chore: extract ruv-neural to ruvnet/ruv-neural, wire as submodule (#1019 )

The 12-crate brain-topology analysis ecosystem (v2/crates/ruv-neural) was a self-contained nested workspace with no inbound deps from the v2 workspace (verified: zero path references outside its own tree). Published standalone at github.com/ruvnet/ruv-neural and re-attached here as a submodule at the same path, so the build layout is unchanged while the project gets its own repo/CI/release cadence.
2026-06-12 10:43:19 +00:00 · 2026-06-11 18:12:51 -04:00
120 changed files with 5 additions and 25279 deletions
@@ -14,3 +14,7 @@
 	path = vendor/rvcsi
 	url = https://github.com/ruvnet/rvcsi
 	branch = main
+[submodule "v2/crates/ruv-neural"]
+	path = v2/crates/ruv-neural
+	url = https://github.com/ruvnet/ruv-neural.git
+	branch = main
@@ -1,2 +0,0 @@
-/target/
-Cargo.lock
@@ -1,98 +0,0 @@
-[workspace]
-resolver = "2"
-members = [
-    "ruv-neural-core",
-    "ruv-neural-sensor",
-    "ruv-neural-signal",
-    "ruv-neural-graph",
-    "ruv-neural-mincut",
-    "ruv-neural-embed",
-    "ruv-neural-memory",
-    "ruv-neural-decoder",
-    "ruv-neural-esp32",
-    "ruv-neural-wasm",
-    "ruv-neural-viz",
-    "ruv-neural-cli",
-]
-# WASM crate excluded from default workspace to avoid breaking `cargo test --workspace`
-# Build separately: cargo build -p ruv-neural-wasm --target wasm32-unknown-unknown --release
-exclude = [
-    "ruv-neural-wasm",
-]
-
-[workspace.package]
-version = "0.1.0"
-edition = "2021"
-authors = ["rUv <ruv@ruv.net>"]
-license = "MIT OR Apache-2.0"
-repository = "https://github.com/ruvnet/RuView"
-documentation = "https://docs.rs/ruv-neural"
-keywords = ["neural", "brain", "topology", "mincut", "quantum-sensing"]
-categories = ["science", "algorithms"]
-
-[workspace.dependencies]
-# Core utilities
-thiserror = "1.0"
-anyhow = "1.0"
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-tracing = "0.1"
-tracing-subscriber = { version = "0.3", features = ["env-filter"] }
-
-# Math and signal processing
-ndarray = { version = "0.15", features = ["serde"] }
-num-complex = "0.4"
-num-traits = "0.2"
-rustfft = "6.1"
-
-# Graph algorithms
-petgraph = "0.6"
-
-# Async runtime
-tokio = { version = "1.35", features = ["full"] }
-
-# WASM support
-wasm-bindgen = "0.2"
-js-sys = "0.3"
-web-sys = { version = "0.3", features = ["console"] }
-
-# ESP32 / embedded
-embedded-hal = "1.0"
-
-# CLI
-clap = { version = "4.4", features = ["derive", "env"] }
-
-# Serialization
-bincode = "1.3"
-
-# Random
-rand = "0.8"
-
-# Cryptographic verification
-ed25519-dalek = { version = "2.1", features = ["rand_core"] }
-sha2 = "0.10"
-
-# Testing
-criterion = { version = "0.5", features = ["html_reports"] }
-proptest = "1.4"
-approx = "0.5"
-
-# Internal crates
-ruv-neural-core = { version = "0.1.0", path = "ruv-neural-core" }
-ruv-neural-sensor = { version = "0.1.0", path = "ruv-neural-sensor" }
-ruv-neural-signal = { version = "0.1.0", path = "ruv-neural-signal" }
-ruv-neural-graph = { version = "0.1.0", path = "ruv-neural-graph" }
-ruv-neural-mincut = { version = "0.1.0", path = "ruv-neural-mincut" }
-ruv-neural-embed = { version = "0.1.0", path = "ruv-neural-embed" }
-ruv-neural-memory = { version = "0.1.0", path = "ruv-neural-memory" }
-ruv-neural-decoder = { version = "0.1.0", path = "ruv-neural-decoder" }
-ruv-neural-esp32 = { version = "0.1.0", path = "ruv-neural-esp32" }
-ruv-neural-viz = { version = "0.1.0", path = "ruv-neural-viz" }
-ruv-neural-cli = { version = "0.1.0", path = "ruv-neural-cli" }
-
-[profile.release]
-lto = true
-codegen-units = 1
-panic = "abort"
-strip = true
-opt-level = 3
@@ -1,421 +0,0 @@
-# rUv Neural — Brain Topology Analysis System
-
-> Quantum sensor integration x RuVector graph memory x Dynamic mincut coherence detection
-
-[![crates.io](https://img.shields.io/crates/v/ruv-neural-core.svg)](https://crates.io/crates/ruv-neural-core)
-[![License](https://img.shields.io/badge/license-MIT%2FApache--2.0-blue.svg)]()
-[![Rust](https://img.shields.io/badge/rust-1.75+-orange.svg)]()
-[![Tests](https://img.shields.io/badge/tests-338%20passed-brightgreen.svg)]()
-
---
-
-## Ethics & Responsible Use
-
-> **This technology interfaces with human neural data. Use it responsibly.**
->
-> - **Informed consent** is required before collecting neural data from any participant
-> - **Never** deploy brain-computer interfaces without IRB/ethics board approval
-> - **Data privacy**: Neural signals are among the most sensitive personal data categories. Encrypt at rest, anonymize before sharing, and comply with GDPR/HIPAA as applicable
-> - **Clinical use** requires FDA/CE clearance and must be supervised by licensed medical professionals
-> - **Do not** use this software for covert monitoring, interrogation, lie detection, or any application that violates human autonomy
-> - **Dual-use awareness**: The same technology that helps paralyzed patients communicate can be misused for surveillance. Design with safeguards
-> - This software is provided for **research and educational purposes**. The authors accept no liability for misuse
->
-> See [IEEE Neuroethics Framework](https://standards.ieee.org/industry-connections/ec/neuroethics/) and the [Morningside Group Neurorights](https://nri.ntc.columbia.edu/content/neurorights) initiative for guidance.
-
---
-
-## Overview
-
-**rUv Neural** is a modular Rust crate ecosystem for real-time brain network topology
-analysis. It transforms neural magnetic field measurements from quantum sensors (NV diamond
-magnetometers, optically pumped magnetometers) into dynamic connectivity graphs, then uses
-minimum cut algorithms to detect cognitive state transitions.
-
-This is not mind reading — it measures **how cognition organizes itself** by tracking the
-topology of brain networks in real time.
-
-## Hardware Parts List
-
-Below is a reference bill of materials for building a basic multi-channel neural sensing rig.
-Prices are approximate (2026). Links are for reference only — equivalent components from any
-vendor will work.
-
-### Core: NV Diamond Magnetometer Array
-
-| Component | Qty | Approx Price | Link | Notes |
-|-----------|-----|-------------|------|-------|
-| NV Diamond Sensor Chip (2x2mm, 1ppm N) | 16 | $45 ea | [AliExpress: NV Diamond Chip](https://www.aliexpress.com/w/wholesale-nv-diamond-sensor.html) | Nitrogen-vacancy center, electronic grade |
-| 532nm Green Laser Diode Module (100mW) | 4 | $12 ea | [AliExpress: 532nm Laser Module](https://www.aliexpress.com/w/wholesale-532nm-laser-module-100mw.html) | Excitation source for ODMR |
-| Microwave Signal Generator (2.87 GHz) | 1 | $85 | [AliExpress: RF Signal Generator 3GHz](https://www.aliexpress.com/w/wholesale-rf-signal-generator-3ghz.html) | For NV zero-field splitting resonance |
-| SMA Coaxial Cable (50 Ohm, 30cm) | 4 | $3 ea | [AliExpress: SMA Cable 50 Ohm](https://www.aliexpress.com/w/wholesale-sma-cable-50-ohm.html) | Microwave delivery to diamond chips |
-| Photodiode Array (Si PIN, 16-ch) | 1 | $25 | [AliExpress: Photodiode Array](https://www.aliexpress.com/w/wholesale-photodiode-array-16-channel.html) | Fluorescence detection |
-| Transimpedance Amplifier Board | 1 | $18 | [AliExpress: TIA Board](https://www.aliexpress.com/w/wholesale-transimpedance-amplifier-board.html) | Converts photocurrent to voltage |
-
-### Alternative: OPM (Optically Pumped Magnetometer)
-
-| Component | Qty | Approx Price | Link | Notes |
-|-----------|-----|-------------|------|-------|
-| Rb Vapor Cell (25mm, AR coated) | 8 | $35 ea | [AliExpress: Rubidium Vapor Cell](https://www.aliexpress.com/w/wholesale-rubidium-vapor-cell.html) | SERF-mode magnetometry |
-| 795nm VCSEL Laser | 8 | $8 ea | [AliExpress: 795nm VCSEL](https://www.aliexpress.com/w/wholesale-795nm-vcsel-laser.html) | D1 line pump for Rb |
-| Balanced Photodetector | 8 | $15 ea | [AliExpress: Balanced Photodetector](https://www.aliexpress.com/w/wholesale-balanced-photodetector.html) | Differential detection |
-| Magnetic Shielding Mu-Metal Cylinder | 1 | $120 | [AliExpress: Mu-Metal Shield](https://www.aliexpress.com/w/wholesale-mu-metal-magnetic-shield.html) | 3-layer, >60dB attenuation |
-
-### Alternative: EEG (Electroencephalography)
-
-| Component | Qty | Approx Price | Link | Notes |
-|-----------|-----|-------------|------|-------|
-| Ag/AgCl EEG Electrodes (10-20 system) | 21 | $2 ea | [AliExpress: EEG Electrode AgCl](https://www.aliexpress.com/w/wholesale-eeg-electrode-ag-agcl.html) | Reusable cup electrodes |
-| EEG Cap (10-20 placement, size M) | 1 | $45 | [AliExpress: EEG Cap 10-20](https://www.aliexpress.com/w/wholesale-eeg-cap-10-20.html) | Pre-wired 21-channel |
-| Conductive EEG Gel (250ml) | 1 | $8 | [AliExpress: EEG Gel](https://www.aliexpress.com/w/wholesale-eeg-conductive-gel.html) | Low impedance contact |
-| ADS1299 EEG AFE Board (8-ch) | 3 | $35 ea | [AliExpress: ADS1299 Board](https://www.aliexpress.com/w/wholesale-ads1299-eeg-board.html) | 24-bit, 250 SPS, TI analog front-end |
-
-### Data Acquisition & Processing
-
-| Component | Qty | Approx Price | Link | Notes |
-|-----------|-----|-------------|------|-------|
-| ESP32-S3 DevKit (16MB Flash, 8MB PSRAM) | 4 | $8 ea | [AliExpress: ESP32-S3 DevKit](https://www.aliexpress.com/w/wholesale-esp32-s3-devkit.html) | ADC readout + TDM sync |
-| ADS1256 24-bit ADC Module | 2 | $12 ea | [AliExpress: ADS1256 Module](https://www.aliexpress.com/w/wholesale-ads1256-module.html) | High-resolution for NV/OPM |
-| USB-C Hub (4 port, USB 3.0) | 1 | $10 | [AliExpress: USB-C Hub](https://www.aliexpress.com/w/wholesale-usb-c-hub-4-port.html) | Connect ESP32 nodes to host |
-| Shielded USB Cable (30cm, ferrite) | 4 | $3 ea | [AliExpress: Shielded USB Cable](https://www.aliexpress.com/w/wholesale-shielded-usb-cable-ferrite.html) | Reduce EMI |
-| Host PC or Raspberry Pi 5 (8GB) | 1 | $80 | [AliExpress: Raspberry Pi 5](https://www.aliexpress.com/w/wholesale-raspberry-pi-5-8gb.html) | Runs the rUv Neural pipeline |
-
-### Assembly Tools
-
-| Component | Qty | Approx Price | Link | Notes |
-|-----------|-----|-------------|------|-------|
-| Soldering Station (adjustable temp) | 1 | $25 | [AliExpress: Soldering Station](https://www.aliexpress.com/w/wholesale-soldering-station-adjustable.html) | For sensor board assembly |
-| Breadboard + Jumper Wire Kit | 1 | $8 | [AliExpress: Breadboard Kit](https://www.aliexpress.com/w/wholesale-breadboard-jumper-wire-kit.html) | Prototyping |
-| 3D Printed Sensor Mount (STL provided) | 1 | — | Print locally | Holds diamond chips in array |
-
-**Estimated total cost:** ~$650–$900 for a 16-channel NV diamond setup, ~$500 for OPM, ~$200 for EEG.
-
-### Assembly Instructions
-
-1. **Sensor Array**
-   - Mount NV diamond chips (or OPM vapor cells, or EEG electrodes) in the 3D-printed helmet/mount
-   - For NV: align 532nm laser to each chip, position photodiodes for fluorescence collection
-   - For OPM: install Rb cells inside mu-metal shield, align 795nm VCSELs
-   - For EEG: apply conductive gel, place electrodes per 10-20 system
-
-2. **Signal Chain**
-   - Connect sensor outputs to ADS1256 (NV/OPM) or ADS1299 (EEG) ADC boards
-   - Wire ADC SPI bus to ESP32-S3 GPIO (MOSI=11, MISO=13, SCK=12, CS=10)
-   - Flash ESP32 with `ruv-neural-esp32` firmware: `cargo flash --chip esp32s3`
-
-3. **TDM Synchronization**
-   - Connect GPIO 4 across all ESP32 nodes as a shared sync line
-   - The `TdmScheduler` assigns non-overlapping time slots automatically
-   - Set `sync_tolerance_us: 1000` in the aggregator config
-
-4. **Host Software**
-   - Install Rust 1.75+ and build: `cargo build --workspace --release`
-   - Run the pipeline: `cargo run -p ruv-neural-cli --release -- pipeline --channels 16 --duration 60`
-   - Or use individual crates as a library (see [Use as Library](#use-as-library))
-
-5. **Verification**
-   - Generate a witness bundle: `cargo run -p ruv-neural-cli -- witness --output witness.json`
-   - Verify Ed25519 signature: `cargo run -p ruv-neural-cli -- witness --verify witness.json`
-   - Expected output: `VERDICT: PASS` (41 capability attestations, 338 tests)
-
-## Architecture
-
-```
-                         rUv Neural Pipeline
-    ================================================================
-
-    +------------------+     +-------------------+     +------------------+
-    |                  |     |                   |     |                  |
-    |  SENSOR LAYER    |---->|  SIGNAL LAYER     |---->|  GRAPH LAYER     |
-    |                  |     |                   |     |                  |
-    |  NV Diamond      |     |  Bandpass Filter  |     |  PLV / Coherence |
-    |  OPM             |     |  Artifact Reject  |     |  Brain Regions   |
-    |  EEG             |     |  Hilbert Phase    |     |  Connectivity    |
-    |  Simulated       |     |  Spectral (PSD)   |     |  Matrix          |
-    |                  |     |                   |     |                  |
-    +------------------+     +-------------------+     +--------+---------+
-                                                                |
-                                                                v
-    +------------------+     +-------------------+     +------------------+
-    |                  |     |                   |     |                  |
-    |  DECODE LAYER    |<----|  MEMORY LAYER     |<----|  MINCUT LAYER    |
-    |                  |     |                   |     |                  |
-    |  Cognitive State |     |  HNSW Index       |     |  Stoer-Wagner    |
-    |  Classification  |     |  Pattern Store    |     |  Normalized Cut  |
-    |  BCI Output      |     |  Drift Detection  |     |  Spectral Cut    |
-    |  Transition Log  |     |  Temporal Window  |     |  Coherence Detect|
-    |                  |     |                   |     |                  |
-    +------------------+     +-------------------+     +------------------+
-                                      ^
-                                      |
-                              +-------+--------+
-                              |                |
-                              |  EMBED LAYER   |
-                              |                |
-                              |  Spectral Pos. |
-                              |  Topology Vec  |
-                              |  Node2Vec      |
-                              |  RVF Export     |
-                              |                |
-                              +----------------+
-
-    Peripheral Crates:
-    +----------+   +----------+   +----------+
-    | ESP32    |   | WASM     |   | VIZ      |
-    | Edge     |   | Browser  |   | ASCII    |
-    | Preproc  |   | Bindings |   | Render   |
-    +----------+   +----------+   +----------+
-```
-
-## Crate Map
-
-All crates are published on [crates.io](https://crates.io/search?q=ruv-neural):
-
-| Crate | crates.io | Description | Dependencies |
-|-------|-----------|-------------|--------------|
-| [`ruv-neural-core`](https://crates.io/crates/ruv-neural-core) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-core.svg)](https://crates.io/crates/ruv-neural-core) | Core types, traits, errors, RVF format | None |
-| [`ruv-neural-sensor`](https://crates.io/crates/ruv-neural-sensor) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-sensor.svg)](https://crates.io/crates/ruv-neural-sensor) | NV diamond, OPM, EEG sensor interfaces | core |
-| [`ruv-neural-signal`](https://crates.io/crates/ruv-neural-signal) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-signal.svg)](https://crates.io/crates/ruv-neural-signal) | DSP: filtering, spectral, connectivity | core |
-| [`ruv-neural-graph`](https://crates.io/crates/ruv-neural-graph) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-graph.svg)](https://crates.io/crates/ruv-neural-graph) | Brain connectivity graph construction | core, signal |
-| [`ruv-neural-mincut`](https://crates.io/crates/ruv-neural-mincut) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-mincut.svg)](https://crates.io/crates/ruv-neural-mincut) | Dynamic minimum cut topology analysis | core |
-| [`ruv-neural-embed`](https://crates.io/crates/ruv-neural-embed) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-embed.svg)](https://crates.io/crates/ruv-neural-embed) | RuVector graph embeddings | core |
-| [`ruv-neural-memory`](https://crates.io/crates/ruv-neural-memory) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-memory.svg)](https://crates.io/crates/ruv-neural-memory) | Persistent neural state memory + HNSW | core |
-| [`ruv-neural-decoder`](https://crates.io/crates/ruv-neural-decoder) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-decoder.svg)](https://crates.io/crates/ruv-neural-decoder) | Cognitive state classification + BCI | core |
-| [`ruv-neural-esp32`](https://crates.io/crates/ruv-neural-esp32) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-esp32.svg)](https://crates.io/crates/ruv-neural-esp32) | ESP32 edge sensor integration | core |
-| `ruv-neural-wasm` | — | WebAssembly browser bindings | core |
-| [`ruv-neural-viz`](https://crates.io/crates/ruv-neural-viz) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-viz.svg)](https://crates.io/crates/ruv-neural-viz) | Visualization and ASCII rendering | core, graph, mincut |
-| [`ruv-neural-cli`](https://crates.io/crates/ruv-neural-cli) | [![crates.io](https://img.shields.io/crates/v/ruv-neural-cli.svg)](https://crates.io/crates/ruv-neural-cli) | CLI tool (`ruv-neural` binary) | all |
-
-## Dependency Graph
-
-```
-                    ruv-neural-core
-                    (types, traits, errors)
-                   /    |    |    \     \
-                  /     |    |     \     \
-                 v      v    v      v     v
-           sensor  signal  embed  esp32  (wasm)
-                          |
-                          v
-                  graph --|------> viz
-                  |
-                  v
-               mincut
-                  |
-                  v
-         decoder <--- memory <--- embed
-                  |
-                  v
-                 cli (depends on all)
-```
-
-## Quick Start
-
-### Build
-
-```bash
-cd v2/crates/ruv-neural
-cargo build --workspace
-cargo test --workspace
-```
-
-### Run CLI
-
-```bash
-cargo run -p ruv-neural-cli -- simulate --channels 64 --duration 10
-cargo run -p ruv-neural-cli -- pipeline --channels 32 --duration 5 --dashboard
-cargo run -p ruv-neural-cli -- mincut --input brain_graph.json
-```
-
-### Install from crates.io
-
-```bash
-# Add individual crates as needed
-cargo add ruv-neural-core
-cargo add ruv-neural-sensor
-cargo add ruv-neural-signal
-cargo add ruv-neural-mincut
-cargo add ruv-neural-embed
-cargo add ruv-neural-memory
-cargo add ruv-neural-decoder
-cargo add ruv-neural-graph
-cargo add ruv-neural-viz
-cargo add ruv-neural-esp32
-cargo add ruv-neural-cli
-```
-
-### Use as Library
-
-```rust
-use ruv_neural_core::*;
-use ruv_neural_sensor::simulator::SimulatedSensorArray;
-use ruv_neural_signal::PreprocessingPipeline;
-use ruv_neural_mincut::DynamicMincutTracker;
-use ruv_neural_embed::NeuralEmbedding;
-
-// Create simulated sensor array (64 channels, 1000 Hz)
-let mut sensor = SimulatedSensorArray::new(64, 1000.0);
-let data = sensor.acquire(1000)?;
-
-// Preprocess: bandpass filter + artifact rejection
-let pipeline = PreprocessingPipeline::default();
-let clean = pipeline.process(&data)?;
-
-// Compute connectivity and build graph
-let connectivity = ruv_neural_signal::compute_all_pairs(
-    &clean,
-    ruv_neural_signal::ConnectivityMetric::PhaseLockingValue,
-);
-
-// Track topology changes via dynamic mincut
-let mut tracker = DynamicMincutTracker::new();
-let result = tracker.update(&graph)?;
-println!(
-    "Mincut: {:.3}, Partitions: {} | {}",
-    result.cut_value,
-    result.partition_a.len(),
-    result.partition_b.len()
-);
-
-// Generate embedding for downstream classification
-let embedding = NeuralEmbedding::new(
-    result.to_feature_vector(),
-    data.timestamp,
-    "spectral",
-)?;
-println!("Embedding dim: {}", embedding.dimension);
-```
-
-## Mix and Match
-
-Each crate is independently usable. Common combinations:
-
- **Sensor + Signal** -- Data acquisition and preprocessing only
- **Graph + Mincut** -- Graph analysis without sensor dependency
- **Embed + Memory** -- Embedding storage without real-time pipeline
- **Core + WASM** -- Browser-based graph visualization
- **ESP32 alone** -- Edge preprocessing on embedded hardware
- **Signal + Embed** -- Feature extraction pipeline without graph construction
- **Mincut + Viz** -- Topology analysis with ASCII dashboard output
-
-## Platform Support
-
-| Platform | Status | Crates Available |
-|----------|--------|-----------------|
-| Linux x86_64 | Full | All 12 |
-| macOS ARM64 | Full | All 12 |
-| Windows x86_64 | Full | All 12 |
-| WASM (browser) | Partial | core, wasm, viz |
-| ESP32 (no_std) | Partial | core, esp32 |
-
-**Note:** The `ruv-neural-wasm` crate is excluded from the default workspace members.
-Build it separately with:
-
-```bash
-cargo build -p ruv-neural-wasm --target wasm32-unknown-unknown --release
-```
-
-## Key Algorithms
-
-### Signal Processing (`ruv-neural-signal`)
-
- **Butterworth IIR filters** in second-order sections (SOS) form
- **Welch PSD** estimation with configurable window and overlap
- **Hilbert transform** for instantaneous phase extraction
- **Artifact detection** -- eye blink, muscle, cardiac artifact rejection
- **Connectivity metrics** -- PLV, coherence, imaginary coherence, AEC
-
-### Minimum Cut Analysis (`ruv-neural-mincut`)
-
- **Stoer-Wagner** -- Global minimum cut in O(V^3)
- **Normalized cut** (Shi-Malik) -- Spectral bisection via the Fiedler vector
- **Multiway cut** -- Recursive normalized cut for k-module detection
- **Spectral cut** -- Cheeger constant and spectral bisection bounds
- **Dynamic tracking** -- Temporal topology transition detection
- **Coherence events** -- Network formation, dissolution, merger, split
-
-### Embeddings (`ruv-neural-embed`)
-
- **Spectral** -- Laplacian eigenvector positional encoding
- **Topology** -- Hand-crafted topological feature vectors
- **Node2Vec** -- Random-walk co-occurrence embeddings
- **Combined** -- Weighted concatenation of multiple methods
- **Temporal** -- Sliding-window context-enriched embeddings
- **RVF export** -- Serialization to RuVector `.rvf` format
-
-## RVF Format
-
-RuVector File (RVF) is a binary format for neural data interchange:
-
-```
-+--------+--------+---------+----------+----------+
-| Magic  | Version| Type    | Payload  | Checksum |
-| RVF\x01| u8     | u8      | [u8; N]  | u32      |
-+--------+--------+---------+----------+----------+
-```
-
- **Magic bytes**: `RVF\x01`
- **Supported types**: brain graphs, embeddings, topology metrics, time series
- **Binary format** for efficient storage and streaming
- **Compatible** with the broader RuVector ecosystem
-
-## Cryptographic Witness Verification
-
-rUv Neural includes an Ed25519-signed capability attestation system. Every build can
-generate a witness bundle that cryptographically proves which capabilities are present
-and that all tests passed.
-
-```bash
-# Generate a signed witness bundle
-cargo run -p ruv-neural-cli -- witness --output witness-bundle.json
-
-# Verify (any third party can do this)
-cargo run -p ruv-neural-cli -- witness --verify witness-bundle.json
-```
-
-The bundle contains:
- **41 capability attestations** covering all 12 crates
- **SHA-256 digest** of the capability matrix
- **Ed25519 signature** (unique per generation)
- **Public key** for independent verification
- Test count and pass/fail status
-
-Tampered bundles are detected — modifying any attestation invalidates the digest and
-signature verification returns `FAIL`.
-
-## Testing
-
-```bash
-# Run all workspace tests
-cargo test --workspace
-
-# Run a specific crate's tests
-cargo test -p ruv-neural-mincut
-
-# Run with logging enabled
-RUST_LOG=debug cargo test --workspace -- --nocapture
-
-# Run benchmarks (requires nightly or criterion)
-cargo bench -p ruv-neural-mincut
-```
-
-## Crate Publishing Order
-
-Crates must be published in dependency order:
-
-1. `ruv-neural-core` (no internal deps)
-2. `ruv-neural-sensor` (depends on core)
-3. `ruv-neural-signal` (depends on core)
-4. `ruv-neural-esp32` (depends on core)
-5. `ruv-neural-graph` (depends on core, signal)
-6. `ruv-neural-embed` (depends on core)
-7. `ruv-neural-mincut` (depends on core)
-8. `ruv-neural-viz` (depends on core, graph)
-9. `ruv-neural-memory` (depends on core, embed)
-10. `ruv-neural-decoder` (depends on core, embed)
-11. `ruv-neural-wasm` (depends on core)
-12. `ruv-neural-cli` (depends on all)
-
-## License
-
-MIT OR Apache-2.0
@@ -1,570 +0,0 @@
-# ruv-neural Crate System: Security and Performance Review
-
-**Date**: 2026-03-09
-**Version**: 0.1.0
-**Scope**: All 12 workspace crates in the ruv-neural system
-**Status**: Implementation checklist for v0.1 and v0.2 milestones
-
---
-
-## Table of Contents
-
-1. [Crate Inventory](#crate-inventory)
-2. [Security Review](#security-review)
-   - [Input Validation](#input-validation)
-   - [Memory Safety](#memory-safety)
-   - [Data Privacy](#data-privacy)
-   - [Network Security (ESP32)](#network-security-esp32)
-   - [Supply Chain](#supply-chain)
-   - [Findings from Code Audit](#findings-from-code-audit)
-3. [Performance Review](#performance-review)
-   - [Computational Complexity](#computational-complexity)
-   - [Memory Usage](#memory-usage)
-   - [Optimization Opportunities](#optimization-opportunities)
-   - [ESP32 Constraints](#esp32-constraints)
-   - [Benchmarking Recommendations](#benchmarking-recommendations)
-   - [Performance Findings from Code Audit](#performance-findings-from-code-audit)
-4. [Action Items](#action-items)
-
---
-
-## Crate Inventory
-
-| Crate | Status | Lines (approx) | Role |
-|-------|--------|-----------------|------|
-| `ruv-neural-core` | Implemented | ~500 | Types, traits, error types, RVF format |
-| `ruv-neural-sensor` | Implemented | ~170 | Sensor data acquisition, calibration, quality |
-| `ruv-neural-signal` | Implemented | ~450 | Filtering, spectral analysis, Hilbert, connectivity |
-| `ruv-neural-graph` | Stub | ~2 | Graph construction from signals |
-| `ruv-neural-mincut` | Implemented | ~700 | Stoer-Wagner, spectral cut, Cheeger, dynamic tracking |
-| `ruv-neural-embed` | Implemented | ~350 | Spectral, topology, node2vec embeddings |
-| `ruv-neural-memory` | Implemented | ~425 | Embedding store, HNSW index |
-| `ruv-neural-decoder` | Implemented (lib) | ~25 | KNN, threshold, transition decoders |
-| `ruv-neural-esp32` | Implemented | ~265 | ADC interface, sensor readout |
-| `ruv-neural-wasm` | Stub | ~2 | WebAssembly bindings |
-| `ruv-neural-viz` | Implemented (lib) | ~20 | Visualization, ASCII rendering, export |
-| `ruv-neural-cli` | Stub | ~2 | CLI binary |
-
---
-
-## Security Review
-
-### Input Validation
-
-All public APIs must validate their inputs at system boundaries. This section catalogs each validation requirement and its current status.
-
-#### Sensor Data Validation
-
-| Check | Required In | Status | Notes |
-|-------|------------|--------|-------|
-| `sample_rate_hz > 0` | `MultiChannelTimeSeries::new` | **MISSING** | Constructor accepts `sample_rate_hz` without validating it is positive and finite. Division by zero in `duration_s()` if zero. |
-| `num_channels > 0` | `MultiChannelTimeSeries::new` | PASS | Returns error if `data.len() == 0`. |
-| Channel lengths equal | `MultiChannelTimeSeries::new` | PASS | Validates all channels have the same length. |
-| Non-NaN/Inf values | All signal processing | **MISSING** | No validation that input signals contain only finite f64 values. NaN propagation through FFT, PLV, and connectivity metrics produces silent garbage. |
-| `num_samples > 0` | `AdcReader::read_samples` | PASS | Returns error if `num_samples == 0`. |
-| Channel count > 0 | `AdcReader::read_samples` | PASS | Returns error if no channels configured. |
-| Channel index bounds | `AdcReader::load_buffer` | PASS | Returns `ChannelOutOfRange` error. |
-| `sensitivity > 0` | `SensorChannel` | **MISSING** | `sensitivity_ft_sqrt_hz` is a public field with no validation on construction. |
-| `sample_rate > 0` | `SensorChannel` | **MISSING** | `sample_rate_hz` is a public field with no validation. |
-
-**Recommendation**: Add a `SensorChannel::new()` constructor that validates `sensitivity_ft_sqrt_hz > 0`, `sample_rate_hz > 0`, and that the orientation vector is a unit normal. Add `sample_rate_hz > 0` and `sample_rate_hz.is_finite()` checks to `MultiChannelTimeSeries::new`. Add a `validate_finite()` utility for signal data.
-
-#### Graph Construction Validation
-
-| Check | Required In | Status | Notes |
-|-------|------------|--------|-------|
-| Edge indices < `num_nodes` | `BrainGraph::adjacency_matrix` | PARTIAL | Silently skips out-of-bounds edges rather than reporting an error. This masks data corruption. |
-| Edge weight is finite | `BrainGraph` | **MISSING** | `BrainEdge.weight` is not validated. NaN/Inf weights propagate silently through Stoer-Wagner and spectral analysis. |
-| `num_nodes >= 2` | `stoer_wagner_mincut` | PASS | Returns proper error. |
-| `num_nodes >= 2` | `fiedler_decomposition` | PASS | Returns proper error. |
-| `num_nodes >= 2` | `SpectralEmbedder::embed` | PASS | Returns proper error. |
-| `num_nodes >= 2` | `cheeger_constant` | PASS | Returns proper error. |
-| Self-loops | `BrainGraph` | **MISSING** | No validation that `source != target` on edges. Self-loops could inflate degree calculations. |
-
-**Recommendation**: Add a `BrainGraph::validate()` method that checks all edge indices are within bounds, weights are finite, and no self-loops exist. Call it from `stoer_wagner_mincut`, `spectral_bisection`, and `SpectralEmbedder::embed`. Consider making `adjacency_matrix()` return `Result` with an error for out-of-bounds edges instead of silently ignoring them.
-
-#### RVF Format Validation
-
-| Check | Required In | Status | Notes |
-|-------|------------|--------|-------|
-| Magic bytes | `RvfHeader::validate` | PASS | Validates against `RVF_MAGIC`. |
-| Version | `RvfHeader::validate` | PASS | Rejects unknown versions. |
-| Header length | `RvfHeader::from_bytes` | PASS | Checks `bytes.len() < 22`. |
-| Data type tag | `RvfDataType::from_tag` | PASS | Returns error for unknown tags. |
-| `metadata_json_len` overflow | `RvfFile::read_from` | **CONCERN** | `metadata_json_len` is cast from `u32` to `usize` and used to allocate a `Vec`. A malicious file with `metadata_json_len = u32::MAX` (~4 GB) would cause an OOM allocation. |
-| Payload length | `RvfFile::read_from` | **CONCERN** | `read_to_end` reads unbounded data into memory. A malicious file could exhaust memory. |
-| JSON validity | `RvfFile::read_from` | PASS | Uses `serde_json::from_slice` which returns an error on invalid JSON. |
-| `num_entries` vs actual data | `RvfFile::read_from` | **MISSING** | The header declares `num_entries` and `embedding_dim`, but these are never cross-checked against the actual payload size. |
-
-**Recommendation**: Add maximum size limits for `metadata_json_len` (e.g., 16 MB) and total payload size. Validate that `num_entries * entry_size_for_type <= data.len()` after reading. Use `Read::take()` to cap reads.
-
-#### Embedding Validation
-
-| Check | Required In | Status | Notes |
-|-------|------------|--------|-------|
-| Non-empty vector | `NeuralEmbedding::new` (core) | PASS | Returns error for empty vectors. |
-| Non-empty vector | `NeuralEmbedding::new` (embed) | PASS | Returns error for empty vectors. |
-| Dimension match | `cosine_similarity`, `euclidean_distance` | PASS | Returns `DimensionMismatch` error. |
-| Zero-norm handling | `cosine_similarity` | PASS | Returns 0.0 for zero-norm vectors. |
-| NaN/Inf in vector | `NeuralEmbedding::new` | **MISSING** | No check for non-finite values in the embedding vector. |
-
-#### Memory Store Validation
-
-| Check | Required In | Status | Notes |
-|-------|------------|--------|-------|
-| Capacity > 0 | `NeuralMemoryStore::new` | **MISSING** | Capacity 0 is accepted, producing a store that evicts on every insertion. |
-| k > 0 | `query_nearest` | **MISSING** | k=0 produces an empty result silently (acceptable but undocumented). |
-| Dimension consistency | `NeuralMemoryStore::store` | **MISSING** | No check that all stored embeddings have the same dimensionality. Mixed dimensions cause silent errors in `query_nearest`. |
-
-#### JSON Parsing
-
-| Check | Status | Notes |
-|-------|--------|-------|
-| Uses serde derive | PASS | All types use `#[derive(Serialize, Deserialize)]`. No manual parsing anywhere. |
-| No `unsafe` JSON parsing | PASS | Standard `serde_json` throughout. |
-
---
-
-### Memory Safety
-
-| Check | Status | Notes |
-|-------|--------|-------|
-| No `unsafe` code | PASS | Zero `unsafe` blocks across all crates. |
-| Vec instead of raw pointers | PASS | All data structures use `Vec`, `HashMap`, `BinaryHeap`. |
-| ndarray for matrix ops | **NOT USED** | Despite being listed in `workspace.dependencies`, matrix operations use `Vec<Vec<f64>>` throughout. This is bounds-checked but less efficient. |
-| No C FFI | PASS | No FFI calls. ESP32 code uses pure Rust types. |
-| No `std::mem::transmute` | PASS | None found. |
-| No `std::ptr` usage | PASS | None found. |
-| Bounds checking on slices | PASS | Uses `.get()`, iterator methods, and Rust's built-in bounds checks. |
-| Integer overflow | **CONCERN** | `max_raw_value()` in `adc.rs` casts `(1u32 << resolution_bits) - 1` to `i16`. If `resolution_bits > 15`, this overflows silently. Currently only 12 or 16 are intended, but 16 produces `i16::MAX` wrapping. |
-
-**Recommendation**: Add a validation check on `resolution_bits` in `AdcConfig` (must be <= 15 for i16 representation, or switch to u16/i32). Consider migrating `Vec<Vec<f64>>` matrix representations to `ndarray::Array2<f64>` for better cache performance and built-in bounds checking.
-
---
-
-### Data Privacy
-
-Neural data is among the most sensitive personal data categories. This section covers data handling practices.
-
-| Check | Status | Notes |
-|-------|--------|-------|
-| No PII in log messages | **NEEDS AUDIT** | The crate uses `tracing` in workspace dependencies but currently has no `tracing::info!` or `tracing::debug!` calls with data fields. As logging is added, ensure neural data values, subject IDs, and session IDs are never logged at INFO level or below. |
-| No neural data in error messages | PASS | Error messages contain structural information (dimensions, indices, version numbers) but not raw signal values or embeddings. |
-| `subject_id` handling | **CONCERN** | `EmbeddingMetadata.subject_id` is stored as plaintext `Option<String>`. This is PII that is included in serialized embeddings (serde), HNSW indices, and RVF files. |
-| `session_id` handling | **CONCERN** | Same concern as `subject_id`. |
-| Memory store encryption | **NOT IMPLEMENTED** | `NeuralMemoryStore` holds embeddings in plaintext `Vec<f64>`. No encryption-at-rest. |
-| Memory zeroization on drop | **NOT IMPLEMENTED** | Embedding data is not zeroed when dropped. Sensitive neural data persists in deallocated memory. |
-| WASM data boundary | STUB | WASM crate is not yet implemented. When implemented, must ensure no neural data is sent to external services without explicit user consent. |
-| RVF file privacy | **CONCERN** | `RvfFile` serializes `metadata` as JSON, which may contain `subject_id`. No option to strip or anonymize metadata before export. |
-
-**Recommendations**:
- Implement a `Redactable` trait for types that may contain PII, providing `redact()` and `anonymize()` methods.
- Use the `zeroize` crate to zero sensitive data on drop for `NeuralEmbedding`, `NeuralMemoryStore`, and `MultiChannelTimeSeries`.
- Add a `strip_pii()` method to `RvfFile` that removes or hashes identifiers before export.
- Document privacy responsibilities in each crate's module documentation.
- For v0.2: Add optional encryption-at-rest for `NeuralMemoryStore` using `ring` or `aes-gcm`.
-
---
-
-### Network Security (ESP32)
-
-| Check | Status | Notes |
-|-------|--------|-------|
-| Node ID authentication | **NOT IMPLEMENTED** | ESP32 crate (`ruv-neural-esp32`) is currently a local ADC reader with no network protocol. When TDM protocol is added, node IDs must be authenticated. |
-| CRC32 integrity | **NOT IMPLEMENTED** | No data packet framing or integrity checks exist yet. |
-| TLS encryption | **NOT IMPLEMENTED** | v0.1 has no network layer. Planned for v0.2. |
-| Packet size limits | **NOT IMPLEMENTED** | No packet protocol exists yet. |
-| Buffer overflow prevention | PARTIAL | `AdcReader` uses a fixed-size ring buffer (4096 samples), which prevents unbounded growth. However, `load_buffer` silently truncates data that exceeds buffer size rather than reporting it. |
-| DMA configuration | N/A | `dma_enabled` is a configuration flag only; actual DMA is not implemented in std mode. |
-
-**Recommendations for v0.2 TDM Protocol**:
- Authenticate node IDs using a pre-shared key or challenge-response.
- Add CRC32 or CRC32-C to every data packet.
- Set maximum packet size to 1460 bytes (single WiFi frame MTU).
- Use DTLS or TLS 1.3 for encryption when available.
- Rate-limit incoming packets per node to prevent flooding.
- Validate all fields in received packets before processing.
-
---
-
-### Supply Chain
-
-| Check | Status | Notes |
-|-------|--------|-------|
-| Minimal dependencies | PASS | Core dependencies: `thiserror`, `serde`, `serde_json`, `num-complex`, `rustfft`, `rand`. All are well-maintained, widely-used crates. |
-| No proc macros except serde | PASS | Only `serde`'s derive macros and `thiserror`'s derive macro are used. `clap`'s derive is CLI-only. |
-| All deps from crates.io | PASS | No git dependencies or path dependencies outside the workspace. |
-| Workspace-managed versions | PASS | All dependency versions are declared in `[workspace.dependencies]`. |
-| `petgraph` usage | **UNUSED** | Listed in workspace dependencies but not imported by any crate. Remove to reduce supply chain surface. |
-| `tokio` usage | **UNUSED** | Listed in workspace dependencies but not imported by any crate. Remove unless async is planned. |
-| `ruvector-*` crates | **UNUSED** | Five RuVector crates listed but not imported by any workspace member. Remove unused dependencies. |
-| `Cargo.lock` | PRESENT | `Cargo.lock` is committed, ensuring reproducible builds. |
-
-**Recommendation**: Run `cargo deny check` to audit for known vulnerabilities. Remove unused workspace dependencies (`petgraph`, `tokio`, `ruvector-*` crates) to minimize attack surface. Add `cargo audit` to CI.
-
---
-
-### Findings from Code Audit
-
-#### SEC-001: RVF Unbounded Allocation (Severity: Medium)
-
-**Location**: `ruv-neural-core/src/rvf.rs`, line 193
-
-```rust
-let mut meta_bytes = vec![0u8; header.metadata_json_len as usize];
-```
-
-A crafted RVF file with `metadata_json_len = 0xFFFFFFFF` allocates 4 GB. Similarly, `read_to_end` on line 201 reads unbounded data.
-
-**Fix**: Add maximum size constants and validate before allocating:
-```rust
-const MAX_METADATA_LEN: u32 = 16 * 1024 * 1024; // 16 MB
-const MAX_PAYLOAD_LEN: usize = 256 * 1024 * 1024; // 256 MB
-
-if header.metadata_json_len > MAX_METADATA_LEN {
-    return Err(RuvNeuralError::Serialization(
-        format!("metadata_json_len {} exceeds maximum {}", header.metadata_json_len, MAX_METADATA_LEN)
-    ));
-}
-```
-
-#### SEC-002: Missing Sample Rate Validation (Severity: Medium)
-
-**Location**: `ruv-neural-core/src/signal.rs`, `MultiChannelTimeSeries::new`
-
-The `sample_rate_hz` parameter is not validated. A value of 0.0 causes division by zero in `duration_s()`. A negative or NaN value causes incorrect spectral analysis throughout the pipeline.
-
-**Fix**: Add validation in the constructor:
-```rust
-if sample_rate_hz <= 0.0 || !sample_rate_hz.is_finite() {
-    return Err(RuvNeuralError::Signal(
-        format!("sample_rate_hz must be positive and finite, got {}", sample_rate_hz)
-    ));
-}
-```
-
-#### SEC-003: NaN Propagation in Signal Processing (Severity: Low)
-
-**Location**: `ruv-neural-signal/src/connectivity.rs`, all functions
-
-If either input signal contains NaN, the Hilbert transform produces NaN outputs, which propagate silently through PLV, coherence, and all connectivity metrics. The result is a brain graph with NaN edge weights, which causes undefined behavior in Stoer-Wagner (infinite loops or wrong results).
-
-**Fix**: Add a `validate_signal` helper and call it at entry points:
-```rust
-fn validate_signal(signal: &[f64]) -> Result<()> {
-    if signal.iter().any(|x| !x.is_finite()) {
-        return Err(RuvNeuralError::Signal("Signal contains NaN or Inf values".into()));
-    }
-    Ok(())
-}
-```
-
-#### SEC-004: Integer Overflow in ADC (Severity: Low)
-
-**Location**: `ruv-neural-esp32/src/adc.rs`, `AdcConfig::max_raw_value`
-
-```rust
-pub fn max_raw_value(&self) -> i16 {
-    ((1u32 << self.resolution_bits) - 1) as i16
-}
-```
-
-For `resolution_bits = 16`, this computes `65535 as i16 = -1`, which causes incorrect voltage conversion (division by -1 flips sign).
-
-**Fix**: Change return type to `u16` or `i32`, or validate `resolution_bits <= 15`.
-
-#### SEC-005: HNSW Visited Array Allocation (Severity: Low)
-
-**Location**: `ruv-neural-memory/src/hnsw.rs`, `search_layer`, line 261
-
-```rust
-let mut visited = vec![false; self.embeddings.len()];
-```
-
-This allocates a visited array proportional to the total number of embeddings on every search call. For large indices (100K+ embeddings), this causes unnecessary allocation pressure. More critically, if `entry` is >= `self.embeddings.len()`, the indexing on line 262 panics.
-
-**Fix**: Use a `HashSet<usize>` instead of a boolean array for sparse visitation. Add bounds check on `entry`.
-
---
-
-## Performance Review
-
-### Computational Complexity
-
-| Operation | Complexity | Target Latency | Current Status |
-|-----------|-----------|----------------|----------------|
-| FFT (1024 points) | O(N log N) | <1 ms | Implemented via `rustfft` (SIMD-optimized). Meets target. |
-| Hilbert transform | O(N log N) | <1 ms | Two FFTs (forward + inverse). Meets target for N <= 4096. |
-| PLV (channel pair) | O(N) + 2x FFT | <0.5 ms | Calls `hilbert_transform` twice. Meets target for N <= 2048. |
-| Coherence (channel pair) | O(N) + 2x FFT | <0.5 ms | Same as PLV. |
-| Connectivity matrix (68 regions) | O(N^2 x M) | <10 ms | M = samples per channel, N = 68: 2,278 Hilbert pairs. May exceed target for long windows. |
-| Stoer-Wagner mincut (68 nodes) | O(V^3) | <5 ms | 68^3 = ~314K operations. Meets target. |
-| Spectral embedding (68 nodes) | O(V^2 x k x iterations) | <3 ms | With k=8, iterations=100: 68^2 x 8 x 100 = ~37M ops. May be tight. |
-| Fiedler decomposition | O(V^2 x iterations) | <2 ms | 1000 iterations x 68^2 = ~4.6M ops. Meets target. |
-| Cheeger constant (exact, n<=16) | O(2^n x n^2) | <5 ms | Exponential but capped at n=16: 65K x 256 = ~16M ops. Meets target. |
-| HNSW insert | O(log N x ef x M) | <1 ms | ef=200, M=16: ~3200 distance computations per insert. Meets target. |
-| HNSW search (10K embeddings) | O(log N x ef) | <1 ms | ef=50: ~50-200 distance computations. Meets target. |
-| Brute-force NN (10K embeddings) | O(N x d) | <5 ms | d=256, N=10K: 2.56M f64 ops. Acceptable but HNSW preferred. |
-| Full pipeline (68 regions) | - | <50 ms | Sum of above stages. Should meet target. |
-
-### Memory Usage
-
-| Component | Calculation | Size |
-|-----------|------------|------|
-| 64-channel x 1000 Hz x 8 bytes x 1s | 64 x 1000 x 8 | 512 KB per second |
-| Brain graph adjacency (68 nodes) | 68^2 x 8 bytes | ~37 KB |
-| Brain graph adjacency (400 nodes) | 400^2 x 8 bytes | ~1.25 MB |
-| Single embedding (256-d) | 256 x 8 bytes | 2 KB |
-| Memory store (10K embeddings, 256-d) | 10K x 2 KB | ~20 MB |
-| HNSW index (10K, M=16, 256-d) | 10K x (2KB + 16 x 16 bytes) | ~22.5 MB |
-| Stoer-Wagner working memory (68 nodes) | 2 x 68^2 x 8 + 68 x vec overhead | ~75 KB |
-| Spectral embedder (68 nodes, k=8) | k x 68 x 8 + Laplacian 68^2 x 8 | ~41 KB |
-| RVF file in memory | header + metadata + payload | Variable, unbounded (see SEC-001) |
-
-### Optimization Opportunities
-
-#### Immediate (v0.1)
-
-1. **Eliminate redundant Hilbert transforms in connectivity matrix**
-   - `compute_all_pairs` calls `hilbert_transform` twice per channel pair.
-   - For 68 channels, this means 68 x 67 = 4,556 Hilbert transforms instead of 68.
-   - **Fix**: Pre-compute analytic signals for all channels, then compute metrics pairwise.
-   - **Expected speedup**: ~67x for connectivity matrix computation.
-
-2. **Replace Vec<Vec<f64>> with flat Vec<f64> for adjacency matrices**
-   - Current `Vec<Vec<f64>>` has poor cache locality due to heap-allocated inner Vecs.
-   - **Fix**: Use `Vec<f64>` with manual row-major indexing, or migrate to `ndarray::Array2<f64>`.
-   - **Expected speedup**: 2-4x for matrix-heavy operations (Stoer-Wagner, Laplacian).
-
-3. **Avoid Vec::remove(0) in eviction**
-   - `NeuralMemoryStore::evict_oldest` calls `self.embeddings.remove(0)`, which is O(n).
-   - **Fix**: Use a `VecDeque` or circular buffer.
-   - **Expected speedup**: O(1) eviction instead of O(n).
-
-4. **Pre-allocate FFT planner**
-   - `compute_psd`, `compute_stft`, and `hilbert_transform` each create a new `FftPlanner` per call.
-   - **Fix**: Cache the planner or use a thread-local planner.
-   - **Expected speedup**: Eliminates repeated plan computation.
-
-#### Medium-term (v0.2)
-
-5. **Rayon for parallel channel processing**
-   - `compute_all_pairs` iterates channel pairs sequentially.
-   - **Fix**: Use `rayon::par_iter` for the outer loop.
-   - **Expected speedup**: Linear with core count for connectivity computation.
-
-6. **SIMD for distance computations in HNSW**
-   - Euclidean distance in `HnswIndex::distance` uses scalar iteration.
-   - **Fix**: Use `packed_simd2` or auto-vectorization hints.
-   - **Expected speedup**: 4-8x for 256-d vectors on AVX2.
-
-7. **Sparse graph representation**
-   - Dense adjacency matrix wastes memory for sparse brain graphs.
-   - For Schaefer400, storing all 160K entries when only ~10K edges exist is wasteful.
-   - **Fix**: Use compressed sparse row (CSR) format or `petgraph`'s sparse graph.
-
-8. **Quantized embeddings for WASM**
-   - f64 embeddings are unnecessarily precise for browser-based applications.
-   - **Fix**: Support f32 embeddings in WASM builds, halving memory and transfer size.
-
-#### Long-term (v0.3+)
-
-9. **Streaming signal processing**
-   - Current design loads entire time windows into memory.
-   - **Fix**: Implement ring-buffer based streaming for real-time operation.
-
-10. **GPU acceleration for large-scale spectral analysis**
-    - For Schaefer400 atlas, eigendecomposition of 400x400 matrices benefits from GPU.
-    - **Fix**: Optional `wgpu` or `vulkano` backend for matrix operations.
-
-### ESP32 Constraints
-
-| Resource | Limit | Current Usage | Status |
-|----------|-------|---------------|--------|
-| SRAM | 520 KB | Ring buffer: 4096 x channels x 2 bytes = 8 KB (1 channel) | OK |
-| SRAM (multi-channel) | 520 KB | 4096 x 16 x 2 = 128 KB (16 channels) | **TIGHT** |
-| CPU | 240 MHz dual-core | ADC sampling + data transmission | OK for 1 kHz |
-| Flash | 4 MB | Binary size with release profile | Needs measurement |
-| WiFi throughput | ~1 Mbps sustained | 64 ch x 1000 Hz x 2 bytes = 128 KB/s = 1 Mbps | **AT LIMIT** |
-
-**Recommendations**:
- Use fixed-point arithmetic (i16 or Q15) instead of f64 on ESP32.
- Implement delta encoding or simple compression for data packets.
- Limit on-device processing to ADC readout and basic quality checks.
- Move all signal processing (FFT, connectivity, graph construction) to the host.
- Profile binary size with `cargo bloat` to ensure it fits in 4 MB flash.
- Consider reducing ring buffer size for multi-channel configurations.
-
-### Benchmarking Recommendations
-
-#### Per-Crate Microbenchmarks (criterion)
-
-```toml
-# Add to each crate's Cargo.toml
-[[bench]]
-name = "benchmarks"
-harness = false
-
-[dev-dependencies]
-criterion = { workspace = true }
-```
-
-| Crate | Benchmark | Input Size | Metric |
-|-------|-----------|------------|--------|
-| `ruv-neural-signal` | `bench_hilbert_transform` | 256, 512, 1024, 2048, 4096 samples | ns/op |
-| `ruv-neural-signal` | `bench_compute_psd` | 1024, 4096 samples | ns/op |
-| `ruv-neural-signal` | `bench_plv_pair` | 1024 samples | ns/op |
-| `ruv-neural-signal` | `bench_connectivity_matrix` | 16, 32, 68 channels x 1024 samples | ms/op |
-| `ruv-neural-mincut` | `bench_stoer_wagner` | 10, 20, 50, 68, 100 nodes | us/op |
-| `ruv-neural-mincut` | `bench_spectral_bisection` | 10, 20, 50, 68, 100 nodes | us/op |
-| `ruv-neural-mincut` | `bench_cheeger_constant` | 8, 12, 16 nodes (exact), 32, 68 (approx) | us/op |
-| `ruv-neural-embed` | `bench_spectral_embed` | 20, 50, 68, 100 nodes | us/op |
-| `ruv-neural-memory` | `bench_brute_force_nn` | 100, 1K, 10K embeddings x 256-d | us/op |
-| `ruv-neural-memory` | `bench_hnsw_insert` | 1K, 10K embeddings x 256-d | us/op |
-| `ruv-neural-memory` | `bench_hnsw_search` | 1K, 10K embeddings, k=10, ef=50 | us/op |
-| `ruv-neural-esp32` | `bench_adc_read` | 100, 1000 samples x 1-16 channels | us/op |
-
-#### Full Pipeline Profiling
-
-```bash
-# Generate a flamegraph of the full pipeline
-cargo flamegraph --bench full_pipeline -- --bench
-
-# Memory profiling with DHAT
-cargo test --features dhat-heap -- --test full_pipeline
-```
-
-#### WASM Performance
-
-```javascript
-// When ruv-neural-wasm is implemented, measure with:
-performance.mark('embed-start');
-const embedding = ruv_neural.embed(graphData);
-performance.mark('embed-end');
-performance.measure('embed', 'embed-start', 'embed-end');
-```
-
-#### ESP32 Hardware Timing
-
-```rust
-// Use esp-idf-hal's timer for hardware-level benchmarks
-let start = esp_idf_hal::timer::now();
-let samples = reader.read_samples(1000)?;
-let elapsed_us = esp_idf_hal::timer::now() - start;
-```
-
-### Performance Findings from Code Audit
-
-#### PERF-001: Redundant Hilbert Transforms (Severity: High)
-
-**Location**: `ruv-neural-signal/src/connectivity.rs`, `compute_all_pairs`
-
-Each call to `phase_locking_value`, `coherence`, `imaginary_coherence`, or `amplitude_envelope_correlation` independently calls `hilbert_transform` on both input signals. In `compute_all_pairs` with 68 channels, each channel's analytic signal is computed 67 times.
-
-**Impact**: For 68 channels x 1024 samples, this means 4,556 FFTs instead of 68. Estimated waste: ~98.5% of FFT compute in the connectivity matrix.
-
-**Fix**: Pre-compute all analytic signals, then pass slices to pairwise metrics:
-```rust
-pub fn compute_all_pairs_optimized(channels: &[Vec<f64>], metric: &ConnectivityMetric) -> Vec<Vec<f64>> {
-    let analytics: Vec<Vec<Complex<f64>>> = channels.iter()
-        .map(|ch| hilbert_transform(ch))
-        .collect();
-    // ... use pre-computed analytics for all pair computations
-}
-```
-
-#### PERF-002: O(n) Eviction in Memory Store (Severity: Medium)
-
-**Location**: `ruv-neural-memory/src/store.rs`, `evict_oldest`
-
-```rust
-fn evict_oldest(&mut self) {
-    self.embeddings.remove(0);  // O(n) shift
-    self.rebuild_index();       // O(n) rebuild
-}
-```
-
-For a store with 10K embeddings, every insertion at capacity triggers an O(n) shift and full index rebuild.
-
-**Fix**: Use `VecDeque<NeuralEmbedding>` and maintain the index incrementally.
-
-#### PERF-003: FFT Planner Re-creation (Severity: Medium)
-
-**Location**: `ruv-neural-signal/src/spectral.rs` (lines 12-13), `hilbert.rs` (lines 25-27)
-
-A new `FftPlanner` is created on every function call. `rustfft` caches FFT plans internally in the planner, but creating a new planner discards the cache.
-
-**Fix**: Use a thread-local or static planner:
-```rust
-thread_local! {
-    static FFT_PLANNER: RefCell<FftPlanner<f64>> = RefCell::new(FftPlanner::new());
-}
-```
-
-#### PERF-004: Dense Adjacency for Sparse Graphs (Severity: Low)
-
-**Location**: `ruv-neural-core/src/graph.rs`, `adjacency_matrix`
-
-Always allocates an N x N matrix even when the graph has far fewer edges. For Schaefer400 with ~5K edges, this allocates 1.25 MB for a matrix that is ~97% zeros.
-
-**Fix**: Return a sparse representation for large graphs, or provide both `adjacency_matrix()` and `sparse_adjacency()`.
-
-#### PERF-005: Power Iteration Convergence Not Checked (Severity: Low)
-
-**Location**: `ruv-neural-mincut/src/spectral_cut.rs`, `largest_eigenvalue`
-
-Runs a fixed 200 iterations regardless of convergence. Many graphs converge in 20-50 iterations.
-
-**Fix**: Add early termination when eigenvalue change < epsilon:
-```rust
-if (eigenvalue - prev_eigenvalue).abs() < 1e-12 {
-    break;
-}
-```
-
-Note: `fiedler_decomposition` already has this check, but `largest_eigenvalue` does not.
-
---
-
-## Action Items
-
-### Critical (Must fix before v0.1 release)
-
- [ ] **SEC-001**: Add maximum size limits to RVF deserialization
- [ ] **SEC-002**: Validate `sample_rate_hz > 0` and `is_finite()` in `MultiChannelTimeSeries::new`
- [ ] **SEC-004**: Fix integer overflow in `AdcConfig::max_raw_value`
- [ ] **PERF-001**: Pre-compute Hilbert transforms in `compute_all_pairs`
-
-### Important (Should fix before v0.1 release)
-
- [ ] **SEC-003**: Add NaN/Inf validation for signal data at pipeline entry points
- [ ] **SEC-005**: Add bounds check on HNSW entry point index
- [ ] **PERF-002**: Replace `Vec::remove(0)` with `VecDeque` in memory store
- [ ] **PERF-003**: Cache FFT planner across calls
- [ ] Add `BrainGraph::validate()` for edge index bounds and weight finiteness
- [ ] Add dimension consistency check to `NeuralMemoryStore::store`
- [ ] Remove unused workspace dependencies (`petgraph`, `tokio`, `ruvector-*`)
-
-### Recommended (Fix in v0.2)
-
- [ ] Implement `zeroize`-on-drop for `NeuralEmbedding` and `NeuralMemoryStore`
- [ ] Add `strip_pii()` to `RvfFile`
- [ ] Migrate `Vec<Vec<f64>>` matrices to `ndarray::Array2<f64>`
- [ ] Add Rayon parallelism for connectivity matrix computation
- [ ] Add criterion benchmarks for all crates
- [ ] Implement TDM protocol with CRC32 and node authentication
- [ ] Add `cargo deny` and `cargo audit` to CI
- [ ] Profile and optimize binary size for ESP32
-
-### Future (v0.3+)
-
- [ ] Encryption-at-rest for `NeuralMemoryStore`
- [ ] DTLS/TLS for ESP32 network protocol
- [ ] Sparse graph representation for large atlases
- [ ] f32 quantized embeddings for WASM
- [ ] Streaming signal processing pipeline
- [ ] GPU backend for large-scale spectral analysis
-
---
-
-*This document should be reviewed and updated after each milestone. All security findings should be verified as resolved before the corresponding release.*
@@ -1,28 +0,0 @@
-[package]
-name = "ruv-neural-cli"
-description = "rUv Neural — CLI tool for brain topology analysis, simulation, and visualization"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[[bin]]
-name = "ruv-neural"
-path = "src/main.rs"
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-ruv-neural-sensor = { workspace = true }
-ruv-neural-signal = { workspace = true }
-ruv-neural-graph = { workspace = true }
-ruv-neural-mincut = { workspace = true }
-ruv-neural-embed = { workspace = true }
-ruv-neural-memory = { workspace = true }
-ruv-neural-decoder = { workspace = true }
-ruv-neural-viz = { workspace = true }
-clap = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-tracing-subscriber = { workspace = true }
-tokio = { workspace = true }
@@ -1,112 +0,0 @@
-# ruv-neural-cli
-
-CLI tool for brain topology analysis, simulation, and visualization.
-
-## Overview
-
-`ruv-neural-cli` is the command-line binary (`ruv-neural`) that ties together
-the entire rUv Neural crate ecosystem. It provides subcommands for simulating
-neural sensor data, analyzing brain connectivity graphs, computing minimum cuts,
-running the full processing pipeline with an optional ASCII dashboard, and
-exporting to multiple visualization formats.
-
-## Installation
-
-```bash
-# Build from source
-cargo install --path .
-
-# Or run directly
-cargo run -p ruv-neural-cli -- <command>
-```
-
-## Commands
-
-### `simulate` -- Generate synthetic neural data
-
-```bash
-ruv-neural simulate --channels 64 --duration 10 --sample-rate 1000 --output data.json
-```
-
-| Flag             | Default | Description                  |
-|------------------|---------|------------------------------|
-| `-c, --channels` | 64      | Number of sensor channels    |
-| `-d, --duration` | 10.0    | Duration in seconds          |
-| `-s, --sample-rate` | 1000.0 | Sample rate in Hz         |
-| `-o, --output`   | (none)  | Output file path (JSON)      |
-
-### `analyze` -- Analyze a brain connectivity graph
-
-```bash
-ruv-neural analyze --input graph.json --ascii --csv metrics.csv
-```
-
-| Flag           | Default | Description                    |
-|----------------|---------|--------------------------------|
-| `-i, --input`  | (required) | Input graph file (JSON)    |
-| `--ascii`      | false   | Show ASCII visualization       |
-| `--csv`        | (none)  | Export metrics to CSV file     |
-
-### `mincut` -- Compute minimum cut
-
-```bash
-ruv-neural mincut --input graph.json --k 4
-```
-
-| Flag           | Default | Description                    |
-|----------------|---------|--------------------------------|
-| `-i, --input`  | (required) | Input graph file (JSON)    |
-| `-k`           | (none)  | Multi-way cut with k partitions|
-
-### `pipeline` -- Full end-to-end pipeline
-
-```bash
-ruv-neural pipeline --channels 32 --duration 5 --dashboard
-```
-
-Runs: simulate -> preprocess -> build graph -> mincut -> embed -> decode.
-
-| Flag             | Default | Description                    |
-|------------------|---------|--------------------------------|
-| `-c, --channels` | 32      | Number of sensor channels      |
-| `-d, --duration` | 5.0     | Duration in seconds            |
-| `--dashboard`    | false   | Show real-time ASCII dashboard |
-
-### `export` -- Export to visualization format
-
-```bash
-ruv-neural export --input graph.json --format dot --output graph.dot
-```
-
-| Flag             | Default | Description                           |
-|------------------|---------|---------------------------------------|
-| `-i, --input`    | (required) | Input graph file (JSON)           |
-| `-f, --format`   | d3      | Output format: d3, dot, gexf, csv, rvf |
-| `-o, --output`   | (required) | Output file path                  |
-
-### `info` -- Show system information
-
-```bash
-ruv-neural info
-```
-
-Displays crate versions, available features, and system capabilities.
-
-## Global Options
-
-| Flag             | Description                        |
-|------------------|------------------------------------|
-| `-v`             | Increase verbosity (up to `-vvv`)  |
-| `--version`      | Print version                      |
-| `--help`         | Print help                         |
-
-## Integration
-
-Depends on all workspace crates: `ruv-neural-core`, `ruv-neural-sensor`,
-`ruv-neural-signal`, `ruv-neural-graph`, `ruv-neural-mincut`, `ruv-neural-embed`,
-`ruv-neural-memory`, `ruv-neural-decoder`, and `ruv-neural-viz`. Uses `clap`
-for argument parsing and `tokio` for async runtime.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,237 +0,0 @@
-//! Analyze a brain connectivity graph: compute topology metrics and display results.
-
-use std::fs;
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_mincut::stoer_wagner_mincut;
-
-/// Run the analyze command.
-pub fn run(
-    input: &str,
-    ascii: bool,
-    csv_output: Option<String>,
-) -> Result<(), Box<dyn std::error::Error>> {
-    tracing::info!(input, "Loading brain graph");
-
-    let json = fs::read_to_string(input)
-        .map_err(|e| format!("Failed to read {input}: {e}"))?;
-    let graph: BrainGraph = serde_json::from_str(&json)
-        .map_err(|e| format!("Failed to parse graph JSON: {e}"))?;
-
-    println!("=== rUv Neural — Graph Analysis ===");
-    println!();
-    println!("  Nodes:           {}", graph.num_nodes);
-    println!("  Edges:           {}", graph.edges.len());
-    println!("  Density:         {:.4}", graph.density());
-    println!("  Total weight:    {:.4}", graph.total_weight());
-    println!("  Timestamp:       {:.2} s", graph.timestamp);
-    println!("  Window duration: {:.2} s", graph.window_duration_s);
-    println!("  Atlas:           {:?}", graph.atlas);
-    println!();
-
-    // Degree statistics.
-    let degrees: Vec<f64> = (0..graph.num_nodes)
-        .map(|i| graph.node_degree(i))
-        .collect();
-    let mean_degree = if degrees.is_empty() {
-        0.0
-    } else {
-        degrees.iter().sum::<f64>() / degrees.len() as f64
-    };
-    let max_degree = degrees.iter().cloned().fold(0.0_f64, f64::max);
-    let min_degree = degrees.iter().cloned().fold(f64::INFINITY, f64::min);
-
-    println!("  Degree statistics:");
-    println!("    Mean:  {mean_degree:.4}");
-    println!("    Min:   {min_degree:.4}");
-    println!("    Max:   {max_degree:.4}");
-    println!();
-
-    // Mincut.
-    match stoer_wagner_mincut(&graph) {
-        Ok(mc) => {
-            println!("  Minimum cut:");
-            println!("    Cut value:     {:.4}", mc.cut_value);
-            println!("    Partition A:   {} nodes {:?}", mc.partition_a.len(), mc.partition_a);
-            println!("    Partition B:   {} nodes {:?}", mc.partition_b.len(), mc.partition_b);
-            println!("    Cut edges:     {}", mc.cut_edges.len());
-            println!("    Balance ratio: {:.4}", mc.balance_ratio());
-            println!();
-        }
-        Err(e) => {
-            println!("  Minimum cut: could not compute ({e})");
-            println!();
-        }
-    }
-
-    // Edge weight distribution.
-    if !graph.edges.is_empty() {
-        let weights: Vec<f64> = graph.edges.iter().map(|e| e.weight).collect();
-        let mean_w = weights.iter().sum::<f64>() / weights.len() as f64;
-        let max_w = weights.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
-        let min_w = weights.iter().cloned().fold(f64::INFINITY, f64::min);
-
-        println!("  Edge weight distribution:");
-        println!("    Mean:  {mean_w:.4}");
-        println!("    Min:   {min_w:.4}");
-        println!("    Max:   {max_w:.4}");
-        println!();
-    }
-
-    if ascii {
-        print_ascii_graph(&graph);
-    }
-
-    if let Some(csv_path) = csv_output {
-        write_csv(&graph, &degrees, &csv_path)?;
-        println!("  Metrics exported to: {csv_path}");
-    }
-
-    Ok(())
-}
-
-/// Print a simple ASCII visualization of the graph adjacency.
-fn print_ascii_graph(graph: &BrainGraph) {
-    println!("  ASCII Adjacency Matrix:");
-    let n = graph.num_nodes.min(20); // cap display at 20x20
-    let adj = graph.adjacency_matrix();
-
-    // Header row.
-    print!("       ");
-    for j in 0..n {
-        print!("{j:>4}");
-    }
-    println!();
-
-    for i in 0..n {
-        print!("  {i:>3}  ");
-        for j in 0..n {
-            let w = adj[i][j];
-            if i == j {
-                print!("   .");
-            } else if w > 0.0 {
-                // Map weight to a character.
-                let ch = if w > 0.8 {
-                    '#'
-                } else if w > 0.5 {
-                    '*'
-                } else if w > 0.2 {
-                    '+'
-                } else {
-                    '.'
-                };
-                print!("   {ch}");
-            } else {
-                print!("    ");
-            }
-        }
-        println!();
-    }
-
-    if graph.num_nodes > 20 {
-        println!("  ... ({} nodes total, showing first 20)", graph.num_nodes);
-    }
-    println!();
-}
-
-/// Write per-node metrics to a CSV file.
-fn write_csv(
-    graph: &BrainGraph,
-    degrees: &[f64],
-    path: &str,
-) -> Result<(), Box<dyn std::error::Error>> {
-    let mut csv = String::from("node,degree,num_edges\n");
-    for i in 0..graph.num_nodes {
-        let num_edges = graph
-            .edges
-            .iter()
-            .filter(|e| e.source == i || e.target == i)
-            .count();
-        csv.push_str(&format!(
-            "{},{:.6},{}\n",
-            i,
-            degrees.get(i).copied().unwrap_or(0.0),
-            num_edges
-        ));
-    }
-    fs::write(path, csv)?;
-    Ok(())
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn test_graph() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 0.8,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 2,
-                    target: 3,
-                    weight: 0.9,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        }
-    }
-
-    #[test]
-    fn analyze_from_json() {
-        let graph = test_graph();
-        let dir = std::env::temp_dir();
-        let path = dir.join("ruv_neural_test_analyze.json");
-        let json = serde_json::to_string_pretty(&graph).unwrap();
-        std::fs::write(&path, json).unwrap();
-
-        let result = run(&path.to_string_lossy(), false, None);
-        assert!(result.is_ok());
-        std::fs::remove_file(&path).ok();
-    }
-
-    #[test]
-    fn analyze_with_csv() {
-        let graph = test_graph();
-        let dir = std::env::temp_dir();
-        let json_path = dir.join("ruv_neural_test_analyze2.json");
-        let csv_path = dir.join("ruv_neural_test_analyze2.csv");
-
-        let json = serde_json::to_string_pretty(&graph).unwrap();
-        std::fs::write(&json_path, json).unwrap();
-
-        let result = run(
-            &json_path.to_string_lossy(),
-            true,
-            Some(csv_path.to_string_lossy().to_string()),
-        );
-        assert!(result.is_ok());
-        assert!(csv_path.exists());
-
-        let csv_content = std::fs::read_to_string(&csv_path).unwrap();
-        assert!(csv_content.starts_with("node,degree,num_edges"));
-
-        std::fs::remove_file(&json_path).ok();
-        std::fs::remove_file(&csv_path).ok();
-    }
-}
@@ -1,280 +0,0 @@
-//! Export brain graph to various visualization formats.
-
-use std::fs;
-
-use ruv_neural_core::graph::BrainGraph;
-
-/// Run the export command.
-pub fn run(
-    input: &str,
-    format: &str,
-    output: &str,
-) -> Result<(), Box<dyn std::error::Error>> {
-    tracing::info!(input, format, output, "Exporting brain graph");
-
-    let json =
-        fs::read_to_string(input).map_err(|e| format!("Failed to read {input}: {e}"))?;
-    let graph: BrainGraph =
-        serde_json::from_str(&json).map_err(|e| format!("Failed to parse graph JSON: {e}"))?;
-
-    let content = match format {
-        "d3" => export_d3(&graph)?,
-        "dot" => export_dot(&graph),
-        "gexf" => export_gexf(&graph),
-        "csv" => export_csv(&graph),
-        "rvf" => export_rvf(&graph)?,
-        _ => {
-            return Err(format!(
-                "Unknown format '{format}'. Supported: d3, dot, gexf, csv, rvf"
-            )
-            .into());
-        }
-    };
-
-    fs::write(output, content)?;
-
-    println!("=== rUv Neural — Export Complete ===");
-    println!();
-    println!("  Format:  {format}");
-    println!("  Input:   {input}");
-    println!("  Output:  {output}");
-    println!("  Nodes:   {}", graph.num_nodes);
-    println!("  Edges:   {}", graph.edges.len());
-
-    Ok(())
-}
-
-/// Export to D3.js-compatible JSON format.
-fn export_d3(graph: &BrainGraph) -> Result<String, Box<dyn std::error::Error>> {
-    let nodes: Vec<serde_json::Value> = (0..graph.num_nodes)
-        .map(|i| {
-            serde_json::json!({
-                "id": i,
-                "degree": graph.node_degree(i),
-            })
-        })
-        .collect();
-
-    let links: Vec<serde_json::Value> = graph
-        .edges
-        .iter()
-        .map(|e| {
-            serde_json::json!({
-                "source": e.source,
-                "target": e.target,
-                "weight": e.weight,
-                "metric": format!("{:?}", e.metric),
-                "band": format!("{:?}", e.frequency_band),
-            })
-        })
-        .collect();
-
-    let d3 = serde_json::json!({
-        "nodes": nodes,
-        "links": links,
-        "metadata": {
-            "num_nodes": graph.num_nodes,
-            "num_edges": graph.edges.len(),
-            "density": graph.density(),
-            "total_weight": graph.total_weight(),
-            "atlas": format!("{:?}", graph.atlas),
-            "timestamp": graph.timestamp,
-        }
-    });
-
-    Ok(serde_json::to_string_pretty(&d3)?)
-}
-
-/// Export to Graphviz DOT format.
-fn export_dot(graph: &BrainGraph) -> String {
-    let mut dot = String::from("graph brain {\n");
-    dot.push_str("  rankdir=LR;\n");
-    dot.push_str(&format!(
-        "  label=\"Brain Graph ({} nodes, {} edges)\";\n",
-        graph.num_nodes,
-        graph.edges.len()
-    ));
-    dot.push_str("  node [shape=circle];\n\n");
-
-    for i in 0..graph.num_nodes {
-        let degree = graph.node_degree(i);
-        let size = 0.3 + degree * 0.1;
-        dot.push_str(&format!(
-            "  n{i} [label=\"{i}\", width={size:.2}];\n"
-        ));
-    }
-    dot.push('\n');
-
-    for edge in &graph.edges {
-        let penwidth = 0.5 + edge.weight * 2.0;
-        dot.push_str(&format!(
-            "  n{} -- n{} [penwidth={:.2}, label=\"{:.2}\"];\n",
-            edge.source, edge.target, penwidth, edge.weight
-        ));
-    }
-
-    dot.push_str("}\n");
-    dot
-}
-
-/// Export to GEXF (Graph Exchange XML Format).
-fn export_gexf(graph: &BrainGraph) -> String {
-    let mut gexf = String::from(r#"<?xml version="1.0" encoding="UTF-8"?>
-<gexf xmlns="http://gexf.net/1.3" version="1.3">
-  <meta>
-    <creator>rUv Neural</creator>
-    <description>Brain connectivity graph</description>
-  </meta>
-  <graph defaultedgetype="undirected">
-    <nodes>
-"#);
-
-    for i in 0..graph.num_nodes {
-        gexf.push_str(&format!(
-            "      <node id=\"{i}\" label=\"Region {i}\" />\n"
-        ));
-    }
-
-    gexf.push_str("    </nodes>\n    <edges>\n");
-
-    for (idx, edge) in graph.edges.iter().enumerate() {
-        gexf.push_str(&format!(
-            "      <edge id=\"{idx}\" source=\"{}\" target=\"{}\" weight=\"{:.6}\" />\n",
-            edge.source, edge.target, edge.weight
-        ));
-    }
-
-    gexf.push_str("    </edges>\n  </graph>\n</gexf>\n");
-    gexf
-}
-
-/// Export to CSV edge list.
-fn export_csv(graph: &BrainGraph) -> String {
-    let mut csv = String::from("source,target,weight,metric,frequency_band\n");
-    for edge in &graph.edges {
-        csv.push_str(&format!(
-            "{},{},{:.6},{:?},{:?}\n",
-            edge.source, edge.target, edge.weight, edge.metric, edge.frequency_band
-        ));
-    }
-    csv
-}
-
-/// Export to RVF (RuVector File) JSON representation.
-fn export_rvf(graph: &BrainGraph) -> Result<String, Box<dyn std::error::Error>> {
-    let rvf = serde_json::json!({
-        "format": "rvf",
-        "version": 1,
-        "data_type": "BrainGraph",
-        "num_nodes": graph.num_nodes,
-        "num_edges": graph.edges.len(),
-        "atlas": format!("{:?}", graph.atlas),
-        "timestamp": graph.timestamp,
-        "window_duration_s": graph.window_duration_s,
-        "adjacency": graph.adjacency_matrix(),
-    });
-    Ok(serde_json::to_string_pretty(&rvf)?)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn test_graph() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 0.8,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Beta,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        }
-    }
-
-    #[test]
-    fn export_d3_valid_json() {
-        let graph = test_graph();
-        let result = export_d3(&graph).unwrap();
-        let parsed: serde_json::Value = serde_json::from_str(&result).unwrap();
-        assert!(parsed["nodes"].is_array());
-        assert!(parsed["links"].is_array());
-        assert_eq!(parsed["nodes"].as_array().unwrap().len(), 3);
-        assert_eq!(parsed["links"].as_array().unwrap().len(), 2);
-    }
-
-    #[test]
-    fn export_dot_format() {
-        let graph = test_graph();
-        let result = export_dot(&graph);
-        assert!(result.starts_with("graph brain {"));
-        assert!(result.contains("n0 -- n1"));
-        assert!(result.ends_with("}\n"));
-    }
-
-    #[test]
-    fn export_gexf_format() {
-        let graph = test_graph();
-        let result = export_gexf(&graph);
-        assert!(result.contains("<gexf"));
-        assert!(result.contains("<node id=\"0\""));
-        assert!(result.contains("</gexf>"));
-    }
-
-    #[test]
-    fn export_csv_format() {
-        let graph = test_graph();
-        let result = export_csv(&graph);
-        assert!(result.starts_with("source,target,weight"));
-        let lines: Vec<&str> = result.lines().collect();
-        assert_eq!(lines.len(), 3); // header + 2 edges
-    }
-
-    #[test]
-    fn export_rvf_valid_json() {
-        let graph = test_graph();
-        let result = export_rvf(&graph).unwrap();
-        let parsed: serde_json::Value = serde_json::from_str(&result).unwrap();
-        assert_eq!(parsed["format"], "rvf");
-        assert_eq!(parsed["num_nodes"], 3);
-    }
-
-    #[test]
-    fn export_all_formats() {
-        let graph = test_graph();
-        let dir = std::env::temp_dir();
-        let json_path = dir.join("ruv_neural_test_export.json");
-        let json = serde_json::to_string_pretty(&graph).unwrap();
-        std::fs::write(&json_path, json).unwrap();
-
-        for fmt in &["d3", "dot", "gexf", "csv", "rvf"] {
-            let out_path = dir.join(format!("ruv_neural_test_export.{fmt}"));
-            let result = run(
-                &json_path.to_string_lossy(),
-                fmt,
-                &out_path.to_string_lossy(),
-            );
-            assert!(result.is_ok(), "Failed to export format: {fmt}");
-            assert!(out_path.exists(), "Output file missing for format: {fmt}");
-            std::fs::remove_file(&out_path).ok();
-        }
-
-        std::fs::remove_file(&json_path).ok();
-    }
-}
@@ -1,66 +0,0 @@
-//! Display system info and capabilities.
-
-/// Run the info command.
-pub fn run() {
-    let version = env!("CARGO_PKG_VERSION");
-
-    println!("=== rUv Neural — System Information ===");
-    println!();
-    println!("  Version:     {version}");
-    println!("  Binary:      ruv-neural");
-    println!();
-    println!("  Crate Versions:");
-    println!("    ruv-neural-core     {version}");
-    println!("    ruv-neural-sensor   {version}");
-    println!("    ruv-neural-signal   {version}");
-    println!("    ruv-neural-graph    {version}");
-    println!("    ruv-neural-mincut   {version}");
-    println!("    ruv-neural-embed    {version}");
-    println!("    ruv-neural-memory   {version}");
-    println!("    ruv-neural-decoder  {version}");
-    println!("    ruv-neural-viz      {version}");
-    println!("    ruv-neural-cli      {version}");
-    println!();
-    println!("  Features:");
-    println!("    Sensor simulation       [available]");
-    println!("    Signal processing       [available]");
-    println!("    Bandpass filtering       [available]  (Butterworth IIR, SOS form)");
-    println!("    Artifact rejection       [available]  (eye blink, muscle, cardiac)");
-    println!("    PLV connectivity         [available]  (phase locking value)");
-    println!("    Coherence metrics        [available]  (coherence, imaginary coherence)");
-    println!("    Stoer-Wagner mincut      [available]  (global minimum cut)");
-    println!("    Normalized cut           [available]  (Shi-Malik spectral bisection)");
-    println!("    Multi-way cut            [available]  (recursive normalized cut)");
-    println!("    Spectral embedding       [available]  (Laplacian eigenvector encoding)");
-    println!("    Topology embedding       [available]  (hand-crafted topological features)");
-    println!("    Node2Vec embedding       [available]  (random walk co-occurrence)");
-    println!("    Threshold decoder        [available]  (rule-based cognitive state)");
-    println!("    KNN decoder              [available]  (k-nearest neighbor classifier)");
-    println!("    Force-directed layout    [available]  (Fruchterman-Reingold)");
-    println!("    Anatomical layout        [available]  (MNI coordinate-based)");
-    println!();
-    println!("  Export Formats:");
-    println!("    D3.js JSON              [available]");
-    println!("    Graphviz DOT            [available]");
-    println!("    GEXF (Graph Exchange)   [available]");
-    println!("    CSV edge list           [available]");
-    println!("    RVF (RuVector File)     [available]");
-    println!();
-    println!("  Pipeline:");
-    println!("    simulate -> filter -> PLV graph -> mincut -> embed -> decode");
-    println!();
-    println!("  Platform:");
-    println!("    OS:           {}", std::env::consts::OS);
-    println!("    Arch:         {}", std::env::consts::ARCH);
-    println!("    Family:       {}", std::env::consts::FAMILY);
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn info_runs_without_panic() {
-        run();
-    }
-}
@@ -1,184 +0,0 @@
-//! Compute minimum cut on a brain connectivity graph.
-
-use std::fs;
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_mincut::{multiway_cut, stoer_wagner_mincut};
-
-/// Run the mincut command.
-pub fn run(input: &str, k: Option<usize>) -> Result<(), Box<dyn std::error::Error>> {
-    tracing::info!(input, ?k, "Computing minimum cut");
-
-    let json =
-        fs::read_to_string(input).map_err(|e| format!("Failed to read {input}: {e}"))?;
-    let graph: BrainGraph =
-        serde_json::from_str(&json).map_err(|e| format!("Failed to parse graph JSON: {e}"))?;
-
-    println!("=== rUv Neural — Minimum Cut Analysis ===");
-    println!();
-    println!("  Graph: {} nodes, {} edges", graph.num_nodes, graph.edges.len());
-    println!();
-
-    match k {
-        Some(k_val) if k_val > 2 => {
-            // Multi-way cut.
-            let result = multiway_cut(&graph, k_val)
-                .map_err(|e| format!("Multiway cut failed: {e}"))?;
-
-            println!("  Multi-way cut (k={k_val}):");
-            println!("    Total cut value: {:.4}", result.cut_value);
-            println!("    Modularity:      {:.4}", result.modularity);
-            println!("    Partitions:      {}", result.num_partitions());
-            println!();
-
-            for (i, partition) in result.partitions.iter().enumerate() {
-                println!("    Partition {i}: {} nodes {:?}", partition.len(), partition);
-            }
-            println!();
-
-            // ASCII visualization of partitions.
-            print_partition_ascii(&graph, &result.partitions);
-        }
-        _ => {
-            // Standard two-way Stoer-Wagner.
-            let mc = stoer_wagner_mincut(&graph)
-                .map_err(|e| format!("Stoer-Wagner mincut failed: {e}"))?;
-
-            println!("  Stoer-Wagner minimum cut:");
-            println!("    Cut value:     {:.4}", mc.cut_value);
-            println!("    Partition A:   {} nodes {:?}", mc.partition_a.len(), mc.partition_a);
-            println!("    Partition B:   {} nodes {:?}", mc.partition_b.len(), mc.partition_b);
-            println!("    Balance ratio: {:.4}", mc.balance_ratio());
-            println!();
-
-            println!("  Cut edges:");
-            for (src, tgt, weight) in &mc.cut_edges {
-                println!("    {src} -- {tgt}  (weight: {weight:.4})");
-            }
-            println!();
-
-            // ASCII visualization of the two partitions.
-            print_partition_ascii(&graph, &[mc.partition_a.clone(), mc.partition_b.clone()]);
-        }
-    }
-
-    Ok(())
-}
-
-/// Print an ASCII visualization of the graph partitions.
-fn print_partition_ascii(graph: &BrainGraph, partitions: &[Vec<usize>]) {
-    println!("  Partition layout:");
-
-    // Build a node-to-partition map.
-    let mut node_partition = vec![0usize; graph.num_nodes];
-    for (pid, partition) in partitions.iter().enumerate() {
-        for &node in partition {
-            if node < graph.num_nodes {
-                node_partition[node] = pid;
-            }
-        }
-    }
-
-    // Label characters for partitions.
-    let labels = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'];
-
-    let n = graph.num_nodes.min(40);
-    print!("    ");
-    for i in 0..n {
-        let pid = node_partition[i];
-        let ch = labels.get(pid).copied().unwrap_or('?');
-        print!("{ch}");
-    }
-    println!();
-
-    if graph.num_nodes > 40 {
-        println!("    ... ({} nodes total)", graph.num_nodes);
-    }
-
-    println!();
-    for (pid, partition) in partitions.iter().enumerate() {
-        let ch = labels.get(pid).copied().unwrap_or('?');
-        println!("    {ch} = {} nodes", partition.len());
-    }
-    println!();
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn test_graph() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 6,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 5.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 5.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 3,
-                    target: 4,
-                    weight: 5.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 4,
-                    target: 5,
-                    weight: 5.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 2,
-                    target: 3,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        }
-    }
-
-    #[test]
-    fn mincut_two_way() {
-        let graph = test_graph();
-        let dir = std::env::temp_dir();
-        let path = dir.join("ruv_neural_test_mincut.json");
-        let json = serde_json::to_string_pretty(&graph).unwrap();
-        std::fs::write(&path, json).unwrap();
-
-        let result = run(&path.to_string_lossy(), None);
-        assert!(result.is_ok());
-        std::fs::remove_file(&path).ok();
-    }
-
-    #[test]
-    fn mincut_multiway() {
-        let graph = test_graph();
-        let dir = std::env::temp_dir();
-        let path = dir.join("ruv_neural_test_mincut_k.json");
-        let json = serde_json::to_string_pretty(&graph).unwrap();
-        std::fs::write(&path, json).unwrap();
-
-        let result = run(&path.to_string_lossy(), Some(3));
-        assert!(result.is_ok());
-        std::fs::remove_file(&path).ok();
-    }
-}
@@ -1,9 +0,0 @@
-//! CLI command implementations.
-
-pub mod analyze;
-pub mod export;
-pub mod info;
-pub mod mincut;
-pub mod pipeline;
-pub mod simulate;
-pub mod witness;
@@ -1,377 +0,0 @@
-//! Full end-to-end pipeline: simulate -> process -> analyze -> decode.
-
-use std::f64::consts::PI;
-
-use ruv_neural_core::brain::Atlas;
-use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-use ruv_neural_core::signal::{FrequencyBand, MultiChannelTimeSeries};
-use ruv_neural_core::topology::CognitiveState;
-use ruv_neural_decoder::ThresholdDecoder;
-use ruv_neural_embed::spectral_embed::SpectralEmbedder;
-use ruv_neural_embed::topology_embed::TopologyEmbedder;
-use ruv_neural_mincut::stoer_wagner_mincut;
-use ruv_neural_signal::connectivity::phase_locking_value;
-use ruv_neural_signal::filter::BandpassFilter;
-
-/// Run the full pipeline command.
-pub fn run(
-    channels: usize,
-    duration: f64,
-    dashboard: bool,
-) -> Result<(), Box<dyn std::error::Error>> {
-    let sample_rate = 1000.0;
-    let num_samples = (duration * sample_rate) as usize;
-
-    println!("=== rUv Neural — Full Pipeline ===");
-    println!();
-
-    // Step 1: Generate simulated sensor data.
-    println!("  [1/7] Generating simulated sensor data...");
-    let raw_data = generate_data(channels, num_samples, sample_rate);
-    let ts = MultiChannelTimeSeries::new(raw_data.clone(), sample_rate, 0.0)
-        .map_err(|e| format!("Time series creation failed: {e}"))?;
-    println!("        {channels} channels, {num_samples} samples, {duration:.1}s");
-
-    // Step 2: Preprocess (bandpass filter 1-100 Hz).
-    println!("  [2/7] Preprocessing (bandpass 1-100 Hz)...");
-    let filter = BandpassFilter::new(4, 1.0, 100.0, sample_rate);
-    let filtered: Vec<Vec<f64>> = raw_data
-        .iter()
-        .map(|ch| {
-            use ruv_neural_signal::filter::SignalProcessor;
-            filter.process(ch)
-        })
-        .collect();
-    println!("        Bandpass filter applied to all channels");
-
-    // Step 3: Construct brain graph via PLV connectivity.
-    println!("  [3/7] Constructing brain connectivity graph (PLV)...");
-    let graph = build_plv_graph(&filtered, sample_rate);
-    println!(
-        "        {} nodes, {} edges, density {:.4}",
-        graph.num_nodes,
-        graph.edges.len(),
-        graph.density()
-    );
-
-    // Step 4: Compute mincut and topology metrics.
-    println!("  [4/7] Computing minimum cut and topology metrics...");
-    let mc = stoer_wagner_mincut(&graph)
-        .map_err(|e| format!("Mincut failed: {e}"))?;
-    println!("        Cut value: {:.4}, balance: {:.4}", mc.cut_value, mc.balance_ratio());
-    println!(
-        "        Partition A: {} nodes, Partition B: {} nodes",
-        mc.partition_a.len(),
-        mc.partition_b.len()
-    );
-
-    // Step 5: Generate embedding.
-    println!("  [5/7] Generating topology embedding...");
-    let embedder = TopologyEmbedder::new();
-    let embedding = embedder.embed_graph(&graph)
-        .map_err(|e| format!("Embedding failed: {e}"))?;
-    println!("        Dimension: {}, norm: {:.4}", embedding.dimension, embedding.norm());
-
-    // Also generate spectral embedding.
-    let spectral_dim = channels.min(8).max(2);
-    let spectral = SpectralEmbedder::new(spectral_dim);
-    let spectral_emb = spectral.embed_graph(&graph)
-        .map_err(|e| format!("Spectral embedding failed: {e}"))?;
-    println!(
-        "        Spectral embedding: dim={}, norm={:.4}",
-        spectral_emb.dimension,
-        spectral_emb.norm()
-    );
-
-    // Step 6: Decode cognitive state.
-    println!("  [6/7] Decoding cognitive state...");
-    let decoder = build_default_decoder();
-    let metrics = ruv_neural_core::topology::TopologyMetrics {
-        global_mincut: mc.cut_value,
-        modularity: estimate_modularity(&graph),
-        global_efficiency: estimate_efficiency(&graph),
-        local_efficiency: 0.0,
-        graph_entropy: estimate_entropy(&graph),
-        fiedler_value: 0.0,
-        num_modules: 2,
-        timestamp: graph.timestamp,
-    };
-    let (state, confidence) = decoder.decode(&metrics);
-    println!("        State:      {state:?}");
-    println!("        Confidence: {confidence:.4}");
-
-    // Step 7: Display results.
-    println!("  [7/7] Results summary");
-    println!();
-
-    println!("  ┌─────────────────────────────────────────┐");
-    println!("  │         Pipeline Results Summary         │");
-    println!("  ├─────────────────────────────────────────┤");
-    println!("  │  Channels:         {:<20} │", channels);
-    println!("  │  Duration:         {:<20} │", format!("{duration:.1} s"));
-    println!("  │  Graph density:    {:<20} │", format!("{:.4}", graph.density()));
-    println!("  │  Mincut value:     {:<20} │", format!("{:.4}", mc.cut_value));
-    println!("  │  Balance ratio:    {:<20} │", format!("{:.4}", mc.balance_ratio()));
-    println!("  │  Modularity:       {:<20} │", format!("{:.4}", metrics.modularity));
-    println!("  │  Graph entropy:    {:<20} │", format!("{:.4}", metrics.graph_entropy));
-    println!("  │  Embedding dim:    {:<20} │", embedding.dimension);
-    println!("  │  Cognitive state:  {:<20} │", format!("{state:?}"));
-    println!("  │  Confidence:       {:<20} │", format!("{confidence:.4}"));
-    println!("  └─────────────────────────────────────────┘");
-    println!();
-
-    if dashboard {
-        print_dashboard(&ts, &graph, &mc, &metrics);
-    }
-
-    Ok(())
-}
-
-/// Generate synthetic multi-channel neural data.
-fn generate_data(channels: usize, num_samples: usize, sample_rate: f64) -> Vec<Vec<f64>> {
-    let mut data = Vec::with_capacity(channels);
-    for ch in 0..channels {
-        let mut channel_data = Vec::with_capacity(num_samples);
-        let phase = (ch as f64) * PI / (channels as f64);
-        let mut rng: u64 = (ch as u64).wrapping_mul(2862933555777941757).wrapping_add(3037000493);
-
-        for i in 0..num_samples {
-            let t = i as f64 / sample_rate;
-            let alpha = 50.0 * (2.0 * PI * 10.0 * t + phase).sin();
-            let beta = 30.0 * (2.0 * PI * 20.0 * t + phase * 1.3).sin();
-            let gamma = 15.0 * (2.0 * PI * 40.0 * t + phase * 0.7).sin();
-
-            rng = rng.wrapping_mul(6364136223846793005).wrapping_add(1442695040888963407);
-            let u1 = (rng >> 11) as f64 / (1u64 << 53) as f64;
-            rng = rng.wrapping_mul(6364136223846793005).wrapping_add(1442695040888963407);
-            let u2 = (rng >> 11) as f64 / (1u64 << 53) as f64;
-            let noise = if u1 > 1e-15 {
-                5.0 * (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos()
-            } else {
-                0.0
-            };
-
-            channel_data.push(alpha + beta + gamma + noise);
-        }
-        data.push(channel_data);
-    }
-    data
-}
-
-/// Build a brain graph from PLV connectivity between all channel pairs.
-fn build_plv_graph(channels: &[Vec<f64>], sample_rate: f64) -> BrainGraph {
-    let n = channels.len();
-    let mut edges = Vec::new();
-    let plv_threshold = 0.3;
-
-    for i in 0..n {
-        for j in (i + 1)..n {
-            let plv = phase_locking_value(&channels[i], &channels[j], sample_rate, FrequencyBand::Alpha);
-            if plv > plv_threshold {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: plv,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-    }
-
-    BrainGraph {
-        num_nodes: n,
-        edges,
-        timestamp: 0.0,
-        window_duration_s: 1.0,
-        atlas: Atlas::Custom(n),
-    }
-}
-
-/// Estimate modularity using a simple degree-based partition.
-fn estimate_modularity(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return 0.0;
-    }
-    let total = graph.total_weight();
-    if total < 1e-12 {
-        return 0.0;
-    }
-
-    let adj = graph.adjacency_matrix();
-    let degrees: Vec<f64> = (0..n).map(|i| graph.node_degree(i)).collect();
-    let two_m = 2.0 * total;
-
-    // Simple bisection: first half vs second half.
-    let mid = n / 2;
-    let mut q = 0.0;
-    for i in 0..n {
-        for j in 0..n {
-            let same_community = (i < mid && j < mid) || (i >= mid && j >= mid);
-            if same_community {
-                q += adj[i][j] - degrees[i] * degrees[j] / two_m;
-            }
-        }
-    }
-    q / two_m
-}
-
-/// Estimate global efficiency (mean inverse shortest path).
-fn estimate_efficiency(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return 0.0;
-    }
-    // Use adjacency weights directly as a rough proxy.
-    let adj = graph.adjacency_matrix();
-    let mut sum = 0.0;
-    let mut count = 0;
-    for i in 0..n {
-        for j in (i + 1)..n {
-            if adj[i][j] > 0.0 {
-                sum += adj[i][j]; // weight as proxy for efficiency
-            }
-            count += 1;
-        }
-    }
-    if count == 0 {
-        return 0.0;
-    }
-    sum / count as f64
-}
-
-/// Estimate graph entropy from edge weight distribution.
-fn estimate_entropy(graph: &BrainGraph) -> f64 {
-    let total = graph.total_weight();
-    if total < 1e-12 || graph.edges.is_empty() {
-        return 0.0;
-    }
-    let mut entropy = 0.0;
-    for edge in &graph.edges {
-        let p = edge.weight / total;
-        if p > 1e-15 {
-            entropy -= p * p.ln();
-        }
-    }
-    entropy
-}
-
-/// Build a threshold decoder with default state definitions.
-fn build_default_decoder() -> ThresholdDecoder {
-    let mut decoder = ThresholdDecoder::new();
-
-    decoder.set_threshold(
-        CognitiveState::Rest,
-        ruv_neural_decoder::TopologyThreshold {
-            mincut_range: (0.0, 5.0),
-            modularity_range: (0.2, 0.6),
-            efficiency_range: (0.1, 0.4),
-            entropy_range: (1.0, 3.0),
-        },
-    );
-
-    decoder.set_threshold(
-        CognitiveState::Focused,
-        ruv_neural_decoder::TopologyThreshold {
-            mincut_range: (3.0, 15.0),
-            modularity_range: (0.4, 0.8),
-            efficiency_range: (0.3, 0.7),
-            entropy_range: (2.0, 4.0),
-        },
-    );
-
-    decoder.set_threshold(
-        CognitiveState::MotorPlanning,
-        ruv_neural_decoder::TopologyThreshold {
-            mincut_range: (2.0, 10.0),
-            modularity_range: (0.3, 0.7),
-            efficiency_range: (0.2, 0.6),
-            entropy_range: (1.5, 3.5),
-        },
-    );
-
-    decoder
-}
-
-/// Print a real-time-style ASCII dashboard.
-fn print_dashboard(
-    ts: &MultiChannelTimeSeries,
-    graph: &BrainGraph,
-    mc: &ruv_neural_core::topology::MincutResult,
-    metrics: &ruv_neural_core::topology::TopologyMetrics,
-) {
-    println!("  ╔═══════════════════════════════════════════════════╗");
-    println!("  ║           rUv Neural — Live Dashboard             ║");
-    println!("  ╠═══════════════════════════════════════════════════╣");
-    println!("  ║                                                   ║");
-
-    // Signal sparkline for first few channels.
-    let display_channels = ts.num_channels.min(6);
-    let display_samples = ts.num_samples.min(50);
-    let sparkline_chars = ['▁', '▂', '▃', '▄', '▅', '▆', '▇', '█'];
-
-    for ch in 0..display_channels {
-        let data = &ts.data[ch];
-        let min_val = data.iter().cloned().fold(f64::INFINITY, f64::min);
-        let max_val = data.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
-        let range = max_val - min_val;
-
-        let step = ts.num_samples / display_samples;
-        let mut sparkline = String::new();
-        for i in 0..display_samples {
-            let val = data[i * step];
-            let normalized = if range > 1e-12 {
-                ((val - min_val) / range * 7.0) as usize
-            } else {
-                4
-            };
-            sparkline.push(sparkline_chars[normalized.min(7)]);
-        }
-        println!("  ║  Ch{ch:02}: {sparkline} ║");
-    }
-
-    println!("  ║                                                   ║");
-    println!("  ║  Graph:  {} nodes, {} edges              ║",
-        format!("{:>3}", graph.num_nodes),
-        format!("{:>4}", graph.edges.len()),
-    );
-    println!("  ║  Mincut: {:.4}  Balance: {:.4}              ║", mc.cut_value, mc.balance_ratio());
-    println!("  ║  Modularity: {:.4}  Entropy: {:.4}          ║", metrics.modularity, metrics.graph_entropy);
-    println!("  ║                                                   ║");
-    println!("  ╚═══════════════════════════════════════════════════╝");
-    println!();
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn pipeline_runs_end_to_end() {
-        let result = run(4, 1.0, false);
-        assert!(result.is_ok());
-    }
-
-    #[test]
-    fn pipeline_with_dashboard() {
-        let result = run(4, 0.5, true);
-        assert!(result.is_ok());
-    }
-
-    #[test]
-    fn plv_graph_has_edges() {
-        let data = generate_data(4, 1000, 1000.0);
-        let graph = build_plv_graph(&data, 1000.0);
-        assert_eq!(graph.num_nodes, 4);
-        // Channels with similar phase should have some PLV connectivity.
-    }
-
-    #[test]
-    fn entropy_non_negative() {
-        let data = generate_data(4, 1000, 1000.0);
-        let graph = build_plv_graph(&data, 1000.0);
-        let e = estimate_entropy(&graph);
-        assert!(e >= 0.0);
-    }
-}
@@ -1,156 +0,0 @@
-//! Simulate neural sensor data and write to JSON or stdout.
-
-use std::f64::consts::PI;
-use std::fs;
-
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-
-/// Run the simulate command.
-///
-/// Generates synthetic multi-channel neural data with configurable alpha,
-/// beta, and gamma oscillations plus realistic noise.
-pub fn run(
-    channels: usize,
-    duration: f64,
-    sample_rate: f64,
-    output: Option<String>,
-) -> Result<(), Box<dyn std::error::Error>> {
-    let num_samples = (duration * sample_rate) as usize;
-    if num_samples == 0 {
-        return Err("Duration and sample rate must produce at least one sample".into());
-    }
-
-    tracing::info!(
-        channels,
-        num_samples,
-        sample_rate,
-        duration,
-        "Generating simulated neural data"
-    );
-
-    let data = generate_neural_data(channels, num_samples, sample_rate);
-
-    let ts = MultiChannelTimeSeries::new(data.clone(), sample_rate, 0.0).map_err(|e| {
-        Box::<dyn std::error::Error>::from(format!("Failed to create time series: {e}"))
-    })?;
-
-    // Compute summary statistics.
-    let mut channel_rms = Vec::with_capacity(channels);
-    for ch in 0..channels {
-        let rms = (data[ch].iter().map(|x| x * x).sum::<f64>() / num_samples as f64).sqrt();
-        channel_rms.push(rms);
-    }
-    let mean_rms = channel_rms.iter().sum::<f64>() / channels as f64;
-
-    println!("=== rUv Neural — Simulation Complete ===");
-    println!();
-    println!("  Channels:      {channels}");
-    println!("  Samples:       {num_samples}");
-    println!("  Duration:      {duration:.2} s");
-    println!("  Sample rate:   {sample_rate:.1} Hz");
-    println!("  Mean RMS:      {mean_rms:.4} fT");
-    println!();
-
-    // Show frequency content summary.
-    println!("  Frequency content:");
-    println!("    Alpha (8-13 Hz):   10 Hz sinusoid, 50 fT amplitude");
-    println!("    Beta  (13-30 Hz):  20 Hz sinusoid, 30 fT amplitude");
-    println!("    Gamma (30-100 Hz): 40 Hz sinusoid, 15 fT amplitude");
-    println!("    Noise floor:       ~10 fT/sqrt(Hz) white noise");
-    println!();
-
-    match output {
-        Some(ref path) => {
-            let json = serde_json::to_string_pretty(&ts)?;
-            fs::write(path, json)?;
-            println!("  Output written to: {path}");
-        }
-        None => {
-            println!("  (Use -o <file> to save output to JSON)");
-        }
-    }
-
-    Ok(())
-}
-
-/// Generate synthetic neural data with realistic oscillations and noise.
-fn generate_neural_data(channels: usize, num_samples: usize, sample_rate: f64) -> Vec<Vec<f64>> {
-    // Use a deterministic seed based on channel index for reproducibility.
-    let mut data = Vec::with_capacity(channels);
-
-    for ch in 0..channels {
-        let mut channel_data = Vec::with_capacity(num_samples);
-        // Phase offsets vary by channel to simulate spatial diversity.
-        let phase_offset = (ch as f64) * PI / (channels as f64);
-
-        // Simple LCG for deterministic pseudo-random noise per channel.
-        let mut rng_state: u64 = (ch as u64).wrapping_mul(6364136223846793005).wrapping_add(1);
-
-        for i in 0..num_samples {
-            let t = i as f64 / sample_rate;
-
-            // Alpha rhythm: 10 Hz, 50 fT
-            let alpha = 50.0 * (2.0 * PI * 10.0 * t + phase_offset).sin();
-
-            // Beta rhythm: 20 Hz, 30 fT
-            let beta = 30.0 * (2.0 * PI * 20.0 * t + phase_offset * 1.3).sin();
-
-            // Gamma rhythm: 40 Hz, 15 fT
-            let gamma = 15.0 * (2.0 * PI * 40.0 * t + phase_offset * 0.7).sin();
-
-            // White noise (~10 fT/sqrt(Hz) density).
-            // Approximate Gaussian via Box-Muller with LCG.
-            rng_state = rng_state.wrapping_mul(6364136223846793005).wrapping_add(1442695040888963407);
-            let u1 = (rng_state >> 11) as f64 / (1u64 << 53) as f64;
-            rng_state = rng_state.wrapping_mul(6364136223846793005).wrapping_add(1442695040888963407);
-            let u2 = (rng_state >> 11) as f64 / (1u64 << 53) as f64;
-
-            let noise_amplitude = 10.0 * (sample_rate / 2.0).sqrt();
-            let gaussian = if u1 > 1e-15 {
-                (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos()
-            } else {
-                0.0
-            };
-            let noise = noise_amplitude * gaussian / (num_samples as f64).sqrt() * 0.1;
-
-            channel_data.push(alpha + beta + gamma + noise);
-        }
-
-        data.push(channel_data);
-    }
-
-    data
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn generate_correct_shape() {
-        let data = generate_neural_data(8, 500, 1000.0);
-        assert_eq!(data.len(), 8);
-        for ch in &data {
-            assert_eq!(ch.len(), 500);
-        }
-    }
-
-    #[test]
-    fn simulate_produces_output() {
-        let result = run(4, 1.0, 500.0, None);
-        assert!(result.is_ok());
-    }
-
-    #[test]
-    fn simulate_writes_json() {
-        let dir = std::env::temp_dir();
-        let path = dir.join("ruv_neural_test_sim.json");
-        let path_str = path.to_string_lossy().to_string();
-        let result = run(2, 0.5, 250.0, Some(path_str.clone()));
-        assert!(result.is_ok());
-        assert!(path.exists());
-        let contents = std::fs::read_to_string(&path).unwrap();
-        let _ts: MultiChannelTimeSeries = serde_json::from_str(&contents).unwrap();
-        std::fs::remove_file(&path).ok();
-    }
-}
@@ -1,91 +0,0 @@
-//! Generate and verify Ed25519-signed capability witness bundles.
-
-use ruv_neural_core::witness::{attest_capabilities, WitnessBundle};
-use std::path::PathBuf;
-
-/// Run the witness command.
-pub fn run(
-    output: Option<PathBuf>,
-    verify: Option<PathBuf>,
-) -> Result<(), Box<dyn std::error::Error>> {
-    if let Some(path) = verify {
-        // Verify mode
-        let json = std::fs::read_to_string(&path)?;
-        let bundle: WitnessBundle = serde_json::from_str(&json)?;
-
-        println!("=== rUv Neural \u{2014} Witness Verification ===\n");
-        println!("  Version:   {}", bundle.version);
-        println!("  Commit:    {}", bundle.commit);
-        println!(
-            "  Tests:     {}/{} passed",
-            bundle.tests_passed, bundle.total_tests
-        );
-        println!("  Caps:      {} attestations", bundle.capabilities.len());
-        println!(
-            "  Public Key: {}...{}",
-            &bundle.public_key[..8],
-            &bundle.public_key[bundle.public_key.len() - 8..]
-        );
-        println!();
-
-        // Verify digest
-        let digest_ok = bundle.verify_digest();
-        println!(
-            "  Digest integrity: {}",
-            if digest_ok { "PASS" } else { "FAIL" }
-        );
-
-        // Verify signature
-        match bundle.verify() {
-            Ok(true) => println!("  Ed25519 signature: PASS"),
-            Ok(false) => println!("  Ed25519 signature: FAIL"),
-            Err(e) => println!("  Ed25519 signature: ERROR ({e})"),
-        }
-
-        let verdict = match bundle.verify_full() {
-            Ok(true) => "PASS",
-            _ => "FAIL",
-        };
-        println!("\n  VERDICT: {verdict}");
-
-        if verdict == "FAIL" {
-            std::process::exit(1);
-        }
-    } else {
-        // Generate mode
-        let caps = attest_capabilities();
-        let bundle = WitnessBundle::new(
-            env!("CARGO_PKG_VERSION"),
-            "0.1.0",
-            333,
-            333,
-            0,
-            caps,
-        );
-
-        let json = serde_json::to_string_pretty(&bundle)?;
-
-        if let Some(path) = output {
-            std::fs::write(&path, &json)?;
-            println!("Witness bundle written to {}", path.display());
-        } else {
-            println!("{json}");
-        }
-
-        println!("\n  Attestations: {}", bundle.capabilities.len());
-        println!("  Digest: {}", bundle.capabilities_digest);
-        println!(
-            "  Signature: {}...{}",
-            &bundle.signature[..16],
-            &bundle.signature[bundle.signature.len() - 16..]
-        );
-        println!(
-            "  Public Key: {}...{}",
-            &bundle.public_key[..8],
-            &bundle.public_key[bundle.public_key.len() - 8..]
-        );
-        println!("\n  VERDICT: SIGNED");
-    }
-
-    Ok(())
-}
@@ -1,301 +0,0 @@
-//! rUv Neural CLI — Brain topology analysis, simulation, and visualization.
-
-mod commands;
-
-use clap::{Parser, Subcommand};
-
-#[derive(Parser)]
-#[command(name = "ruv-neural")]
-#[command(about = "rUv Neural — Brain Topology Analysis System")]
-#[command(version)]
-struct Cli {
-    #[command(subcommand)]
-    command: Commands,
-
-    /// Verbosity level
-    #[arg(short, long, action = clap::ArgAction::Count)]
-    verbose: u8,
-}
-
-#[derive(Subcommand)]
-enum Commands {
-    /// Simulate neural sensor data
-    Simulate {
-        /// Number of channels
-        #[arg(short, long, default_value = "64")]
-        channels: usize,
-        /// Duration in seconds
-        #[arg(short, long, default_value = "10.0")]
-        duration: f64,
-        /// Sample rate in Hz
-        #[arg(short, long, default_value = "1000.0")]
-        sample_rate: f64,
-        /// Output file (JSON)
-        #[arg(short, long)]
-        output: Option<String>,
-    },
-    /// Analyze a brain connectivity graph
-    Analyze {
-        /// Input graph file (JSON)
-        #[arg(short, long)]
-        input: String,
-        /// Show ASCII visualization
-        #[arg(long)]
-        ascii: bool,
-        /// Export metrics to CSV
-        #[arg(long)]
-        csv: Option<String>,
-    },
-    /// Compute minimum cut on brain graph
-    Mincut {
-        /// Input graph file (JSON)
-        #[arg(short, long)]
-        input: String,
-        /// Multi-way cut with k partitions
-        #[arg(short, long)]
-        k: Option<usize>,
-    },
-    /// Run full pipeline: simulate -> process -> analyze -> decode
-    Pipeline {
-        /// Number of channels
-        #[arg(short, long, default_value = "32")]
-        channels: usize,
-        /// Duration in seconds
-        #[arg(short, long, default_value = "5.0")]
-        duration: f64,
-        /// Show real-time ASCII dashboard
-        #[arg(long)]
-        dashboard: bool,
-    },
-    /// Export brain graph to visualization format
-    Export {
-        /// Input graph file (JSON)
-        #[arg(short, long)]
-        input: String,
-        /// Output format: d3, dot, gexf, csv, rvf
-        #[arg(short, long, default_value = "d3")]
-        format: String,
-        /// Output file
-        #[arg(short, long)]
-        output: String,
-    },
-    /// Show system info and capabilities
-    Info,
-    /// Generate or verify Ed25519-signed capability witness bundles
-    Witness {
-        /// Output file path for generated witness bundle (JSON)
-        #[arg(short, long)]
-        output: Option<String>,
-        /// Path to a witness bundle to verify
-        #[arg(long)]
-        verify: Option<String>,
-    },
-}
-
-fn init_tracing(verbose: u8) {
-    let level = match verbose {
-        0 => tracing::Level::WARN,
-        1 => tracing::Level::INFO,
-        2 => tracing::Level::DEBUG,
-        _ => tracing::Level::TRACE,
-    };
-    tracing_subscriber::fmt()
-        .with_max_level(level)
-        .with_target(false)
-        .init();
-}
-
-#[tokio::main]
-async fn main() {
-    let cli = Cli::parse();
-    init_tracing(cli.verbose);
-
-    let result = match cli.command {
-        Commands::Simulate {
-            channels,
-            duration,
-            sample_rate,
-            output,
-        } => commands::simulate::run(channels, duration, sample_rate, output),
-        Commands::Analyze { input, ascii, csv } => commands::analyze::run(&input, ascii, csv),
-        Commands::Mincut { input, k } => commands::mincut::run(&input, k),
-        Commands::Pipeline {
-            channels,
-            duration,
-            dashboard,
-        } => commands::pipeline::run(channels, duration, dashboard),
-        Commands::Export {
-            input,
-            format,
-            output,
-        } => commands::export::run(&input, &format, &output),
-        Commands::Info => {
-            commands::info::run();
-            Ok(())
-        }
-        Commands::Witness { output, verify } => {
-            commands::witness::run(
-                output.map(std::path::PathBuf::from),
-                verify.map(std::path::PathBuf::from),
-            )
-        }
-    };
-
-    if let Err(e) = result {
-        eprintln!("Error: {e}");
-        std::process::exit(1);
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use clap::CommandFactory;
-
-    #[test]
-    fn verify_cli() {
-        Cli::command().debug_assert();
-    }
-
-    #[test]
-    fn parse_simulate_defaults() {
-        let cli = Cli::try_parse_from(["ruv-neural", "simulate"]).unwrap();
-        match cli.command {
-            Commands::Simulate {
-                channels,
-                duration,
-                sample_rate,
-                output,
-            } => {
-                assert_eq!(channels, 64);
-                assert!((duration - 10.0).abs() < 1e-9);
-                assert!((sample_rate - 1000.0).abs() < 1e-9);
-                assert!(output.is_none());
-            }
-            _ => panic!("Expected Simulate command"),
-        }
-    }
-
-    #[test]
-    fn parse_simulate_with_args() {
-        let cli = Cli::try_parse_from([
-            "ruv-neural",
-            "simulate",
-            "-c",
-            "32",
-            "-d",
-            "5.0",
-            "-s",
-            "500.0",
-            "-o",
-            "out.json",
-        ])
-        .unwrap();
-        match cli.command {
-            Commands::Simulate {
-                channels,
-                duration,
-                sample_rate,
-                output,
-            } => {
-                assert_eq!(channels, 32);
-                assert!((duration - 5.0).abs() < 1e-9);
-                assert!((sample_rate - 500.0).abs() < 1e-9);
-                assert_eq!(output.as_deref(), Some("out.json"));
-            }
-            _ => panic!("Expected Simulate command"),
-        }
-    }
-
-    #[test]
-    fn parse_analyze() {
-        let cli =
-            Cli::try_parse_from(["ruv-neural", "analyze", "-i", "graph.json", "--ascii"]).unwrap();
-        match cli.command {
-            Commands::Analyze { input, ascii, csv } => {
-                assert_eq!(input, "graph.json");
-                assert!(ascii);
-                assert!(csv.is_none());
-            }
-            _ => panic!("Expected Analyze command"),
-        }
-    }
-
-    #[test]
-    fn parse_mincut() {
-        let cli = Cli::try_parse_from(["ruv-neural", "mincut", "-i", "graph.json", "-k", "4"])
-            .unwrap();
-        match cli.command {
-            Commands::Mincut { input, k } => {
-                assert_eq!(input, "graph.json");
-                assert_eq!(k, Some(4));
-            }
-            _ => panic!("Expected Mincut command"),
-        }
-    }
-
-    #[test]
-    fn parse_pipeline() {
-        let cli = Cli::try_parse_from([
-            "ruv-neural",
-            "pipeline",
-            "-c",
-            "16",
-            "-d",
-            "3.0",
-            "--dashboard",
-        ])
-        .unwrap();
-        match cli.command {
-            Commands::Pipeline {
-                channels,
-                duration,
-                dashboard,
-            } => {
-                assert_eq!(channels, 16);
-                assert!((duration - 3.0).abs() < 1e-9);
-                assert!(dashboard);
-            }
-            _ => panic!("Expected Pipeline command"),
-        }
-    }
-
-    #[test]
-    fn parse_export() {
-        let cli = Cli::try_parse_from([
-            "ruv-neural",
-            "export",
-            "-i",
-            "graph.json",
-            "-f",
-            "dot",
-            "-o",
-            "out.dot",
-        ])
-        .unwrap();
-        match cli.command {
-            Commands::Export {
-                input,
-                format,
-                output,
-            } => {
-                assert_eq!(input, "graph.json");
-                assert_eq!(format, "dot");
-                assert_eq!(output, "out.dot");
-            }
-            _ => panic!("Expected Export command"),
-        }
-    }
-
-    #[test]
-    fn parse_info() {
-        let cli = Cli::try_parse_from(["ruv-neural", "info"]).unwrap();
-        assert!(matches!(cli.command, Commands::Info));
-    }
-
-    #[test]
-    fn parse_verbose() {
-        let cli = Cli::try_parse_from(["ruv-neural", "-vvv", "info"]).unwrap();
-        assert_eq!(cli.verbose, 3);
-    }
-}
@@ -1,25 +0,0 @@
-[package]
-name = "ruv-neural-core"
-description = "rUv Neural — Core types, traits, and error types for brain topology analysis"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-repository.workspace = true
-keywords = ["neural", "brain", "topology", "types", "core"]
-
-[features]
-default = ["std"]
-std = []
-no_std = []  # For ESP32/embedded targets
-wasm = []    # For WASM targets
-rvf = []     # RuVector RVF format support
-
-[dependencies]
-thiserror = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-num-traits = { workspace = true }
-ed25519-dalek = { workspace = true }
-sha2 = { workspace = true }
-rand = { workspace = true }
@@ -1,102 +0,0 @@
-# ruv-neural-core
-
-Core types, traits, and error types for the rUv Neural brain topology analysis system.
-
-## Overview
-
-`ruv-neural-core` is the foundation crate of the rUv Neural workspace. It defines all
-shared data types, trait interfaces, and the RVF binary file format used across the
-other eleven crates. This crate has **zero** internal dependencies -- every other
-ruv-neural crate depends on it.
-
-## Features
-
- **Sensor types**: `SensorType`, `SensorChannel`, `SensorArray` with sensitivity specs
-  for NV diamond, OPM, SQUID MEG, and EEG sensors
- **Signal types**: `MultiChannelTimeSeries`, `FrequencyBand` (delta through gamma + custom),
-  `SpectralFeatures`, `TimeFrequencyMap`
- **Brain atlas**: `Atlas` (Desikan-Killiany 68, Destrieux 148, Schaefer 100/200/400, custom),
-  `BrainRegion`, `Parcellation` with hemisphere and lobe queries
- **Graph types**: `BrainGraph` with adjacency matrix, density, and degree methods;
-  `BrainEdge`, `ConnectivityMetric`, `BrainGraphSequence`
- **Topology types**: `MincutResult`, `MultiPartition`, `TopologyMetrics`, `CognitiveState`,
-  `SleepStage`
- **Embedding types**: `NeuralEmbedding` with cosine similarity and Euclidean distance,
-  `EmbeddingTrajectory`, `EmbeddingMetadata`
- **RVF format**: Binary RuVector File format with magic bytes, versioned headers,
-  typed payloads, and read/write round-trip support
- **Trait definitions**: `SensorSource`, `SignalProcessor`, `GraphConstructor`,
-  `TopologyAnalyzer`, `EmbeddingGenerator`, `NeuralMemory`, `StateDecoder`,
-  `RvfSerializable`
- **Error handling**: `RuvNeuralError` enum with `DimensionMismatch`, `ChannelOutOfRange`,
-  `InsufficientData`, and domain-specific variants
- **Feature flags**: `std` (default), `no_std` (ESP32/embedded), `wasm`, `rvf`
-
-## Usage
-
-```rust
-use ruv_neural_core::{
-    BrainGraph, BrainEdge, ConnectivityMetric, FrequencyBand, Atlas,
-    NeuralEmbedding, EmbeddingMetadata, CognitiveState,
-    MultiChannelTimeSeries, RvfFile, RvfDataType,
-};
-
-// Create a brain graph
-let graph = BrainGraph {
-    num_nodes: 3,
-    edges: vec![BrainEdge {
-        source: 0, target: 1, weight: 0.8,
-        metric: ConnectivityMetric::PhaseLockingValue,
-        frequency_band: FrequencyBand::Alpha,
-    }],
-    timestamp: 0.0,
-    window_duration_s: 1.0,
-    atlas: Atlas::DesikanKilliany68,
-};
-let matrix = graph.adjacency_matrix();
-let density = graph.density();
-
-// Create a neural embedding
-let meta = EmbeddingMetadata {
-    subject_id: Some("sub-01".into()),
-    session_id: None,
-    cognitive_state: Some(CognitiveState::Focused),
-    source_atlas: Atlas::Schaefer100,
-    embedding_method: "spectral".into(),
-};
-let emb = NeuralEmbedding::new(vec![3.0, 4.0], 1000.0, meta).unwrap();
-assert_eq!(emb.dimension, 2);
-assert!((emb.norm() - 5.0).abs() < 1e-10);
-
-// Write/read RVF files
-let mut rvf = RvfFile::new(RvfDataType::BrainGraph);
-rvf.data = serde_json::to_vec(&graph).unwrap();
-let mut buf = Vec::new();
-rvf.write_to(&mut buf).unwrap();
-```
-
-## API Reference
-
-| Module      | Key Types                                                      |
-|-------------|----------------------------------------------------------------|
-| `sensor`    | `SensorType`, `SensorChannel`, `SensorArray`                   |
-| `signal`    | `MultiChannelTimeSeries`, `FrequencyBand`, `SpectralFeatures`  |
-| `brain`     | `Atlas`, `BrainRegion`, `Parcellation`, `Hemisphere`, `Lobe`   |
-| `graph`     | `BrainGraph`, `BrainEdge`, `ConnectivityMetric`                |
-| `topology`  | `MincutResult`, `TopologyMetrics`, `CognitiveState`            |
-| `embedding` | `NeuralEmbedding`, `EmbeddingTrajectory`, `EmbeddingMetadata`  |
-| `rvf`       | `RvfFile`, `RvfHeader`, `RvfDataType`                          |
-| `traits`    | `SensorSource`, `SignalProcessor`, `EmbeddingGenerator`, etc.  |
-| `error`     | `RuvNeuralError`, `Result<T>`                                  |
-
-## Integration
-
-This crate is a dependency of every other crate in the ruv-neural workspace.
-It provides the shared type vocabulary that allows crates to interoperate --
-for example, `ruv-neural-signal` produces `MultiChannelTimeSeries` values,
-`ruv-neural-graph` consumes them, and `ruv-neural-embed` outputs
-`NeuralEmbedding` values that `ruv-neural-memory` stores.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,103 +0,0 @@
-//! Brain region and atlas types for parcellation.
-
-use serde::{Deserialize, Serialize};
-
-/// Brain atlas defining a parcellation scheme.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum Atlas {
-    /// Desikan-Killiany atlas (68 cortical regions).
-    DesikanKilliany68,
-    /// Destrieux atlas (148 cortical regions).
-    Destrieux148,
-    /// Schaefer 100-parcel atlas.
-    Schaefer100,
-    /// Schaefer 200-parcel atlas.
-    Schaefer200,
-    /// Schaefer 400-parcel atlas.
-    Schaefer400,
-    /// Custom atlas with a specified number of regions.
-    Custom(usize),
-}
-
-impl Atlas {
-    /// Number of regions in this atlas.
-    pub fn num_regions(&self) -> usize {
-        match self {
-            Atlas::DesikanKilliany68 => 68,
-            Atlas::Destrieux148 => 148,
-            Atlas::Schaefer100 => 100,
-            Atlas::Schaefer200 => 200,
-            Atlas::Schaefer400 => 400,
-            Atlas::Custom(n) => *n,
-        }
-    }
-}
-
-/// Cerebral hemisphere.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum Hemisphere {
-    Left,
-    Right,
-    Midline,
-}
-
-/// Brain lobe classification.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum Lobe {
-    Frontal,
-    Parietal,
-    Temporal,
-    Occipital,
-    Limbic,
-    Subcortical,
-    Cerebellar,
-}
-
-/// A single brain region (parcel) within an atlas.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct BrainRegion {
-    /// Region index within the atlas.
-    pub id: usize,
-    /// Human-readable name (e.g., "superiorfrontal").
-    pub name: String,
-    /// Hemisphere.
-    pub hemisphere: Hemisphere,
-    /// Lobe classification.
-    pub lobe: Lobe,
-    /// Centroid in MNI coordinates (x, y, z in mm).
-    pub centroid: [f64; 3],
-}
-
-/// A full brain parcellation (atlas + all regions).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct Parcellation {
-    /// Atlas used.
-    pub atlas: Atlas,
-    /// All regions in the parcellation.
-    pub regions: Vec<BrainRegion>,
-}
-
-impl Parcellation {
-    /// Number of regions.
-    pub fn num_regions(&self) -> usize {
-        self.regions.len()
-    }
-
-    /// Get a region by its id.
-    pub fn get_region(&self, id: usize) -> Option<&BrainRegion> {
-        self.regions.iter().find(|r| r.id == id)
-    }
-
-    /// Get all regions in a given hemisphere.
-    pub fn regions_in_hemisphere(&self, hemisphere: Hemisphere) -> Vec<&BrainRegion> {
-        self.regions
-            .iter()
-            .filter(|r| r.hemisphere == hemisphere)
-            .collect()
-    }
-
-    /// Get all regions in a given lobe.
-    pub fn regions_in_lobe(&self, lobe: Lobe) -> Vec<&BrainRegion> {
-        self.regions.iter().filter(|r| r.lobe == lobe).collect()
-    }
-}
@@ -1,126 +0,0 @@
-//! Vector embedding types for neural state representations.
-
-use serde::{Deserialize, Serialize};
-
-use crate::brain::Atlas;
-use crate::error::{Result, RuvNeuralError};
-use crate::topology::CognitiveState;
-
-/// Neural state embedding vector.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct NeuralEmbedding {
-    /// The embedding vector.
-    pub vector: Vec<f64>,
-    /// Dimensionality of the embedding.
-    pub dimension: usize,
-    /// Timestamp (Unix time).
-    pub timestamp: f64,
-    /// Associated metadata.
-    pub metadata: EmbeddingMetadata,
-}
-
-impl NeuralEmbedding {
-    /// Create a new embedding, validating dimension consistency.
-    pub fn new(vector: Vec<f64>, timestamp: f64, metadata: EmbeddingMetadata) -> Result<Self> {
-        let dimension = vector.len();
-        if dimension == 0 {
-            return Err(RuvNeuralError::Embedding(
-                "Embedding vector must not be empty".into(),
-            ));
-        }
-        Ok(Self {
-            vector,
-            dimension,
-            timestamp,
-            metadata,
-        })
-    }
-
-    /// L2 norm of the embedding vector.
-    pub fn norm(&self) -> f64 {
-        self.vector.iter().map(|x| x * x).sum::<f64>().sqrt()
-    }
-
-    /// Cosine similarity to another embedding.
-    pub fn cosine_similarity(&self, other: &NeuralEmbedding) -> Result<f64> {
-        if self.dimension != other.dimension {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: self.dimension,
-                got: other.dimension,
-            });
-        }
-        let dot: f64 = self
-            .vector
-            .iter()
-            .zip(other.vector.iter())
-            .map(|(a, b)| a * b)
-            .sum();
-        let norm_a = self.norm();
-        let norm_b = other.norm();
-        if norm_a == 0.0 || norm_b == 0.0 {
-            return Ok(0.0);
-        }
-        Ok(dot / (norm_a * norm_b))
-    }
-
-    /// Euclidean distance to another embedding.
-    pub fn euclidean_distance(&self, other: &NeuralEmbedding) -> Result<f64> {
-        if self.dimension != other.dimension {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: self.dimension,
-                got: other.dimension,
-            });
-        }
-        let sum_sq: f64 = self
-            .vector
-            .iter()
-            .zip(other.vector.iter())
-            .map(|(a, b)| (a - b) * (a - b))
-            .sum();
-        Ok(sum_sq.sqrt())
-    }
-}
-
-/// Metadata associated with a neural embedding.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct EmbeddingMetadata {
-    /// Subject identifier.
-    pub subject_id: Option<String>,
-    /// Session identifier.
-    pub session_id: Option<String>,
-    /// Decoded cognitive state (if available).
-    pub cognitive_state: Option<CognitiveState>,
-    /// Atlas used for the source graph.
-    pub source_atlas: Atlas,
-    /// Name of the embedding method (e.g., "spectral", "node2vec").
-    pub embedding_method: String,
-}
-
-/// Temporal sequence of embeddings (trajectory through embedding space).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct EmbeddingTrajectory {
-    /// Ordered sequence of embeddings.
-    pub embeddings: Vec<NeuralEmbedding>,
-    /// Timestamps for each embedding.
-    pub timestamps: Vec<f64>,
-}
-
-impl EmbeddingTrajectory {
-    /// Number of time points.
-    pub fn len(&self) -> usize {
-        self.embeddings.len()
-    }
-
-    /// Returns true if the trajectory is empty.
-    pub fn is_empty(&self) -> bool {
-        self.embeddings.is_empty()
-    }
-
-    /// Total duration in seconds.
-    pub fn duration_s(&self) -> f64 {
-        if self.timestamps.len() < 2 {
-            return 0.0;
-        }
-        self.timestamps.last().unwrap() - self.timestamps.first().unwrap()
-    }
-}
@@ -1,46 +0,0 @@
-//! Error types for the ruv-neural pipeline.
-
-use thiserror::Error;
-
-/// Top-level error type for the ruv-neural system.
-#[derive(Error, Debug)]
-pub enum RuvNeuralError {
-    #[error("Sensor error: {0}")]
-    Sensor(String),
-
-    #[error("Signal processing error: {0}")]
-    Signal(String),
-
-    #[error("Graph construction error: {0}")]
-    Graph(String),
-
-    #[error("Mincut computation error: {0}")]
-    Mincut(String),
-
-    #[error("Embedding error: {0}")]
-    Embedding(String),
-
-    #[error("Memory error: {0}")]
-    Memory(String),
-
-    #[error("Decoder error: {0}")]
-    Decoder(String),
-
-    #[error("Serialization error: {0}")]
-    Serialization(String),
-
-    #[error("Invalid configuration: {0}")]
-    Config(String),
-
-    #[error("Dimension mismatch: expected {expected}, got {got}")]
-    DimensionMismatch { expected: usize, got: usize },
-
-    #[error("Channel {channel} out of range (max {max})")]
-    ChannelOutOfRange { channel: usize, max: usize },
-
-    #[error("Insufficient data: need {needed} samples, have {have}")]
-    InsufficientData { needed: usize, have: usize },
-}
-
-/// Convenience result type for the ruv-neural system.
-pub type Result<T> = std::result::Result<T, RuvNeuralError>;
@@ -1,171 +0,0 @@
-//! Brain connectivity graph types.
-
-use serde::{Deserialize, Serialize};
-
-use crate::brain::Atlas;
-use crate::error::{Result, RuvNeuralError};
-use crate::signal::FrequencyBand;
-
-/// Connectivity metric used to compute edge weights.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum ConnectivityMetric {
-    /// Phase locking value.
-    PhaseLockingValue,
-    /// Amplitude envelope correlation.
-    AmplitudeEnvelopeCorrelation,
-    /// Weighted phase lag index.
-    WeightedPhaseLagIndex,
-    /// Coherence.
-    Coherence,
-    /// Granger causality.
-    GrangerCausality,
-    /// Transfer entropy.
-    TransferEntropy,
-    /// Mutual information.
-    MutualInformation,
-}
-
-/// An edge in the brain connectivity graph.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct BrainEdge {
-    /// Source node index.
-    pub source: usize,
-    /// Target node index.
-    pub target: usize,
-    /// Edge weight (connectivity strength).
-    pub weight: f64,
-    /// Metric used to compute this edge.
-    pub metric: ConnectivityMetric,
-    /// Frequency band for this connectivity estimate.
-    pub frequency_band: FrequencyBand,
-}
-
-/// Brain connectivity graph at a single time window.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct BrainGraph {
-    /// Number of nodes (brain regions).
-    pub num_nodes: usize,
-    /// Edges with connectivity weights.
-    pub edges: Vec<BrainEdge>,
-    /// Timestamp of this graph window (Unix time).
-    pub timestamp: f64,
-    /// Duration of the analysis window in seconds.
-    pub window_duration_s: f64,
-    /// Atlas used for parcellation.
-    pub atlas: Atlas,
-}
-
-impl BrainGraph {
-    /// Validate graph integrity: edge bounds, weight finiteness, no self-loops.
-    pub fn validate(&self) -> Result<()> {
-        for (i, edge) in self.edges.iter().enumerate() {
-            if edge.source >= self.num_nodes {
-                return Err(RuvNeuralError::Graph(format!(
-                    "Edge {i}: source {} out of bounds (num_nodes={})",
-                    edge.source, self.num_nodes
-                )));
-            }
-            if edge.target >= self.num_nodes {
-                return Err(RuvNeuralError::Graph(format!(
-                    "Edge {i}: target {} out of bounds (num_nodes={})",
-                    edge.target, self.num_nodes
-                )));
-            }
-            if edge.source == edge.target {
-                return Err(RuvNeuralError::Graph(format!(
-                    "Edge {i}: self-loop on node {}",
-                    edge.source
-                )));
-            }
-            if !edge.weight.is_finite() {
-                return Err(RuvNeuralError::Graph(format!(
-                    "Edge {i}: non-finite weight {}",
-                    edge.weight
-                )));
-            }
-        }
-        Ok(())
-    }
-
-    /// Build a dense adjacency matrix (num_nodes x num_nodes).
-    /// For duplicate edges, the last one wins.
-    pub fn adjacency_matrix(&self) -> Vec<Vec<f64>> {
-        let n = self.num_nodes;
-        let mut mat = vec![vec![0.0; n]; n];
-        for edge in &self.edges {
-            if edge.source < n && edge.target < n {
-                mat[edge.source][edge.target] = edge.weight;
-                mat[edge.target][edge.source] = edge.weight;
-            }
-        }
-        mat
-    }
-
-    /// Get the weight of the edge between source and target, if it exists.
-    pub fn edge_weight(&self, source: usize, target: usize) -> Option<f64> {
-        self.edges
-            .iter()
-            .find(|e| {
-                (e.source == source && e.target == target)
-                    || (e.source == target && e.target == source)
-            })
-            .map(|e| e.weight)
-    }
-
-    /// Weighted degree of a node (sum of incident edge weights).
-    pub fn node_degree(&self, node: usize) -> f64 {
-        self.edges
-            .iter()
-            .filter(|e| e.source == node || e.target == node)
-            .map(|e| e.weight)
-            .sum()
-    }
-
-    /// Graph density: ratio of actual edges to possible edges.
-    pub fn density(&self) -> f64 {
-        if self.num_nodes < 2 {
-            return 0.0;
-        }
-        let max_edges = self.num_nodes * (self.num_nodes - 1) / 2;
-        if max_edges == 0 {
-            return 0.0;
-        }
-        self.edges.len() as f64 / max_edges as f64
-    }
-
-    /// Total weight of all edges.
-    pub fn total_weight(&self) -> f64 {
-        self.edges.iter().map(|e| e.weight).sum()
-    }
-}
-
-/// Temporal sequence of brain graphs.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct BrainGraphSequence {
-    /// Ordered sequence of graphs.
-    pub graphs: Vec<BrainGraph>,
-    /// Step between successive windows in seconds.
-    pub window_step_s: f64,
-}
-
-impl BrainGraphSequence {
-    /// Number of time points.
-    pub fn len(&self) -> usize {
-        self.graphs.len()
-    }
-
-    /// Returns true if the sequence is empty.
-    pub fn is_empty(&self) -> bool {
-        self.graphs.is_empty()
-    }
-
-    /// Total duration covered by the sequence in seconds.
-    pub fn duration_s(&self) -> f64 {
-        if self.graphs.is_empty() {
-            return 0.0;
-        }
-        let first = self.graphs.first().unwrap();
-        let last = self.graphs.last().unwrap();
-        (last.timestamp - first.timestamp) + last.window_duration_s
-    }
-}
@@ -1,646 +0,0 @@
-//! # ruv-neural-core
-//!
-//! Core types, traits, and error types for the ruv-neural brain topology
-//! analysis system.
-//!
-//! This crate is the foundation of the ruv-neural workspace. It has **zero**
-//! internal dependencies — all other ruv-neural crates depend on this one.
-//!
-//! ## Modules
-//!
-//! | Module      | Contents                                          |
-//! |-------------|---------------------------------------------------|
-//! | `error`     | `RuvNeuralError` enum, `Result<T>` alias           |
-//! | `sensor`    | `SensorType`, `SensorChannel`, `SensorArray`       |
-//! | `signal`    | `MultiChannelTimeSeries`, `FrequencyBand`, spectra |
-//! | `brain`     | `Atlas`, `BrainRegion`, `Parcellation`             |
-//! | `graph`     | `BrainGraph`, `BrainEdge`, `ConnectivityMetric`    |
-//! | `topology`  | `MincutResult`, `CognitiveState`, `TopologyMetrics`|
-//! | `embedding` | `NeuralEmbedding`, `EmbeddingTrajectory`           |
-//! | `rvf`       | RuVector File format header and I/O                |
-//! | `traits`    | Pipeline trait definitions for all crates          |
-
-pub mod brain;
-pub mod embedding;
-pub mod error;
-pub mod graph;
-pub mod rvf;
-pub mod sensor;
-pub mod signal;
-pub mod topology;
-pub mod traits;
-pub mod witness;
-
-// Re-export the most commonly used types at crate root.
-pub use brain::{Atlas, BrainRegion, Hemisphere, Lobe, Parcellation};
-pub use embedding::{EmbeddingMetadata, EmbeddingTrajectory, NeuralEmbedding};
-pub use error::{Result, RuvNeuralError};
-pub use graph::{BrainEdge, BrainGraph, BrainGraphSequence, ConnectivityMetric};
-pub use rvf::{RvfDataType, RvfFile, RvfHeader};
-pub use sensor::{SensorArray, SensorChannel, SensorType};
-pub use signal::{FrequencyBand, MultiChannelTimeSeries, SpectralFeatures, TimeFrequencyMap};
-pub use topology::{
-    CognitiveState, MincutResult, MultiPartition, SleepStage, TopologyMetrics,
-};
-pub use traits::{
-    EmbeddingGenerator, GraphConstructor, NeuralMemory, RvfSerializable, SensorSource,
-    SignalProcessor, StateDecoder, TopologyAnalyzer,
-};
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    // ── Error tests ─────────────────────────────────────────────────
-
-    #[test]
-    fn error_display_formatting() {
-        let err = RuvNeuralError::Sensor("calibration failed".into());
-        assert!(err.to_string().contains("Sensor error"));
-        assert!(err.to_string().contains("calibration failed"));
-
-        let err = RuvNeuralError::DimensionMismatch {
-            expected: 68,
-            got: 100,
-        };
-        assert!(err.to_string().contains("68"));
-        assert!(err.to_string().contains("100"));
-
-        let err = RuvNeuralError::ChannelOutOfRange {
-            channel: 5,
-            max: 3,
-        };
-        assert!(err.to_string().contains("5"));
-        assert!(err.to_string().contains("3"));
-
-        let err = RuvNeuralError::InsufficientData {
-            needed: 1000,
-            have: 500,
-        };
-        assert!(err.to_string().contains("1000"));
-        assert!(err.to_string().contains("500"));
-    }
-
-    // ── Sensor tests ────────────────────────────────────────────────
-
-    #[test]
-    fn sensor_type_sensitivity() {
-        assert!(SensorType::SquidMeg.typical_sensitivity_ft_sqrt_hz() < 5.0);
-        assert!(SensorType::Eeg.typical_sensitivity_ft_sqrt_hz() > 100.0);
-    }
-
-    #[test]
-    fn sensor_array_operations() {
-        let array = SensorArray {
-            channels: vec![
-                SensorChannel {
-                    id: 0,
-                    sensor_type: SensorType::Opm,
-                    position: [0.0, 0.0, 0.1],
-                    orientation: [0.0, 0.0, 1.0],
-                    sensitivity_ft_sqrt_hz: 7.0,
-                    sample_rate_hz: 1000.0,
-                    label: "OPM-001".into(),
-                },
-                SensorChannel {
-                    id: 1,
-                    sensor_type: SensorType::Opm,
-                    position: [0.05, 0.0, 0.12],
-                    orientation: [0.0, 0.0, 1.0],
-                    sensitivity_ft_sqrt_hz: 7.0,
-                    sample_rate_hz: 1000.0,
-                    label: "OPM-002".into(),
-                },
-            ],
-            sensor_type: SensorType::Opm,
-            name: "OPM array".into(),
-        };
-
-        assert_eq!(array.num_channels(), 2);
-        assert!(!array.is_empty());
-        assert_eq!(array.get_channel(0).unwrap().label, "OPM-001");
-        assert!(array.get_channel(5).is_none());
-
-        let (min, max) = array.bounding_box().unwrap();
-        assert_eq!(min[0], 0.0);
-        assert_eq!(max[0], 0.05);
-    }
-
-    #[test]
-    fn sensor_serialize_roundtrip() {
-        let ch = SensorChannel {
-            id: 0,
-            sensor_type: SensorType::NvDiamond,
-            position: [1.0, 2.0, 3.0],
-            orientation: [0.0, 0.0, 1.0],
-            sensitivity_ft_sqrt_hz: 10.0,
-            sample_rate_hz: 2000.0,
-            label: "NV-001".into(),
-        };
-        let json = serde_json::to_string(&ch).unwrap();
-        let ch2: SensorChannel = serde_json::from_str(&json).unwrap();
-        assert_eq!(ch2.id, 0);
-        assert_eq!(ch2.sensor_type, SensorType::NvDiamond);
-    }
-
-    // ── Signal tests ────────────────────────────────────────────────
-
-    #[test]
-    fn frequency_band_ranges() {
-        assert_eq!(FrequencyBand::Delta.range_hz(), (1.0, 4.0));
-        assert_eq!(FrequencyBand::Alpha.range_hz(), (8.0, 13.0));
-        assert_eq!(FrequencyBand::Gamma.range_hz(), (30.0, 100.0));
-        assert_eq!(
-            FrequencyBand::Custom {
-                low_hz: 50.0,
-                high_hz: 70.0
-            }
-            .range_hz(),
-            (50.0, 70.0)
-        );
-    }
-
-    #[test]
-    fn frequency_band_center_and_bandwidth() {
-        assert!((FrequencyBand::Alpha.center_hz() - 10.5).abs() < 1e-10);
-        assert!((FrequencyBand::Alpha.bandwidth_hz() - 5.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn time_series_creation_valid() {
-        let data = vec![vec![1.0, 2.0, 3.0], vec![4.0, 5.0, 6.0]];
-        let ts = MultiChannelTimeSeries::new(data, 100.0, 1000.0).unwrap();
-        assert_eq!(ts.num_channels, 2);
-        assert_eq!(ts.num_samples, 3);
-        assert!((ts.duration_s() - 0.03).abs() < 1e-10);
-    }
-
-    #[test]
-    fn time_series_dimension_mismatch() {
-        let data = vec![vec![1.0, 2.0], vec![3.0]];
-        let result = MultiChannelTimeSeries::new(data, 100.0, 0.0);
-        assert!(result.is_err());
-    }
-
-    #[test]
-    fn time_series_channel_access() {
-        let data = vec![vec![10.0, 20.0], vec![30.0, 40.0]];
-        let ts = MultiChannelTimeSeries::new(data, 100.0, 0.0).unwrap();
-        assert_eq!(ts.channel(0).unwrap(), &[10.0, 20.0]);
-        assert!(ts.channel(5).is_err());
-    }
-
-    // ── Brain / Atlas tests ─────────────────────────────────────────
-
-    #[test]
-    fn atlas_region_counts() {
-        assert_eq!(Atlas::DesikanKilliany68.num_regions(), 68);
-        assert_eq!(Atlas::Destrieux148.num_regions(), 148);
-        assert_eq!(Atlas::Schaefer100.num_regions(), 100);
-        assert_eq!(Atlas::Schaefer200.num_regions(), 200);
-        assert_eq!(Atlas::Schaefer400.num_regions(), 400);
-        assert_eq!(Atlas::Custom(42).num_regions(), 42);
-    }
-
-    #[test]
-    fn parcellation_query() {
-        let parcellation = Parcellation {
-            atlas: Atlas::Custom(3),
-            regions: vec![
-                BrainRegion {
-                    id: 0,
-                    name: "left_frontal".into(),
-                    hemisphere: Hemisphere::Left,
-                    lobe: Lobe::Frontal,
-                    centroid: [-30.0, 20.0, 40.0],
-                },
-                BrainRegion {
-                    id: 1,
-                    name: "right_frontal".into(),
-                    hemisphere: Hemisphere::Right,
-                    lobe: Lobe::Frontal,
-                    centroid: [30.0, 20.0, 40.0],
-                },
-                BrainRegion {
-                    id: 2,
-                    name: "left_temporal".into(),
-                    hemisphere: Hemisphere::Left,
-                    lobe: Lobe::Temporal,
-                    centroid: [-50.0, -10.0, 0.0],
-                },
-            ],
-        };
-
-        assert_eq!(parcellation.num_regions(), 3);
-        assert_eq!(
-            parcellation.regions_in_hemisphere(Hemisphere::Left).len(),
-            2
-        );
-        assert_eq!(parcellation.regions_in_lobe(Lobe::Frontal).len(), 2);
-        assert_eq!(parcellation.regions_in_lobe(Lobe::Temporal).len(), 1);
-        assert!(parcellation.get_region(1).is_some());
-        assert!(parcellation.get_region(99).is_none());
-    }
-
-    #[test]
-    fn brain_region_serialize_roundtrip() {
-        let region = BrainRegion {
-            id: 42,
-            name: "postcentral".into(),
-            hemisphere: Hemisphere::Left,
-            lobe: Lobe::Parietal,
-            centroid: [-40.0, -25.0, 55.0],
-        };
-        let json = serde_json::to_string(&region).unwrap();
-        let r2: BrainRegion = serde_json::from_str(&json).unwrap();
-        assert_eq!(r2.id, 42);
-        assert_eq!(r2.hemisphere, Hemisphere::Left);
-    }
-
-    // ── Graph tests ─────────────────────────────────────────────────
-
-    #[test]
-    fn brain_graph_adjacency_matrix() {
-        let graph = BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 0.8,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Beta,
-                },
-            ],
-            timestamp: 100.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        };
-
-        let mat = graph.adjacency_matrix();
-        assert_eq!(mat.len(), 3);
-        assert!((mat[0][1] - 0.8).abs() < 1e-10);
-        assert!((mat[1][0] - 0.8).abs() < 1e-10);
-        assert!((mat[1][2] - 0.5).abs() < 1e-10);
-        assert!((mat[0][2] - 0.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn brain_graph_edge_weight_lookup() {
-        let graph = BrainGraph {
-            num_nodes: 2,
-            edges: vec![BrainEdge {
-                source: 0,
-                target: 1,
-                weight: 0.9,
-                metric: ConnectivityMetric::MutualInformation,
-                frequency_band: FrequencyBand::Gamma,
-            }],
-            timestamp: 0.0,
-            window_duration_s: 0.5,
-            atlas: Atlas::Custom(2),
-        };
-
-        assert!((graph.edge_weight(0, 1).unwrap() - 0.9).abs() < 1e-10);
-        assert!((graph.edge_weight(1, 0).unwrap() - 0.9).abs() < 1e-10);
-        assert!(graph.edge_weight(0, 0).is_none());
-    }
-
-    #[test]
-    fn brain_graph_node_degree() {
-        let graph = BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 0.3,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 0,
-                    target: 2,
-                    weight: 0.7,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        };
-
-        assert!((graph.node_degree(0) - 1.0).abs() < 1e-10);
-        assert!((graph.node_degree(1) - 0.3).abs() < 1e-10);
-        assert!((graph.node_degree(2) - 0.7).abs() < 1e-10);
-    }
-
-    #[test]
-    fn brain_graph_density() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 2,
-                    target: 3,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 0,
-                    target: 3,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        assert!((graph.density() - 0.5).abs() < 1e-10);
-    }
-
-    #[test]
-    fn graph_sequence_duration() {
-        let seq = BrainGraphSequence {
-            graphs: vec![
-                BrainGraph {
-                    num_nodes: 2,
-                    edges: vec![],
-                    timestamp: 0.0,
-                    window_duration_s: 1.0,
-                    atlas: Atlas::Custom(2),
-                },
-                BrainGraph {
-                    num_nodes: 2,
-                    edges: vec![],
-                    timestamp: 0.5,
-                    window_duration_s: 1.0,
-                    atlas: Atlas::Custom(2),
-                },
-                BrainGraph {
-                    num_nodes: 2,
-                    edges: vec![],
-                    timestamp: 1.0,
-                    window_duration_s: 1.0,
-                    atlas: Atlas::Custom(2),
-                },
-            ],
-            window_step_s: 0.5,
-        };
-
-        assert_eq!(seq.len(), 3);
-        assert!(!seq.is_empty());
-        assert!((seq.duration_s() - 2.0).abs() < 1e-10);
-    }
-
-    // ── Topology tests ──────────────────────────────────────────────
-
-    #[test]
-    fn mincut_result_properties() {
-        let result = MincutResult {
-            cut_value: 1.5,
-            partition_a: vec![0, 1],
-            partition_b: vec![2, 3, 4],
-            cut_edges: vec![(1, 2, 0.8), (0, 3, 0.7)],
-            timestamp: 100.0,
-        };
-
-        assert_eq!(result.num_nodes(), 5);
-        assert_eq!(result.num_cut_edges(), 2);
-        assert!((result.balance_ratio() - 2.0 / 3.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn multi_partition_properties() {
-        let mp = MultiPartition {
-            partitions: vec![vec![0, 1], vec![2, 3], vec![4]],
-            cut_value: 2.0,
-            modularity: 0.4,
-        };
-        assert_eq!(mp.num_partitions(), 3);
-        assert_eq!(mp.num_nodes(), 5);
-    }
-
-    #[test]
-    fn cognitive_state_serialize_roundtrip() {
-        let states = vec![
-            CognitiveState::Rest,
-            CognitiveState::Focused,
-            CognitiveState::Sleep(SleepStage::Rem),
-            CognitiveState::Unknown,
-        ];
-        let json = serde_json::to_string(&states).unwrap();
-        let deserialized: Vec<CognitiveState> = serde_json::from_str(&json).unwrap();
-        assert_eq!(states, deserialized);
-    }
-
-    // ── Embedding tests ─────────────────────────────────────────────
-
-    #[test]
-    fn embedding_creation_and_norm() {
-        let meta = EmbeddingMetadata {
-            subject_id: Some("sub-01".into()),
-            session_id: Some("ses-01".into()),
-            cognitive_state: Some(CognitiveState::Focused),
-            source_atlas: Atlas::Schaefer100,
-            embedding_method: "spectral".into(),
-        };
-        let emb = NeuralEmbedding::new(vec![3.0, 4.0], 1000.0, meta).unwrap();
-        assert_eq!(emb.dimension, 2);
-        assert!((emb.norm() - 5.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn embedding_cosine_similarity() {
-        let meta = || EmbeddingMetadata {
-            subject_id: None,
-            session_id: None,
-            cognitive_state: None,
-            source_atlas: Atlas::Custom(2),
-            embedding_method: "test".into(),
-        };
-
-        let a = NeuralEmbedding::new(vec![1.0, 0.0], 0.0, meta()).unwrap();
-        let b = NeuralEmbedding::new(vec![1.0, 0.0], 0.0, meta()).unwrap();
-        let c = NeuralEmbedding::new(vec![0.0, 1.0], 0.0, meta()).unwrap();
-
-        assert!((a.cosine_similarity(&b).unwrap() - 1.0).abs() < 1e-10);
-        assert!((a.cosine_similarity(&c).unwrap() - 0.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn embedding_euclidean_distance() {
-        let meta = || EmbeddingMetadata {
-            subject_id: None,
-            session_id: None,
-            cognitive_state: None,
-            source_atlas: Atlas::Custom(2),
-            embedding_method: "test".into(),
-        };
-
-        let a = NeuralEmbedding::new(vec![0.0, 0.0], 0.0, meta()).unwrap();
-        let b = NeuralEmbedding::new(vec![3.0, 4.0], 0.0, meta()).unwrap();
-        assert!((a.euclidean_distance(&b).unwrap() - 5.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn embedding_dimension_mismatch() {
-        let meta = || EmbeddingMetadata {
-            subject_id: None,
-            session_id: None,
-            cognitive_state: None,
-            source_atlas: Atlas::Custom(2),
-            embedding_method: "test".into(),
-        };
-
-        let a = NeuralEmbedding::new(vec![1.0, 2.0], 0.0, meta()).unwrap();
-        let b = NeuralEmbedding::new(vec![1.0, 2.0, 3.0], 0.0, meta()).unwrap();
-        assert!(a.cosine_similarity(&b).is_err());
-        assert!(a.euclidean_distance(&b).is_err());
-    }
-
-    #[test]
-    fn embedding_trajectory() {
-        let meta = || EmbeddingMetadata {
-            subject_id: None,
-            session_id: None,
-            cognitive_state: None,
-            source_atlas: Atlas::Custom(2),
-            embedding_method: "test".into(),
-        };
-
-        let traj = EmbeddingTrajectory {
-            embeddings: vec![
-                NeuralEmbedding::new(vec![1.0], 0.0, meta()).unwrap(),
-                NeuralEmbedding::new(vec![2.0], 1.0, meta()).unwrap(),
-                NeuralEmbedding::new(vec![3.0], 2.0, meta()).unwrap(),
-            ],
-            timestamps: vec![0.0, 1.0, 2.0],
-        };
-
-        assert_eq!(traj.len(), 3);
-        assert!(!traj.is_empty());
-        assert!((traj.duration_s() - 2.0).abs() < 1e-10);
-    }
-
-    // ── RVF tests ───────────────────────────────────────────────────
-
-    #[test]
-    fn rvf_data_type_tag_roundtrip() {
-        for dt in [
-            RvfDataType::BrainGraph,
-            RvfDataType::NeuralEmbedding,
-            RvfDataType::TopologyMetrics,
-            RvfDataType::MincutResult,
-            RvfDataType::TimeSeriesChunk,
-        ] {
-            let tag = dt.to_tag();
-            let recovered = RvfDataType::from_tag(tag).unwrap();
-            assert_eq!(dt, recovered);
-        }
-        assert!(RvfDataType::from_tag(255).is_err());
-    }
-
-    #[test]
-    fn rvf_header_encode_decode() {
-        let header = RvfHeader::new(RvfDataType::NeuralEmbedding, 42, 128);
-        let bytes = header.to_bytes();
-        assert_eq!(bytes.len(), 22);
-
-        let decoded = RvfHeader::from_bytes(&bytes).unwrap();
-        assert_eq!(decoded.magic, rvf::RVF_MAGIC);
-        assert_eq!(decoded.version, rvf::RVF_VERSION);
-        assert_eq!(decoded.data_type, RvfDataType::NeuralEmbedding);
-        assert_eq!(decoded.num_entries, 42);
-        assert_eq!(decoded.embedding_dim, 128);
-    }
-
-    #[test]
-    fn rvf_header_validation() {
-        let mut header = RvfHeader::new(RvfDataType::BrainGraph, 1, 0);
-        assert!(header.validate().is_ok());
-
-        header.magic = [0, 0, 0, 0];
-        assert!(header.validate().is_err());
-    }
-
-    #[test]
-    fn rvf_file_write_read_roundtrip() {
-        let mut file = RvfFile::new(RvfDataType::TopologyMetrics);
-        file.header.num_entries = 1;
-        file.metadata = serde_json::json!({ "subject": "sub-01" });
-        file.data = vec![1, 2, 3, 4, 5];
-
-        let mut buf = Vec::new();
-        file.write_to(&mut buf).unwrap();
-
-        let mut cursor = std::io::Cursor::new(buf);
-        let recovered = RvfFile::read_from(&mut cursor).unwrap();
-
-        assert_eq!(recovered.header.data_type, RvfDataType::TopologyMetrics);
-        assert_eq!(recovered.header.num_entries, 1);
-        assert_eq!(recovered.metadata["subject"], "sub-01");
-        assert_eq!(recovered.data, vec![1, 2, 3, 4, 5]);
-    }
-
-    // ── Serialization roundtrip tests ───────────────────────────────
-
-    #[test]
-    fn graph_serialize_roundtrip() {
-        let graph = BrainGraph {
-            num_nodes: 2,
-            edges: vec![BrainEdge {
-                source: 0,
-                target: 1,
-                weight: 0.42,
-                metric: ConnectivityMetric::TransferEntropy,
-                frequency_band: FrequencyBand::Theta,
-            }],
-            timestamp: 999.0,
-            window_duration_s: 2.0,
-            atlas: Atlas::Schaefer200,
-        };
-        let json = serde_json::to_string(&graph).unwrap();
-        let g2: BrainGraph = serde_json::from_str(&json).unwrap();
-        assert_eq!(g2.num_nodes, 2);
-        assert_eq!(g2.edges.len(), 1);
-        assert!((g2.edges[0].weight - 0.42).abs() < 1e-10);
-    }
-
-    #[test]
-    fn topology_metrics_serialize_roundtrip() {
-        let metrics = TopologyMetrics {
-            global_mincut: 3.14,
-            modularity: 0.55,
-            global_efficiency: 0.72,
-            local_efficiency: 0.68,
-            graph_entropy: 2.3,
-            fiedler_value: 0.12,
-            num_modules: 4,
-            timestamp: 500.0,
-        };
-        let json = serde_json::to_string(&metrics).unwrap();
-        let m2: TopologyMetrics = serde_json::from_str(&json).unwrap();
-        assert!((m2.global_mincut - 3.14).abs() < 1e-10);
-        assert_eq!(m2.num_modules, 4);
-    }
-}
@@ -1,232 +0,0 @@
-//! RuVector File (RVF) format types for serialization.
-
-use serde::{Deserialize, Serialize};
-
-use crate::error::{Result, RuvNeuralError};
-
-/// Magic bytes for the RVF file format.
-pub const RVF_MAGIC: [u8; 4] = [b'R', b'V', b'F', 0x01];
-
-/// Current RVF format version.
-pub const RVF_VERSION: u8 = 1;
-
-/// Maximum allowed metadata JSON length (16 MiB).
-pub const MAX_METADATA_LEN: u32 = 16 * 1024 * 1024;
-
-/// Maximum allowed payload length when reading (256 MiB).
-pub const MAX_PAYLOAD_LEN: usize = 256 * 1024 * 1024;
-
-/// Data type stored in an RVF file.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum RvfDataType {
-    /// Brain connectivity graph.
-    BrainGraph,
-    /// Neural embedding vector.
-    NeuralEmbedding,
-    /// Topology metrics snapshot.
-    TopologyMetrics,
-    /// Mincut result.
-    MincutResult,
-    /// Time series chunk.
-    TimeSeriesChunk,
-}
-
-impl RvfDataType {
-    /// Convert to a byte tag for binary encoding.
-    pub fn to_tag(&self) -> u8 {
-        match self {
-            RvfDataType::BrainGraph => 0,
-            RvfDataType::NeuralEmbedding => 1,
-            RvfDataType::TopologyMetrics => 2,
-            RvfDataType::MincutResult => 3,
-            RvfDataType::TimeSeriesChunk => 4,
-        }
-    }
-
-    /// Parse a byte tag back to a data type.
-    pub fn from_tag(tag: u8) -> Result<Self> {
-        match tag {
-            0 => Ok(RvfDataType::BrainGraph),
-            1 => Ok(RvfDataType::NeuralEmbedding),
-            2 => Ok(RvfDataType::TopologyMetrics),
-            3 => Ok(RvfDataType::MincutResult),
-            4 => Ok(RvfDataType::TimeSeriesChunk),
-            _ => Err(RuvNeuralError::Serialization(format!(
-                "Unknown RVF data type tag: {}",
-                tag
-            ))),
-        }
-    }
-}
-
-/// RVF file header (fixed-size, 20 bytes).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct RvfHeader {
-    /// Magic bytes: `b"RVF\x01"`.
-    pub magic: [u8; 4],
-    /// Format version.
-    pub version: u8,
-    /// Type of data stored.
-    pub data_type: RvfDataType,
-    /// Number of entries in the file.
-    pub num_entries: u64,
-    /// Embedding dimensionality (0 if not applicable).
-    pub embedding_dim: u32,
-    /// Length of the JSON metadata section in bytes.
-    pub metadata_json_len: u32,
-}
-
-impl RvfHeader {
-    /// Create a new header with default magic and version.
-    pub fn new(data_type: RvfDataType, num_entries: u64, embedding_dim: u32) -> Self {
-        Self {
-            magic: RVF_MAGIC,
-            version: RVF_VERSION,
-            data_type,
-            num_entries,
-            embedding_dim,
-            metadata_json_len: 0,
-        }
-    }
-
-    /// Validate that this header has correct magic bytes and a known version.
-    pub fn validate(&self) -> Result<()> {
-        if self.magic != RVF_MAGIC {
-            return Err(RuvNeuralError::Serialization(
-                "Invalid RVF magic bytes".into(),
-            ));
-        }
-        if self.version != RVF_VERSION {
-            return Err(RuvNeuralError::Serialization(format!(
-                "Unsupported RVF version: {} (expected {})",
-                self.version, RVF_VERSION
-            )));
-        }
-        Ok(())
-    }
-
-    /// Encode the header to bytes (little-endian).
-    pub fn to_bytes(&self) -> Vec<u8> {
-        let mut buf = Vec::with_capacity(20);
-        buf.extend_from_slice(&self.magic);
-        buf.push(self.version);
-        buf.push(self.data_type.to_tag());
-        buf.extend_from_slice(&self.num_entries.to_le_bytes());
-        buf.extend_from_slice(&self.embedding_dim.to_le_bytes());
-        buf.extend_from_slice(&self.metadata_json_len.to_le_bytes());
-        buf
-    }
-
-    /// Decode a header from bytes.
-    pub fn from_bytes(bytes: &[u8]) -> Result<Self> {
-        if bytes.len() < 22 {
-            return Err(RuvNeuralError::Serialization(format!(
-                "RVF header too short: {} bytes (need 22)",
-                bytes.len()
-            )));
-        }
-        let mut magic = [0u8; 4];
-        magic.copy_from_slice(&bytes[0..4]);
-        let version = bytes[4];
-        let data_type = RvfDataType::from_tag(bytes[5])?;
-        let num_entries = u64::from_le_bytes(bytes[6..14].try_into().unwrap());
-        let embedding_dim = u32::from_le_bytes(bytes[14..18].try_into().unwrap());
-        let metadata_json_len = u32::from_le_bytes(bytes[18..22].try_into().unwrap());
-
-        Ok(Self {
-            magic,
-            version,
-            data_type,
-            num_entries,
-            embedding_dim,
-            metadata_json_len,
-        })
-    }
-}
-
-/// An RVF file containing header, metadata, and binary data.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct RvfFile {
-    /// File header.
-    pub header: RvfHeader,
-    /// JSON metadata.
-    pub metadata: serde_json::Value,
-    /// Raw binary payload.
-    pub data: Vec<u8>,
-}
-
-impl RvfFile {
-    /// Create a new empty RVF file for a given data type.
-    pub fn new(data_type: RvfDataType) -> Self {
-        Self {
-            header: RvfHeader::new(data_type, 0, 0),
-            metadata: serde_json::Value::Object(serde_json::Map::new()),
-            data: Vec::new(),
-        }
-    }
-
-    /// Write the RVF file to a writer.
-    pub fn write_to<W: std::io::Write>(&self, writer: &mut W) -> Result<()> {
-        let meta_bytes = serde_json::to_vec(&self.metadata)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        let mut header = self.header.clone();
-        header.metadata_json_len = meta_bytes.len() as u32;
-
-        writer
-            .write_all(&header.to_bytes())
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-        writer
-            .write_all(&meta_bytes)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-        writer
-            .write_all(&self.data)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        Ok(())
-    }
-
-    /// Read an RVF file from a reader.
-    pub fn read_from<R: std::io::Read>(reader: &mut R) -> Result<Self> {
-        let mut header_bytes = [0u8; 22];
-        reader
-            .read_exact(&mut header_bytes)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        let header = RvfHeader::from_bytes(&header_bytes)?;
-        header.validate()?;
-
-        if header.metadata_json_len > MAX_METADATA_LEN {
-            return Err(RuvNeuralError::Serialization(format!(
-                "RVF metadata length {} exceeds maximum {}",
-                header.metadata_json_len, MAX_METADATA_LEN
-            )));
-        }
-
-        let mut meta_bytes = vec![0u8; header.metadata_json_len as usize];
-        reader
-            .read_exact(&mut meta_bytes)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        let metadata: serde_json::Value = serde_json::from_slice(&meta_bytes)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        let mut data = Vec::new();
-        reader
-            .read_to_end(&mut data)
-            .map_err(|e| RuvNeuralError::Serialization(e.to_string()))?;
-
-        if data.len() > MAX_PAYLOAD_LEN {
-            return Err(RuvNeuralError::Serialization(format!(
-                "RVF payload length {} exceeds maximum {}",
-                data.len(), MAX_PAYLOAD_LEN
-            )));
-        }
-
-        Ok(Self {
-            header,
-            metadata,
-            data,
-        })
-    }
-}
@@ -1,98 +0,0 @@
-//! Sensor types for brain signal acquisition.
-
-use serde::{Deserialize, Serialize};
-
-/// Sensor technology type.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum SensorType {
-    /// Nitrogen-vacancy diamond magnetometer.
-    NvDiamond,
-    /// Optically pumped magnetometer.
-    Opm,
-    /// Electroencephalography.
-    Eeg,
-    /// Superconducting quantum interference device MEG.
-    SquidMeg,
-    /// Atom interferometer for gravitational neural sensing.
-    AtomInterferometer,
-}
-
-impl SensorType {
-    /// Typical sensitivity in fT/sqrt(Hz) for this sensor technology.
-    pub fn typical_sensitivity_ft_sqrt_hz(&self) -> f64 {
-        match self {
-            SensorType::NvDiamond => 10.0,
-            SensorType::Opm => 7.0,
-            SensorType::Eeg => 1000.0,
-            SensorType::SquidMeg => 3.0,
-            SensorType::AtomInterferometer => 1.0,
-        }
-    }
-}
-
-/// Sensor channel metadata.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct SensorChannel {
-    /// Channel index.
-    pub id: usize,
-    /// Type of sensor.
-    pub sensor_type: SensorType,
-    /// Position in head-frame coordinates (x, y, z in meters).
-    pub position: [f64; 3],
-    /// Orientation unit normal vector.
-    pub orientation: [f64; 3],
-    /// Sensitivity in fT/sqrt(Hz).
-    pub sensitivity_ft_sqrt_hz: f64,
-    /// Sampling rate in Hz.
-    pub sample_rate_hz: f64,
-    /// Human-readable label (e.g., "Fz", "OPM-L01").
-    pub label: String,
-}
-
-/// Sensor array configuration (a collection of channels of one type).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct SensorArray {
-    /// All channels in the array.
-    pub channels: Vec<SensorChannel>,
-    /// Sensor technology used by this array.
-    pub sensor_type: SensorType,
-    /// Human-readable name for the array.
-    pub name: String,
-}
-
-impl SensorArray {
-    /// Number of channels in the array.
-    pub fn num_channels(&self) -> usize {
-        self.channels.len()
-    }
-
-    /// Returns true if the array has no channels.
-    pub fn is_empty(&self) -> bool {
-        self.channels.is_empty()
-    }
-
-    /// Get a channel by its index within this array.
-    pub fn get_channel(&self, index: usize) -> Option<&SensorChannel> {
-        self.channels.get(index)
-    }
-
-    /// Get the bounding box of channel positions as ([min_x, min_y, min_z], [max_x, max_y, max_z]).
-    pub fn bounding_box(&self) -> Option<([f64; 3], [f64; 3])> {
-        if self.channels.is_empty() {
-            return None;
-        }
-        let mut min = [f64::INFINITY; 3];
-        let mut max = [f64::NEG_INFINITY; 3];
-        for ch in &self.channels {
-            for i in 0..3 {
-                if ch.position[i] < min[i] {
-                    min[i] = ch.position[i];
-                }
-                if ch.position[i] > max[i] {
-                    max[i] = ch.position[i];
-                }
-            }
-        }
-        Some((min, max))
-    }
-}
@@ -1,157 +0,0 @@
-//! Time series and signal types for neural data.
-
-use serde::{Deserialize, Serialize};
-
-use crate::error::{Result, RuvNeuralError};
-
-/// Multi-channel time series data.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct MultiChannelTimeSeries {
-    /// Raw data: `data[channel][sample]`.
-    pub data: Vec<Vec<f64>>,
-    /// Sampling rate in Hz.
-    pub sample_rate_hz: f64,
-    /// Number of channels.
-    pub num_channels: usize,
-    /// Number of samples per channel.
-    pub num_samples: usize,
-    /// Unix timestamp of the first sample.
-    pub timestamp_start: f64,
-}
-
-impl MultiChannelTimeSeries {
-    /// Create a new time series, validating dimensions.
-    pub fn new(data: Vec<Vec<f64>>, sample_rate_hz: f64, timestamp_start: f64) -> Result<Self> {
-        if !sample_rate_hz.is_finite() || sample_rate_hz <= 0.0 {
-            return Err(RuvNeuralError::Signal(
-                "sample_rate_hz must be finite and positive".into(),
-            ));
-        }
-        let num_channels = data.len();
-        if num_channels == 0 {
-            return Err(RuvNeuralError::Signal(
-                "Time series must have at least one channel".into(),
-            ));
-        }
-        let num_samples = data[0].len();
-        for (i, ch) in data.iter().enumerate() {
-            if ch.len() != num_samples {
-                return Err(RuvNeuralError::DimensionMismatch {
-                    expected: num_samples,
-                    got: ch.len(),
-                });
-            }
-            let _ = i; // suppress unused warning
-        }
-        Ok(Self {
-            data,
-            sample_rate_hz,
-            num_channels,
-            num_samples,
-            timestamp_start,
-        })
-    }
-
-    /// Duration in seconds.
-    pub fn duration_s(&self) -> f64 {
-        self.num_samples as f64 / self.sample_rate_hz
-    }
-
-    /// Get a single channel's data.
-    pub fn channel(&self, index: usize) -> Result<&[f64]> {
-        if index >= self.num_channels {
-            return Err(RuvNeuralError::ChannelOutOfRange {
-                channel: index,
-                max: self.num_channels.saturating_sub(1),
-            });
-        }
-        Ok(&self.data[index])
-    }
-}
-
-/// Frequency band definition for neural oscillations.
-#[derive(Debug, Clone, Copy, PartialEq, Serialize, Deserialize)]
-pub enum FrequencyBand {
-    /// Delta: 1-4 Hz (deep sleep, unconscious processing).
-    Delta,
-    /// Theta: 4-8 Hz (memory, navigation, meditation).
-    Theta,
-    /// Alpha: 8-13 Hz (relaxation, idling, inhibition).
-    Alpha,
-    /// Beta: 13-30 Hz (active thinking, focus, motor planning).
-    Beta,
-    /// Gamma: 30-100 Hz (binding, perception, consciousness).
-    Gamma,
-    /// High gamma: 100-200 Hz (cortical processing, fine motor).
-    HighGamma,
-    /// Custom frequency range.
-    Custom {
-        /// Lower bound in Hz.
-        low_hz: f64,
-        /// Upper bound in Hz.
-        high_hz: f64,
-    },
-}
-
-impl FrequencyBand {
-    /// Returns the (low, high) frequency range in Hz.
-    pub fn range_hz(&self) -> (f64, f64) {
-        match self {
-            FrequencyBand::Delta => (1.0, 4.0),
-            FrequencyBand::Theta => (4.0, 8.0),
-            FrequencyBand::Alpha => (8.0, 13.0),
-            FrequencyBand::Beta => (13.0, 30.0),
-            FrequencyBand::Gamma => (30.0, 100.0),
-            FrequencyBand::HighGamma => (100.0, 200.0),
-            FrequencyBand::Custom { low_hz, high_hz } => (*low_hz, *high_hz),
-        }
-    }
-
-    /// Center frequency in Hz.
-    pub fn center_hz(&self) -> f64 {
-        let (lo, hi) = self.range_hz();
-        (lo + hi) / 2.0
-    }
-
-    /// Bandwidth in Hz.
-    pub fn bandwidth_hz(&self) -> f64 {
-        let (lo, hi) = self.range_hz();
-        hi - lo
-    }
-}
-
-/// Spectral features for one channel at one time window.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct SpectralFeatures {
-    /// Power in each frequency band.
-    pub band_powers: Vec<(FrequencyBand, f64)>,
-    /// Spectral entropy (measure of signal complexity).
-    pub spectral_entropy: f64,
-    /// Peak frequency in Hz.
-    pub peak_frequency_hz: f64,
-    /// Total power across all bands.
-    pub total_power: f64,
-}
-
-/// Time-frequency representation (spectrogram-like).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct TimeFrequencyMap {
-    /// Data matrix: `data[time_window][frequency_bin]`.
-    pub data: Vec<Vec<f64>>,
-    /// Time points in seconds.
-    pub time_points: Vec<f64>,
-    /// Frequency bin centers in Hz.
-    pub frequency_bins: Vec<f64>,
-}
-
-impl TimeFrequencyMap {
-    /// Number of time windows.
-    pub fn num_time_points(&self) -> usize {
-        self.time_points.len()
-    }
-
-    /// Number of frequency bins.
-    pub fn num_frequency_bins(&self) -> usize {
-        self.frequency_bins.len()
-    }
-}
@@ -1,110 +0,0 @@
-//! Topology analysis result types (mincut, partition, metrics).
-
-use serde::{Deserialize, Serialize};
-
-/// Result of a minimum cut computation on a brain graph.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct MincutResult {
-    /// Value of the minimum cut.
-    pub cut_value: f64,
-    /// Node indices in partition A.
-    pub partition_a: Vec<usize>,
-    /// Node indices in partition B.
-    pub partition_b: Vec<usize>,
-    /// Cut edges: (source, target, weight).
-    pub cut_edges: Vec<(usize, usize, f64)>,
-    /// Timestamp of the source graph.
-    pub timestamp: f64,
-}
-
-impl MincutResult {
-    /// Total number of nodes across both partitions.
-    pub fn num_nodes(&self) -> usize {
-        self.partition_a.len() + self.partition_b.len()
-    }
-
-    /// Number of edges crossing the cut.
-    pub fn num_cut_edges(&self) -> usize {
-        self.cut_edges.len()
-    }
-
-    /// Balance ratio: min(|A|, |B|) / max(|A|, |B|).
-    pub fn balance_ratio(&self) -> f64 {
-        let a = self.partition_a.len() as f64;
-        let b = self.partition_b.len() as f64;
-        if a == 0.0 || b == 0.0 {
-            return 0.0;
-        }
-        a.min(b) / a.max(b)
-    }
-}
-
-/// Multi-way partition result.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct MultiPartition {
-    /// Each inner vec is a set of node indices forming one partition.
-    pub partitions: Vec<Vec<usize>>,
-    /// Total cut value.
-    pub cut_value: f64,
-    /// Newman-Girvan modularity score.
-    pub modularity: f64,
-}
-
-impl MultiPartition {
-    /// Number of partitions (modules).
-    pub fn num_partitions(&self) -> usize {
-        self.partitions.len()
-    }
-
-    /// Total number of nodes.
-    pub fn num_nodes(&self) -> usize {
-        self.partitions.iter().map(|p| p.len()).sum()
-    }
-}
-
-/// Cognitive state derived from brain topology analysis.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum CognitiveState {
-    Rest,
-    Focused,
-    MotorPlanning,
-    SpeechProcessing,
-    MemoryEncoding,
-    MemoryRetrieval,
-    Creative,
-    Stressed,
-    Fatigued,
-    Sleep(SleepStage),
-    Unknown,
-}
-
-/// Sleep stage classification.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash, Serialize, Deserialize)]
-pub enum SleepStage {
-    Wake,
-    N1,
-    N2,
-    N3,
-    Rem,
-}
-
-/// Topology metrics computed from a brain graph at a single time point.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct TopologyMetrics {
-    /// Global minimum cut value.
-    pub global_mincut: f64,
-    /// Newman-Girvan modularity.
-    pub modularity: f64,
-    /// Global efficiency (inverse path length).
-    pub global_efficiency: f64,
-    /// Mean local efficiency.
-    pub local_efficiency: f64,
-    /// Graph entropy (edge weight distribution).
-    pub graph_entropy: f64,
-    /// Fiedler value (algebraic connectivity, second smallest Laplacian eigenvalue).
-    pub fiedler_value: f64,
-    /// Number of detected modules.
-    pub num_modules: usize,
-    /// Timestamp of the source graph.
-    pub timestamp: f64,
-}
@@ -1,93 +0,0 @@
-//! Pipeline trait definitions that downstream crates implement.
-
-use crate::embedding::NeuralEmbedding;
-use crate::error::Result;
-use crate::graph::BrainGraph;
-use crate::rvf::RvfFile;
-use crate::sensor::SensorType;
-use crate::signal::MultiChannelTimeSeries;
-use crate::topology::{CognitiveState, MincutResult, TopologyMetrics};
-
-/// Trait for sensor data sources (hardware or simulated).
-pub trait SensorSource {
-    /// The sensor technology used by this source.
-    fn sensor_type(&self) -> SensorType;
-
-    /// Number of channels available.
-    fn num_channels(&self) -> usize;
-
-    /// Sampling rate in Hz.
-    fn sample_rate_hz(&self) -> f64;
-
-    /// Read a chunk of `num_samples` from the source.
-    fn read_chunk(&mut self, num_samples: usize) -> Result<MultiChannelTimeSeries>;
-}
-
-/// Trait for signal processors (filters, artifact removal, etc.).
-pub trait SignalProcessor {
-    /// Process input time series, returning transformed output.
-    fn process(&self, input: &MultiChannelTimeSeries) -> Result<MultiChannelTimeSeries>;
-}
-
-/// Trait for graph constructors (builds connectivity graphs from signals).
-pub trait GraphConstructor {
-    /// Construct a brain graph from multi-channel time series data.
-    fn construct(&self, signals: &MultiChannelTimeSeries) -> Result<BrainGraph>;
-}
-
-/// Trait for topology analyzers (computes graph-theoretic metrics).
-pub trait TopologyAnalyzer {
-    /// Compute full topology metrics for a brain graph.
-    fn analyze(&self, graph: &BrainGraph) -> Result<TopologyMetrics>;
-
-    /// Compute the minimum cut of a brain graph.
-    fn mincut(&self, graph: &BrainGraph) -> Result<MincutResult>;
-}
-
-/// Trait for embedding generators (maps brain graphs to vector space).
-pub trait EmbeddingGenerator {
-    /// Generate an embedding vector from a brain graph.
-    fn embed(&self, graph: &BrainGraph) -> Result<NeuralEmbedding>;
-
-    /// Dimensionality of the output embedding.
-    fn embedding_dim(&self) -> usize;
-}
-
-/// Trait for state decoders (classifies cognitive state from embeddings).
-pub trait StateDecoder {
-    /// Decode the most likely cognitive state from an embedding.
-    fn decode(&self, embedding: &NeuralEmbedding) -> Result<CognitiveState>;
-
-    /// Decode with a confidence score in [0, 1].
-    fn decode_with_confidence(
-        &self,
-        embedding: &NeuralEmbedding,
-    ) -> Result<(CognitiveState, f64)>;
-}
-
-/// Trait for neural state memory (stores and queries embedding history).
-pub trait NeuralMemory {
-    /// Store an embedding in memory.
-    fn store(&mut self, embedding: &NeuralEmbedding) -> Result<()>;
-
-    /// Find the k nearest embeddings to the query.
-    fn query_nearest(
-        &self,
-        embedding: &NeuralEmbedding,
-        k: usize,
-    ) -> Result<Vec<NeuralEmbedding>>;
-
-    /// Find all stored embeddings matching a cognitive state.
-    fn query_by_state(&self, state: CognitiveState) -> Result<Vec<NeuralEmbedding>>;
-}
-
-/// Trait for RVF serialization support.
-pub trait RvfSerializable {
-    /// Serialize this value to an RVF file.
-    fn to_rvf(&self) -> Result<RvfFile>;
-
-    /// Deserialize from an RVF file.
-    fn from_rvf(file: &RvfFile) -> Result<Self>
-    where
-        Self: Sized;
-}
@@ -1,543 +0,0 @@
-//! Cryptographic witness attestation for capability verification.
-//!
-//! Generates Ed25519-signed proof bundles that attest to the capabilities
-//! present in this build. Third parties can verify the signature against
-//! the embedded public key to confirm that capability tests passed at
-//! build time.
-
-use serde::{Deserialize, Serialize};
-use sha2::{Digest, Sha256};
-
-/// A single capability attestation.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct CapabilityAttestation {
-    /// Crate that provides this capability.
-    pub crate_name: String,
-    /// Human-readable capability name.
-    pub capability: String,
-    /// Evidence: function or test that proves this capability.
-    pub evidence: String,
-    /// SHA-256 hash of the source file containing the evidence.
-    pub source_hash: String,
-    /// Status: "verified" or "unverified".
-    pub status: String,
-}
-
-/// Complete witness bundle with Ed25519 signature.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct WitnessBundle {
-    /// Version of the witness format.
-    pub version: String,
-    /// ISO 8601 timestamp of when the witness was generated.
-    pub timestamp: String,
-    /// Git commit hash (short).
-    pub commit: String,
-    /// Workspace version.
-    pub workspace_version: String,
-    /// Total test count.
-    pub total_tests: u32,
-    /// Tests passed.
-    pub tests_passed: u32,
-    /// Tests failed.
-    pub tests_failed: u32,
-    /// List of attested capabilities.
-    pub capabilities: Vec<CapabilityAttestation>,
-    /// SHA-256 hash of the serialized capabilities array (the "message" that was signed).
-    pub capabilities_digest: String,
-    /// Ed25519 signature of capabilities_digest (hex-encoded).
-    pub signature: String,
-    /// Ed25519 public key (hex-encoded) for verification.
-    pub public_key: String,
-}
-
-impl WitnessBundle {
-    /// Create a new witness bundle, signing the capabilities with the given keypair.
-    pub fn new(
-        commit: &str,
-        workspace_version: &str,
-        total_tests: u32,
-        tests_passed: u32,
-        tests_failed: u32,
-        capabilities: Vec<CapabilityAttestation>,
-    ) -> Self {
-        use ed25519_dalek::{Signer, SigningKey};
-        use rand::rngs::OsRng;
-
-        // Serialize capabilities to JSON for hashing
-        let caps_json = serde_json::to_string(&capabilities).unwrap_or_default();
-
-        // SHA-256 digest of capabilities
-        let mut hasher = Sha256::new();
-        hasher.update(caps_json.as_bytes());
-        let digest = hasher.finalize();
-        let digest_hex = hex_encode(&digest);
-
-        // Generate Ed25519 keypair and sign
-        let signing_key = SigningKey::generate(&mut OsRng);
-        let signature = signing_key.sign(digest.as_slice());
-        let public_key = signing_key.verifying_key();
-
-        Self {
-            version: "1.0.0".to_string(),
-            timestamp: epoch_timestamp(),
-            commit: commit.to_string(),
-            workspace_version: workspace_version.to_string(),
-            total_tests,
-            tests_passed,
-            tests_failed,
-            capabilities,
-            capabilities_digest: digest_hex,
-            signature: hex_encode(signature.to_bytes().as_slice()),
-            public_key: hex_encode(public_key.to_bytes().as_slice()),
-        }
-    }
-
-    /// Verify the Ed25519 signature on this witness bundle.
-    pub fn verify(&self) -> Result<bool, String> {
-        use ed25519_dalek::{Signature, Verifier, VerifyingKey};
-
-        let pubkey_bytes =
-            hex_decode(&self.public_key).map_err(|e| format!("Invalid public key hex: {e}"))?;
-        let sig_bytes =
-            hex_decode(&self.signature).map_err(|e| format!("Invalid signature hex: {e}"))?;
-        let digest_bytes = hex_decode(&self.capabilities_digest)
-            .map_err(|e| format!("Invalid digest hex: {e}"))?;
-
-        let pubkey_arr: [u8; 32] = pubkey_bytes
-            .try_into()
-            .map_err(|_| "Public key must be 32 bytes".to_string())?;
-        let sig_arr: [u8; 64] = sig_bytes
-            .try_into()
-            .map_err(|_| "Signature must be 64 bytes".to_string())?;
-
-        let verifying_key = VerifyingKey::from_bytes(&pubkey_arr)
-            .map_err(|e| format!("Invalid public key: {e}"))?;
-        let signature = Signature::from_bytes(&sig_arr);
-
-        Ok(verifying_key.verify(&digest_bytes, &signature).is_ok())
-    }
-
-    /// Recompute the capabilities digest and check it matches.
-    pub fn verify_digest(&self) -> bool {
-        let caps_json = serde_json::to_string(&self.capabilities).unwrap_or_default();
-        let mut hasher = Sha256::new();
-        hasher.update(caps_json.as_bytes());
-        let digest = hasher.finalize();
-        hex_encode(&digest) == self.capabilities_digest
-    }
-
-    /// Full verification: digest integrity + Ed25519 signature.
-    pub fn verify_full(&self) -> Result<bool, String> {
-        if !self.verify_digest() {
-            return Err(
-                "Capabilities digest mismatch \u{2014} data may be tampered".to_string(),
-            );
-        }
-        self.verify()
-    }
-}
-
-/// Generate the complete capability attestation matrix for ruv-neural.
-pub fn attest_capabilities() -> Vec<CapabilityAttestation> {
-    vec![
-        // Core types
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "Brain graph types (BrainGraph, BrainEdge, BrainRegion)".into(),
-            evidence: "tests::brain_graph_adjacency_matrix, tests::brain_graph_node_degree".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "RVF binary format (read/write with magic, versioning, data types)".into(),
-            evidence: "tests::rvf_file_write_read_roundtrip, tests::rvf_header_validation".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "Neural embedding vectors with cosine/euclidean distance".into(),
-            evidence: "tests::embedding_cosine_similarity, tests::embedding_euclidean_distance"
-                .into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "Multi-channel time series with sample rate validation".into(),
-            evidence: "tests::time_series_creation_valid, SEC-002 validation".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "Brain atlas parcellation (Desikan-Killiany 68, Schaefer 200/400)".into(),
-            evidence: "tests::atlas_region_counts, tests::parcellation_query".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-core".into(),
-            capability: "Ed25519 signed witness attestation".into(),
-            evidence: "witness::tests::witness_sign_and_verify".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Sensor
-        CapabilityAttestation {
-            crate_name: "ruv-neural-sensor".into(),
-            capability: "NV Diamond magnetometer (ODMR signal model, calibration)".into(),
-            evidence: "tests::nv_diamond_sensor_source".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-sensor".into(),
-            capability: "OPM SERF-mode magnetometer (cross-talk compensation)".into(),
-            evidence: "tests::opm_sensor_source".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-sensor".into(),
-            capability: "EEG 10-20 system (21 channels, impedance, re-referencing)".into(),
-            evidence: "tests::eeg_sensor_source".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-sensor".into(),
-            capability: "Signal quality monitoring (SNR, saturation, artifacts)".into(),
-            evidence: "tests::quality_detects_low_snr, tests::quality_saturation_detection".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-sensor".into(),
-            capability: "Calibration (gain/offset, noise floor, cross-calibration)".into(),
-            evidence: "tests::calibration_apply_gain_offset, tests::calibration_cross_calibrate"
-                .into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Signal
-        CapabilityAttestation {
-            crate_name: "ruv-neural-signal".into(),
-            capability: "Hilbert transform (analytic signal extraction)".into(),
-            evidence: "bench_hilbert_transform, connectivity PLV computation".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-signal".into(),
-            capability: "Spectral analysis (PSD, STFT, frequency bands)".into(),
-            evidence: "tests in spectral.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-signal".into(),
-            capability: "Connectivity metrics (PLV, coherence, AEC, imaginary coherence)".into(),
-            evidence: "tests in connectivity.rs, integration::connectivity_matrix_from_signals"
-                .into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-signal".into(),
-            capability: "IIR Butterworth bandpass filtering".into(),
-            evidence: "tests in filtering.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Graph
-        CapabilityAttestation {
-            crate_name: "ruv-neural-graph".into(),
-            capability: "Graph construction from connectivity matrices".into(),
-            evidence: "tests in constructor.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-graph".into(),
-            capability: "Spectral analysis (Laplacian, Fiedler value, spectral gap)".into(),
-            evidence: "tests in spectral.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-graph".into(),
-            capability: "Graph metrics (density, clustering, modularity)".into(),
-            evidence: "tests in metrics.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Mincut
-        CapabilityAttestation {
-            crate_name: "ruv-neural-mincut".into(),
-            capability: "Stoer-Wagner global minimum cut O(V^3)".into(),
-            evidence: "tests::stoer_wagner_basic_cut, bench_stoer_wagner".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-mincut".into(),
-            capability: "Spectral bisection (Fiedler vector)".into(),
-            evidence: "tests::spectral_bisection_*, bench_spectral_bisection".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-mincut".into(),
-            capability: "Normalized cut (Shi-Malik)".into(),
-            evidence: "tests::normalized_cut_*".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-mincut".into(),
-            capability: "Cheeger constant (exact and approximate)".into(),
-            evidence: "tests::cheeger_*, bench_cheeger_constant".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-mincut".into(),
-            capability: "Dynamic mincut tracking with coherence events".into(),
-            evidence: "tests::dynamic_tracker_*".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Embed
-        CapabilityAttestation {
-            crate_name: "ruv-neural-embed".into(),
-            capability: "Spectral embedding (eigendecomposition)".into(),
-            evidence: "tests in spectral_embed.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-embed".into(),
-            capability: "Topology embedding (mincut + spectral features)".into(),
-            evidence: "tests in topology_embed.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-embed".into(),
-            capability: "Node2Vec random-walk embedding".into(),
-            evidence: "tests in node2vec.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-embed".into(),
-            capability: "RVF export (embeddings to binary format)".into(),
-            evidence: "tests in rvf_export.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Memory
-        CapabilityAttestation {
-            crate_name: "ruv-neural-memory".into(),
-            capability: "HNSW approximate nearest neighbor index".into(),
-            evidence: "tests in hnsw.rs, bench_hnsw_search".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-memory".into(),
-            capability: "Embedding store with capacity management".into(),
-            evidence: "tests in store.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Decoder
-        CapabilityAttestation {
-            crate_name: "ruv-neural-decoder".into(),
-            capability: "KNN decoder (majority-vote cognitive state)".into(),
-            evidence: "KnnDecoder tests".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-decoder".into(),
-            capability: "Threshold decoder (boundary-based classification)".into(),
-            evidence: "ThresholdDecoder tests".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-decoder".into(),
-            capability: "Transition decoder (HMM-style state tracking)".into(),
-            evidence: "TransitionDecoder tests".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-decoder".into(),
-            capability: "Clinical scorer (multi-domain neurological assessment)".into(),
-            evidence: "ClinicalScorer tests".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // ESP32
-        CapabilityAttestation {
-            crate_name: "ruv-neural-esp32".into(),
-            capability: "ADC sensor readout with femtotesla conversion".into(),
-            evidence: "tests::test_to_femtotesla_known_value".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-esp32".into(),
-            capability: "TDM time-division multiplexing scheduler".into(),
-            evidence: "tests in tdm.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-esp32".into(),
-            capability: "Neural data packet protocol with checksum".into(),
-            evidence: "tests::packet_roundtrip, tests::verify_checksum".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-esp32".into(),
-            capability: "Multi-node aggregation with timestamp sync".into(),
-            evidence: "tests::test_assemble_two_nodes, tests::test_assemble_with_tolerance".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        CapabilityAttestation {
-            crate_name: "ruv-neural-esp32".into(),
-            capability: "Power management (duty cycling, deep sleep)".into(),
-            evidence: "tests in power.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // Viz
-        CapabilityAttestation {
-            crate_name: "ruv-neural-viz".into(),
-            capability: "Export formats (JSON, CSV, DOT, GEXF, D3)".into(),
-            evidence: "tests in export.rs".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // CLI
-        CapabilityAttestation {
-            crate_name: "ruv-neural-cli".into(),
-            capability: "Full pipeline: sensor -> signal -> graph -> mincut -> embed -> decode"
-                .into(),
-            evidence: "tests::pipeline_runs_end_to_end".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-        // WASM
-        CapabilityAttestation {
-            crate_name: "ruv-neural-wasm".into(),
-            capability: "WebAssembly bindings for browser visualization".into(),
-            evidence: "wasm-bindgen exports compile to wasm32-unknown-unknown".into(),
-            source_hash: "".into(),
-            status: "verified".into(),
-        },
-    ]
-}
-
-/// Encode bytes as lowercase hex string.
-fn hex_encode(bytes: &[u8]) -> String {
-    bytes.iter().map(|b| format!("{:02x}", b)).collect()
-}
-
-/// Decode a hex string into bytes.
-fn hex_decode(hex: &str) -> std::result::Result<Vec<u8>, String> {
-    if hex.len() % 2 != 0 {
-        return Err("Odd-length hex string".into());
-    }
-    (0..hex.len())
-        .step_by(2)
-        .map(|i| u8::from_str_radix(&hex[i..i + 2], 16).map_err(|e| e.to_string()))
-        .collect()
-}
-
-/// Return a simple epoch-based timestamp (no chrono dependency).
-fn epoch_timestamp() -> String {
-    use std::time::{SystemTime, UNIX_EPOCH};
-    let secs = SystemTime::now()
-        .duration_since(UNIX_EPOCH)
-        .unwrap_or_default()
-        .as_secs();
-    format!("epoch:{secs}")
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn witness_sign_and_verify() {
-        let caps = attest_capabilities();
-        let bundle = WitnessBundle::new("abc123", "0.1.0", 333, 333, 0, caps);
-
-        assert_eq!(bundle.version, "1.0.0");
-        assert_eq!(bundle.tests_passed, 333);
-        assert_eq!(bundle.tests_failed, 0);
-        assert!(!bundle.capabilities_digest.is_empty());
-        assert!(!bundle.signature.is_empty());
-        assert!(!bundle.public_key.is_empty());
-
-        // Verify signature
-        assert!(bundle.verify_digest(), "Digest should match");
-        assert!(bundle.verify().unwrap(), "Signature should verify");
-        assert!(
-            bundle.verify_full().unwrap(),
-            "Full verification should pass"
-        );
-    }
-
-    #[test]
-    fn tampered_bundle_fails_verification() {
-        let caps = attest_capabilities();
-        let mut bundle = WitnessBundle::new("abc123", "0.1.0", 333, 333, 0, caps);
-
-        // Tamper with capabilities
-        bundle.capabilities[0].status = "tampered".to_string();
-
-        // Digest should no longer match
-        assert!(!bundle.verify_digest(), "Tampered digest should fail");
-        assert!(
-            bundle.verify_full().is_err(),
-            "Full verification should fail"
-        );
-    }
-
-    #[test]
-    fn attestation_matrix_covers_all_crates() {
-        let caps = attest_capabilities();
-        let crate_names: std::collections::HashSet<&str> =
-            caps.iter().map(|c| c.crate_name.as_str()).collect();
-
-        assert!(crate_names.contains("ruv-neural-core"));
-        assert!(crate_names.contains("ruv-neural-sensor"));
-        assert!(crate_names.contains("ruv-neural-signal"));
-        assert!(crate_names.contains("ruv-neural-graph"));
-        assert!(crate_names.contains("ruv-neural-mincut"));
-        assert!(crate_names.contains("ruv-neural-embed"));
-        assert!(crate_names.contains("ruv-neural-memory"));
-        assert!(crate_names.contains("ruv-neural-decoder"));
-        assert!(crate_names.contains("ruv-neural-esp32"));
-        assert!(crate_names.contains("ruv-neural-viz"));
-        assert!(crate_names.contains("ruv-neural-cli"));
-        assert!(crate_names.contains("ruv-neural-wasm"));
-    }
-
-    #[test]
-    fn hex_roundtrip() {
-        let data = b"hello world";
-        let encoded = hex_encode(data);
-        let decoded = hex_decode(&encoded).unwrap();
-        assert_eq!(decoded, data);
-    }
-}
@@ -1,25 +0,0 @@
-[package]
-name = "ruv-neural-decoder"
-description = "rUv Neural — Cognitive state classification and BCI decoding from neural topology embeddings"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-wasm = []
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-# ruv-neural-embed and ruv-neural-memory are available for future integration
-# but not currently required for core decoder functionality
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-rand = { workspace = true }
-num-traits = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
@@ -1,93 +0,0 @@
-# ruv-neural-decoder
-
-Cognitive state classification and BCI decoding from neural topology embeddings.
-
-## Overview
-
-`ruv-neural-decoder` classifies cognitive states from brain graph embeddings and
-topology metrics. It provides multiple decoding strategies -- KNN classification
-from labeled exemplars, threshold-based rule systems, temporal transition detection,
-and clinical biomarker scoring -- plus an ensemble pipeline that combines all
-strategies for robust real-time brain-computer interface (BCI) output.
-
-## Features
-
- **KNN decoder** (`knn_decoder`): K-nearest neighbor classification using stored
-  labeled embeddings from `ruv-neural-memory`; supports configurable k and distance
-  metrics
- **Threshold decoder** (`threshold_decoder`): Rule-based classification from
-  topology metric ranges (mincut value, modularity, efficiency, Fiedler value)
-  with configurable `TopologyThreshold` bounds per cognitive state
- **Transition decoder** (`transition_decoder`): Detects cognitive state transitions
-  from temporal topology dynamics; outputs `StateTransition` events matching
-  known `TransitionPattern` templates
- **Clinical scorer** (`clinical`): `ClinicalScorer` for biomarker detection via
-  deviation from healthy baseline distributions; flags abnormal topology patterns
- **Ensemble pipeline** (`pipeline`): `DecoderPipeline` combining all decoder
-  strategies with confidence-weighted voting; produces `DecoderOutput` with
-  classified state, confidence score, and contributing decoder votes
-
-## Usage
-
-```rust
-use ruv_neural_decoder::{
-    KnnDecoder, ThresholdDecoder, TopologyThreshold,
-    TransitionDecoder, ClinicalScorer, DecoderPipeline, DecoderOutput,
-};
-use ruv_neural_core::topology::{CognitiveState, TopologyMetrics};
-
-// Threshold-based decoding from topology metrics
-let mut decoder = ThresholdDecoder::new();
-decoder.add_threshold(TopologyThreshold {
-    state: CognitiveState::Focused,
-    min_modularity: 0.3,
-    max_modularity: 0.5,
-    min_efficiency: 0.6,
-    ..Default::default()
-});
-let state = decoder.decode(&metrics);
-
-// KNN-based decoding from embeddings
-let mut knn = KnnDecoder::new(5); // k=5
-knn.add_exemplar(embedding, CognitiveState::Rest);
-let predicted = knn.classify(&query_embedding);
-
-// Transition detection from temporal sequences
-let mut transition_decoder = TransitionDecoder::new();
-if let Some(transition) = transition_decoder.check(&current_metrics) {
-    println!("Transition: {:?} -> {:?}", transition.from, transition.to);
-}
-
-// Full ensemble pipeline
-let mut pipeline = DecoderPipeline::new();
-let output: DecoderOutput = pipeline.decode(&metrics, &embedding);
-println!("State: {:?}, confidence: {:.2}", output.state, output.confidence);
-```
-
-## API Reference
-
-| Module               | Key Types                                                  |
-|----------------------|------------------------------------------------------------|
-| `knn_decoder`        | `KnnDecoder`                                               |
-| `threshold_decoder`  | `ThresholdDecoder`, `TopologyThreshold`                    |
-| `transition_decoder` | `TransitionDecoder`, `StateTransition`, `TransitionPattern`|
-| `clinical`           | `ClinicalScorer`                                           |
-| `pipeline`           | `DecoderPipeline`, `DecoderOutput`                         |
-
-## Feature Flags
-
-| Feature | Default | Description                      |
-|---------|---------|----------------------------------|
-| `std`   | Yes     | Standard library support         |
-| `wasm`  | No      | WASM-compatible decoding         |
-
-## Integration
-
-Depends on `ruv-neural-core` for `CognitiveState`, `TopologyMetrics`, and
-`NeuralEmbedding` types. Consumes embeddings from `ruv-neural-embed` and
-topology results from `ruv-neural-mincut`. The KNN decoder can query stored
-exemplars from `ruv-neural-memory`.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,357 +0,0 @@
-//! Clinical biomarker detection from brain topology deviations.
-
-use ruv_neural_core::topology::TopologyMetrics;
-
-/// Clinical biomarker scorer based on topology deviation from a healthy baseline.
-///
-/// Computes z-scores of current topology metrics relative to a learned
-/// healthy population baseline, then derives disease-specific risk scores
-/// and a composite brain health index.
-pub struct ClinicalScorer {
-    /// Mean topology metrics from healthy population.
-    healthy_baseline: TopologyMetrics,
-    /// Standard deviation of topology metrics from healthy population.
-    healthy_std: TopologyMetrics,
-}
-
-impl ClinicalScorer {
-    /// Create a scorer with explicit baseline mean and standard deviation.
-    pub fn new(baseline: TopologyMetrics, std: TopologyMetrics) -> Self {
-        Self {
-            healthy_baseline: baseline,
-            healthy_std: std,
-        }
-    }
-
-    /// Learn the healthy baseline from a set of healthy topology observations.
-    ///
-    /// Computes the mean and standard deviation of each metric across the
-    /// provided samples.
-    pub fn learn_baseline(&mut self, healthy_data: &[TopologyMetrics]) {
-        if healthy_data.is_empty() {
-            return;
-        }
-
-        let n = healthy_data.len() as f64;
-
-        // Compute means.
-        let mean_mincut = healthy_data.iter().map(|m| m.global_mincut).sum::<f64>() / n;
-        let mean_mod = healthy_data.iter().map(|m| m.modularity).sum::<f64>() / n;
-        let mean_eff = healthy_data.iter().map(|m| m.global_efficiency).sum::<f64>() / n;
-        let mean_loc = healthy_data.iter().map(|m| m.local_efficiency).sum::<f64>() / n;
-        let mean_ent = healthy_data.iter().map(|m| m.graph_entropy).sum::<f64>() / n;
-        let mean_fiedler = healthy_data.iter().map(|m| m.fiedler_value).sum::<f64>() / n;
-
-        self.healthy_baseline = TopologyMetrics {
-            global_mincut: mean_mincut,
-            modularity: mean_mod,
-            global_efficiency: mean_eff,
-            local_efficiency: mean_loc,
-            graph_entropy: mean_ent,
-            fiedler_value: mean_fiedler,
-            num_modules: 0,
-            timestamp: 0.0,
-        };
-
-        // Compute standard deviations.
-        let std_mincut = std_dev(healthy_data.iter().map(|m| m.global_mincut), mean_mincut);
-        let std_mod = std_dev(healthy_data.iter().map(|m| m.modularity), mean_mod);
-        let std_eff = std_dev(
-            healthy_data.iter().map(|m| m.global_efficiency),
-            mean_eff,
-        );
-        let std_loc = std_dev(
-            healthy_data.iter().map(|m| m.local_efficiency),
-            mean_loc,
-        );
-        let std_ent = std_dev(healthy_data.iter().map(|m| m.graph_entropy), mean_ent);
-        let std_fiedler = std_dev(
-            healthy_data.iter().map(|m| m.fiedler_value),
-            mean_fiedler,
-        );
-
-        self.healthy_std = TopologyMetrics {
-            global_mincut: std_mincut,
-            modularity: std_mod,
-            global_efficiency: std_eff,
-            local_efficiency: std_loc,
-            graph_entropy: std_ent,
-            fiedler_value: std_fiedler,
-            num_modules: 0,
-            timestamp: 0.0,
-        };
-    }
-
-    /// Composite deviation score (mean absolute z-score across all metrics).
-    ///
-    /// Higher values indicate greater deviation from healthy baseline.
-    pub fn deviation_score(&self, current: &TopologyMetrics) -> f64 {
-        let z_scores = self.z_scores(current);
-        z_scores.iter().map(|z| z.abs()).sum::<f64>() / z_scores.len() as f64
-    }
-
-    /// Alzheimer's disease risk score in `[0, 1]`.
-    ///
-    /// Based on characteristic patterns: reduced global efficiency,
-    /// increased modularity (network fragmentation), reduced mincut.
-    pub fn alzheimer_risk(&self, current: &TopologyMetrics) -> f64 {
-        let z = self.z_scores(current);
-        // z[0]=mincut, z[1]=modularity, z[2]=global_eff, z[3]=local_eff, z[4]=entropy, z[5]=fiedler
-
-        // Alzheimer's: decreased efficiency (negative z), decreased mincut (negative z),
-        // increased modularity (positive z = fragmentation).
-        let efficiency_component = sigmoid(-z[2], 2.0);
-        let mincut_component = sigmoid(-z[0], 2.0);
-        let modularity_component = sigmoid(z[1], 2.0);
-        let fiedler_component = sigmoid(-z[5], 1.5);
-
-        let risk = 0.35 * efficiency_component
-            + 0.25 * mincut_component
-            + 0.25 * modularity_component
-            + 0.15 * fiedler_component;
-
-        risk.clamp(0.0, 1.0)
-    }
-
-    /// Epilepsy risk score in `[0, 1]`.
-    ///
-    /// Based on characteristic patterns: hypersynchrony (increased mincut),
-    /// decreased modularity, increased local efficiency.
-    pub fn epilepsy_risk(&self, current: &TopologyMetrics) -> f64 {
-        let z = self.z_scores(current);
-
-        // Epilepsy: increased mincut (hypersynchrony), decreased modularity,
-        // increased local efficiency.
-        let mincut_component = sigmoid(z[0], 2.0);
-        let modularity_component = sigmoid(-z[1], 2.0);
-        let local_eff_component = sigmoid(z[3], 2.0);
-
-        let risk = 0.4 * mincut_component
-            + 0.3 * modularity_component
-            + 0.3 * local_eff_component;
-
-        risk.clamp(0.0, 1.0)
-    }
-
-    /// Depression risk score in `[0, 1]`.
-    ///
-    /// Based on characteristic patterns: reduced global efficiency,
-    /// altered entropy, reduced Fiedler value (weaker connectivity).
-    pub fn depression_risk(&self, current: &TopologyMetrics) -> f64 {
-        let z = self.z_scores(current);
-
-        // Depression: decreased efficiency, decreased Fiedler value,
-        // altered entropy (can go either way, use absolute deviation).
-        let efficiency_component = sigmoid(-z[2], 2.0);
-        let fiedler_component = sigmoid(-z[5], 2.0);
-        let entropy_component = sigmoid(z[4].abs(), 1.5);
-
-        let risk = 0.4 * efficiency_component
-            + 0.35 * fiedler_component
-            + 0.25 * entropy_component;
-
-        risk.clamp(0.0, 1.0)
-    }
-
-    /// General brain health index in `[0, 1]`.
-    ///
-    /// `0.0` = severe abnormality, `1.0` = perfectly healthy (all metrics
-    /// within normal range).
-    pub fn brain_health_index(&self, current: &TopologyMetrics) -> f64 {
-        let deviation = self.deviation_score(current);
-        // Map deviation to health: 0 deviation = 1.0 health, large deviation = ~0.0.
-        let health = (-0.5 * deviation).exp();
-        health.clamp(0.0, 1.0)
-    }
-
-    /// Compute z-scores for all topology metrics.
-    ///
-    /// Order: [mincut, modularity, global_efficiency, local_efficiency, entropy, fiedler].
-    fn z_scores(&self, current: &TopologyMetrics) -> [f64; 6] {
-        [
-            z_score(
-                current.global_mincut,
-                self.healthy_baseline.global_mincut,
-                self.healthy_std.global_mincut,
-            ),
-            z_score(
-                current.modularity,
-                self.healthy_baseline.modularity,
-                self.healthy_std.modularity,
-            ),
-            z_score(
-                current.global_efficiency,
-                self.healthy_baseline.global_efficiency,
-                self.healthy_std.global_efficiency,
-            ),
-            z_score(
-                current.local_efficiency,
-                self.healthy_baseline.local_efficiency,
-                self.healthy_std.local_efficiency,
-            ),
-            z_score(
-                current.graph_entropy,
-                self.healthy_baseline.graph_entropy,
-                self.healthy_std.graph_entropy,
-            ),
-            z_score(
-                current.fiedler_value,
-                self.healthy_baseline.fiedler_value,
-                self.healthy_std.fiedler_value,
-            ),
-        ]
-    }
-}
-
-/// Compute the z-score: (value - mean) / std.
-///
-/// Returns 0.0 if std is near zero.
-fn z_score(value: f64, mean: f64, std: f64) -> f64 {
-    if std.abs() < 1e-10 {
-        return 0.0;
-    }
-    (value - mean) / std
-}
-
-/// Standard deviation from an iterator of values and a precomputed mean.
-fn std_dev(values: impl Iterator<Item = f64>, mean: f64) -> f64 {
-    let vals: Vec<f64> = values.collect();
-    if vals.len() < 2 {
-        return 1.0; // Default to 1.0 to avoid division by zero.
-    }
-    let n = vals.len() as f64;
-    let variance = vals.iter().map(|v| (v - mean).powi(2)).sum::<f64>() / (n - 1.0);
-    let s = variance.sqrt();
-    if s < 1e-10 { 1.0 } else { s }
-}
-
-/// Sigmoid function mapping a z-score to `[0, 1]`.
-///
-/// `scale` controls the steepness of the transition.
-fn sigmoid(z: f64, scale: f64) -> f64 {
-    1.0 / (1.0 + (-scale * z).exp())
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    fn make_metrics(
-        mincut: f64,
-        modularity: f64,
-        efficiency: f64,
-        entropy: f64,
-    ) -> TopologyMetrics {
-        TopologyMetrics {
-            global_mincut: mincut,
-            modularity,
-            global_efficiency: efficiency,
-            local_efficiency: 0.3,
-            graph_entropy: entropy,
-            fiedler_value: 0.5,
-            num_modules: 4,
-            timestamp: 0.0,
-        }
-    }
-
-    fn make_baseline_scorer() -> ClinicalScorer {
-        ClinicalScorer::new(
-            make_metrics(5.0, 0.4, 0.3, 2.0),
-            make_metrics(1.0, 0.1, 0.05, 0.3),
-        )
-    }
-
-    #[test]
-    fn test_healthy_deviation_near_zero() {
-        let scorer = make_baseline_scorer();
-        let healthy = make_metrics(5.0, 0.4, 0.3, 2.0);
-        let deviation = scorer.deviation_score(&healthy);
-        assert!(
-            deviation < 0.5,
-            "Healthy metrics should have low deviation, got {}",
-            deviation
-        );
-    }
-
-    #[test]
-    fn test_abnormal_deviation_high() {
-        let scorer = make_baseline_scorer();
-        let abnormal = make_metrics(15.0, 1.5, 0.9, 8.0);
-        let deviation = scorer.deviation_score(&abnormal);
-        assert!(
-            deviation > 2.0,
-            "Abnormal metrics should have high deviation, got {}",
-            deviation
-        );
-    }
-
-    #[test]
-    fn test_brain_health_healthy() {
-        let scorer = make_baseline_scorer();
-        let healthy = make_metrics(5.0, 0.4, 0.3, 2.0);
-        let health = scorer.brain_health_index(&healthy);
-        assert!(
-            health > 0.8,
-            "Healthy metrics should yield high health index, got {}",
-            health
-        );
-    }
-
-    #[test]
-    fn test_brain_health_abnormal() {
-        let scorer = make_baseline_scorer();
-        let abnormal = make_metrics(15.0, 1.5, 0.9, 8.0);
-        let health = scorer.brain_health_index(&abnormal);
-        assert!(
-            health < 0.5,
-            "Abnormal metrics should yield low health index, got {}",
-            health
-        );
-    }
-
-    #[test]
-    fn test_disease_risks_in_range() {
-        let scorer = make_baseline_scorer();
-        let current = make_metrics(3.0, 0.6, 0.15, 2.5);
-
-        let alz = scorer.alzheimer_risk(&current);
-        let epi = scorer.epilepsy_risk(&current);
-        let dep = scorer.depression_risk(&current);
-
-        assert!(alz >= 0.0 && alz <= 1.0, "Alzheimer risk out of range: {}", alz);
-        assert!(epi >= 0.0 && epi <= 1.0, "Epilepsy risk out of range: {}", epi);
-        assert!(dep >= 0.0 && dep <= 1.0, "Depression risk out of range: {}", dep);
-    }
-
-    #[test]
-    fn test_learn_baseline() {
-        let mut scorer = ClinicalScorer::new(
-            make_metrics(0.0, 0.0, 0.0, 0.0),
-            make_metrics(1.0, 1.0, 1.0, 1.0),
-        );
-
-        let data = vec![
-            make_metrics(5.0, 0.4, 0.3, 2.0),
-            make_metrics(5.2, 0.42, 0.31, 2.1),
-            make_metrics(4.8, 0.38, 0.29, 1.9),
-        ];
-        scorer.learn_baseline(&data);
-
-        // After learning, healthy data should have low deviation.
-        let deviation = scorer.deviation_score(&make_metrics(5.0, 0.4, 0.3, 2.0));
-        assert!(deviation < 1.0, "Post-learning deviation too high: {}", deviation);
-    }
-
-    #[test]
-    fn test_health_index_range() {
-        let scorer = make_baseline_scorer();
-        // Test extreme values.
-        for mincut in [0.0, 5.0, 20.0] {
-            for mod_val in [0.0, 0.4, 1.0] {
-                let m = make_metrics(mincut, mod_val, 0.3, 2.0);
-                let h = scorer.brain_health_index(&m);
-                assert!(h >= 0.0 && h <= 1.0, "Health index out of range: {}", h);
-            }
-        }
-    }
-}
@@ -1,222 +0,0 @@
-//! K-Nearest Neighbor decoder for cognitive state classification.
-
-use std::collections::HashMap;
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::topology::CognitiveState;
-use ruv_neural_core::traits::StateDecoder;
-
-/// Simple KNN decoder using stored labeled embeddings.
-///
-/// Classifies a query embedding by majority vote among its `k` nearest
-/// neighbors in Euclidean distance.
-pub struct KnnDecoder {
-    labeled_embeddings: Vec<(NeuralEmbedding, CognitiveState)>,
-    k: usize,
-}
-
-impl KnnDecoder {
-    /// Create a new KNN decoder with the given `k` (number of neighbors).
-    pub fn new(k: usize) -> Self {
-        let k = if k == 0 { 1 } else { k };
-        Self {
-            labeled_embeddings: Vec::new(),
-            k,
-        }
-    }
-
-    /// Load labeled training data into the decoder.
-    pub fn train(&mut self, embeddings: Vec<(NeuralEmbedding, CognitiveState)>) {
-        self.labeled_embeddings = embeddings;
-    }
-
-    /// Predict the cognitive state for a query embedding using majority vote.
-    ///
-    /// Returns `CognitiveState::Unknown` if no training data is available.
-    pub fn predict(&self, embedding: &NeuralEmbedding) -> CognitiveState {
-        self.predict_with_confidence(embedding).0
-    }
-
-    /// Predict the cognitive state with a confidence score in `[0, 1]`.
-    ///
-    /// Confidence is the fraction of the `k` nearest neighbors that agree
-    /// on the winning state.
-    pub fn predict_with_confidence(&self, embedding: &NeuralEmbedding) -> (CognitiveState, f64) {
-        if self.labeled_embeddings.is_empty() {
-            return (CognitiveState::Unknown, 0.0);
-        }
-
-        // Compute distances to all stored embeddings.
-        let mut distances: Vec<(f64, &CognitiveState)> = self
-            .labeled_embeddings
-            .iter()
-            .filter_map(|(stored, state)| {
-                let dist = euclidean_distance(&embedding.vector, &stored.vector);
-                Some((dist, state))
-            })
-            .collect();
-
-        // Sort by distance ascending.
-        distances.sort_by(|a, b| a.0.partial_cmp(&b.0).unwrap_or(std::cmp::Ordering::Equal));
-
-        // Take top-k neighbors.
-        let k = self.k.min(distances.len());
-        let neighbors = &distances[..k];
-
-        // Majority vote with distance weighting.
-        let mut vote_counts: HashMap<CognitiveState, f64> = HashMap::new();
-        for (dist, state) in neighbors {
-            // Use inverse distance weighting; add epsilon to avoid division by zero.
-            let weight = 1.0 / (dist + 1e-10);
-            *vote_counts.entry(**state).or_insert(0.0) += weight;
-        }
-
-        // Find the state with the highest weighted vote.
-        let total_weight: f64 = vote_counts.values().sum();
-        let (best_state, best_weight) = vote_counts
-            .into_iter()
-            .max_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal))
-            .unwrap_or((CognitiveState::Unknown, 0.0));
-
-        let confidence = if total_weight > 0.0 {
-            (best_weight / total_weight).clamp(0.0, 1.0)
-        } else {
-            0.0
-        };
-
-        (best_state, confidence)
-    }
-
-    /// Number of stored labeled embeddings.
-    pub fn num_samples(&self) -> usize {
-        self.labeled_embeddings.len()
-    }
-}
-
-impl StateDecoder for KnnDecoder {
-    fn decode(&self, embedding: &NeuralEmbedding) -> Result<CognitiveState> {
-        if self.labeled_embeddings.is_empty() {
-            return Err(RuvNeuralError::Decoder(
-                "KNN decoder has no training data".into(),
-            ));
-        }
-        Ok(self.predict(embedding))
-    }
-
-    fn decode_with_confidence(
-        &self,
-        embedding: &NeuralEmbedding,
-    ) -> Result<(CognitiveState, f64)> {
-        if self.labeled_embeddings.is_empty() {
-            return Err(RuvNeuralError::Decoder(
-                "KNN decoder has no training data".into(),
-            ));
-        }
-        Ok(self.predict_with_confidence(embedding))
-    }
-}
-
-/// Euclidean distance between two vectors of the same length.
-///
-/// If lengths differ, computes distance over the shorter prefix.
-fn euclidean_distance(a: &[f64], b: &[f64]) -> f64 {
-    a.iter()
-        .zip(b.iter())
-        .map(|(x, y)| (x - y) * (x - y))
-        .sum::<f64>()
-        .sqrt()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-
-    fn make_embedding(vector: Vec<f64>) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            0.0,
-            EmbeddingMetadata {
-                subject_id: None,
-                session_id: None,
-                cognitive_state: None,
-                source_atlas: Atlas::DesikanKilliany68,
-                embedding_method: "test".into(),
-            },
-        )
-        .unwrap()
-    }
-
-    #[test]
-    fn test_knn_classifies_correctly() {
-        let mut decoder = KnnDecoder::new(3);
-        decoder.train(vec![
-            (make_embedding(vec![1.0, 0.0, 0.0]), CognitiveState::Rest),
-            (make_embedding(vec![1.1, 0.1, 0.0]), CognitiveState::Rest),
-            (make_embedding(vec![0.9, 0.0, 0.1]), CognitiveState::Rest),
-            (
-                make_embedding(vec![0.0, 1.0, 0.0]),
-                CognitiveState::Focused,
-            ),
-            (
-                make_embedding(vec![0.1, 1.1, 0.0]),
-                CognitiveState::Focused,
-            ),
-            (
-                make_embedding(vec![0.0, 0.9, 0.1]),
-                CognitiveState::Focused,
-            ),
-        ]);
-
-        // Query near the Rest cluster.
-        let query = make_embedding(vec![1.0, 0.05, 0.0]);
-        let (state, confidence) = decoder.predict_with_confidence(&query);
-        assert_eq!(state, CognitiveState::Rest);
-        assert!(confidence > 0.5);
-
-        // Query near the Focused cluster.
-        let query = make_embedding(vec![0.05, 1.0, 0.0]);
-        let state = decoder.predict(&query);
-        assert_eq!(state, CognitiveState::Focused);
-    }
-
-    #[test]
-    fn test_knn_empty_returns_unknown() {
-        let decoder = KnnDecoder::new(3);
-        let query = make_embedding(vec![1.0, 0.0]);
-        assert_eq!(decoder.predict(&query), CognitiveState::Unknown);
-    }
-
-    #[test]
-    fn test_confidence_in_range() {
-        let mut decoder = KnnDecoder::new(3);
-        decoder.train(vec![
-            (make_embedding(vec![1.0, 0.0]), CognitiveState::Rest),
-            (make_embedding(vec![0.0, 1.0]), CognitiveState::Focused),
-        ]);
-        let query = make_embedding(vec![0.5, 0.5]);
-        let (_, confidence) = decoder.predict_with_confidence(&query);
-        assert!(confidence >= 0.0 && confidence <= 1.0);
-    }
-
-    #[test]
-    fn test_state_decoder_trait() {
-        let mut decoder = KnnDecoder::new(1);
-        decoder.train(vec![(
-            make_embedding(vec![1.0, 0.0]),
-            CognitiveState::MotorPlanning,
-        )]);
-        let query = make_embedding(vec![1.0, 0.0]);
-        let result = decoder.decode(&query).unwrap();
-        assert_eq!(result, CognitiveState::MotorPlanning);
-    }
-
-    #[test]
-    fn test_state_decoder_empty_errors() {
-        let decoder = KnnDecoder::new(3);
-        let query = make_embedding(vec![1.0]);
-        assert!(decoder.decode(&query).is_err());
-    }
-}
@@ -1,23 +0,0 @@
-//! rUv Neural Decoder -- Cognitive state classification and BCI decoding
-//! from neural topology embeddings.
-//!
-//! This crate provides multiple decoding strategies for classifying cognitive
-//! states from brain graph embeddings and topology metrics:
-//!
-//! - **KNN Decoder**: K-nearest neighbor classification using stored labeled embeddings
-//! - **Threshold Decoder**: Rule-based classification from topology metric ranges
-//! - **Transition Decoder**: State transition detection from topology dynamics
-//! - **Clinical Scorer**: Biomarker detection via deviation from healthy baselines
-//! - **Pipeline**: End-to-end ensemble decoder combining all strategies
-
-pub mod clinical;
-pub mod knn_decoder;
-pub mod pipeline;
-pub mod threshold_decoder;
-pub mod transition_decoder;
-
-pub use clinical::ClinicalScorer;
-pub use knn_decoder::KnnDecoder;
-pub use pipeline::{DecoderOutput, DecoderPipeline};
-pub use threshold_decoder::{ThresholdDecoder, TopologyThreshold};
-pub use transition_decoder::{StateTransition, TransitionDecoder, TransitionPattern};
@@ -1,369 +0,0 @@
-//! End-to-end decoder pipeline combining multiple decoding strategies.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::topology::{CognitiveState, TopologyMetrics};
-use serde::{Deserialize, Serialize};
-
-use crate::clinical::ClinicalScorer;
-use crate::knn_decoder::KnnDecoder;
-use crate::threshold_decoder::ThresholdDecoder;
-use crate::transition_decoder::{StateTransition, TransitionDecoder};
-
-/// End-to-end decoder pipeline that ensembles multiple decoding strategies.
-///
-/// Combines KNN, threshold, and transition decoders with configurable
-/// ensemble weights, and optionally includes clinical scoring.
-pub struct DecoderPipeline {
-    knn: Option<KnnDecoder>,
-    threshold: Option<ThresholdDecoder>,
-    transition: Option<TransitionDecoder>,
-    clinical: Option<ClinicalScorer>,
-    /// Ensemble weights: [knn_weight, threshold_weight, transition_weight].
-    ensemble_weights: [f64; 3],
-}
-
-/// Output of the decoder pipeline.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct DecoderOutput {
-    /// Decoded cognitive state (ensemble result).
-    pub state: CognitiveState,
-    /// Overall confidence in `[0, 1]`.
-    pub confidence: f64,
-    /// Detected state transition, if any.
-    pub transition: Option<StateTransition>,
-    /// Brain health index from clinical scorer, if configured.
-    pub brain_health_index: Option<f64>,
-    /// Clinical warning flags.
-    pub clinical_flags: Vec<String>,
-    /// Timestamp of the input data.
-    pub timestamp: f64,
-}
-
-impl DecoderPipeline {
-    /// Create an empty pipeline with default ensemble weights.
-    pub fn new() -> Self {
-        Self {
-            knn: None,
-            threshold: None,
-            transition: None,
-            clinical: None,
-            ensemble_weights: [1.0, 1.0, 1.0],
-        }
-    }
-
-    /// Add a KNN decoder to the pipeline.
-    pub fn with_knn(mut self, k: usize) -> Self {
-        self.knn = Some(KnnDecoder::new(k));
-        self
-    }
-
-    /// Add a threshold decoder to the pipeline.
-    pub fn with_thresholds(mut self) -> Self {
-        self.threshold = Some(ThresholdDecoder::new());
-        self
-    }
-
-    /// Add a transition decoder to the pipeline.
-    pub fn with_transitions(mut self, window: usize) -> Self {
-        self.transition = Some(TransitionDecoder::new(window));
-        self
-    }
-
-    /// Add a clinical scorer to the pipeline.
-    pub fn with_clinical(mut self, baseline: TopologyMetrics, std: TopologyMetrics) -> Self {
-        self.clinical = Some(ClinicalScorer::new(baseline, std));
-        self
-    }
-
-    /// Set custom ensemble weights for [knn, threshold, transition].
-    pub fn with_weights(mut self, weights: [f64; 3]) -> Self {
-        self.ensemble_weights = weights;
-        self
-    }
-
-    /// Get a mutable reference to the KNN decoder (for training).
-    pub fn knn_mut(&mut self) -> Option<&mut KnnDecoder> {
-        self.knn.as_mut()
-    }
-
-    /// Get a mutable reference to the threshold decoder (for configuring thresholds).
-    pub fn threshold_mut(&mut self) -> Option<&mut ThresholdDecoder> {
-        self.threshold.as_mut()
-    }
-
-    /// Get a mutable reference to the transition decoder (for registering patterns).
-    pub fn transition_mut(&mut self) -> Option<&mut TransitionDecoder> {
-        self.transition.as_mut()
-    }
-
-    /// Get a mutable reference to the clinical scorer.
-    pub fn clinical_mut(&mut self) -> Option<&mut ClinicalScorer> {
-        self.clinical.as_mut()
-    }
-
-    /// Run the full decoding pipeline on an embedding and topology metrics.
-    pub fn decode(
-        &mut self,
-        embedding: &NeuralEmbedding,
-        metrics: &TopologyMetrics,
-    ) -> DecoderOutput {
-        let mut candidates: Vec<(CognitiveState, f64, f64)> = Vec::new(); // (state, confidence, weight)
-
-        // KNN decoder.
-        if let Some(ref knn) = self.knn {
-            let (state, conf) = knn.predict_with_confidence(embedding);
-            if state != CognitiveState::Unknown {
-                candidates.push((state, conf, self.ensemble_weights[0]));
-            }
-        }
-
-        // Threshold decoder.
-        if let Some(ref threshold) = self.threshold {
-            let (state, conf) = threshold.decode(metrics);
-            if state != CognitiveState::Unknown {
-                candidates.push((state, conf, self.ensemble_weights[1]));
-            }
-        }
-
-        // Transition decoder.
-        let transition = if let Some(ref mut trans) = self.transition {
-            let result = trans.update(metrics.clone());
-            if let Some(ref t) = result {
-                candidates.push((t.to, t.confidence, self.ensemble_weights[2]));
-            }
-            result
-        } else {
-            None
-        };
-
-        // Ensemble: weighted vote.
-        let (state, confidence) = if candidates.is_empty() {
-            (CognitiveState::Unknown, 0.0)
-        } else {
-            weighted_vote(&candidates)
-        };
-
-        // Clinical scoring.
-        let mut brain_health_index = None;
-        let mut clinical_flags = Vec::new();
-
-        if let Some(ref clinical) = self.clinical {
-            let health = clinical.brain_health_index(metrics);
-            brain_health_index = Some(health);
-
-            let alz = clinical.alzheimer_risk(metrics);
-            let epi = clinical.epilepsy_risk(metrics);
-            let dep = clinical.depression_risk(metrics);
-
-            if alz > 0.7 {
-                clinical_flags.push(format!("Elevated Alzheimer risk: {:.2}", alz));
-            }
-            if epi > 0.7 {
-                clinical_flags.push(format!("Elevated epilepsy risk: {:.2}", epi));
-            }
-            if dep > 0.7 {
-                clinical_flags.push(format!("Elevated depression risk: {:.2}", dep));
-            }
-            if health < 0.3 {
-                clinical_flags.push(format!("Low brain health index: {:.2}", health));
-            }
-        }
-
-        DecoderOutput {
-            state,
-            confidence,
-            transition,
-            brain_health_index,
-            clinical_flags,
-            timestamp: metrics.timestamp,
-        }
-    }
-}
-
-impl Default for DecoderPipeline {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-/// Weighted majority vote across candidate predictions.
-///
-/// Returns the state with the highest weighted confidence and the
-/// normalized confidence score.
-fn weighted_vote(candidates: &[(CognitiveState, f64, f64)]) -> (CognitiveState, f64) {
-    use std::collections::HashMap;
-
-    let mut state_scores: HashMap<CognitiveState, f64> = HashMap::new();
-    let mut total_weight = 0.0;
-
-    for &(state, confidence, weight) in candidates {
-        let score = confidence * weight;
-        *state_scores.entry(state).or_insert(0.0) += score;
-        total_weight += score;
-    }
-
-    let (best_state, best_score) = state_scores
-        .into_iter()
-        .max_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal))
-        .unwrap_or((CognitiveState::Unknown, 0.0));
-
-    let normalized = if total_weight > 0.0 {
-        (best_score / total_weight).clamp(0.0, 1.0)
-    } else {
-        0.0
-    };
-
-    (best_state, normalized)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-
-    fn make_embedding(vector: Vec<f64>) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            0.0,
-            EmbeddingMetadata {
-                subject_id: None,
-                session_id: None,
-                cognitive_state: None,
-                source_atlas: Atlas::DesikanKilliany68,
-                embedding_method: "test".into(),
-            },
-        )
-        .unwrap()
-    }
-
-    fn make_metrics(mincut: f64, modularity: f64) -> TopologyMetrics {
-        TopologyMetrics {
-            global_mincut: mincut,
-            modularity,
-            global_efficiency: 0.3,
-            local_efficiency: 0.2,
-            graph_entropy: 2.0,
-            fiedler_value: 0.5,
-            num_modules: 4,
-            timestamp: 0.0,
-        }
-    }
-
-    #[test]
-    fn test_empty_pipeline() {
-        let mut pipeline = DecoderPipeline::new();
-        let emb = make_embedding(vec![1.0, 0.0]);
-        let met = make_metrics(5.0, 0.4);
-        let output = pipeline.decode(&emb, &met);
-        assert_eq!(output.state, CognitiveState::Unknown);
-        assert!(output.confidence >= 0.0 && output.confidence <= 1.0);
-    }
-
-    #[test]
-    fn test_pipeline_with_knn() {
-        let mut pipeline = DecoderPipeline::new().with_knn(3);
-        pipeline.knn_mut().unwrap().train(vec![
-            (make_embedding(vec![1.0, 0.0]), CognitiveState::Rest),
-            (make_embedding(vec![1.1, 0.1]), CognitiveState::Rest),
-            (make_embedding(vec![0.9, 0.0]), CognitiveState::Rest),
-        ]);
-
-        let output = pipeline.decode(&make_embedding(vec![1.0, 0.05]), &make_metrics(5.0, 0.4));
-        assert_eq!(output.state, CognitiveState::Rest);
-        assert!(output.confidence > 0.0);
-    }
-
-    #[test]
-    fn test_pipeline_with_thresholds() {
-        let mut pipeline = DecoderPipeline::new().with_thresholds();
-        pipeline.threshold_mut().unwrap().set_threshold(
-            CognitiveState::Focused,
-            crate::threshold_decoder::TopologyThreshold {
-                mincut_range: (7.0, 9.0),
-                modularity_range: (0.5, 0.7),
-                efficiency_range: (0.2, 0.4),
-                entropy_range: (1.5, 2.5),
-            },
-        );
-
-        let output = pipeline.decode(
-            &make_embedding(vec![0.5, 0.5]),
-            &make_metrics(8.0, 0.6),
-        );
-        assert_eq!(output.state, CognitiveState::Focused);
-    }
-
-    #[test]
-    fn test_pipeline_with_clinical() {
-        let baseline = make_metrics(5.0, 0.4);
-        let std_met = TopologyMetrics {
-            global_mincut: 1.0,
-            modularity: 0.1,
-            global_efficiency: 0.05,
-            local_efficiency: 0.05,
-            graph_entropy: 0.3,
-            fiedler_value: 0.1,
-            num_modules: 1,
-            timestamp: 0.0,
-        };
-        let mut pipeline = DecoderPipeline::new()
-            .with_knn(1)
-            .with_clinical(baseline, std_met);
-        pipeline.knn_mut().unwrap().train(vec![(
-            make_embedding(vec![1.0]),
-            CognitiveState::Rest,
-        )]);
-
-        let output = pipeline.decode(&make_embedding(vec![1.0]), &make_metrics(5.0, 0.4));
-        assert!(output.brain_health_index.is_some());
-        let health = output.brain_health_index.unwrap();
-        assert!(health >= 0.0 && health <= 1.0);
-    }
-
-    #[test]
-    fn test_pipeline_all_decoders() {
-        let baseline = make_metrics(5.0, 0.4);
-        let std_met = TopologyMetrics {
-            global_mincut: 1.0,
-            modularity: 0.1,
-            global_efficiency: 0.05,
-            local_efficiency: 0.05,
-            graph_entropy: 0.3,
-            fiedler_value: 0.1,
-            num_modules: 1,
-            timestamp: 0.0,
-        };
-        let mut pipeline = DecoderPipeline::new()
-            .with_knn(3)
-            .with_thresholds()
-            .with_transitions(5)
-            .with_clinical(baseline, std_met);
-
-        pipeline.knn_mut().unwrap().train(vec![
-            (make_embedding(vec![1.0, 0.0]), CognitiveState::Rest),
-            (make_embedding(vec![1.1, 0.1]), CognitiveState::Rest),
-        ]);
-
-        let output = pipeline.decode(&make_embedding(vec![1.0, 0.05]), &make_metrics(5.0, 0.4));
-        // Should produce some output regardless of which decoders fire.
-        assert!(output.confidence >= 0.0 && output.confidence <= 1.0);
-        assert!(output.brain_health_index.is_some());
-    }
-
-    #[test]
-    fn test_decoder_output_serialization() {
-        let output = DecoderOutput {
-            state: CognitiveState::Rest,
-            confidence: 0.95,
-            transition: None,
-            brain_health_index: Some(0.92),
-            clinical_flags: vec![],
-            timestamp: 1234.5,
-        };
-        let json = serde_json::to_string(&output).unwrap();
-        let parsed: DecoderOutput = serde_json::from_str(&json).unwrap();
-        assert_eq!(parsed.state, CognitiveState::Rest);
-        assert!((parsed.confidence - 0.95).abs() < 1e-10);
-    }
-}
@@ -1,240 +0,0 @@
-//! Threshold-based topology decoder for cognitive state classification.
-
-use std::collections::HashMap;
-
-use ruv_neural_core::topology::{CognitiveState, TopologyMetrics};
-use serde::{Deserialize, Serialize};
-
-/// Decode cognitive states from topology metrics using learned thresholds.
-///
-/// Each cognitive state is associated with expected ranges for key topology
-/// metrics (mincut, modularity, efficiency, entropy). The decoder scores
-/// each candidate state by how well the input metrics fall within the
-/// expected ranges.
-pub struct ThresholdDecoder {
-    thresholds: HashMap<CognitiveState, TopologyThreshold>,
-}
-
-/// Threshold ranges for topology metrics associated with a cognitive state.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct TopologyThreshold {
-    /// Expected range for global minimum cut value.
-    pub mincut_range: (f64, f64),
-    /// Expected range for modularity.
-    pub modularity_range: (f64, f64),
-    /// Expected range for global efficiency.
-    pub efficiency_range: (f64, f64),
-    /// Expected range for graph entropy.
-    pub entropy_range: (f64, f64),
-}
-
-impl TopologyThreshold {
-    /// Score how well a set of metrics matches this threshold.
-    ///
-    /// Returns a value in `[0, 1]` where 1.0 means all metrics fall within
-    /// the expected ranges.
-    fn score(&self, metrics: &TopologyMetrics) -> f64 {
-        let scores = [
-            range_score(metrics.global_mincut, self.mincut_range),
-            range_score(metrics.modularity, self.modularity_range),
-            range_score(metrics.global_efficiency, self.efficiency_range),
-            range_score(metrics.graph_entropy, self.entropy_range),
-        ];
-        scores.iter().sum::<f64>() / scores.len() as f64
-    }
-}
-
-impl ThresholdDecoder {
-    /// Create a new threshold decoder with no thresholds defined.
-    pub fn new() -> Self {
-        Self {
-            thresholds: HashMap::new(),
-        }
-    }
-
-    /// Set the threshold for a specific cognitive state.
-    pub fn set_threshold(&mut self, state: CognitiveState, threshold: TopologyThreshold) {
-        self.thresholds.insert(state, threshold);
-    }
-
-    /// Learn thresholds from labeled topology data.
-    ///
-    /// For each cognitive state present in the data, computes the min/max
-    /// range of each metric with a 10% margin.
-    pub fn learn_thresholds(&mut self, labeled_data: &[(TopologyMetrics, CognitiveState)]) {
-        // Group metrics by state.
-        let mut grouped: HashMap<CognitiveState, Vec<&TopologyMetrics>> = HashMap::new();
-        for (metrics, state) in labeled_data {
-            grouped.entry(*state).or_default().push(metrics);
-        }
-
-        for (state, metrics_vec) in grouped {
-            if metrics_vec.is_empty() {
-                continue;
-            }
-
-            let mincut_range = compute_range(metrics_vec.iter().map(|m| m.global_mincut));
-            let modularity_range = compute_range(metrics_vec.iter().map(|m| m.modularity));
-            let efficiency_range =
-                compute_range(metrics_vec.iter().map(|m| m.global_efficiency));
-            let entropy_range = compute_range(metrics_vec.iter().map(|m| m.graph_entropy));
-
-            self.thresholds.insert(
-                state,
-                TopologyThreshold {
-                    mincut_range,
-                    modularity_range,
-                    efficiency_range,
-                    entropy_range,
-                },
-            );
-        }
-    }
-
-    /// Decode the cognitive state from topology metrics.
-    ///
-    /// Returns the best-matching state and a confidence score in `[0, 1]`.
-    /// If no thresholds are defined, returns `(Unknown, 0.0)`.
-    pub fn decode(&self, metrics: &TopologyMetrics) -> (CognitiveState, f64) {
-        if self.thresholds.is_empty() {
-            return (CognitiveState::Unknown, 0.0);
-        }
-
-        let mut best_state = CognitiveState::Unknown;
-        let mut best_score = -1.0_f64;
-
-        for (state, threshold) in &self.thresholds {
-            let score = threshold.score(metrics);
-            if score > best_score {
-                best_score = score;
-                best_state = *state;
-            }
-        }
-
-        (best_state, best_score.clamp(0.0, 1.0))
-    }
-
-    /// Number of states with defined thresholds.
-    pub fn num_states(&self) -> usize {
-        self.thresholds.len()
-    }
-}
-
-impl Default for ThresholdDecoder {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-/// Compute the range (min, max) from an iterator of values, with a 10% margin.
-fn compute_range(values: impl Iterator<Item = f64>) -> (f64, f64) {
-    let vals: Vec<f64> = values.collect();
-    if vals.is_empty() {
-        return (0.0, 0.0);
-    }
-
-    let min = vals.iter().cloned().fold(f64::INFINITY, f64::min);
-    let max = vals.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
-    let margin = (max - min).abs() * 0.1;
-
-    (min - margin, max + margin)
-}
-
-/// Score how well a value falls within a range.
-///
-/// Returns 1.0 if within range, decays toward 0.0 as the value moves
-/// further outside.
-fn range_score(value: f64, (lo, hi): (f64, f64)) -> f64 {
-    if value >= lo && value <= hi {
-        return 1.0;
-    }
-    let range_width = (hi - lo).abs().max(1e-10);
-    if value < lo {
-        let distance = lo - value;
-        (-distance / range_width).exp()
-    } else {
-        let distance = value - hi;
-        (-distance / range_width).exp()
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    fn make_metrics(mincut: f64, modularity: f64, efficiency: f64, entropy: f64) -> TopologyMetrics {
-        TopologyMetrics {
-            global_mincut: mincut,
-            modularity,
-            global_efficiency: efficiency,
-            local_efficiency: 0.0,
-            graph_entropy: entropy,
-            fiedler_value: 0.0,
-            num_modules: 4,
-            timestamp: 0.0,
-        }
-    }
-
-    #[test]
-    fn test_learn_thresholds() {
-        let mut decoder = ThresholdDecoder::new();
-        let data = vec![
-            (make_metrics(5.0, 0.4, 0.3, 2.0), CognitiveState::Rest),
-            (make_metrics(5.5, 0.45, 0.32, 2.1), CognitiveState::Rest),
-            (make_metrics(5.2, 0.42, 0.31, 2.05), CognitiveState::Rest),
-            (make_metrics(8.0, 0.6, 0.5, 3.0), CognitiveState::Focused),
-            (make_metrics(8.5, 0.65, 0.52, 3.1), CognitiveState::Focused),
-        ];
-
-        decoder.learn_thresholds(&data);
-        assert_eq!(decoder.num_states(), 2);
-
-        // Query with Rest-like metrics.
-        let (state, confidence) = decoder.decode(&make_metrics(5.1, 0.41, 0.31, 2.03));
-        assert_eq!(state, CognitiveState::Rest);
-        assert!(confidence > 0.5);
-    }
-
-    #[test]
-    fn test_set_threshold() {
-        let mut decoder = ThresholdDecoder::new();
-        decoder.set_threshold(
-            CognitiveState::Rest,
-            TopologyThreshold {
-                mincut_range: (4.0, 6.0),
-                modularity_range: (0.3, 0.5),
-                efficiency_range: (0.2, 0.4),
-                entropy_range: (1.5, 2.5),
-            },
-        );
-
-        let (state, confidence) = decoder.decode(&make_metrics(5.0, 0.4, 0.3, 2.0));
-        assert_eq!(state, CognitiveState::Rest);
-        assert!((confidence - 1.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn test_empty_decoder_returns_unknown() {
-        let decoder = ThresholdDecoder::new();
-        let (state, confidence) = decoder.decode(&make_metrics(5.0, 0.4, 0.3, 2.0));
-        assert_eq!(state, CognitiveState::Unknown);
-        assert!((confidence - 0.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn test_confidence_in_range() {
-        let mut decoder = ThresholdDecoder::new();
-        decoder.set_threshold(
-            CognitiveState::Focused,
-            TopologyThreshold {
-                mincut_range: (7.0, 9.0),
-                modularity_range: (0.5, 0.7),
-                efficiency_range: (0.4, 0.6),
-                entropy_range: (2.5, 3.5),
-            },
-        );
-        // Query outside all ranges.
-        let (_, confidence) = decoder.decode(&make_metrics(0.0, 0.0, 0.0, 0.0));
-        assert!(confidence >= 0.0 && confidence <= 1.0);
-    }
-}
@@ -1,298 +0,0 @@
-//! Transition decoder for detecting cognitive state changes from topology dynamics.
-
-use std::collections::HashMap;
-
-use ruv_neural_core::topology::{CognitiveState, TopologyMetrics};
-use serde::{Deserialize, Serialize};
-
-/// Detect cognitive state transitions from topology change patterns.
-///
-/// Monitors a sliding window of topology metrics and compares observed
-/// deltas against registered transition patterns to detect state changes.
-pub struct TransitionDecoder {
-    current_state: CognitiveState,
-    transition_patterns: HashMap<(CognitiveState, CognitiveState), TransitionPattern>,
-    history: Vec<TopologyMetrics>,
-    window_size: usize,
-}
-
-/// A pattern describing the expected topology change during a state transition.
-#[derive(Debug, Clone)]
-pub struct TransitionPattern {
-    /// Expected change in global minimum cut value.
-    pub mincut_delta: f64,
-    /// Expected change in modularity.
-    pub modularity_delta: f64,
-    /// Expected duration of the transition in seconds.
-    pub duration_s: f64,
-}
-
-/// A detected state transition.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct StateTransition {
-    /// State before the transition.
-    pub from: CognitiveState,
-    /// State after the transition.
-    pub to: CognitiveState,
-    /// Confidence of the detection in `[0, 1]`.
-    pub confidence: f64,
-    /// Timestamp when the transition was detected.
-    pub timestamp: f64,
-}
-
-impl TransitionDecoder {
-    /// Create a new transition decoder with a given sliding window size.
-    ///
-    /// The window size determines how many recent topology snapshots are
-    /// retained for computing deltas.
-    pub fn new(window_size: usize) -> Self {
-        let window_size = if window_size < 2 { 2 } else { window_size };
-        Self {
-            current_state: CognitiveState::Unknown,
-            transition_patterns: HashMap::new(),
-            history: Vec::new(),
-            window_size,
-        }
-    }
-
-    /// Register a transition pattern between two states.
-    pub fn register_pattern(
-        &mut self,
-        from: CognitiveState,
-        to: CognitiveState,
-        pattern: TransitionPattern,
-    ) {
-        self.transition_patterns.insert((from, to), pattern);
-    }
-
-    /// Get the current estimated cognitive state.
-    pub fn current_state(&self) -> CognitiveState {
-        self.current_state
-    }
-
-    /// Set the current state explicitly (e.g., from an external decoder).
-    pub fn set_current_state(&mut self, state: CognitiveState) {
-        self.current_state = state;
-    }
-
-    /// Push a new topology snapshot and check for state transitions.
-    ///
-    /// Returns `Some(StateTransition)` if a transition is detected,
-    /// `None` otherwise.
-    pub fn update(&mut self, metrics: TopologyMetrics) -> Option<StateTransition> {
-        self.history.push(metrics);
-
-        // Trim history to window size.
-        if self.history.len() > self.window_size {
-            let excess = self.history.len() - self.window_size;
-            self.history.drain(..excess);
-        }
-
-        // Need at least 2 samples to compute deltas.
-        if self.history.len() < 2 {
-            return None;
-        }
-
-        let oldest = &self.history[0];
-        let newest = self.history.last().unwrap();
-
-        let observed_mincut_delta = newest.global_mincut - oldest.global_mincut;
-        let observed_modularity_delta = newest.modularity - oldest.modularity;
-        let observed_duration = newest.timestamp - oldest.timestamp;
-
-        // Score each registered pattern.
-        let mut best_match: Option<(CognitiveState, f64)> = None;
-
-        for (&(from, to), pattern) in &self.transition_patterns {
-            // Only consider patterns starting from the current state.
-            if from != self.current_state {
-                continue;
-            }
-
-            let score = pattern_match_score(
-                observed_mincut_delta,
-                observed_modularity_delta,
-                observed_duration,
-                pattern,
-            );
-
-            if score > 0.5 {
-                if let Some((_, best_score)) = &best_match {
-                    if score > *best_score {
-                        best_match = Some((to, score));
-                    }
-                } else {
-                    best_match = Some((to, score));
-                }
-            }
-        }
-
-        if let Some((to_state, confidence)) = best_match {
-            let transition = StateTransition {
-                from: self.current_state,
-                to: to_state,
-                confidence: confidence.clamp(0.0, 1.0),
-                timestamp: newest.timestamp,
-            };
-            self.current_state = to_state;
-            Some(transition)
-        } else {
-            None
-        }
-    }
-
-    /// Number of registered transition patterns.
-    pub fn num_patterns(&self) -> usize {
-        self.transition_patterns.len()
-    }
-
-    /// Number of topology snapshots in the history buffer.
-    pub fn history_len(&self) -> usize {
-        self.history.len()
-    }
-}
-
-/// Compute a similarity score between observed deltas and a transition pattern.
-///
-/// Returns a value in `[0, 1]` where 1.0 means a perfect match.
-fn pattern_match_score(
-    observed_mincut_delta: f64,
-    observed_modularity_delta: f64,
-    observed_duration: f64,
-    pattern: &TransitionPattern,
-) -> f64 {
-    let mincut_score = if pattern.mincut_delta.abs() < 1e-10 {
-        if observed_mincut_delta.abs() < 0.5 {
-            1.0
-        } else {
-            0.5
-        }
-    } else {
-        let ratio = observed_mincut_delta / pattern.mincut_delta;
-        gaussian_score(ratio, 1.0, 0.5)
-    };
-
-    let modularity_score = if pattern.modularity_delta.abs() < 1e-10 {
-        if observed_modularity_delta.abs() < 0.05 {
-            1.0
-        } else {
-            0.5
-        }
-    } else {
-        let ratio = observed_modularity_delta / pattern.modularity_delta;
-        gaussian_score(ratio, 1.0, 0.5)
-    };
-
-    let duration_score = if pattern.duration_s.abs() < 1e-10 {
-        1.0
-    } else {
-        let ratio = observed_duration / pattern.duration_s;
-        gaussian_score(ratio, 1.0, 0.5)
-    };
-
-    (mincut_score + modularity_score + duration_score) / 3.0
-}
-
-/// Gaussian-shaped score centered at `center` with width `sigma`.
-fn gaussian_score(value: f64, center: f64, sigma: f64) -> f64 {
-    let diff = value - center;
-    (-0.5 * (diff / sigma).powi(2)).exp()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    fn make_metrics(
-        mincut: f64,
-        modularity: f64,
-        timestamp: f64,
-    ) -> TopologyMetrics {
-        TopologyMetrics {
-            global_mincut: mincut,
-            modularity,
-            global_efficiency: 0.3,
-            local_efficiency: 0.0,
-            graph_entropy: 2.0,
-            fiedler_value: 0.0,
-            num_modules: 4,
-            timestamp,
-        }
-    }
-
-    #[test]
-    fn test_detect_state_transition() {
-        let mut decoder = TransitionDecoder::new(5);
-        decoder.set_current_state(CognitiveState::Rest);
-
-        // Register a pattern: Rest -> Focused causes mincut increase and modularity increase.
-        decoder.register_pattern(
-            CognitiveState::Rest,
-            CognitiveState::Focused,
-            TransitionPattern {
-                mincut_delta: 3.0,
-                modularity_delta: 0.2,
-                duration_s: 2.0,
-            },
-        );
-
-        // Feed metrics that progressively match the pattern.
-        // The transition may fire on any update once deltas are large enough.
-        let updates = vec![
-            make_metrics(5.0, 0.4, 0.0),
-            make_metrics(6.0, 0.45, 0.5),
-            make_metrics(7.0, 0.5, 1.0),
-            make_metrics(8.0, 0.6, 2.0),
-        ];
-
-        let mut detected: Option<StateTransition> = None;
-        for m in updates {
-            if let Some(t) = decoder.update(m) {
-                detected = Some(t);
-            }
-        }
-
-        assert!(detected.is_some(), "Expected a transition to be detected");
-        let transition = detected.unwrap();
-        assert_eq!(transition.from, CognitiveState::Rest);
-        assert_eq!(transition.to, CognitiveState::Focused);
-        assert!(transition.confidence > 0.0 && transition.confidence <= 1.0);
-    }
-
-    #[test]
-    fn test_no_transition_without_pattern() {
-        let mut decoder = TransitionDecoder::new(3);
-        decoder.set_current_state(CognitiveState::Rest);
-
-        let result = decoder.update(make_metrics(5.0, 0.4, 0.0));
-        assert!(result.is_none());
-        let result = decoder.update(make_metrics(8.0, 0.6, 2.0));
-        assert!(result.is_none());
-    }
-
-    #[test]
-    fn test_window_trimming() {
-        let mut decoder = TransitionDecoder::new(3);
-        for i in 0..10 {
-            decoder.update(make_metrics(5.0, 0.4, i as f64));
-        }
-        assert_eq!(decoder.history_len(), 3);
-    }
-
-    #[test]
-    fn test_single_sample_no_transition() {
-        let mut decoder = TransitionDecoder::new(5);
-        decoder.register_pattern(
-            CognitiveState::Rest,
-            CognitiveState::Focused,
-            TransitionPattern {
-                mincut_delta: 3.0,
-                modularity_delta: 0.2,
-                duration_s: 2.0,
-            },
-        );
-        decoder.set_current_state(CognitiveState::Rest);
-        let result = decoder.update(make_metrics(5.0, 0.4, 0.0));
-        assert!(result.is_none());
-    }
-}
@@ -1,25 +0,0 @@
-[package]
-name = "ruv-neural-embed"
-description = "rUv Neural — Graph embedding generation for brain connectivity states using RuVector format"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-wasm = []
-rvf = []
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-ndarray = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-num-traits = { workspace = true }
-rand = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
@@ -1,90 +0,0 @@
-# ruv-neural-embed
-
-Graph embedding generation for brain connectivity states using RuVector format.
-
-## Overview
-
-`ruv-neural-embed` converts brain connectivity graphs into fixed-dimensional
-vector representations suitable for downstream classification, clustering, and
-temporal analysis. It provides multiple embedding methods and supports export
-to the RuVector `.rvf` binary format for interoperability with the broader
-RuVector ecosystem.
-
-## Features
-
- **Spectral embedding** (`spectral_embed`): Laplacian eigenvector-based positional
-  encoding from the graph's normalized Laplacian
- **Topology embedding** (`topology_embed`): Hand-crafted topological feature vectors
-  derived from graph-theoretic metrics
- **Node2Vec** (`node2vec`): Random-walk co-occurrence embeddings using configurable
-  walk length, return parameter (p), and in-out parameter (q)
- **Combined embedding** (`combined`): Weighted concatenation of multiple embedding
-  methods into a single vector
- **Temporal embedding** (`temporal`): Sliding-window context-enriched embeddings
-  that capture graph dynamics over time
- **Distance metrics** (`distance`): Embedding distance and similarity computations
- **RVF export** (`rvf_export`): Serialization of embeddings and trajectories to the
-  RuVector `.rvf` binary format
- **Helper utilities**: `default_metadata` for quick `EmbeddingMetadata` construction
-
-## Usage
-
-```rust
-use ruv_neural_embed::{
-    NeuralEmbedding, EmbeddingMetadata, EmbeddingTrajectory,
-    default_metadata,
-};
-use ruv_neural_core::brain::Atlas;
-
-// Create an embedding with metadata
-let meta = default_metadata("spectral", Atlas::Schaefer100);
-let emb = NeuralEmbedding::new(vec![0.1, 0.5, -0.3, 0.8], 1000.0, meta).unwrap();
-assert_eq!(emb.dimension, 4);
-
-// Compute similarity between embeddings
-let other = NeuralEmbedding::new(
-    vec![0.2, 0.4, -0.2, 0.9],
-    1001.0,
-    default_metadata("spectral", Atlas::Schaefer100),
-).unwrap();
-let similarity = emb.cosine_similarity(&other).unwrap();
-let distance = emb.euclidean_distance(&other).unwrap();
-
-// Build a trajectory from a sequence of embeddings
-let trajectory = EmbeddingTrajectory {
-    embeddings: vec![emb, other],
-    timestamps: vec![1000.0, 1001.0],
-};
-assert_eq!(trajectory.len(), 2);
-```
-
-## API Reference
-
-| Module           | Key Types / Functions                               |
-|------------------|-----------------------------------------------------|
-| `spectral_embed` | Spectral positional encoding from graph Laplacian   |
-| `topology_embed` | Topological feature vector extraction               |
-| `node2vec`       | Random-walk based node embeddings                   |
-| `combined`       | Weighted multi-method embedding concatenation       |
-| `temporal`       | Sliding-window temporal context embeddings          |
-| `distance`       | Distance and similarity computations                |
-| `rvf_export`     | RVF binary format serialization                     |
-
-## Feature Flags
-
-| Feature | Default | Description                         |
-|---------|---------|-------------------------------------|
-| `std`   | Yes     | Standard library support            |
-| `wasm`  | No      | WASM-compatible implementations     |
-| `rvf`   | No      | RuVector RVF format export support  |
-
-## Integration
-
-Depends on `ruv-neural-core` for `NeuralEmbedding`, `BrainGraph`, and
-`EmbeddingGenerator` trait. Receives graphs from `ruv-neural-graph` or
-`ruv-neural-mincut`. Produced embeddings are stored by `ruv-neural-memory`
-and classified by `ruv-neural-decoder`.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,180 +0,0 @@
-//! Combined multi-method embedding.
-//!
-//! Concatenates weighted embeddings from multiple embedding generators
-//! into a single vector representation.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::traits::EmbeddingGenerator;
-
-use crate::default_metadata;
-
-/// Combines multiple embedding methods into a single embedding vector.
-pub struct CombinedEmbedder {
-    embedders: Vec<Box<dyn EmbeddingGenerator>>,
-    weights: Vec<f64>,
-}
-
-impl CombinedEmbedder {
-    /// Create a new empty combined embedder.
-    pub fn new() -> Self {
-        Self {
-            embedders: Vec::new(),
-            weights: Vec::new(),
-        }
-    }
-
-    /// Add an embedding generator with a weight.
-    ///
-    /// The weight scales each element of the generator's output.
-    pub fn add(mut self, embedder: Box<dyn EmbeddingGenerator>, weight: f64) -> Self {
-        self.embedders.push(embedder);
-        self.weights.push(weight);
-        self
-    }
-
-    /// Number of sub-embedders.
-    pub fn num_embedders(&self) -> usize {
-        self.embedders.len()
-    }
-
-    /// Total embedding dimension (sum of all sub-embedder dimensions).
-    pub fn total_dimension(&self) -> usize {
-        self.embedders.iter().map(|e| e.embedding_dim()).sum()
-    }
-
-    /// Generate a combined embedding by concatenating weighted sub-embeddings.
-    pub fn embed_graph(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        if self.embedders.is_empty() {
-            return Err(RuvNeuralError::Embedding(
-                "CombinedEmbedder has no sub-embedders".into(),
-            ));
-        }
-
-        let mut values = Vec::with_capacity(self.total_dimension());
-
-        for (embedder, &weight) in self.embedders.iter().zip(self.weights.iter()) {
-            let sub_emb = embedder.embed(graph)?;
-            for v in &sub_emb.vector {
-                values.push(v * weight);
-            }
-        }
-
-        let meta = default_metadata("combined", graph.atlas);
-        NeuralEmbedding::new(values, graph.timestamp, meta)
-    }
-}
-
-impl Default for CombinedEmbedder {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-impl EmbeddingGenerator for CombinedEmbedder {
-    fn embedding_dim(&self) -> usize {
-        self.total_dimension()
-    }
-
-    fn embed(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        self.embed_graph(graph)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::spectral_embed::SpectralEmbedder;
-    use crate::topology_embed::TopologyEmbedder;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_test_graph() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.8,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 2,
-                    target: 3,
-                    weight: 0.6,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 0,
-                    target: 3,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 1.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        }
-    }
-
-    #[test]
-    fn test_combined_concatenates_correctly() {
-        let graph = make_test_graph();
-        let spectral = SpectralEmbedder::new(2);
-        let topo = TopologyEmbedder::new();
-
-        let spectral_dim = spectral.embedding_dim();
-        let topo_dim = topo.embedding_dim();
-
-        let combined = CombinedEmbedder::new()
-            .add(Box::new(spectral), 1.0)
-            .add(Box::new(topo), 1.0);
-
-        assert_eq!(combined.total_dimension(), spectral_dim + topo_dim);
-
-        let emb = combined.embed(&graph).unwrap();
-        assert_eq!(emb.dimension, spectral_dim + topo_dim);
-        assert_eq!(emb.metadata.embedding_method, "combined");
-    }
-
-    #[test]
-    fn test_combined_weights_scale() {
-        let graph = make_test_graph();
-        let topo = TopologyEmbedder::new();
-
-        let combined = CombinedEmbedder::new().add(Box::new(topo), 2.0);
-        let emb = combined.embed(&graph).unwrap();
-
-        let topo2 = TopologyEmbedder::new();
-        let direct = topo2.embed(&graph).unwrap();
-
-        for (c, d) in emb.vector.iter().zip(direct.vector.iter()) {
-            assert!(
-                (c - 2.0 * d).abs() < 1e-10,
-                "Weight should scale values: {} vs 2*{}",
-                c,
-                d
-            );
-        }
-    }
-
-    #[test]
-    fn test_combined_empty_fails() {
-        let graph = make_test_graph();
-        let combined = CombinedEmbedder::new();
-        assert!(combined.embed(&graph).is_err());
-    }
-}
@@ -1,247 +0,0 @@
-//! Distance metrics for neural embeddings.
-//!
-//! Provides cosine similarity, Euclidean distance, k-nearest-neighbor search,
-//! and a DTW-inspired trajectory distance for comparing embedding sequences.
-
-use ruv_neural_core::embedding::{EmbeddingTrajectory, NeuralEmbedding};
-
-/// Cosine similarity between two embeddings.
-///
-/// Returns a value in [-1, 1] where 1 means identical direction, 0 means
-/// orthogonal, and -1 means opposite.
-///
-/// Returns 0.0 if either embedding has zero norm.
-pub fn cosine_similarity(a: &NeuralEmbedding, b: &NeuralEmbedding) -> f64 {
-    let len = a.vector.len().min(b.vector.len());
-    if len == 0 {
-        return 0.0;
-    }
-
-    let mut dot = 0.0;
-    let mut norm_a = 0.0;
-    let mut norm_b = 0.0;
-
-    for i in 0..len {
-        dot += a.vector[i] * b.vector[i];
-        norm_a += a.vector[i] * a.vector[i];
-        norm_b += b.vector[i] * b.vector[i];
-    }
-
-    let denom = norm_a.sqrt() * norm_b.sqrt();
-    if denom < 1e-12 {
-        return 0.0;
-    }
-
-    dot / denom
-}
-
-/// Euclidean (L2) distance between two embeddings.
-///
-/// If the embeddings have different dimensions, only the overlapping
-/// portion is compared.
-pub fn euclidean_distance(a: &NeuralEmbedding, b: &NeuralEmbedding) -> f64 {
-    let len = a.vector.len().min(b.vector.len());
-    if len == 0 {
-        return 0.0;
-    }
-
-    let mut sum_sq = 0.0;
-    for i in 0..len {
-        let diff = a.vector[i] - b.vector[i];
-        sum_sq += diff * diff;
-    }
-
-    sum_sq.sqrt()
-}
-
-/// Manhattan (L1) distance between two embeddings.
-pub fn manhattan_distance(a: &NeuralEmbedding, b: &NeuralEmbedding) -> f64 {
-    let len = a.vector.len().min(b.vector.len());
-    let mut sum = 0.0;
-    for i in 0..len {
-        sum += (a.vector[i] - b.vector[i]).abs();
-    }
-    sum
-}
-
-/// Find the k nearest neighbors to a query embedding.
-///
-/// Returns a vector of `(index, distance)` tuples sorted by ascending
-/// Euclidean distance. `index` refers to the position in `candidates`.
-pub fn k_nearest(
-    query: &NeuralEmbedding,
-    candidates: &[NeuralEmbedding],
-    k: usize,
-) -> Vec<(usize, f64)> {
-    let mut distances: Vec<(usize, f64)> = candidates
-        .iter()
-        .enumerate()
-        .map(|(i, c)| (i, euclidean_distance(query, c)))
-        .collect();
-
-    distances.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal));
-    distances.truncate(k);
-    distances
-}
-
-/// Dynamic Time Warping (DTW) distance between two embedding trajectories.
-///
-/// Measures the cost of aligning two temporal sequences of embeddings,
-/// allowing for non-linear time warping. The cost at each cell is the
-/// Euclidean distance between the corresponding embeddings.
-pub fn trajectory_distance(a: &EmbeddingTrajectory, b: &EmbeddingTrajectory) -> f64 {
-    let n = a.embeddings.len();
-    let m = b.embeddings.len();
-
-    if n == 0 || m == 0 {
-        return f64::INFINITY;
-    }
-
-    let mut dtw = vec![vec![f64::INFINITY; m + 1]; n + 1];
-    dtw[0][0] = 0.0;
-
-    for i in 1..=n {
-        for j in 1..=m {
-            let cost = euclidean_distance(&a.embeddings[i - 1], &b.embeddings[j - 1]);
-            dtw[i][j] = cost
-                + dtw[i - 1][j]
-                    .min(dtw[i][j - 1])
-                    .min(dtw[i - 1][j - 1]);
-        }
-    }
-
-    dtw[n][m]
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::default_metadata;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::NeuralEmbedding;
-
-    fn emb(values: Vec<f64>) -> NeuralEmbedding {
-        let meta = default_metadata("test", Atlas::Custom(1));
-        NeuralEmbedding::new(values, 0.0, meta).unwrap()
-    }
-
-    #[test]
-    fn test_cosine_similarity_identical() {
-        let a = emb(vec![1.0, 2.0, 3.0]);
-        let b = emb(vec![1.0, 2.0, 3.0]);
-        let sim = cosine_similarity(&a, &b);
-        assert!(
-            (sim - 1.0).abs() < 1e-10,
-            "Identical embeddings: cos sim should be 1.0"
-        );
-    }
-
-    #[test]
-    fn test_cosine_similarity_orthogonal() {
-        let a = emb(vec![1.0, 0.0]);
-        let b = emb(vec![0.0, 1.0]);
-        let sim = cosine_similarity(&a, &b);
-        assert!(
-            sim.abs() < 1e-10,
-            "Orthogonal embeddings: cos sim should be 0.0"
-        );
-    }
-
-    #[test]
-    fn test_cosine_similarity_opposite() {
-        let a = emb(vec![1.0, 2.0]);
-        let b = emb(vec![-1.0, -2.0]);
-        let sim = cosine_similarity(&a, &b);
-        assert!(
-            (sim + 1.0).abs() < 1e-10,
-            "Opposite embeddings: cos sim should be -1.0"
-        );
-    }
-
-    #[test]
-    fn test_euclidean_distance_identical() {
-        let a = emb(vec![1.0, 2.0, 3.0]);
-        let b = emb(vec![1.0, 2.0, 3.0]);
-        let dist = euclidean_distance(&a, &b);
-        assert!(
-            dist.abs() < 1e-10,
-            "Identical embeddings: distance should be 0.0"
-        );
-    }
-
-    #[test]
-    fn test_euclidean_distance_known() {
-        let a = emb(vec![0.0, 0.0]);
-        let b = emb(vec![3.0, 4.0]);
-        let dist = euclidean_distance(&a, &b);
-        assert!((dist - 5.0).abs() < 1e-10, "Distance should be 5.0");
-    }
-
-    #[test]
-    fn test_k_nearest_returns_correct() {
-        let query = emb(vec![0.0, 0.0]);
-        let candidates = vec![
-            emb(vec![10.0, 10.0]),
-            emb(vec![1.0, 0.0]),
-            emb(vec![5.0, 5.0]),
-            emb(vec![0.5, 0.5]),
-        ];
-
-        let nearest = k_nearest(&query, &candidates, 2);
-        assert_eq!(nearest.len(), 2);
-        assert_eq!(nearest[0].0, 3);
-        assert_eq!(nearest[1].0, 1);
-    }
-
-    #[test]
-    fn test_k_nearest_k_larger_than_candidates() {
-        let query = emb(vec![0.0]);
-        let candidates = vec![emb(vec![1.0]), emb(vec![2.0])];
-        let nearest = k_nearest(&query, &candidates, 10);
-        assert_eq!(nearest.len(), 2);
-    }
-
-    #[test]
-    fn test_trajectory_distance_identical() {
-        let traj = EmbeddingTrajectory {
-            embeddings: vec![emb(vec![1.0, 2.0]), emb(vec![3.0, 4.0])],
-            timestamps: vec![0.0, 0.5],
-        };
-        let dist = trajectory_distance(&traj, &traj);
-        assert!(
-            dist.abs() < 1e-10,
-            "Identical trajectories: DTW distance should be 0.0"
-        );
-    }
-
-    #[test]
-    fn test_trajectory_distance_different() {
-        let a = EmbeddingTrajectory {
-            embeddings: vec![emb(vec![0.0, 0.0]), emb(vec![1.0, 0.0])],
-            timestamps: vec![0.0, 0.5],
-        };
-        let b = EmbeddingTrajectory {
-            embeddings: vec![emb(vec![0.0, 0.0]), emb(vec![0.0, 1.0])],
-            timestamps: vec![0.0, 0.5],
-        };
-        let dist = trajectory_distance(&a, &b);
-        assert!(
-            dist > 0.0,
-            "Different trajectories should have non-zero DTW distance"
-        );
-    }
-
-    #[test]
-    fn test_trajectory_distance_empty() {
-        let a = EmbeddingTrajectory {
-            embeddings: vec![],
-            timestamps: vec![],
-        };
-        let b = EmbeddingTrajectory {
-            embeddings: vec![emb(vec![1.0])],
-            timestamps: vec![0.0],
-        };
-        let dist = trajectory_distance(&a, &b);
-        assert!(dist.is_infinite());
-    }
-}
@@ -1,102 +0,0 @@
-//! rUv Neural Embed -- Graph embedding generation for brain connectivity states.
-//!
-//! This crate provides multiple embedding methods to convert brain connectivity
-//! graphs (`BrainGraph`) into fixed-dimensional vector representations suitable
-//! for downstream classification, clustering, and temporal analysis.
-//!
-//! # Embedding Methods
-//!
-//! - **Spectral**: Laplacian eigenvector-based positional encoding
-//! - **Topology**: Hand-crafted topological feature vectors
-//! - **Node2Vec**: Random-walk co-occurrence embeddings
-//! - **Combined**: Weighted concatenation of multiple methods
-//! - **Temporal**: Sliding-window context-enriched embeddings
-//!
-//! # RVF Export
-//!
-//! Embeddings can be serialized to the RuVector `.rvf` format for interoperability
-//! with the broader RuVector ecosystem.
-
-pub mod combined;
-pub mod distance;
-pub mod node2vec;
-pub mod rvf_export;
-pub mod spectral_embed;
-pub mod temporal;
-pub mod topology_embed;
-
-// Re-export core types used throughout this crate.
-pub use ruv_neural_core::embedding::{EmbeddingMetadata, EmbeddingTrajectory, NeuralEmbedding};
-pub use ruv_neural_core::graph::{BrainGraph, BrainGraphSequence};
-pub use ruv_neural_core::traits::EmbeddingGenerator;
-
-/// Helper to build an `EmbeddingMetadata` with just a method name and atlas.
-pub fn default_metadata(
-    method: &str,
-    atlas: ruv_neural_core::brain::Atlas,
-) -> EmbeddingMetadata {
-    EmbeddingMetadata {
-        subject_id: None,
-        session_id: None,
-        cognitive_state: None,
-        source_atlas: atlas,
-        embedding_method: method.to_string(),
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-
-    #[test]
-    fn test_neural_embedding_new() {
-        let meta = default_metadata("test", Atlas::Custom(3));
-        let emb = NeuralEmbedding::new(vec![1.0, 2.0, 3.0], 0.0, meta).unwrap();
-        assert_eq!(emb.dimension, 3);
-        assert_eq!(emb.vector.len(), 3);
-    }
-
-    #[test]
-    fn test_neural_embedding_empty_fails() {
-        let meta = default_metadata("test", Atlas::Custom(1));
-        let result = NeuralEmbedding::new(vec![], 0.0, meta);
-        assert!(result.is_err());
-    }
-
-    #[test]
-    fn test_embedding_norm() {
-        let meta = default_metadata("test", Atlas::Custom(2));
-        let emb = NeuralEmbedding::new(vec![3.0, 4.0], 0.0, meta).unwrap();
-        assert!((emb.norm() - 5.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn test_trajectory() {
-        let traj = EmbeddingTrajectory {
-            embeddings: vec![
-                NeuralEmbedding::new(
-                    vec![0.0; 4],
-                    0.0,
-                    default_metadata("test", Atlas::Custom(4)),
-                )
-                .unwrap(),
-                NeuralEmbedding::new(
-                    vec![0.0; 4],
-                    0.5,
-                    default_metadata("test", Atlas::Custom(4)),
-                )
-                .unwrap(),
-                NeuralEmbedding::new(
-                    vec![0.0; 4],
-                    1.0,
-                    default_metadata("test", Atlas::Custom(4)),
-                )
-                .unwrap(),
-            ],
-            timestamps: vec![0.0, 0.5, 1.0],
-        };
-        assert_eq!(traj.len(), 3);
-        assert!((traj.duration_s() - 1.0).abs() < 1e-10);
-    }
-}
@@ -1,367 +0,0 @@
-//! Node2Vec-inspired random walk embedding.
-//!
-//! Performs biased random walks on the brain graph and constructs a co-occurrence
-//! matrix. The graph-level embedding is obtained via SVD of the co-occurrence
-//! matrix (a simplified skip-gram approximation).
-
-use rand::rngs::StdRng;
-use rand::{Rng, SeedableRng};
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::traits::EmbeddingGenerator;
-
-use crate::default_metadata;
-
-/// Node2Vec-style graph embedder using biased random walks.
-pub struct Node2VecEmbedder {
-    /// Length of each random walk.
-    pub walk_length: usize,
-    /// Number of walks per node.
-    pub num_walks: usize,
-    /// Output embedding dimension.
-    pub embedding_dim: usize,
-    /// Return parameter (higher = more likely to return to previous node).
-    pub p: f64,
-    /// In-out parameter (higher = more likely to explore outward).
-    pub q: f64,
-    /// Random seed for reproducibility.
-    pub seed: u64,
-}
-
-impl Node2VecEmbedder {
-    /// Create a new Node2Vec embedder with default parameters.
-    pub fn new(embedding_dim: usize) -> Self {
-        Self {
-            walk_length: 20,
-            num_walks: 10,
-            embedding_dim,
-            p: 1.0,
-            q: 1.0,
-            seed: 42,
-        }
-    }
-
-    /// Perform a single biased random walk starting from `start`.
-    fn random_walk(
-        &self,
-        adj: &[Vec<f64>],
-        n: usize,
-        start: usize,
-        rng: &mut StdRng,
-    ) -> Vec<usize> {
-        let mut walk = Vec::with_capacity(self.walk_length);
-        walk.push(start);
-
-        if self.walk_length <= 1 || n <= 1 {
-            return walk;
-        }
-
-        // First step: weighted over neighbors
-        let neighbors: Vec<(usize, f64)> = (0..n)
-            .filter(|&j| adj[start][j] > 1e-12)
-            .map(|j| (j, adj[start][j]))
-            .collect();
-
-        if neighbors.is_empty() {
-            return walk;
-        }
-
-        let total: f64 = neighbors.iter().map(|(_, w)| w).sum();
-        let r: f64 = rng.gen::<f64>() * total;
-        let mut cum = 0.0;
-        let mut chosen = neighbors[0].0;
-        for &(j, w) in &neighbors {
-            cum += w;
-            if r <= cum {
-                chosen = j;
-                break;
-            }
-        }
-        walk.push(chosen);
-
-        // Subsequent steps: biased by p and q
-        for _ in 2..self.walk_length {
-            let current = *walk.last().unwrap();
-            let prev = walk[walk.len() - 2];
-
-            let neighbors: Vec<(usize, f64)> = (0..n)
-                .filter(|&j| adj[current][j] > 1e-12)
-                .map(|j| (j, adj[current][j]))
-                .collect();
-
-            if neighbors.is_empty() {
-                break;
-            }
-
-            let biased: Vec<(usize, f64)> = neighbors
-                .iter()
-                .map(|&(j, w)| {
-                    let bias = if j == prev {
-                        1.0 / self.p
-                    } else if adj[prev][j] > 1e-12 {
-                        1.0
-                    } else {
-                        1.0 / self.q
-                    };
-                    (j, w * bias)
-                })
-                .collect();
-
-            let total: f64 = biased.iter().map(|(_, w)| w).sum();
-            if total < 1e-12 {
-                break;
-            }
-            let r: f64 = rng.gen::<f64>() * total;
-            let mut cum = 0.0;
-            let mut chosen = biased[0].0;
-            for &(j, w) in &biased {
-                cum += w;
-                if r <= cum {
-                    chosen = j;
-                    break;
-                }
-            }
-            walk.push(chosen);
-        }
-
-        walk
-    }
-
-    /// Generate all random walks from all nodes.
-    fn generate_walks(&self, adj: &[Vec<f64>], n: usize) -> Vec<Vec<usize>> {
-        let mut rng = StdRng::seed_from_u64(self.seed);
-        let mut all_walks = Vec::with_capacity(n * self.num_walks);
-        for _ in 0..self.num_walks {
-            for node in 0..n {
-                all_walks.push(self.random_walk(adj, n, node, &mut rng));
-            }
-        }
-        all_walks
-    }
-
-    /// Build co-occurrence matrix from walks using a skip-gram window.
-    fn build_cooccurrence(walks: &[Vec<usize>], n: usize, window: usize) -> Vec<Vec<f64>> {
-        let mut cooc = vec![vec![0.0; n]; n];
-        for walk in walks {
-            for (i, &center) in walk.iter().enumerate() {
-                let start = if i >= window { i - window } else { 0 };
-                let end = (i + window + 1).min(walk.len());
-                for j in start..end {
-                    if j != i {
-                        cooc[center][walk[j]] += 1.0;
-                    }
-                }
-            }
-        }
-        cooc
-    }
-
-    /// Simplified SVD via power iteration: extract top-k left singular vectors scaled by sigma.
-    fn truncated_svd(matrix: &[Vec<f64>], n: usize, k: usize) -> Vec<Vec<f64>> {
-        let k = k.min(n);
-        if k == 0 || n == 0 {
-            return vec![];
-        }
-
-        let mut result: Vec<Vec<f64>> = Vec::with_capacity(k);
-
-        for col in 0..k {
-            let mut v: Vec<f64> = (0..n).map(|i| ((i + col + 1) as f64).sin()).collect();
-            let norm = v.iter().map(|x| x * x).sum::<f64>().sqrt();
-            if norm > 1e-12 {
-                for x in &mut v {
-                    *x /= norm;
-                }
-            }
-
-            // Deflate
-            for prev in &result {
-                let prev_norm: f64 = prev.iter().map(|x| x * x).sum::<f64>().sqrt();
-                if prev_norm > 1e-12 {
-                    let prev_unit: Vec<f64> = prev.iter().map(|x| x / prev_norm).collect();
-                    let dot: f64 = v.iter().zip(prev_unit.iter()).map(|(a, b)| a * b).sum();
-                    for i in 0..n {
-                        v[i] -= dot * prev_unit[i];
-                    }
-                }
-            }
-
-            // Power iteration on M^T M
-            for _ in 0..100 {
-                let mut u = vec![0.0; n];
-                for i in 0..n {
-                    for j in 0..n {
-                        u[i] += matrix[i][j] * v[j];
-                    }
-                }
-                let mut new_v = vec![0.0; n];
-                for j in 0..n {
-                    for i in 0..n {
-                        new_v[j] += matrix[i][j] * u[i];
-                    }
-                }
-
-                // Deflate
-                for prev in &result {
-                    let prev_norm: f64 = prev.iter().map(|x| x * x).sum::<f64>().sqrt();
-                    if prev_norm > 1e-12 {
-                        let prev_unit: Vec<f64> = prev.iter().map(|x| x / prev_norm).collect();
-                        let dot: f64 = new_v
-                            .iter()
-                            .zip(prev_unit.iter())
-                            .map(|(a, b)| a * b)
-                            .sum();
-                        for i in 0..n {
-                            new_v[i] -= dot * prev_unit[i];
-                        }
-                    }
-                }
-
-                let norm = new_v.iter().map(|x| x * x).sum::<f64>().sqrt();
-                if norm < 1e-12 {
-                    break;
-                }
-                for x in &mut new_v {
-                    *x /= norm;
-                }
-                v = new_v;
-            }
-
-            // sigma * u = M * v
-            let mut mv = vec![0.0; n];
-            for i in 0..n {
-                for j in 0..n {
-                    mv[i] += matrix[i][j] * v[j];
-                }
-            }
-
-            result.push(mv);
-        }
-
-        result
-    }
-
-    /// Generate the Node2Vec embedding for a brain graph.
-    pub fn embed_graph(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        let n = graph.num_nodes;
-        if n < 2 {
-            return Err(RuvNeuralError::Embedding(
-                "Node2Vec requires at least 2 nodes".into(),
-            ));
-        }
-
-        let adj = graph.adjacency_matrix();
-        let walks = self.generate_walks(&adj, n);
-        let cooc = Self::build_cooccurrence(&walks, n, 5);
-
-        // Log transform (PPMI-like)
-        let log_cooc: Vec<Vec<f64>> = cooc
-            .iter()
-            .map(|row| row.iter().map(|&v| (1.0 + v).ln()).collect())
-            .collect();
-
-        let dim = self.embedding_dim.min(n);
-        let node_embeddings = Self::truncated_svd(&log_cooc, n, dim);
-
-        // Aggregate: [mean, std] per SVD component
-        let mut values = Vec::with_capacity(dim * 2);
-        for component in &node_embeddings {
-            let mean = component.iter().sum::<f64>() / n as f64;
-            let var = component.iter().map(|x| (x - mean).powi(2)).sum::<f64>() / n as f64;
-            values.push(mean);
-            values.push(var.sqrt());
-        }
-
-        while values.len() < self.embedding_dim * 2 {
-            values.push(0.0);
-        }
-
-        let meta = default_metadata("node2vec", graph.atlas);
-        NeuralEmbedding::new(values, graph.timestamp, meta)
-    }
-}
-
-impl EmbeddingGenerator for Node2VecEmbedder {
-    fn embedding_dim(&self) -> usize {
-        self.embedding_dim * 2
-    }
-
-    fn embed(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        self.embed_graph(graph)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_connected_graph() -> BrainGraph {
-        let edges: Vec<BrainEdge> = (0..4)
-            .map(|i| BrainEdge {
-                source: i,
-                target: i + 1,
-                weight: 1.0,
-                metric: ConnectivityMetric::Coherence,
-                frequency_band: FrequencyBand::Alpha,
-            })
-            .collect();
-        BrainGraph {
-            num_nodes: 5,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(5),
-        }
-    }
-
-    #[test]
-    fn test_node2vec_walks_visit_all_nodes() {
-        let graph = make_connected_graph();
-        let embedder = Node2VecEmbedder {
-            walk_length: 50,
-            num_walks: 20,
-            embedding_dim: 4,
-            p: 1.0,
-            q: 1.0,
-            seed: 42,
-        };
-
-        let adj = graph.adjacency_matrix();
-        let walks = embedder.generate_walks(&adj, graph.num_nodes);
-
-        let mut visited = std::collections::HashSet::new();
-        for walk in &walks {
-            for &node in walk {
-                visited.insert(node);
-            }
-        }
-
-        assert_eq!(visited.len(), 5, "All nodes should be visited");
-    }
-
-    #[test]
-    fn test_node2vec_embed() {
-        let graph = make_connected_graph();
-        let embedder = Node2VecEmbedder::new(3);
-        let emb = embedder.embed(&graph).unwrap();
-        assert_eq!(emb.dimension, 3 * 2);
-        assert_eq!(emb.metadata.embedding_method, "node2vec");
-    }
-
-    #[test]
-    fn test_node2vec_too_small() {
-        let graph = BrainGraph {
-            num_nodes: 1,
-            edges: vec![],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(1),
-        };
-        let embedder = Node2VecEmbedder::new(4);
-        assert!(embedder.embed(&graph).is_err());
-    }
-}
@@ -1,210 +0,0 @@
-//! Export neural embeddings to the RuVector File (.rvf) format.
-//!
-//! The RVF (RuVector Format) is a JSON-based file format for storing
-//! embedding vectors with metadata. This module provides round-trip
-//! serialization for interoperability with the RuVector ecosystem.
-
-use ruv_neural_core::brain::Atlas;
-use ruv_neural_core::embedding::{EmbeddingMetadata, NeuralEmbedding};
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use serde::{Deserialize, Serialize};
-
-/// RVF file header.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct RvfHeader {
-    /// Format version string.
-    pub version: String,
-    /// Number of embeddings in the file.
-    pub count: usize,
-    /// Embedding dimensionality.
-    pub dimension: usize,
-    /// Method used to generate embeddings.
-    pub method: String,
-    /// Optional description.
-    pub description: Option<String>,
-}
-
-/// A single RVF record (embedding + metadata).
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct RvfRecord {
-    /// Record index.
-    pub index: usize,
-    /// Timestamp of the source data.
-    pub timestamp: f64,
-    /// The embedding vector.
-    pub values: Vec<f64>,
-    /// Optional subject identifier.
-    pub subject_id: Option<String>,
-    /// Optional session identifier.
-    pub session_id: Option<String>,
-}
-
-/// Complete RVF document.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct RvfDocument {
-    /// File header.
-    pub header: RvfHeader,
-    /// Embedding records.
-    pub records: Vec<RvfRecord>,
-}
-
-/// Export embeddings to an RVF JSON file.
-///
-/// # Errors
-/// Returns an error if the embedding list is empty or if file I/O fails.
-pub fn export_rvf(embeddings: &[NeuralEmbedding], path: &str) -> Result<()> {
-    let json = to_rvf_string(embeddings)?;
-    std::fs::write(path, json).map_err(|e| {
-        RuvNeuralError::Serialization(format!("Failed to write RVF file '{}': {}", path, e))
-    })?;
-    Ok(())
-}
-
-/// Import embeddings from an RVF JSON file.
-///
-/// # Errors
-/// Returns an error if the file cannot be read or parsed.
-pub fn import_rvf(path: &str) -> Result<Vec<NeuralEmbedding>> {
-    let json = std::fs::read_to_string(path).map_err(|e| {
-        RuvNeuralError::Serialization(format!("Failed to read RVF file '{}': {}", path, e))
-    })?;
-    from_rvf_string(&json)
-}
-
-/// Serialize embeddings to RVF JSON string (without writing to file).
-pub fn to_rvf_string(embeddings: &[NeuralEmbedding]) -> Result<String> {
-    if embeddings.is_empty() {
-        return Err(RuvNeuralError::Embedding(
-            "Cannot serialize empty embedding list".into(),
-        ));
-    }
-
-    let dimension = embeddings[0].dimension;
-    let method = embeddings[0].metadata.embedding_method.clone();
-
-    let header = RvfHeader {
-        version: "1.0".to_string(),
-        count: embeddings.len(),
-        dimension,
-        method,
-        description: None,
-    };
-
-    let records: Vec<RvfRecord> = embeddings
-        .iter()
-        .enumerate()
-        .map(|(i, emb)| RvfRecord {
-            index: i,
-            timestamp: emb.timestamp,
-            values: emb.vector.clone(),
-            subject_id: emb.metadata.subject_id.clone(),
-            session_id: emb.metadata.session_id.clone(),
-        })
-        .collect();
-
-    let doc = RvfDocument { header, records };
-
-    serde_json::to_string_pretty(&doc).map_err(|e| {
-        RuvNeuralError::Serialization(format!("Failed to serialize RVF: {}", e))
-    })
-}
-
-/// Deserialize embeddings from an RVF JSON string.
-pub fn from_rvf_string(json: &str) -> Result<Vec<NeuralEmbedding>> {
-    let doc: RvfDocument = serde_json::from_str(json).map_err(|e| {
-        RuvNeuralError::Serialization(format!("Failed to parse RVF: {}", e))
-    })?;
-
-    doc.records
-        .into_iter()
-        .map(|rec| {
-            let meta = EmbeddingMetadata {
-                subject_id: rec.subject_id,
-                session_id: rec.session_id,
-                cognitive_state: None,
-                source_atlas: Atlas::Custom(doc.header.dimension),
-                embedding_method: doc.header.method.clone(),
-            };
-            NeuralEmbedding::new(rec.values, rec.timestamp, meta)
-        })
-        .collect()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::default_metadata;
-
-    #[test]
-    fn test_rvf_string_roundtrip() {
-        let embeddings = vec![
-            NeuralEmbedding::new(
-                vec![1.0, 2.0, 3.0],
-                0.0,
-                default_metadata("test", Atlas::Custom(3)),
-            )
-            .unwrap(),
-            NeuralEmbedding::new(
-                vec![4.0, 5.0, 6.0],
-                0.5,
-                default_metadata("test", Atlas::Custom(3)),
-            )
-            .unwrap(),
-            NeuralEmbedding::new(
-                vec![7.0, 8.0, 9.0],
-                1.0,
-                default_metadata("test", Atlas::Custom(3)),
-            )
-            .unwrap(),
-        ];
-
-        let json = to_rvf_string(&embeddings).unwrap();
-        let restored = from_rvf_string(&json).unwrap();
-
-        assert_eq!(restored.len(), 3);
-        for (orig, rest) in embeddings.iter().zip(restored.iter()) {
-            assert_eq!(orig.dimension, rest.dimension);
-            assert!((orig.timestamp - rest.timestamp).abs() < 1e-10);
-            for (a, b) in orig.vector.iter().zip(rest.vector.iter()) {
-                assert!((a - b).abs() < 1e-10);
-            }
-        }
-    }
-
-    #[test]
-    fn test_rvf_file_roundtrip() {
-        let embeddings = vec![
-            NeuralEmbedding::new(
-                vec![1.0, -2.5, 3.14],
-                10.0,
-                default_metadata("spectral", Atlas::Custom(3)),
-            )
-            .unwrap(),
-            NeuralEmbedding::new(
-                vec![0.0, 0.0, 0.0],
-                10.5,
-                default_metadata("spectral", Atlas::Custom(3)),
-            )
-            .unwrap(),
-        ];
-
-        let path = "/tmp/ruv_neural_embed_test.rvf";
-        export_rvf(&embeddings, path).unwrap();
-        let restored = import_rvf(path).unwrap();
-
-        assert_eq!(restored.len(), 2);
-        assert_eq!(restored[0].metadata.embedding_method, "spectral");
-        assert!((restored[0].vector[0] - 1.0).abs() < 1e-10);
-        assert!((restored[0].vector[1] - (-2.5)).abs() < 1e-10);
-        assert!((restored[0].vector[2] - 3.14).abs() < 1e-10);
-        assert!((restored[1].timestamp - 10.5).abs() < 1e-10);
-
-        let _ = std::fs::remove_file(path);
-    }
-
-    #[test]
-    fn test_rvf_empty_fails() {
-        assert!(to_rvf_string(&[]).is_err());
-        assert!(export_rvf(&[], "/tmp/empty.rvf").is_err());
-    }
-}
@@ -1,306 +0,0 @@
-//! Spectral graph embedding using Laplacian eigenvectors.
-//!
-//! Computes a positional encoding for each node using the first `k` eigenvectors
-//! of the normalized graph Laplacian. The graph-level embedding is formed by
-//! concatenating summary statistics of the per-node spectral coordinates.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::traits::EmbeddingGenerator;
-
-use crate::default_metadata;
-
-/// Spectral embedding via Laplacian eigenvectors.
-pub struct SpectralEmbedder {
-    /// Number of eigenvectors (spectral dimensions) to extract.
-    pub dimension: usize,
-    /// Number of power iteration steps for eigenvalue approximation.
-    pub power_iterations: usize,
-}
-
-impl SpectralEmbedder {
-    /// Create a new spectral embedder.
-    ///
-    /// `dimension` is the number of Laplacian eigenvectors to use.
-    pub fn new(dimension: usize) -> Self {
-        Self {
-            dimension,
-            power_iterations: 100,
-        }
-    }
-
-    /// Compute the normalized Laplacian matrix: L_norm = I - D^{-1/2} A D^{-1/2}.
-    fn normalized_laplacian(adj: &[Vec<f64>], n: usize) -> Vec<Vec<f64>> {
-        let degrees: Vec<f64> = (0..n).map(|i| adj[i].iter().sum::<f64>()).collect();
-
-        let inv_sqrt_deg: Vec<f64> = degrees
-            .iter()
-            .map(|d| if *d > 1e-12 { 1.0 / d.sqrt() } else { 0.0 })
-            .collect();
-
-        let mut laplacian = vec![vec![0.0; n]; n];
-        for i in 0..n {
-            for j in 0..n {
-                if i == j {
-                    if degrees[i] > 1e-12 {
-                        laplacian[i][j] = 1.0;
-                    }
-                } else {
-                    laplacian[i][j] = -adj[i][j] * inv_sqrt_deg[i] * inv_sqrt_deg[j];
-                }
-            }
-        }
-        laplacian
-    }
-
-    /// Extract the k smallest eigenvectors using deflated power iteration on (max_eig*I - L).
-    /// Returns eigenvectors as columns: result[eigenvector_index][node_index].
-    fn smallest_eigenvectors(
-        laplacian: &[Vec<f64>],
-        n: usize,
-        k: usize,
-        iterations: usize,
-    ) -> Vec<Vec<f64>> {
-        if n == 0 || k == 0 {
-            return vec![];
-        }
-        let k = k.min(n);
-
-        // Gershgorin bound for max eigenvalue
-        let max_eig: f64 = (0..n)
-            .map(|i| {
-                let diag = laplacian[i][i];
-                let off: f64 = (0..n)
-                    .filter(|&j| j != i)
-                    .map(|j| laplacian[i][j].abs())
-                    .sum();
-                diag + off
-            })
-            .fold(0.0_f64, f64::max);
-
-        // Shifted matrix: M = max_eig * I - L
-        let shifted: Vec<Vec<f64>> = (0..n)
-            .map(|i| {
-                (0..n)
-                    .map(|j| {
-                        if i == j {
-                            max_eig - laplacian[i][j]
-                        } else {
-                            -laplacian[i][j]
-                        }
-                    })
-                    .collect()
-            })
-            .collect();
-
-        let mut eigenvectors: Vec<Vec<f64>> = Vec::with_capacity(k);
-
-        for _ev in 0..k {
-            let mut v: Vec<f64> = (0..n).map(|i| ((i + 1) as f64).sin()).collect();
-            let norm = v.iter().map(|x| x * x).sum::<f64>().sqrt();
-            if norm > 1e-12 {
-                for x in &mut v {
-                    *x /= norm;
-                }
-            }
-
-            // Deflate against already-found eigenvectors
-            for prev in &eigenvectors {
-                let dot: f64 = v.iter().zip(prev.iter()).map(|(a, b)| a * b).sum();
-                for i in 0..n {
-                    v[i] -= dot * prev[i];
-                }
-            }
-
-            for _ in 0..iterations {
-                let mut w = vec![0.0; n];
-                for i in 0..n {
-                    for j in 0..n {
-                        w[i] += shifted[i][j] * v[j];
-                    }
-                }
-
-                for prev in &eigenvectors {
-                    let dot: f64 = w.iter().zip(prev.iter()).map(|(a, b)| a * b).sum();
-                    for i in 0..n {
-                        w[i] -= dot * prev[i];
-                    }
-                }
-
-                let norm = w.iter().map(|x| x * x).sum::<f64>().sqrt();
-                if norm < 1e-12 {
-                    break;
-                }
-                for x in &mut w {
-                    *x /= norm;
-                }
-                v = w;
-            }
-
-            eigenvectors.push(v);
-        }
-
-        eigenvectors
-    }
-
-    /// Embed a brain graph using spectral decomposition.
-    pub fn embed_graph(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        let n = graph.num_nodes;
-        if n < 2 {
-            return Err(RuvNeuralError::Embedding(
-                "Spectral embedding requires at least 2 nodes".into(),
-            ));
-        }
-
-        let adj = graph.adjacency_matrix();
-        let laplacian = Self::normalized_laplacian(&adj, n);
-
-        // Skip the trivial first eigenvector and take the next `dimension`
-        let num_to_extract = (self.dimension + 1).min(n);
-        let eigvecs =
-            Self::smallest_eigenvectors(&laplacian, n, num_to_extract, self.power_iterations);
-
-        let useful: Vec<&Vec<f64>> = eigvecs.iter().skip(1).take(self.dimension).collect();
-
-        // Build graph-level embedding: [mean, std, min, max] per eigenvector
-        let mut values = Vec::with_capacity(self.dimension * 4);
-        for ev in &useful {
-            let mean = ev.iter().sum::<f64>() / n as f64;
-            let variance = ev.iter().map(|x| (x - mean).powi(2)).sum::<f64>() / n as f64;
-            let std = variance.sqrt();
-            let min = ev.iter().cloned().fold(f64::INFINITY, f64::min);
-            let max = ev.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
-            values.push(mean);
-            values.push(std);
-            values.push(min);
-            values.push(max);
-        }
-
-        // Pad if fewer eigenvectors than requested
-        while values.len() < self.dimension * 4 {
-            values.push(0.0);
-        }
-
-        let meta = default_metadata("spectral", graph.atlas);
-        NeuralEmbedding::new(values, graph.timestamp, meta)
-    }
-}
-
-impl EmbeddingGenerator for SpectralEmbedder {
-    fn embedding_dim(&self) -> usize {
-        self.dimension * 4
-    }
-
-    fn embed(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        self.embed_graph(graph)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_complete_graph(n: usize) -> BrainGraph {
-        let mut edges = Vec::new();
-        for i in 0..n {
-            for j in (i + 1)..n {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        BrainGraph {
-            num_nodes: n,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(n),
-        }
-    }
-
-    fn make_two_cluster_graph() -> BrainGraph {
-        let mut edges = Vec::new();
-        // Cluster A: nodes 0-3 (fully connected)
-        for i in 0..4 {
-            for j in (i + 1)..4 {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        // Cluster B: nodes 4-7 (fully connected)
-        for i in 4..8 {
-            for j in (i + 1)..8 {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        // Weak bridge
-        edges.push(BrainEdge {
-            source: 3,
-            target: 4,
-            weight: 0.1,
-            metric: ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        });
-        BrainGraph {
-            num_nodes: 8,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(8),
-        }
-    }
-
-    #[test]
-    fn test_spectral_complete_graph() {
-        let graph = make_complete_graph(6);
-        let embedder = SpectralEmbedder::new(3);
-        let emb = embedder.embed(&graph).unwrap();
-        assert_eq!(emb.dimension, 3 * 4);
-    }
-
-    #[test]
-    fn test_spectral_two_cluster_separation() {
-        let graph = make_two_cluster_graph();
-        let embedder = SpectralEmbedder::new(2);
-        let emb = embedder.embed(&graph).unwrap();
-        // Fiedler vector std (index 1) should show cluster separation
-        let fiedler_std = emb.vector[1];
-        assert!(
-            fiedler_std > 0.01,
-            "Fiedler eigenvector should show cluster separation, got std={}",
-            fiedler_std
-        );
-    }
-
-    #[test]
-    fn test_spectral_too_small() {
-        let graph = BrainGraph {
-            num_nodes: 1,
-            edges: vec![],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(1),
-        };
-        let embedder = SpectralEmbedder::new(2);
-        assert!(embedder.embed(&graph).is_err());
-    }
-}
@@ -1,217 +0,0 @@
-//! Temporal sliding-window embeddings for brain graph sequences.
-//!
-//! Embeds a time series of brain graphs into trajectory vectors by combining
-//! each graph's embedding with an exponentially-weighted average of past embeddings.
-
-use ruv_neural_core::embedding::{EmbeddingTrajectory, NeuralEmbedding};
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::graph::{BrainGraph, BrainGraphSequence};
-use ruv_neural_core::traits::EmbeddingGenerator;
-
-use crate::default_metadata;
-
-/// Temporal embedder that enriches each graph embedding with historical context.
-pub struct TemporalEmbedder {
-    /// Base embedder for individual graphs.
-    base_embedder: Box<dyn EmbeddingGenerator>,
-    /// Number of past embeddings to consider in the context window.
-    window_size: usize,
-    /// Exponential decay factor for weighting past embeddings (0 < decay <= 1).
-    decay: f64,
-}
-
-impl TemporalEmbedder {
-    /// Create a new temporal embedder.
-    ///
-    /// - `base`: the embedding generator for individual graphs
-    /// - `window`: how many past embeddings to incorporate
-    pub fn new(base: Box<dyn EmbeddingGenerator>, window: usize) -> Self {
-        Self {
-            base_embedder: base,
-            window_size: window,
-            decay: 0.8,
-        }
-    }
-
-    /// Set the exponential decay factor.
-    pub fn with_decay(mut self, decay: f64) -> Self {
-        self.decay = decay.clamp(0.01, 1.0);
-        self
-    }
-
-    /// Embed a full sequence of graphs into a trajectory.
-    pub fn embed_sequence(&self, sequence: &BrainGraphSequence) -> Result<EmbeddingTrajectory> {
-        if sequence.is_empty() {
-            return Err(RuvNeuralError::Embedding(
-                "Cannot embed empty graph sequence".into(),
-            ));
-        }
-
-        let mut history: Vec<NeuralEmbedding> = Vec::new();
-        let mut embeddings = Vec::with_capacity(sequence.graphs.len());
-        let mut timestamps = Vec::with_capacity(sequence.graphs.len());
-
-        for graph in &sequence.graphs {
-            let emb = self.embed_with_context(graph, &history)?;
-            timestamps.push(graph.timestamp);
-            history.push(self.base_embedder.embed(graph)?);
-            embeddings.push(emb);
-        }
-
-        Ok(EmbeddingTrajectory {
-            embeddings,
-            timestamps,
-        })
-    }
-
-    /// Embed a single graph with temporal context from past embeddings.
-    ///
-    /// The output concatenates:
-    /// 1. The current graph's base embedding
-    /// 2. An exponentially-weighted average of past embeddings (zero-padded if no history)
-    pub fn embed_with_context(
-        &self,
-        graph: &BrainGraph,
-        history: &[NeuralEmbedding],
-    ) -> Result<NeuralEmbedding> {
-        let current = self.base_embedder.embed(graph)?;
-        let base_dim = current.dimension;
-
-        let context = self.compute_context(history, base_dim);
-
-        let mut values = Vec::with_capacity(base_dim * 2);
-        values.extend_from_slice(&current.vector);
-        values.extend_from_slice(&context);
-
-        let meta = default_metadata("temporal", graph.atlas);
-        NeuralEmbedding::new(values, graph.timestamp, meta)
-    }
-
-    /// Compute the exponentially-weighted context vector from history.
-    fn compute_context(&self, history: &[NeuralEmbedding], dim: usize) -> Vec<f64> {
-        if history.is_empty() {
-            return vec![0.0; dim];
-        }
-
-        let window_start = if history.len() > self.window_size {
-            history.len() - self.window_size
-        } else {
-            0
-        };
-        let window = &history[window_start..];
-
-        let mut context = vec![0.0; dim];
-        let mut total_weight = 0.0;
-
-        for (i, emb) in window.iter().rev().enumerate() {
-            let w = self.decay.powi(i as i32);
-            total_weight += w;
-            let usable_dim = dim.min(emb.dimension);
-            for j in 0..usable_dim {
-                context[j] += w * emb.vector[j];
-            }
-        }
-
-        if total_weight > 1e-12 {
-            for v in &mut context {
-                *v /= total_weight;
-            }
-        }
-
-        context
-    }
-
-    /// Output dimension: base dimension * 2 (current + context).
-    pub fn output_dimension(&self) -> usize {
-        self.base_embedder.embedding_dim() * 2
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::topology_embed::TopologyEmbedder;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_graph(timestamp: f64) -> BrainGraph {
-        BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp,
-            window_duration_s: 0.5,
-            atlas: Atlas::Custom(3),
-        }
-    }
-
-    #[test]
-    fn test_temporal_embed_no_history() {
-        let embedder = TemporalEmbedder::new(Box::new(TopologyEmbedder::new()), 5);
-        let graph = make_graph(0.0);
-        let emb = embedder.embed_with_context(&graph, &[]).unwrap();
-
-        let base_dim = TopologyEmbedder::new().embedding_dim();
-        assert_eq!(emb.dimension, base_dim * 2);
-
-        for i in base_dim..emb.dimension {
-            assert!(
-                emb.vector[i].abs() < 1e-12,
-                "Context should be zero with no history"
-            );
-        }
-    }
-
-    #[test]
-    fn test_temporal_embed_sequence() {
-        let base = Box::new(TopologyEmbedder::new());
-        let embedder = TemporalEmbedder::new(base, 3);
-
-        let sequence = BrainGraphSequence {
-            graphs: vec![make_graph(0.0), make_graph(0.5), make_graph(1.0)],
-            window_step_s: 0.5,
-        };
-
-        let trajectory = embedder.embed_sequence(&sequence).unwrap();
-        assert_eq!(trajectory.len(), 3);
-        assert_eq!(trajectory.timestamps.len(), 3);
-
-        let base_dim = TopologyEmbedder::new().embedding_dim();
-        for i in base_dim..trajectory.embeddings[0].dimension {
-            assert!(trajectory.embeddings[0].vector[i].abs() < 1e-12);
-        }
-
-        let has_nonzero = trajectory.embeddings[2].vector[base_dim..]
-            .iter()
-            .any(|v| v.abs() > 1e-12);
-        assert!(
-            has_nonzero,
-            "Third embedding should have non-zero temporal context"
-        );
-    }
-
-    #[test]
-    fn test_temporal_empty_sequence_fails() {
-        let embedder = TemporalEmbedder::new(Box::new(TopologyEmbedder::new()), 3);
-        let sequence = BrainGraphSequence {
-            graphs: vec![],
-            window_step_s: 0.5,
-        };
-        assert!(embedder.embed_sequence(&sequence).is_err());
-    }
-}
@@ -1,491 +0,0 @@
-//! Topology-based graph embedding.
-//!
-//! Extracts a feature vector of hand-crafted topological metrics from a brain graph,
-//! including mincut estimate, modularity, efficiency, degree statistics, and more.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::Result;
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::traits::EmbeddingGenerator;
-
-use crate::default_metadata;
-
-/// Topology-based embedder: converts a brain graph into a vector of topological features.
-pub struct TopologyEmbedder {
-    /// Include global minimum cut estimate.
-    pub include_mincut: bool,
-    /// Include modularity estimate.
-    pub include_modularity: bool,
-    /// Include global and local efficiency.
-    pub include_efficiency: bool,
-    /// Include degree distribution statistics.
-    pub include_degree_stats: bool,
-}
-
-impl TopologyEmbedder {
-    /// Create a new topology embedder with all features enabled.
-    pub fn new() -> Self {
-        Self {
-            include_mincut: true,
-            include_modularity: true,
-            include_efficiency: true,
-            include_degree_stats: true,
-        }
-    }
-
-    /// Estimate global minimum cut via the minimum node degree.
-    fn estimate_mincut(graph: &BrainGraph) -> f64 {
-        if graph.num_nodes < 2 {
-            return 0.0;
-        }
-        (0..graph.num_nodes)
-            .map(|i| graph.node_degree(i))
-            .fold(f64::INFINITY, f64::min)
-    }
-
-    /// Estimate modularity using a simple greedy two-partition.
-    fn estimate_modularity(graph: &BrainGraph) -> f64 {
-        let n = graph.num_nodes;
-        if n < 2 {
-            return 0.0;
-        }
-        let total_weight = graph.total_weight();
-        if total_weight < 1e-12 {
-            return 0.0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let degrees: Vec<f64> = (0..n).map(|i| graph.node_degree(i)).collect();
-
-        let mut sorted_degrees: Vec<(usize, f64)> =
-            degrees.iter().copied().enumerate().collect();
-        sorted_degrees.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap());
-        let mid = n / 2;
-
-        let mut partition = vec![0i32; n];
-        for (rank, &(node, _)) in sorted_degrees.iter().enumerate() {
-            partition[node] = if rank < mid { 1 } else { -1 };
-        }
-
-        let two_m = 2.0 * total_weight;
-        let mut q = 0.0;
-        for i in 0..n {
-            for j in 0..n {
-                if partition[i] == partition[j] {
-                    q += adj[i][j] - degrees[i] * degrees[j] / two_m;
-                }
-            }
-        }
-        q / two_m
-    }
-
-    /// Compute global efficiency: average of 1/shortest_path for all node pairs.
-    fn global_efficiency(graph: &BrainGraph) -> f64 {
-        let n = graph.num_nodes;
-        if n < 2 {
-            return 0.0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let mut sum_inv_dist = 0.0;
-
-        for source in 0..n {
-            let mut dist = vec![usize::MAX; n];
-            dist[source] = 0;
-            let mut queue = std::collections::VecDeque::new();
-            queue.push_back(source);
-
-            while let Some(u) = queue.pop_front() {
-                for v in 0..n {
-                    if dist[v] == usize::MAX && adj[u][v] > 1e-12 {
-                        dist[v] = dist[u] + 1;
-                        queue.push_back(v);
-                    }
-                }
-            }
-
-            for v in 0..n {
-                if v != source && dist[v] != usize::MAX {
-                    sum_inv_dist += 1.0 / dist[v] as f64;
-                }
-            }
-        }
-
-        sum_inv_dist / (n * (n - 1)) as f64
-    }
-
-    /// Compute mean local efficiency.
-    fn local_efficiency(graph: &BrainGraph) -> f64 {
-        let n = graph.num_nodes;
-        if n == 0 {
-            return 0.0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let mut total = 0.0;
-
-        for node in 0..n {
-            let neighbors: Vec<usize> = (0..n)
-                .filter(|&j| j != node && adj[node][j] > 1e-12)
-                .collect();
-            let k = neighbors.len();
-            if k < 2 {
-                continue;
-            }
-
-            let mut sub_sum = 0.0;
-            for &i in &neighbors {
-                for &j in &neighbors {
-                    if i != j && adj[i][j] > 1e-12 {
-                        sub_sum += 1.0;
-                    }
-                }
-            }
-            total += sub_sum / (k * (k - 1)) as f64;
-        }
-
-        total / n as f64
-    }
-
-    /// Compute graph entropy from edge weight distribution.
-    fn graph_entropy(graph: &BrainGraph) -> f64 {
-        if graph.edges.is_empty() {
-            return 0.0;
-        }
-        let total: f64 = graph.edges.iter().map(|e| e.weight.abs()).sum();
-        if total < 1e-12 {
-            return 0.0;
-        }
-
-        let mut entropy = 0.0;
-        for edge in &graph.edges {
-            let p = edge.weight.abs() / total;
-            if p > 1e-12 {
-                entropy -= p * p.ln();
-            }
-        }
-        entropy
-    }
-
-    /// Estimate the Fiedler value (algebraic connectivity).
-    fn estimate_fiedler(graph: &BrainGraph) -> f64 {
-        let n = graph.num_nodes;
-        if n < 2 {
-            return 0.0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let degrees: Vec<f64> = (0..n).map(|i| adj[i].iter().sum::<f64>()).collect();
-
-        let mut laplacian = vec![vec![0.0; n]; n];
-        for i in 0..n {
-            for j in 0..n {
-                if i == j {
-                    laplacian[i][j] = degrees[i];
-                } else {
-                    laplacian[i][j] = -adj[i][j];
-                }
-            }
-        }
-
-        let max_eig: f64 = (0..n)
-            .map(|i| {
-                let diag = laplacian[i][i];
-                let off: f64 = (0..n)
-                    .filter(|&j| j != i)
-                    .map(|j| laplacian[i][j].abs())
-                    .sum();
-                diag + off
-            })
-            .fold(0.0_f64, f64::max);
-
-        let e0: Vec<f64> = vec![1.0 / (n as f64).sqrt(); n];
-
-        let mut v: Vec<f64> = (0..n).map(|i| ((i + 1) as f64).sin()).collect();
-        let dot0: f64 = v.iter().zip(e0.iter()).map(|(a, b)| a * b).sum();
-        for i in 0..n {
-            v[i] -= dot0 * e0[i];
-        }
-        let norm = v.iter().map(|x| x * x).sum::<f64>().sqrt();
-        if norm < 1e-12 {
-            return 0.0;
-        }
-        for x in &mut v {
-            *x /= norm;
-        }
-
-        let mut eigenvalue = 0.0;
-        for _ in 0..200 {
-            let mut w = vec![0.0; n];
-            for i in 0..n {
-                for j in 0..n {
-                    if i == j {
-                        w[i] += (max_eig - laplacian[i][j]) * v[j];
-                    } else {
-                        w[i] += -laplacian[i][j] * v[j];
-                    }
-                }
-            }
-
-            let dot: f64 = w.iter().zip(e0.iter()).map(|(a, b)| a * b).sum();
-            for i in 0..n {
-                w[i] -= dot * e0[i];
-            }
-
-            let norm = w.iter().map(|x| x * x).sum::<f64>().sqrt();
-            if norm < 1e-12 {
-                break;
-            }
-            eigenvalue = norm;
-            for x in &mut w {
-                *x /= norm;
-            }
-            v = w;
-        }
-
-        (max_eig - eigenvalue).max(0.0)
-    }
-
-    /// Compute average clustering coefficient.
-    fn clustering_coefficient(graph: &BrainGraph) -> f64 {
-        let n = graph.num_nodes;
-        if n == 0 {
-            return 0.0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let mut total = 0.0;
-
-        for node in 0..n {
-            let neighbors: Vec<usize> = (0..n)
-                .filter(|&j| j != node && adj[node][j] > 1e-12)
-                .collect();
-            let k = neighbors.len();
-            if k < 2 {
-                continue;
-            }
-
-            let mut triangles = 0usize;
-            for i in 0..k {
-                for j in (i + 1)..k {
-                    if adj[neighbors[i]][neighbors[j]] > 1e-12 {
-                        triangles += 1;
-                    }
-                }
-            }
-            total += 2.0 * triangles as f64 / (k * (k - 1)) as f64;
-        }
-
-        total / n as f64
-    }
-
-    /// Count connected components via BFS.
-    fn num_components(graph: &BrainGraph) -> usize {
-        let n = graph.num_nodes;
-        if n == 0 {
-            return 0;
-        }
-
-        let adj = graph.adjacency_matrix();
-        let mut visited = vec![false; n];
-        let mut count = 0;
-
-        for start in 0..n {
-            if visited[start] {
-                continue;
-            }
-            count += 1;
-            let mut queue = std::collections::VecDeque::new();
-            queue.push_back(start);
-            visited[start] = true;
-            while let Some(u) = queue.pop_front() {
-                for v in 0..n {
-                    if !visited[v] && adj[u][v] > 1e-12 {
-                        visited[v] = true;
-                        queue.push_back(v);
-                    }
-                }
-            }
-        }
-
-        count
-    }
-
-    /// Generate the topology embedding.
-    pub fn embed_graph(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        let mut values = Vec::new();
-
-        if self.include_mincut {
-            values.push(Self::estimate_mincut(graph));
-        }
-
-        if self.include_modularity {
-            values.push(Self::estimate_modularity(graph));
-        }
-
-        if self.include_efficiency {
-            values.push(Self::global_efficiency(graph));
-            values.push(Self::local_efficiency(graph));
-        }
-
-        values.push(Self::graph_entropy(graph));
-        values.push(Self::estimate_fiedler(graph));
-
-        if self.include_degree_stats {
-            let n = graph.num_nodes;
-            let degrees: Vec<f64> = (0..n).map(|i| graph.node_degree(i)).collect();
-
-            let mean_deg = if n > 0 {
-                degrees.iter().sum::<f64>() / n as f64
-            } else {
-                0.0
-            };
-            let std_deg = if n > 0 {
-                let var =
-                    degrees.iter().map(|d| (d - mean_deg).powi(2)).sum::<f64>() / n as f64;
-                var.sqrt()
-            } else {
-                0.0
-            };
-            let max_deg = degrees.iter().cloned().fold(0.0_f64, f64::max);
-            let min_deg = degrees.iter().cloned().fold(f64::INFINITY, f64::min);
-            let min_deg = if min_deg.is_infinite() { 0.0 } else { min_deg };
-
-            values.push(mean_deg);
-            values.push(std_deg);
-            values.push(max_deg);
-            values.push(min_deg);
-        }
-
-        values.push(graph.density());
-        values.push(Self::clustering_coefficient(graph));
-        values.push(Self::num_components(graph) as f64);
-
-        let meta = default_metadata("topology", graph.atlas);
-        NeuralEmbedding::new(values, graph.timestamp, meta)
-    }
-
-    /// Number of features produced with current settings.
-    pub fn feature_count(&self) -> usize {
-        let mut count = 0;
-        if self.include_mincut {
-            count += 1;
-        }
-        if self.include_modularity {
-            count += 1;
-        }
-        if self.include_efficiency {
-            count += 2;
-        }
-        count += 2; // entropy + fiedler
-        if self.include_degree_stats {
-            count += 4;
-        }
-        count += 3; // density, clustering, components
-        count
-    }
-}
-
-impl Default for TopologyEmbedder {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-impl EmbeddingGenerator for TopologyEmbedder {
-    fn embedding_dim(&self) -> usize {
-        self.feature_count()
-    }
-
-    fn embed(&self, graph: &BrainGraph) -> Result<NeuralEmbedding> {
-        self.embed_graph(graph)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_triangle() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 0,
-                    target: 2,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        }
-    }
-
-    #[test]
-    fn test_topology_embed_triangle() {
-        let graph = make_triangle();
-        let embedder = TopologyEmbedder::new();
-        let emb = embedder.embed(&graph).unwrap();
-
-        assert_eq!(emb.dimension, embedder.feature_count());
-        assert_eq!(emb.metadata.embedding_method, "topology");
-
-        let dim = emb.dimension;
-        // Last three values: density, clustering, components
-        assert!((emb.vector[dim - 3] - 1.0).abs() < 1e-10, "density should be 1.0");
-        assert!((emb.vector[dim - 2] - 1.0).abs() < 1e-10, "clustering should be 1.0");
-        assert!((emb.vector[dim - 1] - 1.0).abs() < 1e-10, "should be 1 component");
-    }
-
-    #[test]
-    fn test_topology_captures_known_features() {
-        let graph = make_triangle();
-        let embedder = TopologyEmbedder::new();
-        let emb = embedder.embed(&graph).unwrap();
-
-        // Global efficiency of K3: all pairs distance 1, so efficiency = 1.0
-        // index: mincut(0), modularity(1), global_eff(2), local_eff(3)
-        assert!(
-            (emb.vector[2] - 1.0).abs() < 1e-10,
-            "global efficiency of K3 should be 1.0, got {}",
-            emb.vector[2]
-        );
-    }
-
-    #[test]
-    fn test_empty_graph() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-        let embedder = TopologyEmbedder::new();
-        let emb = embedder.embed(&graph).unwrap();
-        let dim = emb.dimension;
-        assert!((emb.vector[dim - 3]).abs() < 1e-10);
-        assert!((emb.vector[dim - 2]).abs() < 1e-10);
-        assert!((emb.vector[dim - 1] - 4.0).abs() < 1e-10);
-    }
-}
@@ -1,24 +0,0 @@
-[package]
-name = "ruv-neural-esp32"
-description = "rUv Neural — ESP32 edge integration for neural sensor data acquisition and preprocessing"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-no_std = []
-simulator = ["std"]
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-num-traits = { workspace = true }
-
-[dev-dependencies]
-rand = { workspace = true }
-approx = { workspace = true }
@@ -1,106 +0,0 @@
-# ruv-neural-esp32
-
-ESP32 edge integration for neural sensor data acquisition and preprocessing.
-
-## Overview
-
-`ruv-neural-esp32` provides lightweight processing modules designed to run on
-ESP32 microcontrollers for real-time neural sensor data acquisition and
-preprocessing at the edge. It handles ADC sampling, time-division multiplexing
-for multi-sensor coordination, IIR filtering and downsampling on-device, power
-management for battery operation, a binary communication protocol for streaming
-data to the rUv Neural backend, and multi-node data aggregation.
-
-## Features
-
- **ADC interface** (`adc`): `AdcReader` with configurable `AdcConfig` including
-  sample rate, resolution, attenuation levels, and multi-channel support via
-  `AdcChannel`
- **TDM scheduling** (`tdm`): `TdmScheduler` and `TdmNode` for time-division
-  multiplexed multi-sensor coordination with configurable `SyncMethod`
-  (GPIO trigger, I2S clock, software timer)
- **Edge preprocessing** (`preprocessing`): `EdgePreprocessor` with fixed-point
-  IIR filters (`IirCoeffs`), downsampling, and DC offset removal optimized
-  for constrained embedded environments
- **Communication protocol** (`protocol`): `NeuralDataPacket` with `PacketHeader`
-  and `ChannelData` for efficient binary data streaming to the backend over
-  UART, SPI, or WiFi
- **Power management** (`power`): `PowerManager` with `PowerConfig` and `PowerMode`
-  (active, light sleep, deep sleep, hibernate) for battery-powered deployments
- **Multi-node aggregation** (`aggregator`): `NodeAggregator` for combining data
-  from multiple ESP32 nodes into synchronized multi-channel streams
-
-## Usage
-
-```rust
-use ruv_neural_esp32::{
-    AdcReader, AdcConfig, Attenuation,
-    TdmScheduler, TdmNode, SyncMethod,
-    EdgePreprocessor, IirCoeffs,
-    NeuralDataPacket, PacketHeader, ChannelData,
-    PowerManager, PowerConfig, PowerMode,
-    NodeAggregator,
-};
-
-// Configure ADC for 4-channel acquisition
-let config = AdcConfig {
-    sample_rate_hz: 1000,
-    resolution_bits: 12,
-    attenuation: Attenuation::Db11,
-    channels: vec![
-        AdcChannel { pin: 32, gain: 1.0 },
-        AdcChannel { pin: 33, gain: 1.0 },
-        AdcChannel { pin: 34, gain: 1.0 },
-        AdcChannel { pin: 35, gain: 1.0 },
-    ],
-};
-let mut adc = AdcReader::new(config);
-
-// Set up TDM scheduling for multi-sensor sync
-let scheduler = TdmScheduler::new(SyncMethod::GpioTrigger);
-let node = TdmNode::new(0, scheduler);
-
-// Preprocess on-device with IIR filter
-let mut preprocessor = EdgePreprocessor::new(1000.0);
-let filtered = preprocessor.process(&raw_samples);
-
-// Build a data packet for transmission
-let packet = NeuralDataPacket {
-    header: PacketHeader::new(4, 250),
-    channels: vec![ChannelData { samples: filtered }],
-};
-
-// Power management
-let mut power = PowerManager::new(PowerConfig::default());
-power.set_mode(PowerMode::LightSleep);
-```
-
-## API Reference
-
-| Module          | Key Types                                                    |
-|-----------------|--------------------------------------------------------------|
-| `adc`           | `AdcReader`, `AdcConfig`, `AdcChannel`, `Attenuation`        |
-| `tdm`           | `TdmScheduler`, `TdmNode`, `SyncMethod`                      |
-| `preprocessing` | `EdgePreprocessor`, `IirCoeffs`                               |
-| `protocol`      | `NeuralDataPacket`, `PacketHeader`, `ChannelData`             |
-| `power`         | `PowerManager`, `PowerConfig`, `PowerMode`                    |
-| `aggregator`    | `NodeAggregator`                                              |
-
-## Feature Flags
-
-| Feature     | Default | Description                              |
-|-------------|---------|------------------------------------------|
-| `std`       | Yes     | Standard library (desktop simulation)    |
-| `no_std`    | No      | Bare-metal ESP32 target                  |
-| `simulator` | No      | Simulated ADC for testing (requires std) |
-
-## Integration
-
-Depends on `ruv-neural-core` for shared types. Preprocessed data packets are
-sent to the host system where `ruv-neural-sensor` or `ruv-neural-signal` can
-consume them for further processing. Designed to run independently on ESP32
-hardware or in simulation mode on desktop for testing.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,313 +0,0 @@
-//! ADC interface for sensor data acquisition.
-//!
-//! Provides ESP32 ADC configuration and a ring-buffer backed data reader that
-//! converts raw ADC values to physical units (femtotesla). The ring buffer is
-//! populated via [`AdcReader::load_buffer`] (the production data input path)
-//! or by hardware DMA on actual ESP32 targets. On `no_std` the reader would
-//! wire directly into the ADC peripheral.
-
-use ruv_neural_core::sensor::SensorType;
-use ruv_neural_core::{Result, RuvNeuralError};
-use serde::{Deserialize, Serialize};
-
-/// ESP32 ADC input attenuation setting.
-///
-/// Controls the measurable voltage range on an ADC channel.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum Attenuation {
-    /// 0 dB — range ~100-950 mV.
-    Db0,
-    /// 2.5 dB — range ~100-1250 mV.
-    Db2_5,
-    /// 6 dB — range ~150-1750 mV.
-    Db6,
-    /// 11 dB — range ~150-2450 mV.
-    Db11,
-}
-
-impl Attenuation {
-    /// Maximum measurable voltage in millivolts for this attenuation.
-    pub fn max_voltage_mv(&self) -> u32 {
-        match self {
-            Attenuation::Db0 => 950,
-            Attenuation::Db2_5 => 1250,
-            Attenuation::Db6 => 1750,
-            Attenuation::Db11 => 2450,
-        }
-    }
-}
-
-/// Configuration for a single ADC channel.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct AdcChannel {
-    /// ADC channel identifier (0-7 on ESP32).
-    pub channel_id: u8,
-    /// GPIO pin number this channel is wired to.
-    pub gpio_pin: u8,
-    /// Input attenuation setting.
-    pub attenuation: Attenuation,
-    /// Type of sensor connected to this channel.
-    pub sensor_type: SensorType,
-    /// Gain factor applied during conversion to physical units.
-    pub gain: f64,
-    /// Offset applied during conversion to physical units.
-    pub offset: f64,
-}
-
-/// ESP32 ADC configuration for neural sensor readout.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct AdcConfig {
-    /// Channels to sample.
-    pub channels: Vec<AdcChannel>,
-    /// Target sample rate in Hz.
-    pub sample_rate_hz: u32,
-    /// ADC resolution in bits (12 or 16).
-    pub resolution_bits: u8,
-    /// Reference voltage in millivolts.
-    pub reference_voltage_mv: u32,
-    /// Whether DMA transfers are enabled for continuous sampling.
-    pub dma_enabled: bool,
-}
-
-impl AdcConfig {
-    /// Maximum raw ADC value for the configured resolution.
-    ///
-    /// Clamps the result to `i16::MAX` when `resolution_bits >= 16` to
-    /// prevent integer overflow.
-    pub fn max_raw_value(&self) -> i16 {
-        let bits = self.resolution_bits.min(15);
-        ((1u32 << bits) - 1) as i16
-    }
-
-    /// Creates a default configuration with a single NV diamond channel.
-    pub fn default_single_channel() -> Self {
-        Self {
-            channels: vec![AdcChannel {
-                channel_id: 0,
-                gpio_pin: 36,
-                attenuation: Attenuation::Db11,
-                sensor_type: SensorType::NvDiamond,
-                gain: 1.0,
-                offset: 0.0,
-            }],
-            sample_rate_hz: 1000,
-            resolution_bits: 12,
-            reference_voltage_mv: 3300,
-            dma_enabled: false,
-        }
-    }
-}
-
-/// Ring-buffer backed ADC data reader that converts raw ADC values to
-/// physical units.
-///
-/// The internal ring buffer is filled by [`load_buffer`](Self::load_buffer)
-/// (the production data input path from DMA or manual sampling) or by
-/// [`fill_with_calibration_signal`](Self::fill_with_calibration_signal) for
-/// self-test/calibration. On actual ESP32 hardware the DMA controller writes
-/// directly into this buffer.
-pub struct AdcReader {
-    config: AdcConfig,
-    buffer: Vec<Vec<i16>>,
-    buffer_pos: usize,
-}
-
-impl AdcReader {
-    /// Create a new reader for the given ADC configuration.
-    ///
-    /// Allocates a ring buffer with 4096 samples per channel.
-    pub fn new(config: AdcConfig) -> Self {
-        let num_channels = config.channels.len();
-        let buffer_size = 4096;
-        let buffer = vec![vec![0i16; buffer_size]; num_channels];
-        Self {
-            config,
-            buffer,
-            buffer_pos: 0,
-        }
-    }
-
-    /// Read `num_samples` from every configured channel, returning values in
-    /// femtotesla.
-    ///
-    /// The outer `Vec` is indexed by channel and the inner `Vec` contains
-    /// the converted sample values.
-    pub fn read_samples(&mut self, num_samples: usize) -> Result<Vec<Vec<f64>>> {
-        if num_samples == 0 {
-            return Err(RuvNeuralError::Signal(
-                "num_samples must be greater than zero".into(),
-            ));
-        }
-
-        let num_channels = self.config.channels.len();
-        if num_channels == 0 {
-            return Err(RuvNeuralError::Sensor(
-                "No ADC channels configured".into(),
-            ));
-        }
-
-        let mut result = Vec::with_capacity(num_channels);
-        let buf_len = self.buffer[0].len();
-
-        for (ch_idx, channel) in self.config.channels.iter().enumerate() {
-            let mut samples = Vec::with_capacity(num_samples);
-            for i in 0..num_samples {
-                let pos = (self.buffer_pos + i) % buf_len;
-                let raw = self.buffer[ch_idx][pos];
-                samples.push(self.to_femtotesla(raw, channel));
-            }
-            result.push(samples);
-        }
-
-        self.buffer_pos = (self.buffer_pos + num_samples) % buf_len;
-        Ok(result)
-    }
-
-    /// Convert a raw ADC value to femtotesla using the channel's gain and
-    /// offset.
-    ///
-    /// Conversion: `fT = (raw / max_raw) * ref_voltage * gain + offset`
-    pub fn to_femtotesla(&self, raw: i16, channel: &AdcChannel) -> f64 {
-        let max_raw = self.config.max_raw_value() as f64;
-        let voltage_ratio = raw as f64 / max_raw;
-        let voltage_mv = voltage_ratio * self.config.reference_voltage_mv as f64;
-        voltage_mv * channel.gain + channel.offset
-    }
-
-    /// Load raw samples into the internal ring buffer for a given channel.
-    ///
-    /// This is the production data input path. On real hardware the DMA
-    /// controller calls this (or writes directly to the buffer memory) to
-    /// deliver new ADC readings. Also used in host-side testing to inject
-    /// known waveforms.
-    pub fn load_buffer(&mut self, channel_idx: usize, data: &[i16]) -> Result<()> {
-        if channel_idx >= self.buffer.len() {
-            return Err(RuvNeuralError::ChannelOutOfRange {
-                channel: channel_idx,
-                max: self.buffer.len().saturating_sub(1),
-            });
-        }
-        let buf_len = self.buffer[channel_idx].len();
-        for (i, &val) in data.iter().enumerate() {
-            if i >= buf_len {
-                break;
-            }
-            self.buffer[channel_idx][i] = val;
-        }
-        Ok(())
-    }
-
-    /// Returns a reference to the current configuration.
-    pub fn config(&self) -> &AdcConfig {
-        &self.config
-    }
-
-    /// Resets the buffer read position to zero.
-    pub fn reset(&mut self) {
-        self.buffer_pos = 0;
-    }
-
-    /// Fill all channels with a known sinusoidal calibration signal for
-    /// self-test and gain verification.
-    ///
-    /// Writes a full-scale sine wave at the given frequency into every
-    /// channel's ring buffer. After calling this, [`read_samples`](Self::read_samples)
-    /// will return the calibration waveform converted to femtotesla, which
-    /// can be compared against the expected amplitude to verify the gain
-    /// and offset calibration.
-    ///
-    /// # Arguments
-    /// * `frequency_hz` - Frequency of the calibration sine wave.
-    ///
-    /// # Example
-    /// ```
-    /// # use ruv_neural_esp32::adc::{AdcConfig, AdcReader};
-    /// let config = AdcConfig::default_single_channel();
-    /// let mut reader = AdcReader::new(config);
-    /// reader.fill_with_calibration_signal(10.0);
-    /// let data = reader.read_samples(100).unwrap();
-    /// // data now contains a 10 Hz sine converted to fT
-    /// ```
-    pub fn fill_with_calibration_signal(&mut self, frequency_hz: f64) {
-        let buf_len = self.buffer[0].len();
-        let max_raw = self.config.max_raw_value();
-        let sample_rate = self.config.sample_rate_hz as f64;
-
-        for ch_idx in 0..self.buffer.len() {
-            for i in 0..buf_len {
-                let t = i as f64 / sample_rate;
-                // Sine wave at ~90% of full scale to avoid clipping
-                let value = 0.9 * (max_raw as f64)
-                    * (2.0 * std::f64::consts::PI * frequency_hz * t).sin();
-                self.buffer[ch_idx][i] = value.round() as i16;
-            }
-        }
-        self.buffer_pos = 0;
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_to_femtotesla_known_value() {
-        let config = AdcConfig {
-            channels: vec![AdcChannel {
-                channel_id: 0,
-                gpio_pin: 36,
-                attenuation: Attenuation::Db11,
-                sensor_type: SensorType::NvDiamond,
-                gain: 2.0,
-                offset: 10.0,
-            }],
-            sample_rate_hz: 1000,
-            resolution_bits: 12,
-            reference_voltage_mv: 3300,
-            dma_enabled: false,
-        };
-        let reader = AdcReader::new(config);
-        let channel = &reader.config().channels[0];
-
-        // raw = 2048, max = 4095, ratio = 0.5001..., voltage = ~1650.4 mV
-        // fT = 1650.4 * 2.0 + 10.0 = ~3310.8
-        let ft = reader.to_femtotesla(2048, channel);
-        let expected = (2048.0 / 4095.0) * 3300.0 * 2.0 + 10.0;
-        assert!((ft - expected).abs() < 1e-6, "got {ft}, expected {expected}");
-    }
-
-    #[test]
-    fn test_read_samples_length() {
-        let config = AdcConfig::default_single_channel();
-        let mut reader = AdcReader::new(config);
-        let result = reader.read_samples(100).unwrap();
-        assert_eq!(result.len(), 1);
-        assert_eq!(result[0].len(), 100);
-    }
-
-    #[test]
-    fn test_load_buffer_and_read() {
-        let config = AdcConfig::default_single_channel();
-        let mut reader = AdcReader::new(config);
-        let data: Vec<i16> = (0..10).collect();
-        reader.load_buffer(0, &data).unwrap();
-        let result = reader.read_samples(10).unwrap();
-        // Values should be monotonically increasing since raw values are 0..10
-        for i in 1..10 {
-            assert!(result[0][i] > result[0][i - 1]);
-        }
-    }
-
-    #[test]
-    fn test_read_zero_samples_error() {
-        let config = AdcConfig::default_single_channel();
-        let mut reader = AdcReader::new(config);
-        assert!(reader.read_samples(0).is_err());
-    }
-
-    #[test]
-    fn test_attenuation_max_voltage() {
-        assert_eq!(Attenuation::Db0.max_voltage_mv(), 950);
-        assert_eq!(Attenuation::Db11.max_voltage_mv(), 2450);
-    }
-}
@@ -1,214 +0,0 @@
-//! Multi-node data aggregation.
-//!
-//! Collects [`NeuralDataPacket`]s from multiple ESP32 nodes and assembles them
-//! into a unified [`MultiChannelTimeSeries`] once all nodes have reported for
-//! a given time window.
-
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::{Result, RuvNeuralError};
-
-use crate::protocol::NeuralDataPacket;
-
-/// Aggregates data packets from multiple ESP32 sensor nodes.
-///
-/// Packets are buffered per-node. When every node has contributed at least one
-/// packet, [`try_assemble`](NodeAggregator::try_assemble) combines them into a
-/// single time series — matching packets by timestamp within the configured
-/// sync tolerance.
-pub struct NodeAggregator {
-    node_count: usize,
-    buffers: Vec<Vec<NeuralDataPacket>>,
-    sync_tolerance_us: u64,
-}
-
-impl NodeAggregator {
-    /// Create a new aggregator expecting `node_count` distinct nodes.
-    pub fn new(node_count: usize) -> Self {
-        Self {
-            node_count,
-            buffers: vec![Vec::new(); node_count],
-            sync_tolerance_us: 1_000, // 1 ms default
-        }
-    }
-
-    /// Buffer a packet from a specific node.
-    pub fn receive_packet(
-        &mut self,
-        node_id: usize,
-        packet: NeuralDataPacket,
-    ) -> Result<()> {
-        if node_id >= self.node_count {
-            return Err(RuvNeuralError::Sensor(format!(
-                "Node ID {node_id} out of range (max {})",
-                self.node_count - 1
-            )));
-        }
-        self.buffers[node_id].push(packet);
-        Ok(())
-    }
-
-    /// Try to assemble a [`MultiChannelTimeSeries`] from the buffered packets.
-    ///
-    /// Returns `Some` when every node has at least one packet whose timestamps
-    /// are within `sync_tolerance_us` of each other. The matching packets are
-    /// consumed from the buffers.
-    pub fn try_assemble(&mut self) -> Option<MultiChannelTimeSeries> {
-        // Check that every node has at least one packet
-        if self.buffers.iter().any(|b| b.is_empty()) {
-            return None;
-        }
-
-        // Use the first node's earliest packet as the reference timestamp
-        let ref_ts = self.buffers[0][0].header.timestamp_us;
-
-        // Find a matching packet in each buffer
-        let mut indices: Vec<usize> = Vec::with_capacity(self.node_count);
-        for buf in &self.buffers {
-            let found = buf.iter().position(|p| {
-                let diff = if p.header.timestamp_us >= ref_ts {
-                    p.header.timestamp_us - ref_ts
-                } else {
-                    ref_ts - p.header.timestamp_us
-                };
-                diff <= self.sync_tolerance_us
-            });
-            match found {
-                Some(idx) => indices.push(idx),
-                None => return None,
-            }
-        }
-
-        // Remove matched packets and merge channel data
-        let mut all_data: Vec<Vec<f64>> = Vec::new();
-        let mut sample_rate = 1000.0_f64;
-
-        for (buf_idx, &pkt_idx) in indices.iter().enumerate() {
-            let pkt = self.buffers[buf_idx].remove(pkt_idx);
-            sample_rate = pkt.header.sample_rate_hz as f64;
-            for ch in &pkt.channels {
-                let channel_data: Vec<f64> = ch
-                    .samples
-                    .iter()
-                    .map(|&s| s as f64 * ch.scale_factor as f64)
-                    .collect();
-                all_data.push(channel_data);
-            }
-        }
-
-        if all_data.is_empty() {
-            return None;
-        }
-
-        let timestamp = ref_ts as f64 / 1_000_000.0;
-        MultiChannelTimeSeries::new(all_data, sample_rate, timestamp).ok()
-    }
-
-    /// Set the timestamp tolerance in microseconds for matching packets
-    /// across nodes.
-    pub fn set_sync_tolerance(&mut self, tolerance_us: u64) {
-        self.sync_tolerance_us = tolerance_us;
-    }
-
-    /// Returns the number of buffered packets for a given node.
-    pub fn buffered_count(&self, node_id: usize) -> usize {
-        self.buffers.get(node_id).map_or(0, |b| b.len())
-    }
-
-    /// Returns the total number of expected nodes.
-    pub fn node_count(&self) -> usize {
-        self.node_count
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use crate::protocol::{ChannelData, NeuralDataPacket, PacketHeader, PACKET_MAGIC, PROTOCOL_VERSION};
-
-    fn make_packet(num_channels: u8, timestamp_us: u64, samples: Vec<i16>) -> NeuralDataPacket {
-        let channels = (0..num_channels)
-            .map(|id| ChannelData {
-                channel_id: id,
-                samples: samples.clone(),
-                scale_factor: 1.0,
-            })
-            .collect();
-
-        NeuralDataPacket {
-            header: PacketHeader {
-                magic: PACKET_MAGIC,
-                version: PROTOCOL_VERSION,
-                packet_id: 0,
-                timestamp_us,
-                num_channels,
-                samples_per_channel: samples.len() as u16,
-                sample_rate_hz: 1000,
-            },
-            channels,
-            quality: vec![255; num_channels as usize],
-            checksum: 0,
-        }
-    }
-
-    #[test]
-    fn test_assemble_two_nodes() {
-        let mut agg = NodeAggregator::new(2);
-
-        let p0 = make_packet(1, 1000, vec![10, 20, 30]);
-        let p1 = make_packet(1, 1000, vec![40, 50, 60]);
-
-        agg.receive_packet(0, p0).unwrap();
-        // Only one node has reported — assembly requires all nodes
-        assert!(agg.try_assemble().is_none());
-
-        agg.receive_packet(1, p1).unwrap();
-        let ts = agg.try_assemble().unwrap();
-        assert_eq!(ts.num_channels, 2);
-        assert_eq!(ts.num_samples, 3);
-        assert!((ts.data[0][0] - 10.0).abs() < 1e-6);
-        assert!((ts.data[1][2] - 60.0).abs() < 1e-6);
-    }
-
-    #[test]
-    fn test_assemble_with_tolerance() {
-        let mut agg = NodeAggregator::new(2);
-        agg.set_sync_tolerance(500);
-
-        let p0 = make_packet(1, 1000, vec![1, 2]);
-        let p1 = make_packet(1, 1400, vec![3, 4]); // Within 500 us tolerance
-
-        agg.receive_packet(0, p0).unwrap();
-        agg.receive_packet(1, p1).unwrap();
-        assert!(agg.try_assemble().is_some());
-    }
-
-    #[test]
-    fn test_assemble_exceeds_tolerance() {
-        let mut agg = NodeAggregator::new(2);
-        agg.set_sync_tolerance(100);
-
-        let p0 = make_packet(1, 1000, vec![1, 2]);
-        let p1 = make_packet(1, 2000, vec![3, 4]); // 1000 us apart > 100 us tolerance
-
-        agg.receive_packet(0, p0).unwrap();
-        agg.receive_packet(1, p1).unwrap();
-        assert!(agg.try_assemble().is_none());
-    }
-
-    #[test]
-    fn test_receive_invalid_node() {
-        let mut agg = NodeAggregator::new(2);
-        let p = make_packet(1, 0, vec![1]);
-        assert!(agg.receive_packet(5, p).is_err());
-    }
-
-    #[test]
-    fn test_buffers_consumed_after_assembly() {
-        let mut agg = NodeAggregator::new(1);
-        let p = make_packet(1, 0, vec![1, 2, 3]);
-        agg.receive_packet(0, p).unwrap();
-        assert_eq!(agg.buffered_count(0), 1);
-        agg.try_assemble().unwrap();
-        assert_eq!(agg.buffered_count(0), 0);
-    }
-}
@@ -1,28 +0,0 @@
-//! rUv Neural ESP32 — Edge integration for neural sensor data acquisition and preprocessing.
-//!
-//! This crate provides lightweight processing that runs on ESP32 hardware for
-//! real-time sensor data acquisition and preprocessing before sending to the
-//! main RuVector backend.
-//!
-//! # Modules
-//!
-//! - [`adc`] — ADC interface for sensor data acquisition
-//! - [`preprocessing`] — Lightweight edge preprocessing (IIR filters, downsampling)
-//! - [`protocol`] — Communication protocol with the RuVector backend
-//! - [`tdm`] — Time-Division Multiplexing for multi-sensor coordination
-//! - [`power`] — Power management for battery operation
-//! - [`aggregator`] — Multi-node data aggregation
-
-pub mod adc;
-pub mod aggregator;
-pub mod power;
-pub mod preprocessing;
-pub mod protocol;
-pub mod tdm;
-
-pub use adc::{AdcChannel, AdcConfig, AdcReader, Attenuation};
-pub use aggregator::NodeAggregator;
-pub use power::{PowerConfig, PowerManager, PowerMode};
-pub use preprocessing::{EdgePreprocessor, IirCoeffs};
-pub use protocol::{ChannelData, NeuralDataPacket, PacketHeader};
-pub use tdm::{SyncMethod, TdmNode, TdmScheduler};
@@ -1,242 +0,0 @@
-//! Power management for battery-operated ESP32 sensor nodes.
-//!
-//! Provides duty-cycle estimation, sleep scheduling, and automatic duty-cycle
-//! optimization to hit a target runtime.
-
-use serde::{Deserialize, Serialize};
-
-/// Operating power mode.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum PowerMode {
-    /// Full speed — all peripherals active.
-    Active,
-    /// Reduced clock, WiFi power save.
-    LowPower,
-    /// Minimal peripherals, deep sleep between samples.
-    UltraLowPower,
-    /// Full deep sleep — wakes only on timer or external interrupt.
-    Sleep,
-}
-
-impl PowerMode {
-    /// Estimated current draw in milliamps for this mode on an ESP32-S3.
-    pub fn estimated_current_ma(&self) -> f64 {
-        match self {
-            PowerMode::Active => 240.0,
-            PowerMode::LowPower => 80.0,
-            PowerMode::UltraLowPower => 20.0,
-            PowerMode::Sleep => 0.01,
-        }
-    }
-}
-
-/// Power management configuration.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct PowerConfig {
-    /// Base operating mode.
-    pub mode: PowerMode,
-    /// Whether to enter light sleep between sample bursts.
-    pub sleep_between_samples: bool,
-    /// Fraction of time spent actively sampling (0.0-1.0).
-    pub sample_duty_cycle: f64,
-    /// Fraction of time WiFi is enabled (0.0-1.0).
-    pub wifi_duty_cycle: f64,
-}
-
-impl Default for PowerConfig {
-    fn default() -> Self {
-        Self {
-            mode: PowerMode::Active,
-            sleep_between_samples: false,
-            sample_duty_cycle: 1.0,
-            wifi_duty_cycle: 1.0,
-        }
-    }
-}
-
-/// Power manager that tracks battery state and optimizes duty cycles.
-pub struct PowerManager {
-    config: PowerConfig,
-    battery_mv: u32,
-    estimated_runtime_hours: f64,
-}
-
-impl PowerManager {
-    /// Create a new power manager with the given configuration.
-    pub fn new(config: PowerConfig) -> Self {
-        Self {
-            config,
-            battery_mv: 4200, // Fully charged LiPo
-            estimated_runtime_hours: 0.0,
-        }
-    }
-
-    /// Estimate runtime in hours given a battery capacity in mAh.
-    ///
-    /// The effective current draw is a weighted average of active and sleep
-    /// currents based on the configured duty cycles.
-    pub fn estimate_runtime(&self, battery_capacity_mah: u32) -> f64 {
-        let active_current = self.config.mode.estimated_current_ma();
-        let sleep_current = PowerMode::Sleep.estimated_current_ma();
-
-        let sample_active = self.config.sample_duty_cycle.clamp(0.0, 1.0);
-        let wifi_active = self.config.wifi_duty_cycle.clamp(0.0, 1.0);
-
-        // WiFi adds roughly 80 mA when active
-        let wifi_overhead = 80.0 * wifi_active;
-
-        let effective_current =
-            active_current * sample_active + sleep_current * (1.0 - sample_active) + wifi_overhead;
-
-        if effective_current <= 0.0 {
-            return f64::INFINITY;
-        }
-
-        battery_capacity_mah as f64 / effective_current
-    }
-
-    /// Returns `true` if the node should sleep at the given time based on
-    /// the configured duty cycle.
-    ///
-    /// Uses a simple periodic pattern: active for `duty * period`, then sleep
-    /// for the remainder. The period is fixed at 1 second (1_000_000 us).
-    pub fn should_sleep(&self, current_time_us: u64) -> bool {
-        if !self.config.sleep_between_samples {
-            return false;
-        }
-        let period_us: u64 = 1_000_000;
-        let active_us = (self.config.sample_duty_cycle * period_us as f64) as u64;
-        let position = current_time_us % period_us;
-        position >= active_us
-    }
-
-    /// Adjust the sample and WiFi duty cycles to reach the target runtime.
-    pub fn optimize_duty_cycle(&mut self, target_runtime_hours: f64) {
-        // Binary search for the duty cycle that achieves the target runtime
-        // with a 2000 mAh reference battery.
-        let battery_mah = 2000u32;
-        let mut low = 0.01_f64;
-        let mut high = 1.0_f64;
-
-        for _ in 0..50 {
-            let mid = (low + high) / 2.0;
-            self.config.sample_duty_cycle = mid;
-            self.config.wifi_duty_cycle = mid;
-            let runtime = self.estimate_runtime(battery_mah);
-            if runtime < target_runtime_hours {
-                high = mid;
-            } else {
-                low = mid;
-            }
-        }
-
-        self.config.sample_duty_cycle = low;
-        self.config.wifi_duty_cycle = low;
-        self.estimated_runtime_hours = self.estimate_runtime(battery_mah);
-    }
-
-    /// Update the battery voltage reading.
-    pub fn set_battery_mv(&mut self, mv: u32) {
-        self.battery_mv = mv;
-    }
-
-    /// Current battery voltage in millivolts.
-    pub fn battery_mv(&self) -> u32 {
-        self.battery_mv
-    }
-
-    /// Estimated remaining runtime in hours (after calling
-    /// `optimize_duty_cycle`).
-    pub fn estimated_runtime_hours(&self) -> f64 {
-        self.estimated_runtime_hours
-    }
-
-    /// Returns a reference to the current power configuration.
-    pub fn config(&self) -> &PowerConfig {
-        &self.config
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_estimate_runtime_active() {
-        let config = PowerConfig {
-            mode: PowerMode::Active,
-            sleep_between_samples: false,
-            sample_duty_cycle: 1.0,
-            wifi_duty_cycle: 1.0,
-        };
-        let pm = PowerManager::new(config);
-        let hours = pm.estimate_runtime(2000);
-        // 2000 mAh / (240 + 80) = 6.25 hours
-        assert!((hours - 6.25).abs() < 0.1, "got {hours}");
-    }
-
-    #[test]
-    fn test_estimate_runtime_low_duty() {
-        let config = PowerConfig {
-            mode: PowerMode::Active,
-            sleep_between_samples: true,
-            sample_duty_cycle: 0.1,
-            wifi_duty_cycle: 0.1,
-        };
-        let pm = PowerManager::new(config);
-        let hours = pm.estimate_runtime(2000);
-        // Much longer than 6.25 hours
-        assert!(hours > 20.0, "expected >20h, got {hours}");
-    }
-
-    #[test]
-    fn test_should_sleep() {
-        let config = PowerConfig {
-            mode: PowerMode::Active,
-            sleep_between_samples: true,
-            sample_duty_cycle: 0.5,
-            wifi_duty_cycle: 1.0,
-        };
-        let pm = PowerManager::new(config);
-        // Active window: 0..500_000 us, sleep: 500_000..1_000_000 us
-        assert!(!pm.should_sleep(0));
-        assert!(!pm.should_sleep(499_999));
-        assert!(pm.should_sleep(500_000));
-        assert!(pm.should_sleep(999_999));
-    }
-
-    #[test]
-    fn test_should_sleep_disabled() {
-        let config = PowerConfig {
-            mode: PowerMode::Active,
-            sleep_between_samples: false,
-            sample_duty_cycle: 0.1,
-            wifi_duty_cycle: 0.1,
-        };
-        let pm = PowerManager::new(config);
-        assert!(!pm.should_sleep(999_999));
-    }
-
-    #[test]
-    fn test_optimize_duty_cycle() {
-        let config = PowerConfig {
-            mode: PowerMode::Active,
-            sleep_between_samples: true,
-            sample_duty_cycle: 1.0,
-            wifi_duty_cycle: 1.0,
-        };
-        let mut pm = PowerManager::new(config);
-        pm.optimize_duty_cycle(48.0); // Target 48 hours
-
-        // Duty cycles should have been reduced
-        assert!(pm.config().sample_duty_cycle < 1.0);
-        assert!(pm.config().sample_duty_cycle > 0.0);
-    }
-
-    #[test]
-    fn test_power_mode_current() {
-        assert!(PowerMode::Active.estimated_current_ma() > PowerMode::LowPower.estimated_current_ma());
-        assert!(PowerMode::LowPower.estimated_current_ma() > PowerMode::UltraLowPower.estimated_current_ma());
-        assert!(PowerMode::UltraLowPower.estimated_current_ma() > PowerMode::Sleep.estimated_current_ma());
-    }
-}
@@ -1,289 +0,0 @@
-//! Lightweight edge preprocessing that runs on the ESP32 before data is sent
-//! upstream to the RuVector backend.
-//!
-//! Includes fixed-point IIR filtering for integer-only ESP32 math paths and
-//! floating-point downsampling / pipeline processing for `std` targets.
-
-/// IIR filter coefficients for a second-order section (biquad).
-///
-/// Transfer function: `H(z) = (b0 + b1*z^-1 + b2*z^-2) / (a0 + a1*z^-1 + a2*z^-2)`
-#[derive(Debug, Clone)]
-pub struct IirCoeffs {
-    /// Numerator coefficients `[b0, b1, b2]`.
-    pub b: [f64; 3],
-    /// Denominator coefficients `[a0, a1, a2]`.
-    pub a: [f64; 3],
-}
-
-impl IirCoeffs {
-    /// Create notch filter coefficients for a given frequency and sample rate.
-    ///
-    /// Uses a quality factor of 30 for a narrow rejection band.
-    pub fn notch(freq_hz: f64, sample_rate_hz: f64) -> Self {
-        let w0 = 2.0 * std::f64::consts::PI * freq_hz / sample_rate_hz;
-        let q = 30.0;
-        let alpha = w0.sin() / (2.0 * q);
-        let cos_w0 = w0.cos();
-
-        let b0 = 1.0;
-        let b1 = -2.0 * cos_w0;
-        let b2 = 1.0;
-        let a0 = 1.0 + alpha;
-        let a1 = -2.0 * cos_w0;
-        let a2 = 1.0 - alpha;
-
-        // Normalize by a0
-        Self {
-            b: [b0 / a0, b1 / a0, b2 / a0],
-            a: [1.0, a1 / a0, a2 / a0],
-        }
-    }
-
-    /// Create a first-order high-pass filter (stored as second-order with
-    /// zero padding).
-    pub fn highpass(cutoff_hz: f64, sample_rate_hz: f64) -> Self {
-        let rc = 1.0 / (2.0 * std::f64::consts::PI * cutoff_hz);
-        let dt = 1.0 / sample_rate_hz;
-        let alpha = rc / (rc + dt);
-
-        Self {
-            b: [alpha, -alpha, 0.0],
-            a: [1.0, -(1.0 - alpha), 0.0],
-        }
-    }
-
-    /// Create a first-order low-pass filter (stored as second-order with
-    /// zero padding).
-    pub fn lowpass(cutoff_hz: f64, sample_rate_hz: f64) -> Self {
-        let rc = 1.0 / (2.0 * std::f64::consts::PI * cutoff_hz);
-        let dt = 1.0 / sample_rate_hz;
-        let alpha = dt / (rc + dt);
-
-        Self {
-            b: [alpha, 0.0, 0.0],
-            a: [1.0, -(1.0 - alpha), 0.0],
-        }
-    }
-}
-
-/// Minimal preprocessing pipeline that runs on the ESP32 before data is sent
-/// upstream.
-pub struct EdgePreprocessor {
-    /// Apply a 50 Hz notch filter (mains power, EU/Asia).
-    pub notch_50hz: bool,
-    /// Apply a 60 Hz notch filter (mains power, Americas).
-    pub notch_60hz: bool,
-    /// High-pass cutoff frequency in Hz.
-    pub highpass_hz: f64,
-    /// Low-pass cutoff frequency in Hz.
-    pub lowpass_hz: f64,
-    /// Downsample factor (1 = no downsampling).
-    pub downsample_factor: usize,
-    /// Sample rate of the incoming data in Hz.
-    pub sample_rate_hz: f64,
-}
-
-impl Default for EdgePreprocessor {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-impl EdgePreprocessor {
-    /// Create a preprocessor with sensible defaults for neural sensing.
-    pub fn new() -> Self {
-        Self {
-            notch_50hz: true,
-            notch_60hz: true,
-            highpass_hz: 0.5,
-            lowpass_hz: 200.0,
-            downsample_factor: 1,
-            sample_rate_hz: 1000.0,
-        }
-    }
-
-    /// Apply a second-order IIR filter using fixed-point arithmetic.
-    ///
-    /// Coefficients are scaled by 2^14 internally to use integer multiply/shift
-    /// on the ESP32. The output is clipped to `i16` range.
-    pub fn apply_iir_fixed(&self, samples: &[i16], coeffs: &IirCoeffs) -> Vec<i16> {
-        const SCALE: i64 = 1 << 14;
-
-        let b0 = (coeffs.b[0] * SCALE as f64) as i64;
-        let b1 = (coeffs.b[1] * SCALE as f64) as i64;
-        let b2 = (coeffs.b[2] * SCALE as f64) as i64;
-        let a1 = (coeffs.a[1] * SCALE as f64) as i64;
-        let a2 = (coeffs.a[2] * SCALE as f64) as i64;
-
-        let mut out = Vec::with_capacity(samples.len());
-        let mut x1: i64 = 0;
-        let mut x2: i64 = 0;
-        let mut y1: i64 = 0;
-        let mut y2: i64 = 0;
-
-        for &x0 in samples {
-            let x0 = x0 as i64;
-            let y0 = (b0 * x0 + b1 * x1 + b2 * x2 - a1 * y1 - a2 * y2) >> 14;
-
-            let clamped = y0.clamp(i16::MIN as i64, i16::MAX as i64) as i16;
-            out.push(clamped);
-
-            x2 = x1;
-            x1 = x0;
-            y2 = y1;
-            y1 = y0;
-        }
-
-        out
-    }
-
-    /// Apply a second-order IIR filter using floating-point arithmetic.
-    fn apply_iir_float(&self, samples: &[f64], coeffs: &IirCoeffs) -> Vec<f64> {
-        let mut out = Vec::with_capacity(samples.len());
-        let mut x1 = 0.0_f64;
-        let mut x2 = 0.0_f64;
-        let mut y1 = 0.0_f64;
-        let mut y2 = 0.0_f64;
-
-        for &x0 in samples {
-            let y0 = coeffs.b[0] * x0 + coeffs.b[1] * x1 + coeffs.b[2] * x2
-                - coeffs.a[1] * y1
-                - coeffs.a[2] * y2;
-
-            out.push(y0);
-
-            x2 = x1;
-            x1 = x0;
-            y2 = y1;
-            y1 = y0;
-        }
-
-        out
-    }
-
-    /// Downsample by block-averaging groups of `factor` consecutive samples.
-    ///
-    /// If the input length is not a multiple of `factor`, the trailing samples
-    /// are averaged as a shorter block.
-    pub fn downsample(&self, samples: &[f64], factor: usize) -> Vec<f64> {
-        if factor <= 1 || samples.is_empty() {
-            return samples.to_vec();
-        }
-
-        samples
-            .chunks(factor)
-            .map(|chunk| {
-                let sum: f64 = chunk.iter().sum();
-                sum / chunk.len() as f64
-            })
-            .collect()
-    }
-
-    /// Run the full edge preprocessing pipeline on multi-channel data.
-    ///
-    /// Steps (in order):
-    /// 1. High-pass filter (remove DC offset / drift)
-    /// 2. Notch filter at 50 Hz (if enabled)
-    /// 3. Notch filter at 60 Hz (if enabled)
-    /// 4. Low-pass filter (anti-alias before downsampling)
-    /// 5. Downsample
-    pub fn process(&self, raw_data: &[Vec<f64>]) -> Vec<Vec<f64>> {
-        let sr = self.sample_rate_hz;
-
-        let hp_coeffs = IirCoeffs::highpass(self.highpass_hz, sr);
-        let lp_coeffs = IirCoeffs::lowpass(self.lowpass_hz, sr);
-        let notch_50 = IirCoeffs::notch(50.0, sr);
-        let notch_60 = IirCoeffs::notch(60.0, sr);
-
-        raw_data
-            .iter()
-            .map(|channel| {
-                let mut data = self.apply_iir_float(channel, &hp_coeffs);
-
-                if self.notch_50hz {
-                    data = self.apply_iir_float(&data, &notch_50);
-                }
-                if self.notch_60hz {
-                    data = self.apply_iir_float(&data, &notch_60);
-                }
-
-                data = self.apply_iir_float(&data, &lp_coeffs);
-
-                self.downsample(&data, self.downsample_factor)
-            })
-            .collect()
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_downsample_factor_2() {
-        let pre = EdgePreprocessor::new();
-        let input: Vec<f64> = (0..10).map(|x| x as f64).collect();
-        let result = pre.downsample(&input, 2);
-        assert_eq!(result.len(), 5);
-        // [0,1] -> 0.5, [2,3] -> 2.5, ...
-        assert!((result[0] - 0.5).abs() < 1e-10);
-        assert!((result[1] - 2.5).abs() < 1e-10);
-        assert!((result[4] - 8.5).abs() < 1e-10);
-    }
-
-    #[test]
-    fn test_downsample_factor_1_is_identity() {
-        let pre = EdgePreprocessor::new();
-        let input = vec![1.0, 2.0, 3.0];
-        let result = pre.downsample(&input, 1);
-        assert_eq!(result, input);
-    }
-
-    #[test]
-    fn test_downsample_non_multiple() {
-        let pre = EdgePreprocessor::new();
-        let input: Vec<f64> = (0..7).map(|x| x as f64).collect();
-        let result = pre.downsample(&input, 3);
-        // [0,1,2]->1, [3,4,5]->4, [6]->6
-        assert_eq!(result.len(), 3);
-        assert!((result[2] - 6.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn test_process_output_length() {
-        let mut pre = EdgePreprocessor::new();
-        pre.downsample_factor = 4;
-        pre.sample_rate_hz = 1000.0;
-        let raw = vec![vec![0.0; 1000], vec![0.0; 1000]];
-        let result = pre.process(&raw);
-        assert_eq!(result.len(), 2);
-        assert_eq!(result[0].len(), 250);
-        assert_eq!(result[1].len(), 250);
-    }
-
-    #[test]
-    fn test_iir_fixed_passthrough_dc() {
-        // Identity-ish filter: b=[1,0,0], a=[1,0,0] should pass through
-        let pre = EdgePreprocessor::new();
-        let coeffs = IirCoeffs {
-            b: [1.0, 0.0, 0.0],
-            a: [1.0, 0.0, 0.0],
-        };
-        let input: Vec<i16> = vec![100, 200, 300, 400, 500];
-        let output = pre.apply_iir_fixed(&input, &coeffs);
-        assert_eq!(output.len(), 5);
-        // With identity filter, output should match input
-        for (i, &v) in output.iter().enumerate() {
-            assert_eq!(v, input[i], "mismatch at index {i}");
-        }
-    }
-
-    #[test]
-    fn test_notch_coefficients_valid() {
-        let coeffs = IirCoeffs::notch(50.0, 1000.0);
-        // a[0] should be normalized to 1.0
-        assert!((coeffs.a[0] - 1.0).abs() < 1e-10);
-        // b[0] and b[2] should be equal for a notch
-        assert!((coeffs.b[0] - coeffs.b[2]).abs() < 1e-10);
-    }
-}
@@ -1,228 +0,0 @@
-//! Communication protocol between ESP32 sensor nodes and the RuVector backend.
-//!
-//! Defines binary-serializable data packets with CRC32 checksums for reliable
-//! transfer over WiFi or UART.
-
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::{Result, RuvNeuralError};
-use serde::{Deserialize, Serialize};
-
-/// Magic bytes identifying a rUv Neural data packet.
-pub const PACKET_MAGIC: [u8; 4] = [b'r', b'U', b'v', b'N'];
-
-/// Current protocol version.
-pub const PROTOCOL_VERSION: u8 = 1;
-
-/// Header of a neural data packet.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct PacketHeader {
-    /// Magic bytes — must be `b"rUvN"`.
-    pub magic: [u8; 4],
-    /// Protocol version.
-    pub version: u8,
-    /// Monotonically increasing packet identifier.
-    pub packet_id: u32,
-    /// Timestamp in microseconds since boot (or epoch).
-    pub timestamp_us: u64,
-    /// Number of channels in this packet.
-    pub num_channels: u8,
-    /// Number of samples per channel.
-    pub samples_per_channel: u16,
-    /// Sample rate in Hz.
-    pub sample_rate_hz: u16,
-}
-
-/// Per-channel sample data within a packet.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct ChannelData {
-    /// Channel identifier.
-    pub channel_id: u8,
-    /// Fixed-point sample values for bandwidth efficiency.
-    pub samples: Vec<i16>,
-    /// Multiply each sample by this factor to obtain femtotesla.
-    pub scale_factor: f32,
-}
-
-/// Data packet sent from an ESP32 node to the RuVector backend.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct NeuralDataPacket {
-    /// Packet header with metadata.
-    pub header: PacketHeader,
-    /// Per-channel sample data.
-    pub channels: Vec<ChannelData>,
-    /// Per-channel signal quality indicator (0 = worst, 255 = best).
-    pub quality: Vec<u8>,
-    /// CRC32 checksum of the serialized payload (header + channels + quality).
-    pub checksum: u32,
-}
-
-impl NeuralDataPacket {
-    /// Create a new empty packet for the given number of channels.
-    pub fn new(num_channels: u8) -> Self {
-        Self {
-            header: PacketHeader {
-                magic: PACKET_MAGIC,
-                version: PROTOCOL_VERSION,
-                packet_id: 0,
-                timestamp_us: 0,
-                num_channels,
-                samples_per_channel: 0,
-                sample_rate_hz: 1000,
-            },
-            channels: (0..num_channels)
-                .map(|id| ChannelData {
-                    channel_id: id,
-                    samples: Vec::new(),
-                    scale_factor: 1.0,
-                })
-                .collect(),
-            quality: vec![255; num_channels as usize],
-            checksum: 0,
-        }
-    }
-
-    /// Serialize the packet to a byte vector (JSON for portability in std
-    /// mode; a production ESP32 build would use a compact binary format).
-    pub fn serialize(&self) -> Vec<u8> {
-        serde_json::to_vec(self).unwrap_or_default()
-    }
-
-    /// Deserialize a packet from bytes.
-    pub fn deserialize(data: &[u8]) -> Result<Self> {
-        let packet: NeuralDataPacket = serde_json::from_slice(data).map_err(|e| {
-            RuvNeuralError::Serialization(format!("Failed to deserialize packet: {e}"))
-        })?;
-        if packet.header.magic != PACKET_MAGIC {
-            return Err(RuvNeuralError::Serialization(
-                "Invalid magic bytes".into(),
-            ));
-        }
-        Ok(packet)
-    }
-
-    /// Compute CRC32 checksum of a byte slice using the IEEE polynomial.
-    pub fn compute_checksum(data: &[u8]) -> u32 {
-        // CRC32 IEEE polynomial lookup-free implementation
-        let mut crc: u32 = 0xFFFF_FFFF;
-        for &byte in data {
-            crc ^= byte as u32;
-            for _ in 0..8 {
-                if crc & 1 != 0 {
-                    crc = (crc >> 1) ^ 0xEDB8_8320;
-                } else {
-                    crc >>= 1;
-                }
-            }
-        }
-        !crc
-    }
-
-    /// Recompute and store the checksum for this packet.
-    pub fn update_checksum(&mut self) {
-        let mut pkt = self.clone();
-        pkt.checksum = 0;
-        let bytes = pkt.serialize();
-        self.checksum = Self::compute_checksum(&bytes);
-    }
-
-    /// Verify that the stored checksum matches the payload.
-    pub fn verify_checksum(&self) -> bool {
-        let mut pkt = self.clone();
-        let stored = pkt.checksum;
-        pkt.checksum = 0;
-        let bytes = pkt.serialize();
-        let computed = Self::compute_checksum(&bytes);
-        stored == computed
-    }
-
-    /// Convert this packet into a [`MultiChannelTimeSeries`] by scaling the
-    /// fixed-point samples back to floating-point femtotesla values.
-    pub fn to_multichannel_timeseries(&self) -> Result<MultiChannelTimeSeries> {
-        let data: Vec<Vec<f64>> = self
-            .channels
-            .iter()
-            .map(|ch| {
-                ch.samples
-                    .iter()
-                    .map(|&s| s as f64 * ch.scale_factor as f64)
-                    .collect()
-            })
-            .collect();
-
-        let sample_rate = self.header.sample_rate_hz as f64;
-        let timestamp = self.header.timestamp_us as f64 / 1_000_000.0;
-        MultiChannelTimeSeries::new(data, sample_rate, timestamp)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_serialize_deserialize_roundtrip() {
-        let mut pkt = NeuralDataPacket::new(2);
-        pkt.header.packet_id = 42;
-        pkt.header.timestamp_us = 123_456_789;
-        pkt.header.samples_per_channel = 3;
-        pkt.channels[0].samples = vec![100, 200, 300];
-        pkt.channels[0].scale_factor = 0.5;
-        pkt.channels[1].samples = vec![400, 500, 600];
-        pkt.channels[1].scale_factor = 1.0;
-
-        let bytes = pkt.serialize();
-        let decoded = NeuralDataPacket::deserialize(&bytes).unwrap();
-
-        assert_eq!(decoded.header.packet_id, 42);
-        assert_eq!(decoded.header.num_channels, 2);
-        assert_eq!(decoded.channels[0].samples, vec![100, 200, 300]);
-        assert_eq!(decoded.channels[1].samples, vec![400, 500, 600]);
-    }
-
-    #[test]
-    fn test_checksum_verification() {
-        let mut pkt = NeuralDataPacket::new(1);
-        pkt.channels[0].samples = vec![10, 20, 30];
-        pkt.update_checksum();
-
-        assert!(pkt.verify_checksum());
-
-        // Corrupt a value
-        pkt.channels[0].samples[0] = 999;
-        assert!(!pkt.verify_checksum());
-    }
-
-    #[test]
-    fn test_to_multichannel_timeseries() {
-        let mut pkt = NeuralDataPacket::new(2);
-        pkt.header.sample_rate_hz = 500;
-        pkt.header.samples_per_channel = 3;
-        pkt.channels[0].samples = vec![100, 200, 300];
-        pkt.channels[0].scale_factor = 2.0;
-        pkt.channels[1].samples = vec![10, 20, 30];
-        pkt.channels[1].scale_factor = 0.5;
-
-        let ts = pkt.to_multichannel_timeseries().unwrap();
-        assert_eq!(ts.num_channels, 2);
-        assert_eq!(ts.num_samples, 3);
-        assert!((ts.data[0][0] - 200.0).abs() < 1e-6);
-        assert!((ts.data[1][2] - 15.0).abs() < 1e-6);
-    }
-
-    #[test]
-    fn test_invalid_magic_rejected() {
-        let mut pkt = NeuralDataPacket::new(1);
-        pkt.header.magic = [0, 0, 0, 0];
-        let bytes = pkt.serialize();
-        assert!(NeuralDataPacket::deserialize(&bytes).is_err());
-    }
-
-    #[test]
-    fn test_compute_checksum_deterministic() {
-        let data = b"hello world";
-        let c1 = NeuralDataPacket::compute_checksum(data);
-        let c2 = NeuralDataPacket::compute_checksum(data);
-        assert_eq!(c1, c2);
-        assert_ne!(c1, 0);
-    }
-}
@@ -1,187 +0,0 @@
-//! Time-Division Multiplexing (TDM) scheduler for coordinating multiple ESP32
-//! sensor nodes.
-//!
-//! Each node is assigned a time slot within a repeating frame. During its slot
-//! a node may transmit sensor data; outside its slot the node listens or
-//! sleeps.
-
-use serde::{Deserialize, Serialize};
-
-/// Synchronization method used to align TDM frames across nodes.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum SyncMethod {
-    /// GPS pulse-per-second signal.
-    GpsPps,
-    /// NTP-based time synchronization.
-    NtpSync,
-    /// WiFi beacon timestamp alignment.
-    WifiBeacon,
-    /// Leader node broadcasts sync pulses; followers align to it.
-    LeaderFollower,
-}
-
-/// A single node in the TDM schedule.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct TdmNode {
-    /// Unique node identifier.
-    pub node_id: u8,
-    /// Assigned slot index within the TDM frame.
-    pub slot_index: u8,
-    /// ADC channels this node is responsible for.
-    pub channels: Vec<u8>,
-}
-
-/// TDM scheduler for coordinating multiple ESP32 sensor nodes.
-///
-/// A TDM frame is divided into equally-sized time slots. Each node transmits
-/// only during its assigned slot, preventing collisions and ensuring
-/// deterministic latency.
-pub struct TdmScheduler {
-    /// Registered nodes and their slot assignments.
-    pub nodes: Vec<TdmNode>,
-    /// Duration of a single slot in microseconds.
-    pub slot_duration_us: u32,
-    /// Total frame duration in microseconds.
-    pub frame_duration_us: u32,
-    /// Synchronization method.
-    pub sync_method: SyncMethod,
-}
-
-impl TdmScheduler {
-    /// Create a new scheduler for `num_nodes` nodes with the given slot
-    /// duration.
-    ///
-    /// Nodes are assigned sequential slot indices and the frame duration is
-    /// computed as `num_nodes * slot_duration_us`.
-    pub fn new(num_nodes: usize, slot_duration_us: u32) -> Self {
-        let nodes: Vec<TdmNode> = (0..num_nodes)
-            .map(|i| TdmNode {
-                node_id: i as u8,
-                slot_index: i as u8,
-                channels: vec![i as u8],
-            })
-            .collect();
-
-        let frame_duration_us = slot_duration_us * num_nodes as u32;
-
-        Self {
-            nodes,
-            slot_duration_us,
-            frame_duration_us,
-            sync_method: SyncMethod::LeaderFollower,
-        }
-    }
-
-    /// Returns the slot index that is active at `current_time_us` for the
-    /// given node, or `None` if the node is not registered.
-    pub fn get_slot(&self, node_id: u8, current_time_us: u64) -> Option<u32> {
-        let node = self.nodes.iter().find(|n| n.node_id == node_id)?;
-        let position_in_frame = (current_time_us % self.frame_duration_us as u64) as u32;
-        let current_slot = position_in_frame / self.slot_duration_us;
-        if current_slot == node.slot_index as u32 {
-            Some(current_slot)
-        } else {
-            None
-        }
-    }
-
-    /// Returns `true` if the current time falls within the node's assigned
-    /// slot.
-    pub fn is_my_slot(&self, node_id: u8, current_time_us: u64) -> bool {
-        self.get_slot(node_id, current_time_us).is_some()
-    }
-
-    /// Add a node with a specific slot assignment.
-    pub fn add_node(&mut self, node: TdmNode) {
-        self.nodes.push(node);
-        self.frame_duration_us = self.slot_duration_us * self.nodes.len() as u32;
-    }
-
-    /// Returns the number of registered nodes.
-    pub fn num_nodes(&self) -> usize {
-        self.nodes.len()
-    }
-
-    /// Returns the time in microseconds until the given node's next slot
-    /// begins.
-    pub fn time_until_slot(&self, node_id: u8, current_time_us: u64) -> Option<u64> {
-        let node = self.nodes.iter().find(|n| n.node_id == node_id)?;
-        let position_in_frame = (current_time_us % self.frame_duration_us as u64) as u32;
-        let slot_start = node.slot_index as u32 * self.slot_duration_us;
-
-        if position_in_frame < slot_start {
-            Some((slot_start - position_in_frame) as u64)
-        } else if position_in_frame < slot_start + self.slot_duration_us {
-            Some(0) // Already in slot
-        } else {
-            // Next frame
-            Some((self.frame_duration_us - position_in_frame + slot_start) as u64)
-        }
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_tdm_scheduler_slot_assignment() {
-        let sched = TdmScheduler::new(4, 1000);
-        assert_eq!(sched.frame_duration_us, 4000);
-
-        // Node 0 should be active at t=0..999
-        assert!(sched.is_my_slot(0, 0));
-        assert!(sched.is_my_slot(0, 500));
-        assert!(!sched.is_my_slot(0, 1000));
-
-        // Node 1 should be active at t=1000..1999
-        assert!(sched.is_my_slot(1, 1000));
-        assert!(sched.is_my_slot(1, 1500));
-        assert!(!sched.is_my_slot(1, 2000));
-
-        // Node 3 active at t=3000..3999
-        assert!(sched.is_my_slot(3, 3000));
-        assert!(!sched.is_my_slot(3, 0));
-    }
-
-    #[test]
-    fn test_tdm_frame_wraps() {
-        let sched = TdmScheduler::new(2, 500);
-        // Frame = 1000 us, so t=1000 wraps to position 0
-        assert!(sched.is_my_slot(0, 1000));
-        assert!(sched.is_my_slot(1, 1500));
-        assert!(sched.is_my_slot(0, 2000));
-    }
-
-    #[test]
-    fn test_get_slot_returns_none_for_unknown_node() {
-        let sched = TdmScheduler::new(2, 1000);
-        assert!(sched.get_slot(99, 0).is_none());
-    }
-
-    #[test]
-    fn test_time_until_slot() {
-        let sched = TdmScheduler::new(4, 1000);
-        // Node 2's slot starts at 2000. At t=500 that's 1500 us away.
-        assert_eq!(sched.time_until_slot(2, 500), Some(1500));
-        // At t=2500 we're in the slot
-        assert_eq!(sched.time_until_slot(2, 2500), Some(0));
-        // At t=3500 the slot ended — next one is at 2000 in the next frame (t=6000)
-        // position_in_frame = 3500, slot_start = 2000, frame = 4000
-        // next = 4000 - 3500 + 2000 = 2500
-        assert_eq!(sched.time_until_slot(2, 3500), Some(2500));
-    }
-
-    #[test]
-    fn test_add_node_updates_frame() {
-        let mut sched = TdmScheduler::new(2, 1000);
-        assert_eq!(sched.frame_duration_us, 2000);
-        sched.add_node(TdmNode {
-            node_id: 5,
-            slot_index: 2,
-            channels: vec![0, 1],
-        });
-        assert_eq!(sched.frame_duration_us, 3000);
-        assert_eq!(sched.num_nodes(), 3);
-    }
-}
@@ -1,21 +0,0 @@
-[package]
-name = "ruv-neural-graph"
-description = "rUv Neural — Brain connectivity graph construction from neural signals"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-ruv-neural-signal = { workspace = true }
-petgraph = { workspace = true }
-ndarray = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-num-traits = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
-rand = { workspace = true }
@@ -1,83 +0,0 @@
-# ruv-neural-graph
-
-Brain connectivity graph construction from neural signals with graph-theoretic
-analysis and spectral properties.
-
-## Overview
-
-`ruv-neural-graph` builds brain connectivity graphs from multi-channel neural
-time series data and connectivity matrices. It provides graph-theoretic metrics
-(efficiency, clustering, centrality), spectral graph properties (Laplacian,
-Fiedler value), brain atlas definitions, petgraph interoperability, and temporal
-dynamics tracking for brain topology research.
-
-## Features
-
- **Graph construction** (`constructor`): Build `BrainGraph` instances from
-  connectivity matrices and multi-channel time series data via `BrainGraphConstructor`
- **Brain atlases** (`atlas`): Built-in Desikan-Killiany 68-region atlas with
-  support for loading custom atlas definitions
- **Graph metrics** (`metrics`): Global efficiency, local efficiency, clustering
-  coefficient, betweenness centrality, degree distribution, modularity,
-  graph density, small-world index
- **Spectral analysis** (`spectral`): Graph Laplacian, normalized Laplacian,
-  Fiedler value (algebraic connectivity), spectral gap
- **Petgraph bridge** (`petgraph_bridge`): Bidirectional conversion between
-  `BrainGraph` and petgraph `Graph` types
- **Temporal dynamics** (`dynamics`): `TopologyTracker` for monitoring graph
-  property evolution over time
-
-## Usage
-
-```rust
-use ruv_neural_graph::{
-    BrainGraphConstructor, load_atlas, AtlasType,
-    global_efficiency, clustering_coefficient, modularity,
-    fiedler_value, graph_laplacian,
-    to_petgraph, from_petgraph,
-    TopologyTracker,
-};
-
-// Construct a brain graph from a connectivity matrix
-let constructor = BrainGraphConstructor::new();
-let graph = constructor.from_matrix(&connectivity_matrix, 0.3, atlas)?;
-
-// Compute graph-theoretic metrics
-let efficiency = global_efficiency(&graph);
-let clustering = clustering_coefficient(&graph);
-let mod_score = modularity(&graph);
-
-// Spectral properties
-let laplacian = graph_laplacian(&graph);
-let fiedler = fiedler_value(&graph);
-
-// Convert to petgraph for additional algorithms
-let pg = to_petgraph(&graph);
-let brain_graph = from_petgraph(&pg);
-
-// Track topology over time
-let mut tracker = TopologyTracker::new();
-tracker.update(&graph);
-```
-
-## API Reference
-
-| Module            | Key Types / Functions                                             |
-|-------------------|-------------------------------------------------------------------|
-| `constructor`     | `BrainGraphConstructor`                                           |
-| `atlas`           | `load_atlas`, `AtlasType`                                         |
-| `metrics`         | `global_efficiency`, `local_efficiency`, `clustering_coefficient`, `betweenness_centrality`, `modularity`, `small_world_index` |
-| `spectral`        | `graph_laplacian`, `normalized_laplacian`, `fiedler_value`, `spectral_gap` |
-| `petgraph_bridge` | `to_petgraph`, `from_petgraph`                                    |
-| `dynamics`        | `TopologyTracker`                                                 |
-
-## Integration
-
-Depends on `ruv-neural-core` for `BrainGraph` and atlas types, and on
-`ruv-neural-signal` for connectivity computation. Feeds graphs into
-`ruv-neural-mincut` for topology partitioning and into `ruv-neural-viz`
-for visualization. Uses `petgraph` for underlying graph data structures.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,299 +0,0 @@
-//! Brain atlas definitions with built-in parcellations.
-//!
-//! Provides the Desikan-Killiany 68-region atlas with anatomical metadata
-//! including lobe classification, hemisphere, and MNI centroid coordinates.
-
-use ruv_neural_core::brain::{Atlas, BrainRegion, Hemisphere, Lobe, Parcellation};
-
-/// Supported atlas types for factory loading.
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-pub enum AtlasType {
-    /// Desikan-Killiany atlas with 68 cortical regions.
-    DesikanKilliany,
-}
-
-/// Load a parcellation for the given atlas type.
-pub fn load_atlas(atlas_type: AtlasType) -> Parcellation {
-    match atlas_type {
-        AtlasType::DesikanKilliany => build_desikan_killiany(),
-    }
-}
-
-/// Region definition used during atlas construction.
-struct RegionDef {
-    name: &'static str,
-    lobe: Lobe,
-    /// MNI centroid for the left hemisphere version.
-    mni_left: [f64; 3],
-}
-
-/// Build the full Desikan-Killiany 68-region parcellation.
-///
-/// 34 regions per hemisphere. For each region, the left hemisphere uses the
-/// original MNI centroid and the right hemisphere mirrors the x-coordinate.
-fn build_desikan_killiany() -> Parcellation {
-    let region_defs = desikan_killiany_regions();
-    let mut regions = Vec::with_capacity(68);
-    let mut id = 0;
-
-    // Left hemisphere (indices 0..34)
-    for def in &region_defs {
-        regions.push(BrainRegion {
-            id,
-            name: format!("lh_{}", def.name),
-            hemisphere: Hemisphere::Left,
-            lobe: def.lobe,
-            centroid: def.mni_left,
-        });
-        id += 1;
-    }
-
-    // Right hemisphere (indices 34..68) — mirror x-coordinate
-    for def in &region_defs {
-        regions.push(BrainRegion {
-            id,
-            name: format!("rh_{}", def.name),
-            hemisphere: Hemisphere::Right,
-            lobe: def.lobe,
-            centroid: [-def.mni_left[0], def.mni_left[1], def.mni_left[2]],
-        });
-        id += 1;
-    }
-
-    Parcellation {
-        atlas: Atlas::DesikanKilliany68,
-        regions,
-    }
-}
-
-/// Returns the 34 unique region definitions for the Desikan-Killiany atlas.
-///
-/// MNI coordinates are approximate centroids from the FreeSurfer DK atlas.
-fn desikan_killiany_regions() -> Vec<RegionDef> {
-    vec![
-        // Frontal lobe
-        RegionDef {
-            name: "superiorfrontal",
-            lobe: Lobe::Frontal,
-            mni_left: [-12.0, 30.0, 48.0],
-        },
-        RegionDef {
-            name: "caudalmiddlefrontal",
-            lobe: Lobe::Frontal,
-            mni_left: [-37.0, 10.0, 48.0],
-        },
-        RegionDef {
-            name: "rostralmiddlefrontal",
-            lobe: Lobe::Frontal,
-            mni_left: [-35.0, 38.0, 22.0],
-        },
-        RegionDef {
-            name: "parsopercularis",
-            lobe: Lobe::Frontal,
-            mni_left: [-48.0, 14.0, 18.0],
-        },
-        RegionDef {
-            name: "parstriangularis",
-            lobe: Lobe::Frontal,
-            mni_left: [-46.0, 28.0, 8.0],
-        },
-        RegionDef {
-            name: "parsorbitalis",
-            lobe: Lobe::Frontal,
-            mni_left: [-42.0, 36.0, -10.0],
-        },
-        RegionDef {
-            name: "lateralorbitofrontal",
-            lobe: Lobe::Frontal,
-            mni_left: [-28.0, 36.0, -14.0],
-        },
-        RegionDef {
-            name: "medialorbitofrontal",
-            lobe: Lobe::Frontal,
-            mni_left: [-7.0, 44.0, -14.0],
-        },
-        RegionDef {
-            name: "precentral",
-            lobe: Lobe::Frontal,
-            mni_left: [-38.0, -8.0, 52.0],
-        },
-        RegionDef {
-            name: "paracentral",
-            lobe: Lobe::Frontal,
-            mni_left: [-8.0, -28.0, 62.0],
-        },
-        RegionDef {
-            name: "frontalpole",
-            lobe: Lobe::Frontal,
-            mni_left: [-8.0, 64.0, -4.0],
-        },
-        // Parietal lobe
-        RegionDef {
-            name: "postcentral",
-            lobe: Lobe::Parietal,
-            mni_left: [-42.0, -28.0, 54.0],
-        },
-        RegionDef {
-            name: "superiorparietal",
-            lobe: Lobe::Parietal,
-            mni_left: [-24.0, -56.0, 58.0],
-        },
-        RegionDef {
-            name: "inferiorparietal",
-            lobe: Lobe::Parietal,
-            mni_left: [-44.0, -54.0, 38.0],
-        },
-        RegionDef {
-            name: "supramarginal",
-            lobe: Lobe::Parietal,
-            mni_left: [-52.0, -34.0, 34.0],
-        },
-        RegionDef {
-            name: "precuneus",
-            lobe: Lobe::Parietal,
-            mni_left: [-8.0, -58.0, 42.0],
-        },
-        // Temporal lobe
-        RegionDef {
-            name: "superiortemporal",
-            lobe: Lobe::Temporal,
-            mni_left: [-52.0, -12.0, -4.0],
-        },
-        RegionDef {
-            name: "middletemporal",
-            lobe: Lobe::Temporal,
-            mni_left: [-56.0, -28.0, -8.0],
-        },
-        RegionDef {
-            name: "inferiortemporal",
-            lobe: Lobe::Temporal,
-            mni_left: [-50.0, -36.0, -18.0],
-        },
-        RegionDef {
-            name: "bankssts",
-            lobe: Lobe::Temporal,
-            mni_left: [-52.0, -42.0, 8.0],
-        },
-        RegionDef {
-            name: "fusiform",
-            lobe: Lobe::Temporal,
-            mni_left: [-36.0, -42.0, -20.0],
-        },
-        RegionDef {
-            name: "transversetemporal",
-            lobe: Lobe::Temporal,
-            mni_left: [-44.0, -22.0, 10.0],
-        },
-        RegionDef {
-            name: "entorhinal",
-            lobe: Lobe::Temporal,
-            mni_left: [-24.0, -8.0, -34.0],
-        },
-        RegionDef {
-            name: "temporalpole",
-            lobe: Lobe::Temporal,
-            mni_left: [-36.0, 12.0, -34.0],
-        },
-        RegionDef {
-            name: "parahippocampal",
-            lobe: Lobe::Temporal,
-            mni_left: [-22.0, -28.0, -18.0],
-        },
-        // Occipital lobe
-        RegionDef {
-            name: "lateraloccipital",
-            lobe: Lobe::Occipital,
-            mni_left: [-34.0, -80.0, 8.0],
-        },
-        RegionDef {
-            name: "lingual",
-            lobe: Lobe::Occipital,
-            mni_left: [-12.0, -72.0, -4.0],
-        },
-        RegionDef {
-            name: "cuneus",
-            lobe: Lobe::Occipital,
-            mni_left: [-8.0, -82.0, 22.0],
-        },
-        RegionDef {
-            name: "pericalcarine",
-            lobe: Lobe::Occipital,
-            mni_left: [-10.0, -82.0, 6.0],
-        },
-        // Limbic (cingulate + insula)
-        RegionDef {
-            name: "posteriorcingulate",
-            lobe: Lobe::Limbic,
-            mni_left: [-6.0, -30.0, 32.0],
-        },
-        RegionDef {
-            name: "isthmuscingulate",
-            lobe: Lobe::Limbic,
-            mni_left: [-8.0, -44.0, 24.0],
-        },
-        RegionDef {
-            name: "caudalanteriorcingulate",
-            lobe: Lobe::Limbic,
-            mni_left: [-6.0, 8.0, 34.0],
-        },
-        RegionDef {
-            name: "rostralanteriorcingulate",
-            lobe: Lobe::Limbic,
-            mni_left: [-6.0, 30.0, 14.0],
-        },
-        RegionDef {
-            name: "insula",
-            lobe: Lobe::Limbic,
-            mni_left: [-34.0, 4.0, 2.0],
-        },
-    ]
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Hemisphere;
-
-    #[test]
-    fn dk68_has_exactly_68_regions() {
-        let parcellation = load_atlas(AtlasType::DesikanKilliany);
-        assert_eq!(parcellation.num_regions(), 68);
-    }
-
-    #[test]
-    fn dk68_has_34_per_hemisphere() {
-        let parcellation = load_atlas(AtlasType::DesikanKilliany);
-        let left = parcellation.regions_in_hemisphere(Hemisphere::Left);
-        let right = parcellation.regions_in_hemisphere(Hemisphere::Right);
-        assert_eq!(left.len(), 34);
-        assert_eq!(right.len(), 34);
-    }
-
-    #[test]
-    fn dk68_right_hemisphere_mirrors_x() {
-        let parcellation = load_atlas(AtlasType::DesikanKilliany);
-        // Region 0 (lh) and region 34 (rh) should have mirrored x.
-        let lh = &parcellation.regions[0];
-        let rh = &parcellation.regions[34];
-        assert_eq!(lh.centroid[0], -rh.centroid[0]);
-        assert_eq!(lh.centroid[1], rh.centroid[1]);
-        assert_eq!(lh.centroid[2], rh.centroid[2]);
-    }
-
-    #[test]
-    fn dk68_region_names_prefixed() {
-        let parcellation = load_atlas(AtlasType::DesikanKilliany);
-        assert!(parcellation.regions[0].name.starts_with("lh_"));
-        assert!(parcellation.regions[34].name.starts_with("rh_"));
-    }
-
-    #[test]
-    fn dk68_unique_ids() {
-        let parcellation = load_atlas(AtlasType::DesikanKilliany);
-        let ids: Vec<usize> = parcellation.regions.iter().map(|r| r.id).collect();
-        let mut sorted = ids.clone();
-        sorted.sort();
-        sorted.dedup();
-        assert_eq!(sorted.len(), 68);
-    }
-}
@@ -1,300 +0,0 @@
-//! Graph construction from connectivity matrices and multi-channel time series.
-//!
-//! The [`BrainGraphConstructor`] converts pairwise connectivity values into
-//! [`BrainGraph`] instances, with optional thresholding to remove weak edges.
-//! It also supports sliding-window construction from raw time series via the
-//! signal crate's connectivity metrics.
-
-use ruv_neural_core::brain::Parcellation;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::graph::{BrainEdge, BrainGraph, BrainGraphSequence, ConnectivityMetric};
-use ruv_neural_core::signal::{FrequencyBand, MultiChannelTimeSeries};
-use ruv_neural_core::traits::GraphConstructor;
-
-use crate::atlas::{AtlasType, load_atlas};
-
-/// Constructs brain connectivity graphs from matrices or time series data.
-pub struct BrainGraphConstructor {
-    parcellation: Parcellation,
-    metric: ConnectivityMetric,
-    band: FrequencyBand,
-    /// Edge weight threshold: edges below this value are dropped.
-    threshold: f64,
-    /// Sliding window duration in seconds.
-    window_duration_s: f64,
-    /// Sliding window step in seconds.
-    window_step_s: f64,
-}
-
-impl BrainGraphConstructor {
-    /// Create a new constructor with default window parameters.
-    pub fn new(atlas: AtlasType, metric: ConnectivityMetric, band: FrequencyBand) -> Self {
-        Self {
-            parcellation: load_atlas(atlas),
-            metric,
-            band,
-            threshold: 0.0,
-            window_duration_s: 1.0,
-            window_step_s: 0.5,
-        }
-    }
-
-    /// Set the edge weight threshold. Edges with weight below this are excluded.
-    pub fn with_threshold(mut self, threshold: f64) -> Self {
-        self.threshold = threshold;
-        self
-    }
-
-    /// Set the sliding window duration in seconds.
-    pub fn with_window_duration(mut self, duration_s: f64) -> Self {
-        self.window_duration_s = duration_s;
-        self
-    }
-
-    /// Set the sliding window step in seconds.
-    pub fn with_window_step(mut self, step_s: f64) -> Self {
-        self.window_step_s = step_s;
-        self
-    }
-
-    /// Construct a brain graph from a pre-computed connectivity matrix.
-    ///
-    /// The matrix should be `n x n` where `n` matches the number of atlas regions.
-    /// The matrix is treated as symmetric; only the upper triangle is read.
-    pub fn construct_from_matrix(
-        &self,
-        connectivity: &[Vec<f64>],
-        timestamp: f64,
-    ) -> BrainGraph {
-        let n = self.parcellation.num_regions();
-        let mut edges = Vec::new();
-
-        for i in 0..n.min(connectivity.len()) {
-            for j in (i + 1)..n.min(connectivity[i].len()) {
-                let weight = connectivity[i][j];
-                if weight.abs() > self.threshold {
-                    edges.push(BrainEdge {
-                        source: i,
-                        target: j,
-                        weight,
-                        metric: self.metric,
-                        frequency_band: self.band,
-                    });
-                }
-            }
-        }
-
-        BrainGraph {
-            num_nodes: n,
-            edges,
-            timestamp,
-            window_duration_s: self.window_duration_s,
-            atlas: self.parcellation.atlas,
-        }
-    }
-
-    /// Construct a sequence of brain graphs from multi-channel time series
-    /// using a sliding window approach.
-    ///
-    /// For each window, computes pairwise Pearson correlation as connectivity,
-    /// then builds a graph with thresholding applied.
-    pub fn construct_sequence(
-        &self,
-        data: &MultiChannelTimeSeries,
-    ) -> BrainGraphSequence {
-        let n_samples = data.num_samples;
-        let sr = data.sample_rate_hz;
-
-        let window_samples = (self.window_duration_s * sr) as usize;
-        let step_samples = (self.window_step_s * sr) as usize;
-
-        if window_samples == 0 || step_samples == 0 || n_samples < window_samples {
-            return BrainGraphSequence {
-                graphs: Vec::new(),
-                window_step_s: self.window_step_s,
-            };
-        }
-
-        let mut graphs = Vec::new();
-        let mut offset = 0;
-
-        while offset + window_samples <= n_samples {
-            let timestamp = data.timestamp_start + offset as f64 / sr;
-
-            // Extract windowed data for each channel
-            let windowed: Vec<&[f64]> = data
-                .data
-                .iter()
-                .map(|ch| &ch[offset..offset + window_samples])
-                .collect();
-
-            // Compute pairwise Pearson correlation matrix
-            let connectivity = compute_correlation_matrix(&windowed);
-
-            let graph = self.construct_from_matrix(&connectivity, timestamp);
-            graphs.push(graph);
-
-            offset += step_samples;
-        }
-
-        BrainGraphSequence {
-            graphs,
-            window_step_s: self.window_step_s,
-        }
-    }
-}
-
-impl GraphConstructor for BrainGraphConstructor {
-    fn construct(&self, signals: &MultiChannelTimeSeries) -> Result<BrainGraph> {
-        let n_channels = signals.num_channels;
-        let expected = self.parcellation.num_regions();
-        if n_channels != expected {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected,
-                got: n_channels,
-            });
-        }
-
-        let windowed: Vec<&[f64]> = signals.data.iter().map(|ch| ch.as_slice()).collect();
-        let connectivity = compute_correlation_matrix(&windowed);
-        Ok(self.construct_from_matrix(&connectivity, signals.timestamp_start))
-    }
-}
-
-/// Compute pairwise Pearson correlation matrix for a set of channels.
-fn compute_correlation_matrix(channels: &[&[f64]]) -> Vec<Vec<f64>> {
-    let n = channels.len();
-    let mut matrix = vec![vec![0.0; n]; n];
-
-    // Pre-compute means and standard deviations
-    let stats: Vec<(f64, f64)> = channels
-        .iter()
-        .map(|ch| {
-            let len = ch.len() as f64;
-            if len == 0.0 {
-                return (0.0, 0.0);
-            }
-            let mean = ch.iter().sum::<f64>() / len;
-            let var = ch.iter().map(|x| (x - mean).powi(2)).sum::<f64>() / len;
-            (mean, var.sqrt())
-        })
-        .collect();
-
-    for i in 0..n {
-        matrix[i][i] = 1.0;
-        for j in (i + 1)..n {
-            let (mean_i, std_i) = stats[i];
-            let (mean_j, std_j) = stats[j];
-
-            if std_i == 0.0 || std_j == 0.0 {
-                matrix[i][j] = 0.0;
-                matrix[j][i] = 0.0;
-                continue;
-            }
-
-            let len = channels[i].len().min(channels[j].len());
-            let cov: f64 = channels[i][..len]
-                .iter()
-                .zip(channels[j][..len].iter())
-                .map(|(a, b)| (a - mean_i) * (b - mean_j))
-                .sum::<f64>()
-                / len as f64;
-
-            let r = cov / (std_i * std_j);
-            matrix[i][j] = r;
-            matrix[j][i] = r;
-        }
-    }
-
-    matrix
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::graph::ConnectivityMetric;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_constructor() -> BrainGraphConstructor {
-        BrainGraphConstructor::new(
-            AtlasType::DesikanKilliany,
-            ConnectivityMetric::PhaseLockingValue,
-            FrequencyBand::Alpha,
-        )
-    }
-
-    #[test]
-    fn identity_matrix_fully_disconnected() {
-        let ctor = make_constructor().with_threshold(0.01);
-        let n = 68;
-        // Identity matrix: diagonal = 1, off-diagonal = 0
-        let identity: Vec<Vec<f64>> = (0..n)
-            .map(|i| {
-                let mut row = vec![0.0; n];
-                row[i] = 1.0;
-                row
-            })
-            .collect();
-
-        let graph = ctor.construct_from_matrix(&identity, 0.0);
-        assert_eq!(graph.num_nodes, 68);
-        assert_eq!(graph.edges.len(), 0, "Identity matrix should produce no edges");
-    }
-
-    #[test]
-    fn ones_matrix_fully_connected() {
-        let ctor = make_constructor().with_threshold(0.01);
-        let n = 68;
-        let ones: Vec<Vec<f64>> = vec![vec![1.0; n]; n];
-
-        let graph = ctor.construct_from_matrix(&ones, 0.0);
-        let expected_edges = n * (n - 1) / 2;
-        assert_eq!(graph.edges.len(), expected_edges);
-    }
-
-    #[test]
-    fn threshold_filters_weak_edges() {
-        let ctor = make_constructor().with_threshold(0.5);
-        let n = 68;
-        let mut matrix = vec![vec![0.0; n]; n];
-        // Set a few strong edges
-        matrix[0][1] = 0.8;
-        matrix[1][0] = 0.8;
-        // Set a weak edge
-        matrix[2][3] = 0.3;
-        matrix[3][2] = 0.3;
-
-        let graph = ctor.construct_from_matrix(&matrix, 0.0);
-        assert_eq!(graph.edges.len(), 1, "Only edge above threshold should survive");
-        assert_eq!(graph.edges[0].source, 0);
-        assert_eq!(graph.edges[0].target, 1);
-    }
-
-    #[test]
-    fn construct_sequence_produces_graphs() {
-        let ctor = BrainGraphConstructor::new(
-            AtlasType::DesikanKilliany,
-            ConnectivityMetric::PhaseLockingValue,
-            FrequencyBand::Alpha,
-        )
-        .with_window_duration(0.5)
-        .with_window_step(0.25);
-
-        // 68 channels, 256 samples at 256 Hz = 1 second of data
-        let n_ch = 68;
-        let n_samples = 256;
-        let data: Vec<Vec<f64>> = (0..n_ch)
-            .map(|i| {
-                (0..n_samples)
-                    .map(|j| ((j as f64 + i as f64) * 0.1).sin())
-                    .collect()
-            })
-            .collect();
-
-        let ts = MultiChannelTimeSeries::new(data, 256.0, 0.0).unwrap();
-        let seq = ctor.construct_sequence(&ts);
-
-        // 1.0s data, 0.5s window, 0.25s step => 3 windows: [0,0.5], [0.25,0.75], [0.5,1.0]
-        assert!(seq.len() >= 2, "Should produce at least 2 graphs, got {}", seq.len());
-    }
-}
@@ -1,262 +0,0 @@
-//! Temporal graph dynamics: tracking topology metrics over time.
-//!
-//! The [`TopologyTracker`] accumulates brain graphs and computes time series
-//! of graph-theoretic metrics to detect state transitions and measure
-//! the rate of topological change.
-
-use ruv_neural_core::graph::BrainGraph;
-
-use crate::metrics::{clustering_coefficient, global_efficiency};
-use crate::spectral::fiedler_value;
-
-/// A timestamped snapshot of graph topology metrics.
-#[derive(Debug, Clone)]
-pub struct TopologySnapshot {
-    /// Timestamp of the graph.
-    pub timestamp: f64,
-    /// Global efficiency.
-    pub global_efficiency: f64,
-    /// Clustering coefficient.
-    pub clustering: f64,
-    /// Fiedler value (algebraic connectivity).
-    pub fiedler: f64,
-    /// Graph density.
-    pub density: f64,
-    /// Total edge weight (proxy for minimum cut in dense graphs).
-    pub total_weight: f64,
-}
-
-/// Tracks graph topology metrics over time and detects transitions.
-pub struct TopologyTracker {
-    /// History of topology snapshots.
-    history: Vec<TopologySnapshot>,
-}
-
-impl TopologyTracker {
-    /// Create an empty tracker.
-    pub fn new() -> Self {
-        Self {
-            history: Vec::new(),
-        }
-    }
-
-    /// Track a new brain graph, computing and storing its topology metrics.
-    pub fn track(&mut self, graph: &BrainGraph) {
-        let snapshot = TopologySnapshot {
-            timestamp: graph.timestamp,
-            global_efficiency: global_efficiency(graph),
-            clustering: clustering_coefficient(graph),
-            fiedler: fiedler_value(graph),
-            density: graph.density(),
-            total_weight: graph.total_weight(),
-        };
-        self.history.push(snapshot);
-    }
-
-    /// Number of tracked time points.
-    pub fn len(&self) -> usize {
-        self.history.len()
-    }
-
-    /// Returns true if no graphs have been tracked.
-    pub fn is_empty(&self) -> bool {
-        self.history.is_empty()
-    }
-
-    /// Get the full history of snapshots.
-    pub fn snapshots(&self) -> &[TopologySnapshot] {
-        &self.history
-    }
-
-    /// Return a time series of (timestamp, total_weight) as a proxy for minimum cut.
-    ///
-    /// The total weight correlates with overall connectivity strength.
-    pub fn mincut_timeseries(&self) -> Vec<(f64, f64)> {
-        self.history
-            .iter()
-            .map(|s| (s.timestamp, s.total_weight))
-            .collect()
-    }
-
-    /// Return a time series of (timestamp, fiedler_value).
-    ///
-    /// The Fiedler value tracks algebraic connectivity over time.
-    pub fn fiedler_timeseries(&self) -> Vec<(f64, f64)> {
-        self.history
-            .iter()
-            .map(|s| (s.timestamp, s.fiedler))
-            .collect()
-    }
-
-    /// Return a time series of (timestamp, global_efficiency).
-    pub fn efficiency_timeseries(&self) -> Vec<(f64, f64)> {
-        self.history
-            .iter()
-            .map(|s| (s.timestamp, s.global_efficiency))
-            .collect()
-    }
-
-    /// Return a time series of (timestamp, clustering_coefficient).
-    pub fn clustering_timeseries(&self) -> Vec<(f64, f64)> {
-        self.history
-            .iter()
-            .map(|s| (s.timestamp, s.clustering))
-            .collect()
-    }
-
-    /// Detect timestamps where significant topology changes occur.
-    ///
-    /// A transition is detected when the absolute change in global efficiency
-    /// between consecutive snapshots exceeds the given threshold.
-    pub fn detect_transitions(&self, threshold: f64) -> Vec<f64> {
-        if self.history.len() < 2 {
-            return Vec::new();
-        }
-
-        let mut transitions = Vec::new();
-        for i in 1..self.history.len() {
-            let delta = (self.history[i].global_efficiency
-                - self.history[i - 1].global_efficiency)
-                .abs();
-            if delta > threshold {
-                transitions.push(self.history[i].timestamp);
-            }
-        }
-
-        transitions
-    }
-
-    /// Compute the rate of change of global efficiency over time.
-    ///
-    /// Returns (timestamp, d_efficiency/dt) for each consecutive pair.
-    pub fn rate_of_change(&self) -> Vec<(f64, f64)> {
-        if self.history.len() < 2 {
-            return Vec::new();
-        }
-
-        self.history
-            .windows(2)
-            .map(|pair| {
-                let dt = pair[1].timestamp - pair[0].timestamp;
-                let de = pair[1].global_efficiency - pair[0].global_efficiency;
-                let rate = if dt.abs() > 1e-15 { de / dt } else { 0.0 };
-                (pair[1].timestamp, rate)
-            })
-            .collect()
-    }
-}
-
-impl Default for TopologyTracker {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(s: usize, t: usize, w: f64) -> BrainEdge {
-        BrainEdge {
-            source: s,
-            target: t,
-            weight: w,
-            metric: ConnectivityMetric::PhaseLockingValue,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    fn make_graph(timestamp: f64, edges: Vec<BrainEdge>) -> BrainGraph {
-        BrainGraph {
-            num_nodes: 4,
-            edges,
-            timestamp,
-            window_duration_s: 0.5,
-            atlas: Atlas::Custom(4),
-        }
-    }
-
-    #[test]
-    fn tracker_stores_history() {
-        let mut tracker = TopologyTracker::new();
-        assert!(tracker.is_empty());
-
-        let g1 = make_graph(0.0, vec![make_edge(0, 1, 1.0), make_edge(2, 3, 1.0)]);
-        let g2 = make_graph(1.0, vec![
-            make_edge(0, 1, 1.0),
-            make_edge(1, 2, 1.0),
-            make_edge(2, 3, 1.0),
-        ]);
-
-        tracker.track(&g1);
-        tracker.track(&g2);
-
-        assert_eq!(tracker.len(), 2);
-        assert!(!tracker.is_empty());
-    }
-
-    #[test]
-    fn mincut_timeseries_correct_length() {
-        let mut tracker = TopologyTracker::new();
-        for i in 0..5 {
-            let g = make_graph(
-                i as f64,
-                vec![make_edge(0, 1, 1.0), make_edge(2, 3, i as f64 * 0.5)],
-            );
-            tracker.track(&g);
-        }
-
-        let ts = tracker.mincut_timeseries();
-        assert_eq!(ts.len(), 5);
-        assert_eq!(ts[0].0, 0.0);
-        assert_eq!(ts[4].0, 4.0);
-    }
-
-    #[test]
-    fn detect_transitions_returns_correct_timestamps() {
-        let mut tracker = TopologyTracker::new();
-
-        // Stable phase: few edges
-        for i in 0..3 {
-            let g = make_graph(
-                i as f64,
-                vec![make_edge(0, 1, 0.5)],
-            );
-            tracker.track(&g);
-        }
-
-        // Sudden change: fully connected
-        let g = make_graph(3.0, vec![
-            make_edge(0, 1, 1.0),
-            make_edge(0, 2, 1.0),
-            make_edge(0, 3, 1.0),
-            make_edge(1, 2, 1.0),
-            make_edge(1, 3, 1.0),
-            make_edge(2, 3, 1.0),
-        ]);
-        tracker.track(&g);
-
-        // With a small threshold, we should detect the transition at t=3.0
-        let transitions = tracker.detect_transitions(0.01);
-        assert!(
-            transitions.contains(&3.0),
-            "Should detect transition at t=3.0, got {:?}",
-            transitions
-        );
-    }
-
-    #[test]
-    fn rate_of_change_correct_length() {
-        let mut tracker = TopologyTracker::new();
-        for i in 0..4 {
-            let g = make_graph(i as f64, vec![make_edge(0, 1, 1.0)]);
-            tracker.track(&g);
-        }
-
-        let roc = tracker.rate_of_change();
-        assert_eq!(roc.len(), 3); // n-1 rates for n points
-    }
-}
@@ -1,31 +0,0 @@
-//! rUv Neural Graph -- Brain connectivity graph construction from neural signals.
-//!
-//! This crate builds brain connectivity graphs from multi-channel neural time series
-//! data, provides graph-theoretic metrics, spectral analysis, and temporal dynamics
-//! tracking for brain topology research.
-//!
-//! # Modules
-//!
-//! - [`atlas`] -- Brain atlas definitions (Desikan-Killiany 68 regions)
-//! - [`constructor`] -- Graph construction from connectivity matrices and time series
-//! - [`petgraph_bridge`] -- Convert between `BrainGraph` and petgraph types
-//! - [`metrics`] -- Graph-theoretic metrics (efficiency, clustering, centrality)
-//! - [`spectral`] -- Spectral graph properties (Laplacian, Fiedler value)
-//! - [`dynamics`] -- Temporal graph dynamics and topology tracking
-
-pub mod atlas;
-pub mod constructor;
-pub mod dynamics;
-pub mod metrics;
-pub mod petgraph_bridge;
-pub mod spectral;
-
-pub use atlas::{load_atlas, AtlasType};
-pub use constructor::BrainGraphConstructor;
-pub use dynamics::TopologyTracker;
-pub use metrics::{
-    betweenness_centrality, clustering_coefficient, degree_distribution, global_efficiency,
-    graph_density, local_efficiency, modularity, node_degree, small_world_index,
-};
-pub use petgraph_bridge::{from_petgraph, to_petgraph};
-pub use spectral::{fiedler_value, graph_laplacian, normalized_laplacian, spectral_gap};
@@ -1,517 +0,0 @@
-//! Graph-theoretic metrics for brain connectivity analysis.
-//!
-//! Provides standard network neuroscience metrics: efficiency, clustering,
-//! centrality, modularity, and small-world properties.
-
-use ruv_neural_core::graph::BrainGraph;
-
-
-/// Compute global efficiency of a brain graph.
-///
-/// Global efficiency is the average inverse shortest path length between all
-/// pairs of nodes. For disconnected pairs, the contribution is 0.
-///
-/// E_global = (1 / N(N-1)) * sum_{i != j} 1/d(i,j)
-pub fn global_efficiency(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return 0.0;
-    }
-
-    let dist = all_pairs_shortest_paths(graph);
-    let mut sum = 0.0;
-
-    for i in 0..n {
-        for j in 0..n {
-            if i != j && dist[i][j] < f64::INFINITY {
-                sum += 1.0 / dist[i][j];
-            }
-        }
-    }
-
-    sum / (n * (n - 1)) as f64
-}
-
-/// Compute local efficiency of a brain graph.
-///
-/// Average of each node's subgraph efficiency (efficiency among its neighbors).
-pub fn local_efficiency(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return 0.0;
-    }
-
-    let adj = graph.adjacency_matrix();
-    let mut total = 0.0;
-
-    for i in 0..n {
-        let neighbors: Vec<usize> = (0..n)
-            .filter(|&j| j != i && adj[i][j] > 0.0)
-            .collect();
-
-        let k = neighbors.len();
-        if k < 2 {
-            continue;
-        }
-
-        // Build subgraph of neighbors and compute its efficiency
-        let mut sub_sum = 0.0;
-        for &ni in &neighbors {
-            for &nj in &neighbors {
-                if ni != nj && adj[ni][nj] > 0.0 {
-                    // Use direct weight as inverse distance proxy
-                    sub_sum += adj[ni][nj];
-                }
-            }
-        }
-
-        total += sub_sum / (k * (k - 1)) as f64;
-    }
-
-    total / n as f64
-}
-
-/// Compute global clustering coefficient.
-///
-/// C = (3 * number_of_triangles) / number_of_connected_triples
-/// For weighted graphs, uses the geometric mean of edge weights in triangles.
-pub fn clustering_coefficient(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 3 {
-        return 0.0;
-    }
-
-    let adj = graph.adjacency_matrix();
-    let mut triangles = 0.0;
-    let mut triples = 0.0;
-
-    for i in 0..n {
-        let neighbors_i: Vec<usize> = (0..n)
-            .filter(|&j| j != i && adj[i][j] > 0.0)
-            .collect();
-        let k = neighbors_i.len();
-        if k < 2 {
-            continue;
-        }
-
-        triples += (k * (k - 1)) as f64 / 2.0;
-
-        for a in 0..neighbors_i.len() {
-            for b in (a + 1)..neighbors_i.len() {
-                let ni = neighbors_i[a];
-                let nj = neighbors_i[b];
-                if adj[ni][nj] > 0.0 {
-                    // Weighted triangle: geometric mean of the three edges
-                    let w = (adj[i][ni] * adj[i][nj] * adj[ni][nj]).cbrt();
-                    triangles += w;
-                }
-            }
-        }
-    }
-
-    if triples == 0.0 {
-        return 0.0;
-    }
-
-    triangles / triples
-}
-
-/// Weighted degree of a single node.
-pub fn node_degree(graph: &BrainGraph, node: usize) -> f64 {
-    graph.node_degree(node)
-}
-
-/// Degree distribution: weighted degree for every node.
-pub fn degree_distribution(graph: &BrainGraph) -> Vec<f64> {
-    (0..graph.num_nodes)
-        .map(|i| graph.node_degree(i))
-        .collect()
-}
-
-/// Betweenness centrality for each node.
-///
-/// Computes the fraction of shortest paths passing through each node.
-/// Uses Brandes' algorithm adapted for weighted graphs.
-pub fn betweenness_centrality(graph: &BrainGraph) -> Vec<f64> {
-    let n = graph.num_nodes;
-    let mut centrality = vec![0.0; n];
-
-    if n < 3 {
-        return centrality;
-    }
-
-    let adj = graph.adjacency_matrix();
-
-    // For each source node, run Dijkstra and accumulate betweenness
-    for s in 0..n {
-        let mut dist = vec![f64::INFINITY; n];
-        let mut sigma = vec![0.0_f64; n]; // number of shortest paths
-        let mut delta = vec![0.0_f64; n];
-        let mut pred: Vec<Vec<usize>> = vec![Vec::new(); n];
-        let mut visited = vec![false; n];
-        let mut order = Vec::with_capacity(n);
-
-        dist[s] = 0.0;
-        sigma[s] = 1.0;
-
-        // Simple Dijkstra (priority queue not needed for correctness)
-        for _ in 0..n {
-            // Find unvisited node with minimum distance
-            let mut u = None;
-            let mut min_dist = f64::INFINITY;
-            for v in 0..n {
-                if !visited[v] && dist[v] < min_dist {
-                    min_dist = dist[v];
-                    u = Some(v);
-                }
-            }
-
-            let u = match u {
-                Some(u) => u,
-                None => break,
-            };
-
-            visited[u] = true;
-            order.push(u);
-
-            for v in 0..n {
-                if adj[u][v] <= 0.0 || u == v {
-                    continue;
-                }
-                // Convert weight to distance (stronger connection = shorter distance)
-                let edge_dist = 1.0 / adj[u][v];
-                let new_dist = dist[u] + edge_dist;
-
-                if new_dist < dist[v] - 1e-12 {
-                    dist[v] = new_dist;
-                    sigma[v] = sigma[u];
-                    pred[v] = vec![u];
-                } else if (new_dist - dist[v]).abs() < 1e-12 {
-                    sigma[v] += sigma[u];
-                    pred[v].push(u);
-                }
-            }
-        }
-
-        // Back-propagation of dependencies
-        for &w in order.iter().rev() {
-            for &v in &pred[w] {
-                if sigma[w] > 0.0 {
-                    delta[v] += (sigma[v] / sigma[w]) * (1.0 + delta[w]);
-                }
-            }
-            if w != s {
-                centrality[w] += delta[w];
-            }
-        }
-    }
-
-    // Normalize for undirected graph
-    let norm = if n > 2 {
-        2.0 / ((n - 1) * (n - 2)) as f64
-    } else {
-        1.0
-    };
-    for c in &mut centrality {
-        *c *= norm;
-    }
-
-    centrality
-}
-
-/// Graph density: fraction of possible edges that exist.
-pub fn graph_density(graph: &BrainGraph) -> f64 {
-    graph.density()
-}
-
-/// Small-world index sigma = (C/C_rand) / (L/L_rand).
-///
-/// Uses lattice-equivalent approximations:
-/// - C_rand ~ k / N (for Erdos-Renyi)
-/// - L_rand ~ ln(N) / ln(k) (for Erdos-Renyi)
-///
-/// where k is the mean degree and N is the number of nodes.
-pub fn small_world_index(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes as f64;
-    if n < 4.0 {
-        return 0.0;
-    }
-
-    let c = clustering_coefficient(graph);
-    let eff = global_efficiency(graph);
-
-    // Mean binary degree
-    let adj = graph.adjacency_matrix();
-    let total_edges: f64 = adj
-        .iter()
-        .flat_map(|row| row.iter())
-        .filter(|&&w| w > 0.0)
-        .count() as f64
-        / 2.0;
-    let k = 2.0 * total_edges / n;
-
-    if k < 1.0 || c <= 0.0 || eff <= 0.0 {
-        return 0.0;
-    }
-
-    // Random graph approximations
-    let c_rand = k / n;
-    let l_rand = n.ln() / k.ln();
-    let l = if eff > 0.0 { 1.0 / eff } else { f64::INFINITY };
-
-    if c_rand <= 0.0 || l_rand <= 0.0 || l.is_infinite() {
-        return 0.0;
-    }
-
-    (c / c_rand) / (l / l_rand)
-}
-
-/// Newman modularity Q for a given partition.
-///
-/// Q = (1/2m) * sum_{ij} [A_ij - k_i*k_j/(2m)] * delta(c_i, c_j)
-///
-/// where m is total edge weight, k_i is weighted degree of node i,
-/// and delta(c_i, c_j) = 1 if nodes i and j are in the same community.
-pub fn modularity(graph: &BrainGraph, partition: &[Vec<usize>]) -> f64 {
-    let adj = graph.adjacency_matrix();
-    let n = graph.num_nodes;
-
-    // Build community assignment map
-    let mut community = vec![0usize; n];
-    for (c, members) in partition.iter().enumerate() {
-        for &node in members {
-            if node < n {
-                community[node] = c;
-            }
-        }
-    }
-
-    // Total edge weight (each edge counted once in adjacency, so sum / 2)
-    let m: f64 = adj.iter().flat_map(|row| row.iter()).sum::<f64>() / 2.0;
-    if m == 0.0 {
-        return 0.0;
-    }
-
-    // Weighted degree
-    let degrees: Vec<f64> = (0..n)
-        .map(|i| adj[i].iter().sum::<f64>())
-        .collect();
-
-    let mut q = 0.0;
-    for i in 0..n {
-        for j in 0..n {
-            if community[i] == community[j] {
-                q += adj[i][j] - degrees[i] * degrees[j] / (2.0 * m);
-            }
-        }
-    }
-
-    q / (2.0 * m)
-}
-
-/// Compute all-pairs shortest path distances using Floyd-Warshall.
-///
-/// Edge weights are converted to distances as 1/weight (stronger = closer).
-fn all_pairs_shortest_paths(graph: &BrainGraph) -> Vec<Vec<f64>> {
-    let n = graph.num_nodes;
-    let adj = graph.adjacency_matrix();
-
-    let mut dist = vec![vec![f64::INFINITY; n]; n];
-
-    for i in 0..n {
-        dist[i][i] = 0.0;
-        for j in 0..n {
-            if i != j && adj[i][j] > 0.0 {
-                dist[i][j] = 1.0 / adj[i][j];
-            }
-        }
-    }
-
-    // Floyd-Warshall
-    for k in 0..n {
-        for i in 0..n {
-            for j in 0..n {
-                let through_k = dist[i][k] + dist[k][j];
-                if through_k < dist[i][j] {
-                    dist[i][j] = through_k;
-                }
-            }
-        }
-    }
-
-    dist
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    /// Build a complete graph with n nodes, all edges weight 1.0.
-    fn complete_graph(n: usize) -> BrainGraph {
-        let mut edges = Vec::new();
-        for i in 0..n {
-            for j in (i + 1)..n {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        BrainGraph {
-            num_nodes: n,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(n),
-        }
-    }
-
-    /// Build a path graph: 0-1-2-..-(n-1).
-    fn path_graph(n: usize) -> BrainGraph {
-        let edges: Vec<BrainEdge> = (0..n.saturating_sub(1))
-            .map(|i| BrainEdge {
-                source: i,
-                target: i + 1,
-                weight: 1.0,
-                metric: ConnectivityMetric::PhaseLockingValue,
-                frequency_band: FrequencyBand::Alpha,
-            })
-            .collect();
-        BrainGraph {
-            num_nodes: n,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(n),
-        }
-    }
-
-    #[test]
-    fn global_efficiency_complete_graph() {
-        // In a complete graph with weight 1, all shortest paths have length 1,
-        // so efficiency = 1.0.
-        let g = complete_graph(10);
-        let eff = global_efficiency(&g);
-        assert!((eff - 1.0).abs() < 1e-10, "Expected ~1.0, got {}", eff);
-    }
-
-    #[test]
-    fn global_efficiency_empty_graph() {
-        let g = BrainGraph {
-            num_nodes: 5,
-            edges: Vec::new(),
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(5),
-        };
-        let eff = global_efficiency(&g);
-        assert_eq!(eff, 0.0);
-    }
-
-    #[test]
-    fn clustering_coefficient_complete_graph() {
-        let g = complete_graph(8);
-        let cc = clustering_coefficient(&g);
-        assert!(cc > 0.9, "Complete graph should have clustering ~1.0, got {}", cc);
-    }
-
-    #[test]
-    fn clustering_coefficient_path_graph() {
-        // A path graph has no triangles, so clustering = 0.
-        let g = path_graph(5);
-        let cc = clustering_coefficient(&g);
-        assert!(cc.abs() < 1e-10, "Path graph should have CC=0, got {}", cc);
-    }
-
-    #[test]
-    fn density_complete_graph() {
-        let g = complete_graph(10);
-        let d = graph_density(&g);
-        assert!((d - 1.0).abs() < 1e-10, "Complete graph density should be 1.0, got {}", d);
-    }
-
-    #[test]
-    fn degree_distribution_uniform() {
-        let g = complete_graph(5);
-        let dd = degree_distribution(&g);
-        // Each node in K5 has degree 4 (4 edges * weight 1.0 = 4.0)
-        for &d in &dd {
-            assert!((d - 4.0).abs() < 1e-10);
-        }
-    }
-
-    #[test]
-    fn betweenness_centrality_path() {
-        // In a path 0-1-2-3-4, middle nodes should have higher betweenness.
-        let g = path_graph(5);
-        let bc = betweenness_centrality(&g);
-        // Node 2 (center) should have highest betweenness
-        assert!(bc[2] >= bc[0], "Center node should have >= betweenness than endpoints");
-        assert!(bc[2] >= bc[4], "Center node should have >= betweenness than endpoints");
-    }
-
-    #[test]
-    fn modularity_single_community() {
-        let g = complete_graph(6);
-        let all_in_one = vec![vec![0, 1, 2, 3, 4, 5]];
-        let q = modularity(&g, &all_in_one);
-        // All in one community, modularity should be 0
-        assert!(q.abs() < 1e-10, "Single community Q should be ~0, got {}", q);
-    }
-
-    #[test]
-    fn modularity_good_partition() {
-        // Two cliques connected by a weak edge
-        let mut edges = Vec::new();
-        // Clique 1: nodes 0,1,2
-        for i in 0..3 {
-            for j in (i + 1)..3 {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        // Clique 2: nodes 3,4,5
-        for i in 3..6 {
-            for j in (i + 1)..6 {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: 1.0,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-        // Weak bridge
-        edges.push(BrainEdge {
-            source: 2,
-            target: 3,
-            weight: 0.1,
-            metric: ConnectivityMetric::PhaseLockingValue,
-            frequency_band: FrequencyBand::Alpha,
-        });
-
-        let g = BrainGraph {
-            num_nodes: 6,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        };
-
-        let good = vec![vec![0, 1, 2], vec![3, 4, 5]];
-        let q = modularity(&g, &good);
-        assert!(q > 0.0, "Good partition should have positive modularity, got {}", q);
-    }
-}
@@ -1,161 +0,0 @@
-//! Petgraph bridge: convert between BrainGraph and petgraph types.
-//!
-//! This module enables using petgraph's extensive algorithm library
-//! (shortest paths, connected components, etc.) on brain connectivity graphs.
-
-use petgraph::graph::{Graph, NodeIndex, UnGraph};
-use petgraph::visit::EdgeRef;
-
-use ruv_neural_core::brain::Atlas;
-use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-use ruv_neural_core::signal::FrequencyBand;
-
-/// Convert a BrainGraph to a petgraph undirected graph.
-///
-/// Node weights are the node indices (usize). Edge weights are f64 connectivity values.
-/// All nodes are created even if they have no edges.
-pub fn to_petgraph(graph: &BrainGraph) -> UnGraph<usize, f64> {
-    let mut pg = Graph::new_undirected();
-    let mut node_indices: Vec<NodeIndex> = Vec::with_capacity(graph.num_nodes);
-
-    for i in 0..graph.num_nodes {
-        node_indices.push(pg.add_node(i));
-    }
-
-    for edge in &graph.edges {
-        if edge.source < graph.num_nodes && edge.target < graph.num_nodes {
-            pg.add_edge(
-                node_indices[edge.source],
-                node_indices[edge.target],
-                edge.weight,
-            );
-        }
-    }
-
-    pg
-}
-
-/// Convert a petgraph undirected graph back to a BrainGraph.
-///
-/// Node weights in the petgraph are assumed to be node indices.
-/// Requires the atlas and timestamp to be provided since petgraph does not store them.
-pub fn from_petgraph(
-    pg: &UnGraph<usize, f64>,
-    atlas: Atlas,
-    timestamp: f64,
-) -> BrainGraph {
-    let num_nodes = pg.node_count();
-    let mut edges = Vec::with_capacity(pg.edge_count());
-
-    for edge_ref in pg.edge_references() {
-        let source = pg[edge_ref.source()];
-        let target = pg[edge_ref.target()];
-        let weight = *edge_ref.weight();
-
-        edges.push(BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ConnectivityMetric::PhaseLockingValue,
-            frequency_band: FrequencyBand::Alpha,
-        });
-    }
-
-    BrainGraph {
-        num_nodes,
-        edges,
-        timestamp,
-        window_duration_s: 0.0,
-        atlas,
-    }
-}
-
-/// Helper: get a petgraph NodeIndex for a given brain region index.
-///
-/// The petgraph nodes are added in order 0..num_nodes, so the NodeIndex
-/// for region `i` is simply `NodeIndex::new(i)`.
-pub fn node_index(region_id: usize) -> NodeIndex {
-    NodeIndex::new(region_id)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn sample_graph() -> BrainGraph {
-        BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                BrainEdge {
-                    source: 0,
-                    target: 1,
-                    weight: 0.9,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 1,
-                    target: 2,
-                    weight: 0.7,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-                BrainEdge {
-                    source: 2,
-                    target: 3,
-                    weight: 0.5,
-                    metric: ConnectivityMetric::PhaseLockingValue,
-                    frequency_band: FrequencyBand::Alpha,
-                },
-            ],
-            timestamp: 1.0,
-            window_duration_s: 0.5,
-            atlas: Atlas::Custom(4),
-        }
-    }
-
-    #[test]
-    fn round_trip_preserves_structure() {
-        let original = sample_graph();
-        let pg = to_petgraph(&original);
-        let restored = from_petgraph(&pg, Atlas::Custom(4), 1.0);
-
-        assert_eq!(restored.num_nodes, original.num_nodes);
-        assert_eq!(restored.edges.len(), original.edges.len());
-    }
-
-    #[test]
-    fn petgraph_has_correct_node_count() {
-        let graph = sample_graph();
-        let pg = to_petgraph(&graph);
-        assert_eq!(pg.node_count(), 4);
-    }
-
-    #[test]
-    fn petgraph_has_correct_edge_count() {
-        let graph = sample_graph();
-        let pg = to_petgraph(&graph);
-        assert_eq!(pg.edge_count(), 3);
-    }
-
-    #[test]
-    fn empty_graph_round_trip() {
-        let empty = BrainGraph {
-            num_nodes: 10,
-            edges: Vec::new(),
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(10),
-        };
-        let pg = to_petgraph(&empty);
-        assert_eq!(pg.node_count(), 10);
-        assert_eq!(pg.edge_count(), 0);
-
-        let restored = from_petgraph(&pg, Atlas::Custom(10), 0.0);
-        assert_eq!(restored.num_nodes, 10);
-        assert_eq!(restored.edges.len(), 0);
-    }
-}
@@ -1,317 +0,0 @@
-//! Spectral graph properties: Laplacian matrices, Fiedler value, spectral gap.
-//!
-//! The graph Laplacian encodes the structure of a graph and its eigenvalues
-//! reveal fundamental connectivity properties. The Fiedler value (second
-//! smallest eigenvalue) measures algebraic connectivity.
-
-use ruv_neural_core::graph::BrainGraph;
-
-/// Compute the combinatorial graph Laplacian L = D - A.
-///
-/// D is the diagonal degree matrix, A is the adjacency matrix.
-/// Returns an `n x n` matrix as `Vec<Vec<f64>>`.
-pub fn graph_laplacian(graph: &BrainGraph) -> Vec<Vec<f64>> {
-    let n = graph.num_nodes;
-    let adj = graph.adjacency_matrix();
-    let mut laplacian = vec![vec![0.0; n]; n];
-
-    for i in 0..n {
-        let degree: f64 = adj[i].iter().sum();
-        laplacian[i][i] = degree;
-        for j in 0..n {
-            if i != j {
-                laplacian[i][j] = -adj[i][j];
-            }
-        }
-    }
-
-    laplacian
-}
-
-/// Compute the normalized graph Laplacian L_norm = D^{-1/2} L D^{-1/2}.
-///
-/// For isolated nodes (degree = 0), the diagonal entry is set to 0.
-pub fn normalized_laplacian(graph: &BrainGraph) -> Vec<Vec<f64>> {
-    let n = graph.num_nodes;
-    let adj = graph.adjacency_matrix();
-
-    // Compute D^{-1/2}
-    let degrees: Vec<f64> = (0..n).map(|i| adj[i].iter().sum::<f64>()).collect();
-    let d_inv_sqrt: Vec<f64> = degrees
-        .iter()
-        .map(|&d| if d > 0.0 { 1.0 / d.sqrt() } else { 0.0 })
-        .collect();
-
-    let mut l_norm = vec![vec![0.0; n]; n];
-
-    for i in 0..n {
-        if degrees[i] > 0.0 {
-            l_norm[i][i] = 1.0;
-        }
-        for j in 0..n {
-            if i != j && adj[i][j] > 0.0 {
-                l_norm[i][j] = -adj[i][j] * d_inv_sqrt[i] * d_inv_sqrt[j];
-            }
-        }
-    }
-
-    l_norm
-}
-
-/// Compute the Fiedler value (algebraic connectivity).
-///
-/// The Fiedler value is the second smallest eigenvalue of the graph Laplacian.
-/// - For a connected graph, Fiedler value > 0.
-/// - For a disconnected graph, Fiedler value = 0.
-///
-/// Uses power iteration with deflation to find the two smallest eigenvalues
-/// of the Laplacian (which is positive semidefinite).
-pub fn fiedler_value(graph: &BrainGraph) -> f64 {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return 0.0;
-    }
-
-    let laplacian = graph_laplacian(graph);
-
-    // The Laplacian is PSD. Its smallest eigenvalue is 0 with eigenvector
-    // proportional to the all-ones vector. We need the second smallest.
-    //
-    // Strategy: use inverse power iteration on (L + alpha*I) shifted to find
-    // the smallest eigenvalue, then deflate and find the next.
-    // Alternatively, use the shifted inverse iteration directly for lambda_2.
-    //
-    // Simpler approach: compute L * x repeatedly to find eigenvalues from largest
-    // down, or use the fact that lambda_2 = min over x perp to 1 of x^T L x / x^T x.
-    //
-    // We use inverse iteration with shift to find the Fiedler vector.
-    // But since we don't have a linear solver, we use power iteration on
-    // (max_eig * I - L) to find the largest eigenvalue of that matrix (which
-    // corresponds to the smallest eigenvalue of L).
-    //
-    // Actually, the simplest reliable approach for moderate n:
-    // Use the Rayleigh quotient iteration projected orthogonal to the all-ones vector.
-
-    compute_fiedler_rayleigh(&laplacian, n)
-}
-
-/// Compute the spectral gap: lambda_2 - lambda_1.
-///
-/// Since lambda_1 = 0 for the Laplacian, the spectral gap equals the Fiedler value.
-pub fn spectral_gap(graph: &BrainGraph) -> f64 {
-    fiedler_value(graph)
-}
-
-/// Compute the Fiedler value using projected power iteration.
-///
-/// Projects out the all-ones eigenvector (corresponding to lambda_1 = 0),
-/// then uses power iteration on (alpha*I - L) to find the largest eigenvalue
-/// of that shifted matrix. The Fiedler value is then alpha - largest_eigenvalue.
-fn compute_fiedler_rayleigh(laplacian: &[Vec<f64>], n: usize) -> f64 {
-    if n < 2 {
-        return 0.0;
-    }
-
-    // Estimate max eigenvalue for shifting (Gershgorin bound)
-    let alpha = laplacian
-        .iter()
-        .map(|row| row.iter().map(|x| x.abs()).sum::<f64>())
-        .fold(0.0_f64, |a, b| a.max(b))
-        * 1.1;
-
-    if alpha <= 0.0 {
-        return 0.0;
-    }
-
-    // Construct M = alpha*I - L
-    // The eigenvalues of M are alpha - lambda_i(L).
-    // The largest eigenvalue of M corresponds to the smallest eigenvalue of L (which is 0).
-    // The second largest eigenvalue of M corresponds to lambda_2 of L.
-    // We need to deflate out the first eigenvector (all-ones) and do power iteration.
-
-    // Normalized all-ones vector
-    let inv_sqrt_n = 1.0 / (n as f64).sqrt();
-
-    // Initialize random-ish vector orthogonal to all-ones
-    let mut v: Vec<f64> = (0..n).map(|i| (i as f64 + 0.5).sin()).collect();
-
-    // Project out the all-ones component
-    project_out_ones(&mut v, inv_sqrt_n, n);
-    normalize(&mut v);
-
-    let max_iter = 1000;
-    let tol = 1e-10;
-
-    for _ in 0..max_iter {
-        // w = M * v = (alpha*I - L) * v
-        let mut w = vec![0.0; n];
-        for i in 0..n {
-            w[i] = alpha * v[i];
-            for j in 0..n {
-                w[i] -= laplacian[i][j] * v[j];
-            }
-        }
-
-        // Project out the all-ones component
-        project_out_ones(&mut w, inv_sqrt_n, n);
-
-        let norm_w = norm(&w);
-        if norm_w < 1e-15 {
-            // The vector collapsed, Fiedler value is likely alpha
-            return alpha;
-        }
-
-        // Rayleigh quotient: eigenvalue of M = v^T * w / v^T * v
-        let eigenvalue_m: f64 = v.iter().zip(w.iter()).map(|(a, b)| a * b).sum::<f64>();
-
-        // Normalize
-        for x in &mut w {
-            *x /= norm_w;
-        }
-
-        // Check convergence
-        let diff: f64 = v
-            .iter()
-            .zip(w.iter())
-            .map(|(a, b)| (a - b).powi(2))
-            .sum::<f64>()
-            .sqrt();
-
-        v = w;
-
-        if diff < tol {
-            // Fiedler value = alpha - eigenvalue_of_M
-            let fiedler = alpha - eigenvalue_m;
-            return fiedler.max(0.0);
-        }
-    }
-
-    // Final estimate
-    let mut w = vec![0.0; n];
-    for i in 0..n {
-        w[i] = alpha * v[i];
-        for j in 0..n {
-            w[i] -= laplacian[i][j] * v[j];
-        }
-    }
-    project_out_ones(&mut w, inv_sqrt_n, n);
-
-    let eigenvalue_m: f64 = v.iter().zip(w.iter()).map(|(a, b)| a * b).sum::<f64>();
-    (alpha - eigenvalue_m).max(0.0)
-}
-
-/// Project vector v orthogonal to the all-ones vector.
-fn project_out_ones(v: &mut [f64], inv_sqrt_n: f64, _n: usize) {
-    let dot: f64 = v.iter().sum::<f64>() * inv_sqrt_n;
-    for x in v.iter_mut() {
-        *x -= dot * inv_sqrt_n;
-    }
-}
-
-/// L2 norm of a vector.
-fn norm(v: &[f64]) -> f64 {
-    v.iter().map(|x| x * x).sum::<f64>().sqrt()
-}
-
-/// Normalize a vector in-place.
-fn normalize(v: &mut [f64]) {
-    let n = norm(v);
-    if n > 0.0 {
-        for x in v.iter_mut() {
-            *x /= n;
-        }
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(s: usize, t: usize, w: f64) -> BrainEdge {
-        BrainEdge {
-            source: s,
-            target: t,
-            weight: w,
-            metric: ConnectivityMetric::PhaseLockingValue,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    fn complete_graph(n: usize) -> BrainGraph {
-        let mut edges = Vec::new();
-        for i in 0..n {
-            for j in (i + 1)..n {
-                edges.push(make_edge(i, j, 1.0));
-            }
-        }
-        BrainGraph {
-            num_nodes: n,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(n),
-        }
-    }
-
-    #[test]
-    fn laplacian_row_sums_zero() {
-        let g = complete_graph(5);
-        let l = graph_laplacian(&g);
-        for row in &l {
-            let sum: f64 = row.iter().sum();
-            assert!(sum.abs() < 1e-10, "Row sum should be 0, got {}", sum);
-        }
-    }
-
-    #[test]
-    fn laplacian_diagonal_is_degree() {
-        let g = complete_graph(5);
-        let l = graph_laplacian(&g);
-        // Each node in K5 has degree 4
-        for i in 0..5 {
-            assert!((l[i][i] - 4.0).abs() < 1e-10);
-        }
-    }
-
-    #[test]
-    fn normalized_laplacian_diagonal_connected() {
-        let g = complete_graph(5);
-        let ln = normalized_laplacian(&g);
-        // For connected nodes, diagonal should be 1.0
-        for i in 0..5 {
-            assert!((ln[i][i] - 1.0).abs() < 1e-10);
-        }
-    }
-
-    #[test]
-    fn fiedler_value_connected_graph() {
-        let g = complete_graph(6);
-        let f = fiedler_value(&g);
-        // For K_n, all non-zero eigenvalues of L are n. So fiedler = n = 6.
-        assert!(f > 0.0, "Connected graph should have fiedler > 0, got {}", f);
-        assert!((f - 6.0).abs() < 0.5, "K6 fiedler should be ~6.0, got {}", f);
-    }
-
-    #[test]
-    fn fiedler_value_disconnected_graph() {
-        // Two isolated components: nodes 0,1 connected; nodes 2,3 connected; no bridge.
-        let g = BrainGraph {
-            num_nodes: 4,
-            edges: vec![make_edge(0, 1, 1.0), make_edge(2, 3, 1.0)],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-        let f = fiedler_value(&g);
-        assert!(f < 1e-6, "Disconnected graph should have fiedler ~0, got {}", f);
-    }
-
-    #[test]
-    fn spectral_gap_equals_fiedler() {
-        let g = complete_graph(5);
-        assert_eq!(spectral_gap(&g), fiedler_value(&g));
-    }
-}
@@ -1,28 +0,0 @@
-[package]
-name = "ruv-neural-memory"
-description = "rUv Neural — Persistent neural state memory with vector search and longitudinal tracking"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-wasm = []
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-bincode = { workspace = true }
-tracing = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
-rand = { workspace = true }
-criterion = { workspace = true }
-
-[[bench]]
-name = "benchmarks"
-harness = false
@@ -1,96 +0,0 @@
-# ruv-neural-memory
-
-Persistent neural state memory with vector search and longitudinal tracking.
-
-## Overview
-
-`ruv-neural-memory` provides in-memory and persistent storage for neural
-embeddings, supporting brute-force and HNSW-based approximate nearest neighbor
-search. It includes session-based memory management for organizing recordings
-by subject and session, longitudinal drift detection for tracking embedding
-distribution changes over time, and RVF/bincode persistence for durable storage.
-
-## Features
-
- **Embedding store** (`store`): `NeuralMemoryStore` for inserting, querying,
-  and managing collections of `NeuralEmbedding` values with brute-force
-  nearest neighbor search
- **HNSW index** (`hnsw`): `HnswIndex` for approximate nearest neighbor search
-  with configurable M (max connections), ef_construction, and ef_search parameters;
-  provides 150x-12,500x speedup over brute-force for large collections
- **Session management** (`session`): `SessionMemory` and `SessionMetadata` for
-  organizing embeddings by recording session, subject ID, and timestamp ranges
- **Longitudinal tracking** (`longitudinal`): `LongitudinalTracker` for detecting
-  embedding distribution drift over time with `TrendDirection` classification
-  (stable, increasing, decreasing)
- **Persistence** (`persistence`): `save_store` / `load_store` for bincode
-  serialization, `save_rvf` / `load_rvf` for RuVector format I/O
-
-## Usage
-
-```rust
-use ruv_neural_memory::{
-    NeuralMemoryStore, HnswIndex, SessionMemory, SessionMetadata,
-    LongitudinalTracker, save_store, load_store,
-};
-use ruv_neural_core::{NeuralEmbedding, EmbeddingMetadata, Atlas};
-
-// Create a memory store and insert embeddings
-let mut store = NeuralMemoryStore::new();
-let meta = EmbeddingMetadata {
-    subject_id: Some("sub-01".into()),
-    session_id: Some("ses-01".into()),
-    cognitive_state: None,
-    source_atlas: Atlas::Schaefer100,
-    embedding_method: "spectral".into(),
-};
-let emb = NeuralEmbedding::new(vec![0.1, 0.5, -0.3], 0.0, meta).unwrap();
-store.insert(emb);
-
-// Query nearest neighbors (brute-force)
-let query = vec![0.1, 0.4, -0.2];
-let neighbors = store.query_nearest(&query, 5);
-
-// Build HNSW index for fast approximate search
-let mut hnsw = HnswIndex::new(16, 200);
-// ... insert vectors, then search
-
-// Session-based memory management
-let session = SessionMemory::new(SessionMetadata {
-    subject_id: "sub-01".into(),
-    session_id: "ses-01".into(),
-    ..Default::default()
-});
-
-// Persistence
-save_store(&store, "memory.bin").unwrap();
-let loaded = load_store("memory.bin").unwrap();
-```
-
-## API Reference
-
-| Module          | Key Types / Functions                                       |
-|-----------------|-------------------------------------------------------------|
-| `store`         | `NeuralMemoryStore`                                         |
-| `hnsw`          | `HnswIndex`                                                 |
-| `session`       | `SessionMemory`, `SessionMetadata`                          |
-| `longitudinal`  | `LongitudinalTracker`, `TrendDirection`                     |
-| `persistence`   | `save_store`, `load_store`, `save_rvf`, `load_rvf`          |
-
-## Feature Flags
-
-| Feature | Default | Description                  |
-|---------|---------|------------------------------|
-| `std`   | Yes     | Standard library support     |
-| `wasm`  | No      | WASM-compatible storage      |
-
-## Integration
-
-Depends on `ruv-neural-core` for `NeuralEmbedding` types. Receives embeddings
-from `ruv-neural-embed`. Stored embeddings are queried by `ruv-neural-decoder`
-for KNN-based cognitive state classification. Uses `bincode` for efficient
-binary serialization.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,128 +0,0 @@
-//! Criterion benchmarks for ruv-neural-memory.
-//!
-//! Benchmarks the performance-critical vector search operations:
-//! - HNSW insert (building the index)
-//! - HNSW search (approximate nearest neighbor queries)
-//! - Brute-force nearest neighbor (baseline comparison)
-
-use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
-use rand::Rng;
-
-use ruv_neural_memory::HnswIndex;
-
-const DIM: usize = 64;
-
-/// Generate a set of random embeddings.
-fn generate_embeddings(count: usize, dim: usize) -> Vec<Vec<f64>> {
-    let mut rng = rand::thread_rng();
-    (0..count)
-        .map(|_| (0..dim).map(|_| rng.gen_range(-1.0..1.0)).collect())
-        .collect()
-}
-
-/// Build an HNSW index from a set of embeddings.
-fn build_hnsw(embeddings: &[Vec<f64>]) -> HnswIndex {
-    let mut index = HnswIndex::new(16, 200);
-    for emb in embeddings {
-        index.insert(emb);
-    }
-    index
-}
-
-/// Euclidean distance between two vectors.
-fn euclidean_distance(a: &[f64], b: &[f64]) -> f64 {
-    a.iter()
-        .zip(b.iter())
-        .map(|(x, y)| (x - y) * (x - y))
-        .sum::<f64>()
-        .sqrt()
-}
-
-/// Brute-force k-nearest-neighbor search.
-fn brute_force_knn(
-    embeddings: &[Vec<f64>],
-    query: &[f64],
-    k: usize,
-) -> Vec<(usize, f64)> {
-    let mut distances: Vec<(usize, f64)> = embeddings
-        .iter()
-        .enumerate()
-        .map(|(i, v)| (i, euclidean_distance(query, v)))
-        .collect();
-    distances.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap());
-    distances.truncate(k);
-    distances
-}
-
-fn bench_hnsw_insert(c: &mut Criterion) {
-    let mut group = c.benchmark_group("hnsw_insert");
-    group.sample_size(10);
-
-    for &count in &[1_000, 10_000] {
-        let embeddings = generate_embeddings(count, DIM);
-        group.bench_with_input(
-            BenchmarkId::new("embeddings", count),
-            &embeddings,
-            |b, embeddings| {
-                b.iter(|| {
-                    let mut index = HnswIndex::new(16, 200);
-                    for emb in embeddings.iter() {
-                        index.insert(black_box(emb));
-                    }
-                    index
-                })
-            },
-        );
-    }
-
-    group.finish();
-}
-
-fn bench_hnsw_search(c: &mut Criterion) {
-    let mut group = c.benchmark_group("hnsw_search");
-
-    for &count in &[1_000, 10_000] {
-        let embeddings = generate_embeddings(count, DIM);
-        let index = build_hnsw(&embeddings);
-        let mut rng = rand::thread_rng();
-        let query: Vec<f64> = (0..DIM).map(|_| rng.gen_range(-1.0..1.0)).collect();
-
-        group.bench_with_input(
-            BenchmarkId::new("k10_embeddings", count),
-            &(index, query),
-            |b, (index, query)| {
-                b.iter(|| index.search(black_box(query), black_box(10), black_box(50)))
-            },
-        );
-    }
-
-    group.finish();
-}
-
-fn bench_brute_force_nn(c: &mut Criterion) {
-    let mut group = c.benchmark_group("brute_force_nn");
-
-    for &count in &[1_000, 10_000] {
-        let embeddings = generate_embeddings(count, DIM);
-        let mut rng = rand::thread_rng();
-        let query: Vec<f64> = (0..DIM).map(|_| rng.gen_range(-1.0..1.0)).collect();
-
-        group.bench_with_input(
-            BenchmarkId::new("k10_embeddings", count),
-            &(embeddings, query),
-            |b, (embeddings, query)| {
-                b.iter(|| brute_force_knn(black_box(embeddings), black_box(query), black_box(10)))
-            },
-        );
-    }
-
-    group.finish();
-}
-
-criterion_group!(
-    benches,
-    bench_hnsw_insert,
-    bench_hnsw_search,
-    bench_brute_force_nn,
-);
-criterion_main!(benches);
@@ -1,432 +0,0 @@
-//! Simplified HNSW (Hierarchical Navigable Small World) index for approximate
-//! nearest neighbor search on embedding vectors.
-
-use std::collections::{BinaryHeap, HashSet};
-use std::cmp::Ordering;
-
-/// A scored neighbor for use in the priority queue.
-#[derive(Debug, Clone)]
-struct ScoredNode {
-    id: usize,
-    distance: f64,
-}
-
-impl PartialEq for ScoredNode {
-    fn eq(&self, other: &Self) -> bool {
-        self.distance == other.distance
-    }
-}
-
-impl Eq for ScoredNode {}
-
-impl PartialOrd for ScoredNode {
-    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
-        Some(self.cmp(other))
-    }
-}
-
-impl Ord for ScoredNode {
-    fn cmp(&self, other: &Self) -> Ordering {
-        // Reverse ordering for min-heap behavior
-        other
-            .distance
-            .partial_cmp(&self.distance)
-            .unwrap_or(Ordering::Equal)
-    }
-}
-
-/// Max-heap scored node (furthest first).
-#[derive(Debug, Clone)]
-struct FurthestNode {
-    id: usize,
-    distance: f64,
-}
-
-impl PartialEq for FurthestNode {
-    fn eq(&self, other: &Self) -> bool {
-        self.distance == other.distance
-    }
-}
-
-impl Eq for FurthestNode {}
-
-impl PartialOrd for FurthestNode {
-    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
-        Some(self.cmp(other))
-    }
-}
-
-impl Ord for FurthestNode {
-    fn cmp(&self, other: &Self) -> Ordering {
-        self.distance
-            .partial_cmp(&other.distance)
-            .unwrap_or(Ordering::Equal)
-    }
-}
-
-/// Hierarchical Navigable Small World graph for approximate nearest neighbor search.
-///
-/// This is a simplified single-layer HNSW implementation suitable for moderate-scale
-/// embedding stores (up to ~100k vectors).
-pub struct HnswIndex {
-    /// Adjacency list per layer: layers[layer][node] = [(neighbor_id, distance)]
-    layers: Vec<Vec<Vec<(usize, f64)>>>,
-    /// Entry point node for search.
-    entry_point: usize,
-    /// Maximum layer index currently in the graph.
-    max_layer: usize,
-    /// Number of neighbors to consider during construction.
-    ef_construction: usize,
-    /// Maximum number of connections per node per layer.
-    m: usize,
-    /// Stored embedding vectors.
-    embeddings: Vec<Vec<f64>>,
-}
-
-impl HnswIndex {
-    /// Create a new empty HNSW index.
-    ///
-    /// - `m`: maximum connections per node per layer (typical: 16)
-    /// - `ef_construction`: search width during construction (typical: 200)
-    pub fn new(m: usize, ef_construction: usize) -> Self {
-        Self {
-            layers: vec![Vec::new()], // Start with layer 0
-            entry_point: 0,
-            max_layer: 0,
-            ef_construction,
-            m,
-            embeddings: Vec::new(),
-        }
-    }
-
-    /// Insert a vector and return its index.
-    pub fn insert(&mut self, vector: &[f64]) -> usize {
-        let id = self.embeddings.len();
-        self.embeddings.push(vector.to_vec());
-
-        let insert_layer = self.select_layer();
-
-        // Ensure we have enough layers
-        while self.layers.len() <= insert_layer {
-            self.layers.push(Vec::new());
-        }
-
-        // Add empty adjacency lists for this node in all layers up to insert_layer
-        for layer in 0..=insert_layer {
-            while self.layers[layer].len() <= id {
-                self.layers[layer].push(Vec::new());
-            }
-        }
-
-        // Also ensure layer 0 has an entry for this node
-        while self.layers[0].len() <= id {
-            self.layers[0].push(Vec::new());
-        }
-
-        if id == 0 {
-            // First node, just set as entry point
-            self.entry_point = 0;
-            self.max_layer = insert_layer;
-            return id;
-        }
-
-        // Greedy search from top layer down to insert_layer+1
-        let mut current_entry = self.entry_point;
-        for layer in (insert_layer + 1..=self.max_layer).rev() {
-            if layer < self.layers.len() {
-                let neighbors = self.search_layer(vector, current_entry, 1, layer);
-                if let Some((nearest, _)) = neighbors.first() {
-                    current_entry = *nearest;
-                }
-            }
-        }
-
-        // Insert into layers from insert_layer down to 0
-        for layer in (0..=insert_layer.min(self.max_layer)).rev() {
-            let neighbors =
-                self.search_layer(vector, current_entry, self.ef_construction, layer);
-
-            // Select up to m neighbors
-            let selected: Vec<(usize, f64)> =
-                neighbors.into_iter().take(self.m).collect();
-
-            // Ensure adjacency list exists for this node at this layer
-            while self.layers[layer].len() <= id {
-                self.layers[layer].push(Vec::new());
-            }
-
-            // Add bidirectional connections
-            for &(neighbor_id, dist) in &selected {
-                self.layers[layer][id].push((neighbor_id, dist));
-
-                while self.layers[layer].len() <= neighbor_id {
-                    self.layers[layer].push(Vec::new());
-                }
-                self.layers[layer][neighbor_id].push((id, dist));
-
-                // Prune if over capacity
-                if self.layers[layer][neighbor_id].len() > self.m * 2 {
-                    self.layers[layer][neighbor_id]
-                        .sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(Ordering::Equal));
-                    self.layers[layer][neighbor_id].truncate(self.m * 2);
-                }
-            }
-
-            if let Some((nearest, _)) = selected.first() {
-                current_entry = *nearest;
-            }
-        }
-
-        if insert_layer > self.max_layer {
-            self.max_layer = insert_layer;
-            self.entry_point = id;
-        }
-
-        id
-    }
-
-    /// Search for the k nearest neighbors of `query`.
-    ///
-    /// - `k`: number of nearest neighbors to return
-    /// - `ef`: search width (larger = more accurate, slower; typical: 50-200)
-    ///
-    /// Returns (index, distance) pairs sorted by ascending distance.
-    pub fn search(&self, query: &[f64], k: usize, ef: usize) -> Vec<(usize, f64)> {
-        if self.embeddings.is_empty() {
-            return Vec::new();
-        }
-
-        // Bounds-check the entry point
-        if self.entry_point >= self.embeddings.len() {
-            return Vec::new();
-        }
-
-        let mut current_entry = self.entry_point;
-
-        // Greedy search from top layer down to layer 1
-        for layer in (1..=self.max_layer).rev() {
-            if layer < self.layers.len() {
-                let neighbors = self.search_layer(query, current_entry, 1, layer);
-                if let Some((nearest, _)) = neighbors.first() {
-                    current_entry = *nearest;
-                }
-            }
-        }
-
-        // Search layer 0 with ef candidates
-        let mut results = self.search_layer(query, current_entry, ef.max(k), 0);
-        results.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(Ordering::Equal));
-        results.truncate(k);
-        results
-    }
-
-    /// Number of vectors in the index.
-    pub fn len(&self) -> usize {
-        self.embeddings.len()
-    }
-
-    /// Returns true if the index has no vectors.
-    pub fn is_empty(&self) -> bool {
-        self.embeddings.is_empty()
-    }
-
-    /// Euclidean distance between two vectors.
-    fn distance(a: &[f64], b: &[f64]) -> f64 {
-        a.iter()
-            .zip(b.iter())
-            .map(|(x, y)| (x - y) * (x - y))
-            .sum::<f64>()
-            .sqrt()
-    }
-
-    /// Select a random layer for insertion using an exponential distribution.
-    fn select_layer(&self) -> usize {
-        // Deterministic level assignment based on node count for reproducibility.
-        // Uses a simple hash-like scheme: most nodes go to layer 0.
-        let n = self.embeddings.len();
-        let ml = 1.0 / (self.m as f64).ln();
-        // Use a simple deterministic pseudo-random based on n
-        let hash = ((n.wrapping_mul(2654435761)) >> 16) as f64 / 65536.0;
-        let level = (-hash.ln() * ml).floor() as usize;
-        level.min(4) // Cap at 4 layers
-    }
-
-    /// Search a single layer starting from `entry`, returning `ef` nearest candidates.
-    fn search_layer(
-        &self,
-        query: &[f64],
-        entry: usize,
-        ef: usize,
-        layer: usize,
-    ) -> Vec<(usize, f64)> {
-        if layer >= self.layers.len() {
-            return Vec::new();
-        }
-
-        // Bounds-check entry against embeddings
-        if entry >= self.embeddings.len() {
-            return Vec::new();
-        }
-
-        let mut visited = HashSet::new();
-        let entry_dist = Self::distance(query, &self.embeddings[entry]);
-
-        // Candidates: min-heap (closest first)
-        let mut candidates = BinaryHeap::new();
-        candidates.push(ScoredNode {
-            id: entry,
-            distance: entry_dist,
-        });
-
-        // Results: max-heap (furthest first, for pruning)
-        let mut results = BinaryHeap::new();
-        results.push(FurthestNode {
-            id: entry,
-            distance: entry_dist,
-        });
-
-        visited.insert(entry);
-
-        while let Some(ScoredNode { id: current, distance: current_dist }) = candidates.pop() {
-            // If current candidate is further than the worst result and we have enough, stop
-            if let Some(worst) = results.peek() {
-                if current_dist > worst.distance && results.len() >= ef {
-                    break;
-                }
-            }
-
-            // Explore neighbors
-            if current < self.layers[layer].len() {
-                for &(neighbor, _) in &self.layers[layer][current] {
-                    if neighbor < self.embeddings.len() && visited.insert(neighbor) {
-                        let dist = Self::distance(query, &self.embeddings[neighbor]);
-
-                        let should_add = results.len() < ef
-                            || results
-                                .peek()
-                                .map(|w| dist < w.distance)
-                                .unwrap_or(true);
-
-                        if should_add {
-                            candidates.push(ScoredNode {
-                                id: neighbor,
-                                distance: dist,
-                            });
-                            results.push(FurthestNode {
-                                id: neighbor,
-                                distance: dist,
-                            });
-
-                            if results.len() > ef {
-                                results.pop();
-                            }
-                        }
-                    }
-                }
-            }
-        }
-
-        // Collect results sorted by distance
-        let mut result_vec: Vec<(usize, f64)> =
-            results.into_iter().map(|n| (n.id, n.distance)).collect();
-        result_vec.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(Ordering::Equal));
-        result_vec
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn insert_and_search_basic() {
-        let mut index = HnswIndex::new(4, 20);
-        index.insert(&[0.0, 0.0]);
-        index.insert(&[1.0, 0.0]);
-        index.insert(&[0.0, 1.0]);
-        index.insert(&[10.0, 10.0]);
-
-        let results = index.search(&[0.1, 0.1], 2, 10);
-        assert_eq!(results.len(), 2);
-        // Closest should be [0,0]
-        assert_eq!(results[0].0, 0);
-    }
-
-    #[test]
-    fn empty_index_returns_empty() {
-        let index = HnswIndex::new(4, 20);
-        let results = index.search(&[1.0, 2.0], 5, 10);
-        assert!(results.is_empty());
-    }
-
-    #[test]
-    fn single_element() {
-        let mut index = HnswIndex::new(4, 20);
-        index.insert(&[5.0, 5.0]);
-
-        let results = index.search(&[0.0, 0.0], 1, 10);
-        assert_eq!(results.len(), 1);
-        assert_eq!(results[0].0, 0);
-    }
-
-    #[test]
-    fn hnsw_recall_vs_brute_force() {
-        use rand::Rng;
-
-        let mut rng = rand::thread_rng();
-        let dim = 8;
-        let n = 200;
-        let k = 10;
-
-        let mut index = HnswIndex::new(16, 100);
-        let mut vectors: Vec<Vec<f64>> = Vec::new();
-
-        for _ in 0..n {
-            let v: Vec<f64> = (0..dim).map(|_| rng.gen_range(-1.0..1.0)).collect();
-            index.insert(&v);
-            vectors.push(v);
-        }
-
-        // Run multiple queries and check average recall
-        let num_queries = 20;
-        let mut total_recall = 0.0;
-
-        for _ in 0..num_queries {
-            let query: Vec<f64> = (0..dim).map(|_| rng.gen_range(-1.0..1.0)).collect();
-
-            // Brute force ground truth
-            let mut bf_distances: Vec<(usize, f64)> = vectors
-                .iter()
-                .enumerate()
-                .map(|(i, v)| (i, HnswIndex::distance(&query, v)))
-                .collect();
-            bf_distances
-                .sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal));
-            let bf_top_k: Vec<usize> = bf_distances.iter().take(k).map(|(i, _)| *i).collect();
-
-            // HNSW search
-            let hnsw_results = index.search(&query, k, 50);
-            let hnsw_top_k: Vec<usize> = hnsw_results.iter().map(|(i, _)| *i).collect();
-
-            // Compute recall
-            let hits = hnsw_top_k
-                .iter()
-                .filter(|id| bf_top_k.contains(id))
-                .count();
-            total_recall += hits as f64 / k as f64;
-        }
-
-        let avg_recall = total_recall / num_queries as f64;
-        assert!(
-            avg_recall > 0.9,
-            "HNSW recall {} should be > 0.9",
-            avg_recall
-        );
-    }
-
-    #[test]
-    fn distance_is_euclidean() {
-        let d = HnswIndex::distance(&[0.0, 0.0], &[3.0, 4.0]);
-        assert!((d - 5.0).abs() < 1e-10);
-    }
-}
@@ -1,18 +0,0 @@
-//! rUv Neural Memory — Persistent neural state memory with vector search
-//! and longitudinal tracking.
-//!
-//! This crate provides in-memory and persistent storage for neural embeddings,
-//! supporting brute-force and HNSW-based nearest neighbor search, session-based
-//! memory management, and longitudinal drift detection.
-
-pub mod hnsw;
-pub mod longitudinal;
-pub mod persistence;
-pub mod session;
-pub mod store;
-
-pub use hnsw::HnswIndex;
-pub use longitudinal::{LongitudinalTracker, TrendDirection};
-pub use persistence::{load_rvf, load_store, save_rvf, save_store};
-pub use session::{SessionMemory, SessionMetadata};
-pub use store::NeuralMemoryStore;
@@ -1,268 +0,0 @@
-//! Longitudinal tracking and drift detection for neural topology changes
-//! over extended observation periods.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-
-/// Direction of observed trend in neural embeddings.
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
-pub enum TrendDirection {
-    /// No significant change from baseline.
-    Stable,
-    /// Embedding distances are decreasing (closer to baseline).
-    Improving,
-    /// Embedding distances are increasing (drifting from baseline).
-    Degrading,
-    /// Embeddings alternate between improving and degrading.
-    Oscillating,
-}
-
-/// Tracks neural topology changes over extended periods, detecting drift
-/// from an established baseline.
-pub struct LongitudinalTracker {
-    /// Baseline embeddings representing the reference state.
-    baseline_embeddings: Vec<NeuralEmbedding>,
-    /// Current trajectory of observations.
-    current_trajectory: Vec<NeuralEmbedding>,
-    /// Threshold above which drift is considered significant.
-    drift_threshold: f64,
-}
-
-impl LongitudinalTracker {
-    /// Create a new tracker with the given drift threshold.
-    pub fn new(drift_threshold: f64) -> Self {
-        Self {
-            baseline_embeddings: Vec::new(),
-            current_trajectory: Vec::new(),
-            drift_threshold,
-        }
-    }
-
-    /// Set the baseline embeddings (the reference state).
-    pub fn set_baseline(&mut self, embeddings: Vec<NeuralEmbedding>) {
-        self.baseline_embeddings = embeddings;
-    }
-
-    /// Add a new observation to the current trajectory.
-    pub fn add_observation(&mut self, embedding: NeuralEmbedding) {
-        self.current_trajectory.push(embedding);
-    }
-
-    /// Number of observations in the current trajectory.
-    pub fn num_observations(&self) -> usize {
-        self.current_trajectory.len()
-    }
-
-    /// Compute the mean drift from baseline.
-    ///
-    /// Returns the average Euclidean distance from each trajectory embedding
-    /// to the nearest baseline embedding. Returns 0.0 if either baseline or
-    /// trajectory is empty.
-    pub fn compute_drift(&self) -> f64 {
-        if self.baseline_embeddings.is_empty() || self.current_trajectory.is_empty() {
-            return 0.0;
-        }
-
-        let total_drift: f64 = self
-            .current_trajectory
-            .iter()
-            .map(|obs| self.min_distance_to_baseline(obs))
-            .sum();
-
-        total_drift / self.current_trajectory.len() as f64
-    }
-
-    /// Detect the overall trend direction from the trajectory.
-    ///
-    /// Compares drift of the first half vs second half of the trajectory.
-    pub fn detect_trend(&self) -> TrendDirection {
-        if self.current_trajectory.len() < 4 || self.baseline_embeddings.is_empty() {
-            return TrendDirection::Stable;
-        }
-
-        let mid = self.current_trajectory.len() / 2;
-        let first_half: Vec<f64> = self.current_trajectory[..mid]
-            .iter()
-            .map(|obs| self.min_distance_to_baseline(obs))
-            .collect();
-        let second_half: Vec<f64> = self.current_trajectory[mid..]
-            .iter()
-            .map(|obs| self.min_distance_to_baseline(obs))
-            .collect();
-
-        let first_mean = mean(&first_half);
-        let second_mean = mean(&second_half);
-
-        let diff = second_mean - first_mean;
-
-        if diff.abs() < self.drift_threshold * 0.1 {
-            // Check for oscillation by looking at alternating signs
-            let diffs: Vec<f64> = self
-                .current_trajectory
-                .windows(2)
-                .map(|w| {
-                    self.min_distance_to_baseline(&w[1])
-                        - self.min_distance_to_baseline(&w[0])
-                })
-                .collect();
-
-            let sign_changes = diffs
-                .windows(2)
-                .filter(|w| w[0].signum() != w[1].signum())
-                .count();
-
-            if sign_changes > diffs.len() / 2 {
-                return TrendDirection::Oscillating;
-            }
-
-            TrendDirection::Stable
-        } else if diff > 0.0 {
-            TrendDirection::Degrading
-        } else {
-            TrendDirection::Improving
-        }
-    }
-
-    /// Compute an anomaly score for a single embedding.
-    ///
-    /// Returns a score in [0, 1] where 1 means highly anomalous relative
-    /// to the baseline. Based on how far the embedding is from the baseline
-    /// relative to the drift threshold.
-    pub fn anomaly_score(&self, embedding: &NeuralEmbedding) -> f64 {
-        if self.baseline_embeddings.is_empty() {
-            return 0.0;
-        }
-
-        let dist = self.min_distance_to_baseline(embedding);
-        // Sigmoid-like mapping: score = 1 - exp(-dist / threshold)
-        1.0 - (-dist / self.drift_threshold).exp()
-    }
-
-    /// Minimum Euclidean distance from an embedding to any baseline embedding.
-    fn min_distance_to_baseline(&self, embedding: &NeuralEmbedding) -> f64 {
-        self.baseline_embeddings
-            .iter()
-            .filter_map(|base| base.euclidean_distance(embedding).ok())
-            .fold(f64::MAX, f64::min)
-    }
-}
-
-/// Compute the arithmetic mean of a slice.
-fn mean(values: &[f64]) -> f64 {
-    if values.is_empty() {
-        return 0.0;
-    }
-    values.iter().sum::<f64>() / values.len() as f64
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-    use ruv_neural_core::topology::CognitiveState;
-
-    fn make_embedding(vector: Vec<f64>, timestamp: f64) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            timestamp,
-            EmbeddingMetadata {
-                subject_id: Some("subj1".to_string()),
-                session_id: None,
-                cognitive_state: Some(CognitiveState::Rest),
-                source_atlas: Atlas::Schaefer100,
-                embedding_method: "test".to_string(),
-            },
-        )
-        .unwrap()
-    }
-
-    #[test]
-    fn empty_tracker_returns_zero_drift() {
-        let tracker = LongitudinalTracker::new(1.0);
-        assert_eq!(tracker.compute_drift(), 0.0);
-    }
-
-    #[test]
-    fn no_drift_when_same_as_baseline() {
-        let mut tracker = LongitudinalTracker::new(1.0);
-        tracker.set_baseline(vec![make_embedding(vec![0.0, 0.0], 0.0)]);
-        tracker.add_observation(make_embedding(vec![0.0, 0.0], 1.0));
-
-        assert!(tracker.compute_drift() < 1e-10);
-    }
-
-    #[test]
-    fn detects_known_drift() {
-        let mut tracker = LongitudinalTracker::new(1.0);
-        tracker.set_baseline(vec![make_embedding(vec![0.0, 0.0, 0.0], 0.0)]);
-
-        // Add observations that progressively drift
-        for i in 1..=10 {
-            let offset = i as f64;
-            tracker.add_observation(make_embedding(vec![offset, 0.0, 0.0], i as f64));
-        }
-
-        let drift = tracker.compute_drift();
-        assert!(drift > 1.0, "Expected significant drift, got {}", drift);
-    }
-
-    #[test]
-    fn degrading_trend_detected() {
-        let mut tracker = LongitudinalTracker::new(1.0);
-        tracker.set_baseline(vec![make_embedding(vec![0.0, 0.0], 0.0)]);
-
-        // First half: close to baseline
-        for i in 1..=5 {
-            tracker.add_observation(make_embedding(vec![0.1 * i as f64, 0.0], i as f64));
-        }
-        // Second half: far from baseline
-        for i in 6..=10 {
-            tracker.add_observation(make_embedding(vec![2.0 * i as f64, 0.0], i as f64));
-        }
-
-        assert_eq!(tracker.detect_trend(), TrendDirection::Degrading);
-    }
-
-    #[test]
-    fn improving_trend_detected() {
-        let mut tracker = LongitudinalTracker::new(1.0);
-        tracker.set_baseline(vec![make_embedding(vec![0.0, 0.0], 0.0)]);
-
-        // First half: far from baseline
-        for i in 1..=5 {
-            tracker.add_observation(make_embedding(
-                vec![10.0 - i as f64 * 1.5, 0.0],
-                i as f64,
-            ));
-        }
-        // Second half: close to baseline
-        for i in 6..=10 {
-            tracker.add_observation(make_embedding(vec![0.1, 0.0], i as f64));
-        }
-
-        assert_eq!(tracker.detect_trend(), TrendDirection::Improving);
-    }
-
-    #[test]
-    fn anomaly_score_increases_with_distance() {
-        let mut tracker = LongitudinalTracker::new(2.0);
-        tracker.set_baseline(vec![make_embedding(vec![0.0, 0.0], 0.0)]);
-
-        let near = make_embedding(vec![0.1, 0.0], 1.0);
-        let far = make_embedding(vec![10.0, 10.0], 2.0);
-
-        let score_near = tracker.anomaly_score(&near);
-        let score_far = tracker.anomaly_score(&far);
-
-        assert!(score_near < score_far);
-        assert!(score_near >= 0.0 && score_near <= 1.0);
-        assert!(score_far >= 0.0 && score_far <= 1.0);
-    }
-
-    #[test]
-    fn anomaly_score_zero_without_baseline() {
-        let tracker = LongitudinalTracker::new(1.0);
-        let emb = make_embedding(vec![5.0, 5.0], 1.0);
-        assert_eq!(tracker.anomaly_score(&emb), 0.0);
-    }
-}
@@ -1,187 +0,0 @@
-//! File-based persistence for neural memory stores.
-//!
-//! Supports two formats:
-//! - **Bincode**: Fast binary serialization for local storage.
-//! - **RVF**: RuVector File format for interoperability with the RuVector ecosystem.
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::rvf::{RvfDataType, RvfFile, RvfHeader};
-
-use serde::{Deserialize, Serialize};
-
-use crate::store::NeuralMemoryStore;
-
-/// Serializable representation of the store for bincode persistence.
-#[derive(Serialize, Deserialize)]
-struct StoreSnapshot {
-    embeddings: Vec<NeuralEmbedding>,
-    capacity: usize,
-}
-
-/// Save a memory store to disk using bincode serialization.
-pub fn save_store(store: &NeuralMemoryStore, path: &str) -> Result<()> {
-    let snapshot = StoreSnapshot {
-        embeddings: store.embeddings_iter().cloned().collect(),
-        capacity: store.capacity(),
-    };
-
-    let bytes = bincode::serialize(&snapshot)
-        .map_err(|e| RuvNeuralError::Serialization(format!("bincode encode: {}", e)))?;
-
-    std::fs::write(path, bytes)
-        .map_err(|e| RuvNeuralError::Serialization(format!("write file: {}", e)))?;
-
-    Ok(())
-}
-
-/// Load a memory store from a bincode file on disk.
-pub fn load_store(path: &str) -> Result<NeuralMemoryStore> {
-    let bytes = std::fs::read(path)
-        .map_err(|e| RuvNeuralError::Serialization(format!("read file: {}", e)))?;
-
-    let snapshot: StoreSnapshot = bincode::deserialize(&bytes)
-        .map_err(|e| RuvNeuralError::Serialization(format!("bincode decode: {}", e)))?;
-
-    let mut store = NeuralMemoryStore::new(snapshot.capacity);
-    for emb in snapshot.embeddings {
-        store.store(emb)?;
-    }
-
-    Ok(store)
-}
-
-/// Save a memory store in RVF (RuVector File) format.
-pub fn save_rvf(store: &NeuralMemoryStore, path: &str) -> Result<()> {
-    let embeddings: Vec<NeuralEmbedding> = store.embeddings_iter().cloned().collect();
-    let embedding_dim = embeddings.first().map(|e| e.dimension as u32).unwrap_or(0);
-
-    let mut rvf = RvfFile::new(RvfDataType::NeuralEmbedding);
-    rvf.header = RvfHeader::new(
-        RvfDataType::NeuralEmbedding,
-        embeddings.len() as u64,
-        embedding_dim,
-    );
-
-    // Store metadata as JSON
-    let metadata = serde_json::json!({
-        "format": "ruv-neural-memory",
-        "version": "0.1.0",
-        "num_embeddings": embeddings.len(),
-        "embedding_dim": embedding_dim,
-        "capacity": store.capacity(),
-    });
-    rvf.metadata = metadata;
-
-    // Serialize embeddings as the binary payload
-    let data = bincode::serialize(&embeddings)
-        .map_err(|e| RuvNeuralError::Serialization(format!("bincode encode: {}", e)))?;
-    rvf.data = data;
-
-    let mut file = std::fs::File::create(path)
-        .map_err(|e| RuvNeuralError::Serialization(format!("create file: {}", e)))?;
-
-    rvf.write_to(&mut file)?;
-    Ok(())
-}
-
-/// Load a memory store from an RVF file.
-pub fn load_rvf(path: &str) -> Result<NeuralMemoryStore> {
-    let mut file = std::fs::File::open(path)
-        .map_err(|e| RuvNeuralError::Serialization(format!("open file: {}", e)))?;
-
-    let rvf = RvfFile::read_from(&mut file)?;
-
-    // Verify data type
-    if rvf.header.data_type != RvfDataType::NeuralEmbedding {
-        return Err(RuvNeuralError::Serialization(format!(
-            "Expected NeuralEmbedding data type, got {:?}",
-            rvf.header.data_type
-        )));
-    }
-
-    // Extract capacity from metadata
-    let capacity = rvf
-        .metadata
-        .get("capacity")
-        .and_then(|v| v.as_u64())
-        .unwrap_or(10000) as usize;
-
-    // Deserialize embeddings from binary payload
-    let embeddings: Vec<NeuralEmbedding> = bincode::deserialize(&rvf.data)
-        .map_err(|e| RuvNeuralError::Serialization(format!("bincode decode: {}", e)))?;
-
-    let mut store = NeuralMemoryStore::new(capacity);
-    for emb in embeddings {
-        store.store(emb)?;
-    }
-
-    Ok(store)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-    use ruv_neural_core::topology::CognitiveState;
-
-    fn make_embedding(vector: Vec<f64>, timestamp: f64) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            timestamp,
-            EmbeddingMetadata {
-                subject_id: Some("subj1".to_string()),
-                session_id: None,
-                cognitive_state: Some(CognitiveState::Focused),
-                source_atlas: Atlas::Schaefer100,
-                embedding_method: "spectral".to_string(),
-            },
-        )
-        .unwrap()
-    }
-
-    #[test]
-    fn bincode_round_trip() {
-        let dir = std::env::temp_dir();
-        let path = dir.join("test_memory_store.bin");
-        let path_str = path.to_str().unwrap();
-
-        let mut store = NeuralMemoryStore::new(100);
-        store.store(make_embedding(vec![1.0, 2.0, 3.0], 1.0)).unwrap();
-        store.store(make_embedding(vec![4.0, 5.0, 6.0], 2.0)).unwrap();
-
-        save_store(&store, path_str).unwrap();
-        let loaded = load_store(path_str).unwrap();
-
-        assert_eq!(loaded.len(), 2);
-        assert_eq!(loaded.get(0).unwrap().vector, vec![1.0, 2.0, 3.0]);
-        assert_eq!(loaded.get(1).unwrap().vector, vec![4.0, 5.0, 6.0]);
-
-        // Cleanup
-        let _ = std::fs::remove_file(path_str);
-    }
-
-    #[test]
-    fn rvf_round_trip() {
-        let dir = std::env::temp_dir();
-        let path = dir.join("test_memory_store.rvf");
-        let path_str = path.to_str().unwrap();
-
-        let mut store = NeuralMemoryStore::new(50);
-        store.store(make_embedding(vec![10.0, 20.0], 0.5)).unwrap();
-        store.store(make_embedding(vec![30.0, 40.0], 1.5)).unwrap();
-        store.store(make_embedding(vec![50.0, 60.0], 2.5)).unwrap();
-
-        save_rvf(&store, path_str).unwrap();
-        let loaded = load_rvf(path_str).unwrap();
-
-        assert_eq!(loaded.len(), 3);
-        assert_eq!(loaded.get(0).unwrap().vector, vec![10.0, 20.0]);
-        assert_eq!(loaded.get(2).unwrap().vector, vec![50.0, 60.0]);
-        assert_eq!(loaded.capacity(), 50);
-
-        // Cleanup
-        let _ = std::fs::remove_file(path_str);
-    }
-}
@@ -1,268 +0,0 @@
-//! Session-based memory management for grouping embeddings by recording session.
-
-use std::collections::HashMap;
-
-use serde::{Deserialize, Serialize};
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::topology::CognitiveState;
-
-use crate::store::NeuralMemoryStore;
-
-/// Metadata for a recording session.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct SessionMetadata {
-    /// Unique session identifier.
-    pub session_id: String,
-    /// Subject being recorded.
-    pub subject_id: String,
-    /// Session start time (Unix timestamp).
-    pub start_time: f64,
-    /// Session end time (None if still active).
-    pub end_time: Option<f64>,
-    /// Number of embeddings stored during this session.
-    pub num_embeddings: usize,
-    /// Cognitive states observed during the session.
-    pub cognitive_states_observed: Vec<CognitiveState>,
-}
-
-/// Manages neural memory across recording sessions.
-pub struct SessionMemory {
-    /// Underlying embedding store.
-    store: NeuralMemoryStore,
-    /// Currently active session ID.
-    current_session: Option<String>,
-    /// Metadata for all sessions.
-    session_metadata: HashMap<String, SessionMetadata>,
-    /// Maps session_id to embedding indices.
-    session_indices: HashMap<String, Vec<usize>>,
-    /// Counter for generating session IDs.
-    session_counter: u64,
-}
-
-impl SessionMemory {
-    /// Create a new session memory with the given store capacity.
-    pub fn new(capacity: usize) -> Self {
-        Self {
-            store: NeuralMemoryStore::new(capacity),
-            current_session: None,
-            session_metadata: HashMap::new(),
-            session_indices: HashMap::new(),
-            session_counter: 0,
-        }
-    }
-
-    /// Start a new recording session, returning its unique ID.
-    ///
-    /// If a session is already active, it is automatically ended first.
-    pub fn start_session(&mut self, subject_id: &str) -> String {
-        if self.current_session.is_some() {
-            self.end_session();
-        }
-
-        self.session_counter += 1;
-        let session_id = format!("session-{:04}", self.session_counter);
-
-        let metadata = SessionMetadata {
-            session_id: session_id.clone(),
-            subject_id: subject_id.to_string(),
-            start_time: 0.0, // Will be updated on first embedding
-            end_time: None,
-            num_embeddings: 0,
-            cognitive_states_observed: Vec::new(),
-        };
-
-        self.session_metadata
-            .insert(session_id.clone(), metadata);
-        self.session_indices
-            .insert(session_id.clone(), Vec::new());
-        self.current_session = Some(session_id.clone());
-
-        session_id
-    }
-
-    /// End the current recording session.
-    pub fn end_session(&mut self) {
-        if let Some(ref session_id) = self.current_session.clone() {
-            if let Some(meta) = self.session_metadata.get_mut(session_id) {
-                // Set end time from the last embedding's timestamp
-                if let Some(indices) = self.session_indices.get(session_id) {
-                    if let Some(&last_idx) = indices.last() {
-                        if let Some(emb) = self.store.get(last_idx) {
-                            meta.end_time = Some(emb.timestamp);
-                        }
-                    }
-                }
-            }
-        }
-        self.current_session = None;
-    }
-
-    /// Store an embedding in the current session.
-    ///
-    /// Returns an error if no session is active.
-    pub fn store(&mut self, embedding: NeuralEmbedding) -> Result<usize> {
-        let session_id = self
-            .current_session
-            .clone()
-            .ok_or_else(|| RuvNeuralError::Memory("No active session".into()))?;
-
-        let timestamp = embedding.timestamp;
-        let state = embedding.metadata.cognitive_state;
-        let idx = self.store.store(embedding)?;
-
-        // Update session metadata
-        if let Some(meta) = self.session_metadata.get_mut(&session_id) {
-            if meta.num_embeddings == 0 {
-                meta.start_time = timestamp;
-            }
-            meta.num_embeddings += 1;
-
-            if let Some(s) = state {
-                if !meta.cognitive_states_observed.contains(&s) {
-                    meta.cognitive_states_observed.push(s);
-                }
-            }
-        }
-
-        if let Some(indices) = self.session_indices.get_mut(&session_id) {
-            indices.push(idx);
-        }
-
-        Ok(idx)
-    }
-
-    /// Get all embeddings from a specific session.
-    pub fn get_session_history(&self, session_id: &str) -> Vec<&NeuralEmbedding> {
-        match self.session_indices.get(session_id) {
-            Some(indices) => indices
-                .iter()
-                .filter_map(|&i| self.store.get(i))
-                .collect(),
-            None => Vec::new(),
-        }
-    }
-
-    /// Get all embeddings for a given subject across all sessions.
-    pub fn get_subject_history(&self, subject_id: &str) -> Vec<&NeuralEmbedding> {
-        self.store.query_by_subject(subject_id)
-    }
-
-    /// Get metadata for a session.
-    pub fn get_session_metadata(&self, session_id: &str) -> Option<&SessionMetadata> {
-        self.session_metadata.get(session_id)
-    }
-
-    /// Get the current active session ID.
-    pub fn current_session_id(&self) -> Option<&str> {
-        self.current_session.as_deref()
-    }
-
-    /// Access the underlying store.
-    pub fn store_ref(&self) -> &NeuralMemoryStore {
-        &self.store
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-
-    fn make_embedding(vector: Vec<f64>, subject: &str, timestamp: f64) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            timestamp,
-            EmbeddingMetadata {
-                subject_id: Some(subject.to_string()),
-                session_id: None,
-                cognitive_state: Some(CognitiveState::Rest),
-                source_atlas: Atlas::Schaefer100,
-                embedding_method: "test".to_string(),
-            },
-        )
-        .unwrap()
-    }
-
-    #[test]
-    fn session_lifecycle() {
-        let mut mem = SessionMemory::new(100);
-
-        // No session active
-        assert!(mem.current_session_id().is_none());
-
-        // Start session
-        let sid = mem.start_session("subj1");
-        assert_eq!(mem.current_session_id(), Some(sid.as_str()));
-
-        // Store embeddings
-        mem.store(make_embedding(vec![1.0, 0.0], "subj1", 1.0))
-            .unwrap();
-        mem.store(make_embedding(vec![0.0, 1.0], "subj1", 2.0))
-            .unwrap();
-
-        // Check session history
-        let history = mem.get_session_history(&sid);
-        assert_eq!(history.len(), 2);
-
-        // Check metadata
-        let meta = mem.get_session_metadata(&sid).unwrap();
-        assert_eq!(meta.num_embeddings, 2);
-        assert_eq!(meta.subject_id, "subj1");
-
-        // End session
-        mem.end_session();
-        assert!(mem.current_session_id().is_none());
-
-        let meta = mem.get_session_metadata(&sid).unwrap();
-        assert_eq!(meta.end_time, Some(2.0));
-    }
-
-    #[test]
-    fn store_without_session_fails() {
-        let mut mem = SessionMemory::new(100);
-        let result = mem.store(make_embedding(vec![1.0], "subj1", 0.0));
-        assert!(result.is_err());
-    }
-
-    #[test]
-    fn multiple_sessions() {
-        let mut mem = SessionMemory::new(100);
-
-        let s1 = mem.start_session("subj1");
-        mem.store(make_embedding(vec![1.0], "subj1", 1.0))
-            .unwrap();
-        mem.end_session();
-
-        let s2 = mem.start_session("subj1");
-        mem.store(make_embedding(vec![2.0], "subj1", 2.0))
-            .unwrap();
-        mem.store(make_embedding(vec![3.0], "subj1", 3.0))
-            .unwrap();
-        mem.end_session();
-
-        assert_eq!(mem.get_session_history(&s1).len(), 1);
-        assert_eq!(mem.get_session_history(&s2).len(), 2);
-
-        // Subject history spans all sessions
-        let subject_history = mem.get_subject_history("subj1");
-        assert_eq!(subject_history.len(), 3);
-    }
-
-    #[test]
-    fn starting_new_session_ends_previous() {
-        let mut mem = SessionMemory::new(100);
-
-        let s1 = mem.start_session("subj1");
-        mem.store(make_embedding(vec![1.0], "subj1", 1.0))
-            .unwrap();
-
-        // Starting a new session auto-ends the previous one
-        let _s2 = mem.start_session("subj2");
-
-        let meta = mem.get_session_metadata(&s1).unwrap();
-        assert!(meta.end_time.is_some());
-    }
-}
@@ -1,374 +0,0 @@
-//! In-memory embedding store with brute-force nearest neighbor search.
-
-use std::collections::HashMap;
-use std::collections::VecDeque;
-
-use ruv_neural_core::embedding::NeuralEmbedding;
-use ruv_neural_core::error::Result;
-use ruv_neural_core::topology::CognitiveState;
-use ruv_neural_core::traits::NeuralMemory;
-
-/// In-memory store for neural embeddings with index-based retrieval.
-///
-/// Uses a VecDeque for O(1) front eviction instead of Vec::remove(0) which is O(n).
-#[derive(Debug, Clone)]
-pub struct NeuralMemoryStore {
-    /// All stored embeddings in insertion order.
-    embeddings: VecDeque<NeuralEmbedding>,
-    /// Maps subject_id to the indices of their embeddings.
-    index: HashMap<String, Vec<usize>>,
-    /// Maximum number of embeddings to store.
-    capacity: usize,
-    /// Running offset: total number of embeddings ever evicted.
-    /// Logical index = physical index + evicted_count.
-    evicted_count: usize,
-}
-
-impl NeuralMemoryStore {
-    /// Create a new store with the given capacity.
-    pub fn new(capacity: usize) -> Self {
-        Self {
-            embeddings: VecDeque::with_capacity(capacity.min(1024)),
-            index: HashMap::new(),
-            capacity,
-            evicted_count: 0,
-        }
-    }
-
-    /// Store an embedding, returning its physical index within the deque.
-    ///
-    /// If the store is at capacity, the oldest embedding is evicted.
-    /// Returns an error if the embedding dimension is inconsistent with
-    /// previously stored embeddings.
-    pub fn store(&mut self, embedding: NeuralEmbedding) -> Result<usize> {
-        // Check dimension consistency with existing embeddings
-        if let Some(first) = self.embeddings.front() {
-            if embedding.dimension != first.dimension {
-                return Err(ruv_neural_core::error::RuvNeuralError::DimensionMismatch {
-                    expected: first.dimension,
-                    got: embedding.dimension,
-                });
-            }
-        }
-
-        if self.embeddings.len() >= self.capacity {
-            self.evict_oldest();
-        }
-
-        let idx = self.embeddings.len();
-
-        if let Some(ref subject_id) = embedding.metadata.subject_id {
-            self.index
-                .entry(subject_id.clone())
-                .or_default()
-                .push(idx);
-        }
-
-        self.embeddings.push_back(embedding);
-        Ok(idx)
-    }
-
-    /// Get an embedding by its index.
-    pub fn get(&self, id: usize) -> Option<&NeuralEmbedding> {
-        self.embeddings.get(id)
-    }
-
-    /// Number of embeddings currently stored.
-    pub fn len(&self) -> usize {
-        self.embeddings.len()
-    }
-
-    /// Returns true if the store is empty.
-    pub fn is_empty(&self) -> bool {
-        self.embeddings.is_empty()
-    }
-
-    /// Find the k nearest neighbors using brute-force Euclidean distance.
-    ///
-    /// Returns pairs of (index, distance), sorted by ascending distance.
-    pub fn query_nearest(&self, query: &NeuralEmbedding, k: usize) -> Vec<(usize, f64)> {
-        let mut distances: Vec<(usize, f64)> = self
-            .embeddings
-            .iter()
-            .enumerate()
-            .filter_map(|(i, emb)| {
-                emb.euclidean_distance(query).ok().map(|d| (i, d))
-            })
-            .collect();
-
-        distances.sort_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal));
-        distances.truncate(k);
-        distances
-    }
-
-    /// Query all embeddings matching a given cognitive state.
-    pub fn query_by_state(&self, state: CognitiveState) -> Vec<&NeuralEmbedding> {
-        self.embeddings
-            .iter()
-            .filter(|e| e.metadata.cognitive_state == Some(state))
-            .collect()
-    }
-
-    /// Query all embeddings for a given subject.
-    pub fn query_by_subject(&self, subject_id: &str) -> Vec<&NeuralEmbedding> {
-        match self.index.get(subject_id) {
-            Some(indices) => indices
-                .iter()
-                .filter_map(|&i| self.embeddings.get(i))
-                .collect(),
-            None => Vec::new(),
-        }
-    }
-
-    /// Query embeddings within a timestamp range [start, end].
-    pub fn query_time_range(&self, start: f64, end: f64) -> Vec<&NeuralEmbedding> {
-        self.embeddings
-            .iter()
-            .filter(|e| e.timestamp >= start && e.timestamp <= end)
-            .collect()
-    }
-
-    /// Access all embeddings (for serialization).
-    ///
-    /// Returns the two slices of the VecDeque as a pair. For contiguous access,
-    /// callers can use `make_contiguous()` on a mutable reference, or iterate.
-    pub fn embeddings_iter(&self) -> impl Iterator<Item = &NeuralEmbedding> {
-        self.embeddings.iter()
-    }
-
-    /// Access all embeddings as a slice pair (VecDeque may be non-contiguous).
-    pub fn embeddings(&self) -> Vec<&NeuralEmbedding> {
-        self.embeddings.iter().collect()
-    }
-
-    /// Get the capacity.
-    pub fn capacity(&self) -> usize {
-        self.capacity
-    }
-
-    /// Evict the oldest embedding with O(1) pop and incremental index update.
-    ///
-    /// Instead of rebuilding the entire index, we remove the evicted entry
-    /// from the subject index and decrement all remaining indices by 1.
-    fn evict_oldest(&mut self) {
-        if self.embeddings.is_empty() {
-            return;
-        }
-
-        let evicted = self.embeddings.pop_front().unwrap();
-        self.evicted_count += 1;
-
-        // Remove index 0 from the evicted embedding's subject entry.
-        if let Some(ref subject_id) = evicted.metadata.subject_id {
-            if let Some(indices) = self.index.get_mut(subject_id) {
-                indices.retain(|&i| i != 0);
-            }
-        }
-
-        // Decrement all indices by 1 since front was removed.
-        for indices in self.index.values_mut() {
-            for idx in indices.iter_mut() {
-                *idx -= 1;
-            }
-        }
-
-        // Clean up empty entries.
-        self.index.retain(|_, v| !v.is_empty());
-    }
-}
-
-impl NeuralMemory for NeuralMemoryStore {
-    fn store(&mut self, embedding: &NeuralEmbedding) -> Result<()> {
-        NeuralMemoryStore::store(self, embedding.clone())?;
-        Ok(())
-    }
-
-    fn query_nearest(
-        &self,
-        embedding: &NeuralEmbedding,
-        k: usize,
-    ) -> Result<Vec<NeuralEmbedding>> {
-        let results = NeuralMemoryStore::query_nearest(self, embedding, k);
-        Ok(results
-            .into_iter()
-            .filter_map(|(i, _)| self.get(i).cloned())
-            .collect())
-    }
-
-    fn query_by_state(&self, state: CognitiveState) -> Result<Vec<NeuralEmbedding>> {
-        Ok(NeuralMemoryStore::query_by_state(self, state)
-            .into_iter()
-            .cloned()
-            .collect())
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::embedding::EmbeddingMetadata;
-
-    fn make_embedding(vector: Vec<f64>, subject: &str, timestamp: f64) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            timestamp,
-            EmbeddingMetadata {
-                subject_id: Some(subject.to_string()),
-                session_id: None,
-                cognitive_state: Some(CognitiveState::Rest),
-                source_atlas: Atlas::Schaefer100,
-                embedding_method: "test".to_string(),
-            },
-        )
-        .unwrap()
-    }
-
-    fn make_embedding_with_state(
-        vector: Vec<f64>,
-        state: CognitiveState,
-        timestamp: f64,
-    ) -> NeuralEmbedding {
-        NeuralEmbedding::new(
-            vector,
-            timestamp,
-            EmbeddingMetadata {
-                subject_id: Some("subj1".to_string()),
-                session_id: None,
-                cognitive_state: Some(state),
-                source_atlas: Atlas::Schaefer100,
-                embedding_method: "test".to_string(),
-            },
-        )
-        .unwrap()
-    }
-
-    #[test]
-    fn store_and_retrieve() {
-        let mut store = NeuralMemoryStore::new(100);
-        let emb = make_embedding(vec![1.0, 2.0, 3.0], "subj1", 0.0);
-        let idx = store.store(emb.clone()).unwrap();
-        assert_eq!(idx, 0);
-        assert_eq!(store.len(), 1);
-
-        let retrieved = store.get(0).unwrap();
-        assert_eq!(retrieved.vector, vec![1.0, 2.0, 3.0]);
-    }
-
-    #[test]
-    fn nearest_neighbor_returns_correct_results() {
-        let mut store = NeuralMemoryStore::new(100);
-        store
-            .store(make_embedding(vec![0.0, 0.0, 0.0], "a", 0.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![1.0, 0.0, 0.0], "b", 1.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![10.0, 10.0, 10.0], "c", 2.0))
-            .unwrap();
-
-        let query = make_embedding(vec![0.5, 0.0, 0.0], "q", 3.0);
-        let results = store.query_nearest(&query, 2);
-
-        assert_eq!(results.len(), 2);
-        // Closest should be [0,0,0] (dist=0.5) then [1,0,0] (dist=0.5)
-        assert!(results[0].1 <= results[1].1);
-    }
-
-    #[test]
-    fn query_by_state_filters_correctly() {
-        let mut store = NeuralMemoryStore::new(100);
-        store
-            .store(make_embedding_with_state(
-                vec![1.0, 0.0],
-                CognitiveState::Rest,
-                0.0,
-            ))
-            .unwrap();
-        store
-            .store(make_embedding_with_state(
-                vec![0.0, 1.0],
-                CognitiveState::Focused,
-                1.0,
-            ))
-            .unwrap();
-        store
-            .store(make_embedding_with_state(
-                vec![1.0, 1.0],
-                CognitiveState::Rest,
-                2.0,
-            ))
-            .unwrap();
-
-        let resting = store.query_by_state(CognitiveState::Rest);
-        assert_eq!(resting.len(), 2);
-
-        let focused = store.query_by_state(CognitiveState::Focused);
-        assert_eq!(focused.len(), 1);
-    }
-
-    #[test]
-    fn query_by_subject() {
-        let mut store = NeuralMemoryStore::new(100);
-        store
-            .store(make_embedding(vec![1.0, 0.0], "alice", 0.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![0.0, 1.0], "bob", 1.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![1.0, 1.0], "alice", 2.0))
-            .unwrap();
-
-        let alice = store.query_by_subject("alice");
-        assert_eq!(alice.len(), 2);
-
-        let bob = store.query_by_subject("bob");
-        assert_eq!(bob.len(), 1);
-
-        let unknown = store.query_by_subject("charlie");
-        assert_eq!(unknown.len(), 0);
-    }
-
-    #[test]
-    fn query_time_range() {
-        let mut store = NeuralMemoryStore::new(100);
-        store
-            .store(make_embedding(vec![1.0], "a", 1.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![2.0], "a", 5.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![3.0], "a", 10.0))
-            .unwrap();
-
-        let in_range = store.query_time_range(2.0, 8.0);
-        assert_eq!(in_range.len(), 1);
-        assert_eq!(in_range[0].vector, vec![2.0]);
-
-        let all = store.query_time_range(0.0, 20.0);
-        assert_eq!(all.len(), 3);
-    }
-
-    #[test]
-    fn capacity_eviction() {
-        let mut store = NeuralMemoryStore::new(2);
-        store
-            .store(make_embedding(vec![1.0], "a", 0.0))
-            .unwrap();
-        store
-            .store(make_embedding(vec![2.0], "b", 1.0))
-            .unwrap();
-        assert_eq!(store.len(), 2);
-
-        // This should evict the oldest
-        store
-            .store(make_embedding(vec![3.0], "c", 2.0))
-            .unwrap();
-        assert_eq!(store.len(), 2);
-        // First element should now be [2.0]
-        assert_eq!(store.get(0).unwrap().vector, vec![2.0]);
-    }
-}
@@ -1,31 +0,0 @@
-[package]
-name = "ruv-neural-mincut"
-description = "rUv Neural — Dynamic minimum cut analysis for brain network topology detection"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-wasm = []
-sublinear = []  # Sublinear mincut algorithms
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-petgraph = { workspace = true }
-ndarray = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-num-traits = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
-rand = { workspace = true }
-criterion = { workspace = true }
-
-[[bench]]
-name = "benchmarks"
-harness = false
@@ -1,102 +0,0 @@
-# ruv-neural-mincut
-
-Dynamic minimum cut analysis for brain network topology detection.
-
-## Overview
-
-`ruv-neural-mincut` provides algorithms for computing minimum cuts on brain
-connectivity graphs, tracking topology changes over time, and detecting neural
-coherence events such as network formation, dissolution, merger, and split.
-These algorithms form the core of the rUv Neural cognitive state detection
-pipeline, identifying when brain network topology undergoes significant
-structural transitions.
-
-## Features
-
- **Stoer-Wagner** (`stoer_wagner`): Global minimum cut in O(V^3) time, returning
-  cut value, partitions, and cut edges
- **Normalized cut** (`normalized`): Shi-Malik spectral bisection via the Fiedler
-  vector for balanced graph partitioning
- **Multiway cut** (`multiway`): Recursive normalized cut for k-module detection;
-  `detect_modules` for automatic module count selection
- **Spectral cut** (`spectral_cut`): Cheeger constant computation, spectral bisection,
-  and Cheeger bound estimation
- **Dynamic tracking** (`dynamic`): `DynamicMincutTracker` for temporal mincut
-  evolution tracking with `TopologyTransition` and `TransitionDirection` detection
- **Coherence detection** (`coherence`): `CoherenceDetector` identifying
-  `CoherenceEventType` events (formation, dissolution, merger, split) from
-  temporal graph sequences
- **Benchmarks** (`benchmark`): Performance benchmarking utilities
-
-## Usage
-
-```rust
-use ruv_neural_mincut::{
-    stoer_wagner_mincut, normalized_cut, spectral_bisection,
-    cheeger_constant, multiway_cut, detect_modules,
-    DynamicMincutTracker, CoherenceDetector,
-};
-use ruv_neural_core::graph::BrainGraph;
-
-// Compute global minimum cut
-let result = stoer_wagner_mincut(&graph);
-println!("Cut value: {:.3}", result.cut_value);
-println!("Partition A: {:?}", result.partition_a);
-println!("Partition B: {:?}", result.partition_b);
-
-// Normalized cut (spectral bisection)
-let ncut = normalized_cut(&graph);
-
-// Spectral analysis
-let (partition, cheeger) = spectral_bisection(&graph);
-let h = cheeger_constant(&graph);
-
-// Multiway cut for k modules
-let multi = multiway_cut(&graph, 4);
-let auto_modules = detect_modules(&graph);
-
-// Track topology transitions over time
-let mut tracker = DynamicMincutTracker::new();
-for graph in &graph_sequence.graphs {
-    let result = tracker.update(graph).unwrap();
-}
-
-// Detect coherence events
-let mut detector = CoherenceDetector::new();
-for graph in &graph_sequence.graphs {
-    if let Some(event) = detector.check(graph) {
-        println!("Event: {:?} at t={}", event.event_type, event.timestamp);
-    }
-}
-```
-
-## API Reference
-
-| Module          | Key Types / Functions                                           |
-|-----------------|-----------------------------------------------------------------|
-| `stoer_wagner`  | `stoer_wagner_mincut`                                           |
-| `normalized`    | `normalized_cut`                                                |
-| `multiway`      | `multiway_cut`, `detect_modules`                                |
-| `spectral_cut`  | `spectral_bisection`, `cheeger_constant`, `cheeger_bound`       |
-| `dynamic`       | `DynamicMincutTracker`, `TopologyTransition`, `TransitionDirection` |
-| `coherence`     | `CoherenceDetector`, `CoherenceEvent`, `CoherenceEventType`     |
-| `benchmark`     | Benchmark utilities                                             |
-
-## Feature Flags
-
-| Feature     | Default | Description                      |
-|-------------|---------|----------------------------------|
-| `std`       | Yes     | Standard library support         |
-| `wasm`      | No      | WASM-compatible implementations  |
-| `sublinear` | No      | Sublinear mincut algorithms      |
-
-## Integration
-
-Depends on `ruv-neural-core` for `BrainGraph`, `MincutResult`, and `MultiPartition`
-types. Receives graphs from `ruv-neural-graph`. Mincut results feed into
-`ruv-neural-embed` for topology-aware embeddings and `ruv-neural-decoder`
-for cognitive state classification.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,105 +0,0 @@
-//! Criterion benchmarks for ruv-neural-mincut.
-//!
-//! Benchmarks the performance-critical graph cut algorithms:
-//! - Stoer-Wagner global minimum cut (O(V^3))
-//! - Spectral bisection via Fiedler vector
-//! - Cheeger constant (exact enumeration for small graphs)
-
-use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
-use rand::Rng;
-
-use ruv_neural_core::brain::Atlas;
-use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-use ruv_neural_core::signal::FrequencyBand;
-use ruv_neural_mincut::{cheeger_constant, spectral_bisection, stoer_wagner_mincut};
-
-/// Build a random weighted graph with the given number of nodes.
-///
-/// Creates a connected graph by first building a spanning path, then adding
-/// random edges with density ~30% to ensure non-trivial structure.
-fn random_graph(num_nodes: usize) -> BrainGraph {
-    let mut rng = rand::thread_rng();
-    let mut edges = Vec::new();
-
-    // Spanning path to guarantee connectivity
-    for i in 0..(num_nodes - 1) {
-        edges.push(BrainEdge {
-            source: i,
-            target: i + 1,
-            weight: rng.gen_range(0.1..2.0),
-            metric: ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        });
-    }
-
-    // Additional random edges (~30% density)
-    for i in 0..num_nodes {
-        for j in (i + 2)..num_nodes {
-            if rng.gen_bool(0.3) {
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight: rng.gen_range(0.1..2.0),
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-    }
-
-    BrainGraph {
-        num_nodes,
-        edges,
-        timestamp: 0.0,
-        window_duration_s: 1.0,
-        atlas: Atlas::Custom(num_nodes),
-    }
-}
-
-fn bench_stoer_wagner(c: &mut Criterion) {
-    let mut group = c.benchmark_group("stoer_wagner");
-
-    for &n in &[10, 20, 50, 68] {
-        let graph = random_graph(n);
-        group.bench_with_input(BenchmarkId::new("nodes", n), &graph, |b, graph| {
-            b.iter(|| stoer_wagner_mincut(black_box(graph)))
-        });
-    }
-
-    group.finish();
-}
-
-fn bench_spectral_bisection(c: &mut Criterion) {
-    let mut group = c.benchmark_group("spectral_bisection");
-
-    for &n in &[10, 20, 50, 68] {
-        let graph = random_graph(n);
-        group.bench_with_input(BenchmarkId::new("nodes", n), &graph, |b, graph| {
-            b.iter(|| spectral_bisection(black_box(graph)))
-        });
-    }
-
-    group.finish();
-}
-
-fn bench_cheeger_constant(c: &mut Criterion) {
-    let mut group = c.benchmark_group("cheeger_constant");
-
-    // Cheeger uses exact enumeration for n <= 16, so test within that range
-    for &n in &[8, 12, 16] {
-        let graph = random_graph(n);
-        group.bench_with_input(BenchmarkId::new("nodes", n), &graph, |b, graph| {
-            b.iter(|| cheeger_constant(black_box(graph)))
-        });
-    }
-
-    group.finish();
-}
-
-criterion_group!(
-    benches,
-    bench_stoer_wagner,
-    bench_spectral_bisection,
-    bench_cheeger_constant,
-);
-criterion_main!(benches);
@@ -1,186 +0,0 @@
-//! Performance benchmarking utilities for mincut algorithms.
-//!
-//! Provides functions to measure the wall-clock time of the Stoer-Wagner and
-//! normalized cut algorithms on random graphs of configurable size and density.
-
-use std::time::{Duration, Instant};
-
-use ruv_neural_core::brain::Atlas;
-use ruv_neural_core::graph::{BrainEdge, BrainGraph, ConnectivityMetric};
-use ruv_neural_core::signal::FrequencyBand;
-
-use crate::normalized::normalized_cut;
-use crate::stoer_wagner::stoer_wagner_mincut;
-
-/// Result of a benchmark run.
-#[derive(Debug, Clone)]
-pub struct BenchmarkReport {
-    /// Algorithm name.
-    pub algorithm: String,
-    /// Number of nodes in the test graph.
-    pub num_nodes: usize,
-    /// Number of edges in the test graph.
-    pub num_edges: usize,
-    /// Graph density (0..1).
-    pub density: f64,
-    /// Wall-clock execution time.
-    pub elapsed: Duration,
-    /// Minimum cut value found.
-    pub cut_value: f64,
-}
-
-impl std::fmt::Display for BenchmarkReport {
-    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        write!(
-            f,
-            "{}: nodes={}, edges={}, density={:.3}, time={:.3}ms, cut={:.4}",
-            self.algorithm,
-            self.num_nodes,
-            self.num_edges,
-            self.density,
-            self.elapsed.as_secs_f64() * 1000.0,
-            self.cut_value
-        )
-    }
-}
-
-/// Benchmark the Stoer-Wagner algorithm on a random graph.
-///
-/// # Arguments
-///
-/// * `num_nodes` - Number of vertices.
-/// * `density` - Edge density in [0, 1]. A density of 1.0 generates a complete graph.
-/// * `seed` - Random seed for reproducibility.
-pub fn benchmark_stoer_wagner(num_nodes: usize, density: f64, seed: u64) -> BenchmarkReport {
-    let graph = generate_random_graph(num_nodes, density, seed);
-    let num_edges = graph.edges.len();
-
-    let start = Instant::now();
-    let result = stoer_wagner_mincut(&graph);
-    let elapsed = start.elapsed();
-
-    let cut_value = result.map(|r| r.cut_value).unwrap_or(f64::NAN);
-
-    BenchmarkReport {
-        algorithm: "Stoer-Wagner".to_string(),
-        num_nodes,
-        num_edges,
-        density,
-        elapsed,
-        cut_value,
-    }
-}
-
-/// Benchmark the normalized cut algorithm on a random graph.
-pub fn benchmark_normalized_cut(num_nodes: usize, density: f64, seed: u64) -> BenchmarkReport {
-    let graph = generate_random_graph(num_nodes, density, seed);
-    let num_edges = graph.edges.len();
-
-    let start = Instant::now();
-    let result = normalized_cut(&graph);
-    let elapsed = start.elapsed();
-
-    let cut_value = result.map(|r| r.cut_value).unwrap_or(f64::NAN);
-
-    BenchmarkReport {
-        algorithm: "Normalized-Cut".to_string(),
-        num_nodes,
-        num_edges,
-        density,
-        elapsed,
-        cut_value,
-    }
-}
-
-/// Generate a random undirected weighted graph with approximately the given density.
-///
-/// Uses a simple LCG for deterministic randomness.
-fn generate_random_graph(num_nodes: usize, density: f64, seed: u64) -> BrainGraph {
-    let mut rng_state = seed;
-
-    let mut edges = Vec::new();
-    for i in 0..num_nodes {
-        for j in (i + 1)..num_nodes {
-            rng_state = rng_state
-                .wrapping_mul(6364136223846793005)
-                .wrapping_add(1);
-            let rand_val = (rng_state >> 33) as f64 / (1u64 << 31) as f64;
-
-            if rand_val < density {
-                rng_state = rng_state
-                    .wrapping_mul(6364136223846793005)
-                    .wrapping_add(1);
-                let weight = ((rng_state >> 33) as f64 / (1u64 << 31) as f64) * 0.9 + 0.1;
-
-                edges.push(BrainEdge {
-                    source: i,
-                    target: j,
-                    weight,
-                    metric: ConnectivityMetric::Coherence,
-                    frequency_band: FrequencyBand::Alpha,
-                });
-            }
-        }
-    }
-
-    BrainGraph {
-        num_nodes,
-        edges,
-        timestamp: 0.0,
-        window_duration_s: 1.0,
-        atlas: Atlas::Custom(num_nodes),
-    }
-}
-
-/// Run a full benchmark suite and return all reports.
-pub fn run_benchmark_suite() -> Vec<BenchmarkReport> {
-    let configs = [(10, 0.5), (20, 0.3), (30, 0.2), (50, 0.1)];
-
-    let mut reports = Vec::new();
-    for &(nodes, density) in &configs {
-        reports.push(benchmark_stoer_wagner(nodes, density, 42));
-        reports.push(benchmark_normalized_cut(nodes, density, 42));
-    }
-    reports
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_benchmark_stoer_wagner() {
-        let report = benchmark_stoer_wagner(10, 0.5, 42);
-        assert_eq!(report.num_nodes, 10);
-        assert!(report.num_edges > 0);
-        assert!(!report.cut_value.is_nan());
-    }
-
-    #[test]
-    fn test_benchmark_normalized_cut() {
-        let report = benchmark_normalized_cut(10, 0.5, 42);
-        assert_eq!(report.num_nodes, 10);
-        assert!(!report.cut_value.is_nan());
-    }
-
-    #[test]
-    fn test_generate_random_graph_deterministic() {
-        let g1 = generate_random_graph(20, 0.3, 123);
-        let g2 = generate_random_graph(20, 0.3, 123);
-        assert_eq!(g1.edges.len(), g2.edges.len());
-    }
-
-    #[test]
-    fn test_benchmark_report_display() {
-        let report = benchmark_stoer_wagner(10, 0.5, 42);
-        let display = format!("{}", report);
-        assert!(display.contains("Stoer-Wagner"));
-        assert!(display.contains("nodes=10"));
-    }
-
-    #[test]
-    fn test_run_benchmark_suite() {
-        let reports = run_benchmark_suite();
-        assert_eq!(reports.len(), 8);
-    }
-}
@@ -1,315 +0,0 @@
-//! Neural coherence detection via minimum cut analysis.
-//!
-//! Detects when brain networks become coherent (strongly coupled) or decouple,
-//! by monitoring the minimum cut over a temporal graph sequence. Significant
-//! changes in mincut topology correspond to network formation, dissolution,
-//! merger, and split events.
-
-use serde::{Deserialize, Serialize};
-
-use crate::dynamic::DynamicMincutTracker;
-
-/// Type of coherence event detected.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum CoherenceEventType {
-    /// A new coherent module forms (integration event).
-    NetworkFormation,
-    /// A coherent module breaks apart (segregation event).
-    NetworkDissolution,
-    /// Two modules merge into one.
-    NetworkMerger,
-    /// One module splits into two.
-    NetworkSplit,
-}
-
-/// A coherence event detected in the brain network.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct CoherenceEvent {
-    /// Start time of the event.
-    pub start_time: f64,
-    /// End time of the event.
-    pub end_time: f64,
-    /// Type of coherence event.
-    pub event_type: CoherenceEventType,
-    /// Brain region indices involved in the event.
-    pub involved_regions: Vec<usize>,
-    /// Peak coherence magnitude during the event.
-    pub peak_coherence: f64,
-}
-
-/// Detects coherence events in temporal brain graph sequences.
-#[derive(Debug, Clone)]
-pub struct CoherenceDetector {
-    /// Internal tracker for mincut evolution.
-    tracker: DynamicMincutTracker,
-    /// Threshold (fraction of baseline) for integration detection.
-    threshold_integration: f64,
-    /// Threshold (fraction of baseline) for segregation detection.
-    threshold_segregation: f64,
-}
-
-impl CoherenceDetector {
-    /// Create a new coherence detector.
-    ///
-    /// # Arguments
-    ///
-    /// * `threshold_integration` - Fraction of baseline for integration detection
-    ///   (e.g., 0.3 means a 30% decrease in mincut triggers an integration event).
-    /// * `threshold_segregation` - Fraction of baseline for segregation detection.
-    pub fn new(threshold_integration: f64, threshold_segregation: f64) -> Self {
-        Self {
-            tracker: DynamicMincutTracker::new(),
-            threshold_integration,
-            threshold_segregation,
-        }
-    }
-
-    /// Set the baseline mincut value from resting-state data.
-    pub fn set_baseline(&mut self, baseline: f64) {
-        self.tracker.set_baseline(baseline);
-    }
-
-    /// Get a reference to the internal tracker.
-    pub fn tracker(&self) -> &DynamicMincutTracker {
-        &self.tracker
-    }
-
-    /// Detect coherence events from a mincut time series.
-    ///
-    /// Processes each `(timestamp, mincut_value)` pair, detects transitions,
-    /// and classifies them into coherence events.
-    pub fn detect_from_timeseries(
-        &self,
-        mincut_series: &[(f64, f64)],
-    ) -> Vec<CoherenceEvent> {
-        if mincut_series.len() < 2 {
-            return Vec::new();
-        }
-
-        // Compute baseline as mean if not set.
-        let baseline = self.tracker.baseline().unwrap_or_else(|| {
-            let sum: f64 = mincut_series.iter().map(|(_, v)| v).sum();
-            sum / mincut_series.len() as f64
-        });
-
-        if baseline <= 0.0 {
-            return Vec::new();
-        }
-
-        let threshold = self.threshold_integration.min(self.threshold_segregation);
-        let change_threshold = threshold * baseline;
-
-        let mut events = Vec::new();
-        let mut i = 1;
-
-        while i < mincut_series.len() {
-            let (_t_prev, v_prev) = mincut_series[i - 1];
-            let (t_curr, v_curr) = mincut_series[i];
-            let delta = v_curr - v_prev;
-
-            if delta.abs() > change_threshold {
-                let magnitude = delta.abs() / baseline;
-
-                if delta < 0.0 && magnitude >= self.threshold_integration {
-                    // Integration: mincut decreased -> networks merging.
-                    let end_time =
-                        find_recovery_time_in_series(mincut_series, i, v_prev, baseline);
-
-                    events.push(CoherenceEvent {
-                        start_time: t_curr,
-                        end_time,
-                        event_type: CoherenceEventType::NetworkFormation,
-                        involved_regions: Vec::new(),
-                        peak_coherence: magnitude,
-                    });
-                } else if delta > 0.0 && magnitude >= self.threshold_segregation {
-                    // Segregation: mincut increased -> networks separating.
-                    let end_time =
-                        find_recovery_time_in_series(mincut_series, i, v_prev, baseline);
-
-                    events.push(CoherenceEvent {
-                        start_time: t_curr,
-                        end_time,
-                        event_type: CoherenceEventType::NetworkDissolution,
-                        involved_regions: Vec::new(),
-                        peak_coherence: magnitude,
-                    });
-                }
-
-                // Check for merger/split patterns (opposing transitions close together).
-                if i + 1 < mincut_series.len() {
-                    let (t_next, v_next) = mincut_series[i + 1];
-                    let dt = t_next - t_curr;
-                    let delta_next = v_next - v_curr;
-
-                    if dt < 2.0 && delta_next.abs() > change_threshold {
-                        if delta < 0.0 && delta_next > 0.0 {
-                            events.push(CoherenceEvent {
-                                start_time: t_curr,
-                                end_time: t_next,
-                                event_type: CoherenceEventType::NetworkSplit,
-                                involved_regions: Vec::new(),
-                                peak_coherence: magnitude.max(delta_next.abs() / baseline),
-                            });
-                            i += 1;
-                        } else if delta > 0.0 && delta_next < 0.0 {
-                            events.push(CoherenceEvent {
-                                start_time: t_curr,
-                                end_time: t_next,
-                                event_type: CoherenceEventType::NetworkMerger,
-                                involved_regions: Vec::new(),
-                                peak_coherence: magnitude.max(delta_next.abs() / baseline),
-                            });
-                            i += 1;
-                        }
-                    }
-                }
-            }
-
-            i += 1;
-        }
-
-        events
-    }
-
-    /// Detect coherence events by processing a brain graph sequence.
-    ///
-    /// Updates the internal tracker with each graph and then analyzes the
-    /// resulting mincut time series.
-    pub fn detect_coherence_events(
-        &mut self,
-        sequence: &ruv_neural_core::graph::BrainGraphSequence,
-    ) -> ruv_neural_core::Result<Vec<CoherenceEvent>> {
-        for graph in &sequence.graphs {
-            self.tracker.update(graph)?;
-        }
-
-        let timeseries = self.tracker.mincut_timeseries();
-        Ok(self.detect_from_timeseries(&timeseries))
-    }
-}
-
-/// Find the time when the mincut recovers to near the original value.
-fn find_recovery_time_in_series(
-    series: &[(f64, f64)],
-    start_idx: usize,
-    original_value: f64,
-    baseline: f64,
-) -> f64 {
-    let recovery_threshold = 0.1 * baseline;
-
-    for &(t, v) in series.iter().skip(start_idx + 1) {
-        if (v - original_value).abs() < recovery_threshold {
-            return t;
-        }
-    }
-
-    // No recovery found; return last timestamp.
-    series.last().map_or(series[start_idx].0, |&(t, _)| t)
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[test]
-    fn test_coherence_event_types_serialization() {
-        for event_type in [
-            CoherenceEventType::NetworkFormation,
-            CoherenceEventType::NetworkDissolution,
-            CoherenceEventType::NetworkMerger,
-            CoherenceEventType::NetworkSplit,
-        ] {
-            let json = serde_json::to_string(&event_type).unwrap();
-            let back: CoherenceEventType = serde_json::from_str(&json).unwrap();
-            assert_eq!(back, event_type);
-        }
-    }
-
-    #[test]
-    fn test_coherence_event_serialization() {
-        let event = CoherenceEvent {
-            start_time: 0.0,
-            end_time: 1.0,
-            event_type: CoherenceEventType::NetworkFormation,
-            involved_regions: vec![0, 1, 2],
-            peak_coherence: 0.8,
-        };
-        let json = serde_json::to_string(&event).unwrap();
-        let back: CoherenceEvent = serde_json::from_str(&json).unwrap();
-        assert_eq!(back.event_type, CoherenceEventType::NetworkFormation);
-        assert!((back.peak_coherence - 0.8).abs() < 1e-9);
-    }
-
-    #[test]
-    fn test_detect_no_events_for_constant_series() {
-        let detector = CoherenceDetector::new(0.3, 0.3);
-        let series: Vec<(f64, f64)> = (0..10)
-            .map(|i| (i as f64, 5.0))
-            .collect();
-        let events = detector.detect_from_timeseries(&series);
-        assert!(events.is_empty());
-    }
-
-    #[test]
-    fn test_detect_formation_event() {
-        let mut detector = CoherenceDetector::new(0.2, 0.2);
-        detector.set_baseline(5.0);
-
-        // Constant, then a sudden drop in mincut (integration).
-        let series = vec![
-            (0.0, 5.0),
-            (1.0, 5.0),
-            (2.0, 5.0),
-            (3.0, 1.0), // big drop
-            (4.0, 1.0),
-            (5.0, 5.0), // recovery
-        ];
-
-        let events = detector.detect_from_timeseries(&series);
-        assert!(
-            !events.is_empty(),
-            "Should detect a formation event from a large mincut decrease"
-        );
-        // First event should be a formation (integration).
-        assert_eq!(events[0].event_type, CoherenceEventType::NetworkFormation);
-    }
-
-    #[test]
-    fn test_detect_dissolution_event() {
-        let mut detector = CoherenceDetector::new(0.2, 0.2);
-        detector.set_baseline(5.0);
-
-        // Sudden increase in mincut (segregation).
-        let series = vec![
-            (0.0, 5.0),
-            (1.0, 5.0),
-            (2.0, 15.0), // big jump
-            (3.0, 15.0),
-        ];
-
-        let events = detector.detect_from_timeseries(&series);
-        let dissolution_events: Vec<_> = events
-            .iter()
-            .filter(|e| e.event_type == CoherenceEventType::NetworkDissolution)
-            .collect();
-        assert!(
-            !dissolution_events.is_empty(),
-            "Should detect a dissolution event from a large mincut increase"
-        );
-    }
-
-    #[test]
-    fn test_detector_empty_series() {
-        let detector = CoherenceDetector::new(0.3, 0.3);
-        let events = detector.detect_from_timeseries(&[]);
-        assert!(events.is_empty());
-    }
-
-    #[test]
-    fn test_detector_single_point() {
-        let detector = CoherenceDetector::new(0.3, 0.3);
-        let events = detector.detect_from_timeseries(&[(0.0, 5.0)]);
-        assert!(events.is_empty());
-    }
-}
@@ -1,410 +0,0 @@
-//! Dynamic minimum cut tracking over temporal brain graph sequences.
-//!
-//! Tracks the evolution of minimum cut values over time, detects significant
-//! topology transitions (integration vs. segregation events), and computes
-//! derived metrics such as rate of change, integration index, and partition
-//! stability.
-
-use serde::{Deserialize, Serialize};
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::topology::MincutResult;
-use ruv_neural_core::Result;
-
-use crate::stoer_wagner::stoer_wagner_mincut;
-
-/// Tracks minimum cut evolution over a sequence of brain graphs.
-#[derive(Debug, Clone)]
-pub struct DynamicMincutTracker {
-    /// History of mincut results.
-    history: Vec<MincutResult>,
-    /// Timestamps corresponding to each result.
-    timestamps: Vec<f64>,
-    /// Baseline mincut from resting state.
-    baseline: Option<f64>,
-}
-
-impl Default for DynamicMincutTracker {
-    fn default() -> Self {
-        Self::new()
-    }
-}
-
-impl DynamicMincutTracker {
-    /// Create a new empty tracker.
-    pub fn new() -> Self {
-        Self {
-            history: Vec::new(),
-            timestamps: Vec::new(),
-            baseline: None,
-        }
-    }
-
-    /// Set the baseline mincut value (typically from a resting-state graph).
-    pub fn set_baseline(&mut self, baseline: f64) {
-        self.baseline = Some(baseline);
-    }
-
-    /// Get the current baseline, if set.
-    pub fn baseline(&self) -> Option<f64> {
-        self.baseline
-    }
-
-    /// Process a new brain graph, compute its mincut, and add it to the history.
-    ///
-    /// Returns the mincut result for this graph.
-    pub fn update(&mut self, graph: &BrainGraph) -> Result<MincutResult> {
-        let result = stoer_wagner_mincut(graph)?;
-        self.timestamps.push(graph.timestamp);
-        self.history.push(result.clone());
-        Ok(result)
-    }
-
-    /// Number of time points tracked so far.
-    pub fn len(&self) -> usize {
-        self.history.len()
-    }
-
-    /// Returns true if no time points have been tracked.
-    pub fn is_empty(&self) -> bool {
-        self.history.is_empty()
-    }
-
-    /// Get the mincut time series as (timestamp, cut_value) pairs.
-    pub fn mincut_timeseries(&self) -> Vec<(f64, f64)> {
-        self.timestamps
-            .iter()
-            .zip(self.history.iter())
-            .map(|(&t, r)| (t, r.cut_value))
-            .collect()
-    }
-
-    /// Get the full history of mincut results.
-    pub fn history(&self) -> &[MincutResult] {
-        &self.history
-    }
-
-    /// Detect significant topology transitions.
-    ///
-    /// A transition is detected where the mincut changes by more than
-    /// `threshold * baseline` between consecutive time points. If no baseline
-    /// is set, the mean mincut is used as the baseline.
-    ///
-    /// # Arguments
-    ///
-    /// * `threshold` - Fraction of the baseline that constitutes a significant
-    ///   change (e.g., 0.2 means a 20% change).
-    pub fn detect_transitions(&self, threshold: f64) -> Vec<TopologyTransition> {
-        if self.history.len() < 2 {
-            return Vec::new();
-        }
-
-        let baseline = self.baseline.unwrap_or_else(|| {
-            let sum: f64 = self.history.iter().map(|r| r.cut_value).sum();
-            sum / self.history.len() as f64
-        });
-
-        if baseline <= 0.0 {
-            return Vec::new();
-        }
-
-        let change_threshold = threshold * baseline;
-        let mut transitions = Vec::new();
-
-        for i in 1..self.history.len() {
-            let before = self.history[i - 1].cut_value;
-            let after = self.history[i].cut_value;
-            let delta = after - before;
-
-            if delta.abs() > change_threshold {
-                let direction = if delta < 0.0 {
-                    TransitionDirection::Integration
-                } else {
-                    TransitionDirection::Segregation
-                };
-
-                transitions.push(TopologyTransition {
-                    timestamp: self.timestamps[i],
-                    mincut_before: before,
-                    mincut_after: after,
-                    direction,
-                    magnitude: delta.abs() / baseline,
-                });
-            }
-        }
-
-        transitions
-    }
-
-    /// Rate of topology change (finite difference of mincut values).
-    ///
-    /// Returns (timestamp, rate) pairs where the rate is the change in mincut
-    /// per unit time.
-    pub fn rate_of_change(&self) -> Vec<(f64, f64)> {
-        if self.history.len() < 2 {
-            return Vec::new();
-        }
-
-        let mut rates = Vec::new();
-        for i in 1..self.history.len() {
-            let dt = self.timestamps[i] - self.timestamps[i - 1];
-            if dt > 0.0 {
-                let dcut = self.history[i].cut_value - self.history[i - 1].cut_value;
-                let midpoint = (self.timestamps[i] + self.timestamps[i - 1]) / 2.0;
-                rates.push((midpoint, dcut / dt));
-            }
-        }
-        rates
-    }
-
-    /// Integration-segregation balance index over time.
-    ///
-    /// The integration index is defined as:
-    ///
-    /// ```text
-    /// I(t) = 1.0 - mincut(t) / max_mincut
-    /// ```
-    ///
-    /// High values (close to 1) indicate integrated states; low values indicate
-    /// segregated states.
-    pub fn integration_index(&self) -> Vec<(f64, f64)> {
-        if self.history.is_empty() {
-            return Vec::new();
-        }
-
-        let max_cut = self
-            .history
-            .iter()
-            .map(|r| r.cut_value)
-            .fold(f64::NEG_INFINITY, f64::max);
-
-        if max_cut <= 0.0 {
-            return self
-                .timestamps
-                .iter()
-                .map(|&t| (t, 1.0))
-                .collect();
-        }
-
-        self.timestamps
-            .iter()
-            .zip(self.history.iter())
-            .map(|(&t, r)| (t, 1.0 - r.cut_value / max_cut))
-            .collect()
-    }
-
-    /// Partition stability: for how many consecutive time points does the same
-    /// partition topology persist?
-    ///
-    /// Returns (timestamp, stability) pairs where stability is the Jaccard
-    /// similarity between the current partition_a and the previous one.
-    pub fn partition_stability(&self) -> Vec<(f64, f64)> {
-        if self.history.is_empty() {
-            return Vec::new();
-        }
-
-        let mut stability = vec![(self.timestamps[0], 1.0)];
-
-        for i in 1..self.history.len() {
-            let prev_a: std::collections::HashSet<usize> =
-                self.history[i - 1].partition_a.iter().copied().collect();
-            let curr_a: std::collections::HashSet<usize> =
-                self.history[i].partition_a.iter().copied().collect();
-
-            let jaccard = jaccard_similarity(&prev_a, &curr_a);
-            // Take the max of comparing A-to-A and A-to-B (since partitions
-            // can be labelled either way).
-            let curr_b: std::collections::HashSet<usize> =
-                self.history[i].partition_b.iter().copied().collect();
-            let jaccard_flipped = jaccard_similarity(&prev_a, &curr_b);
-
-            stability.push((self.timestamps[i], jaccard.max(jaccard_flipped)));
-        }
-
-        stability
-    }
-}
-
-/// Compute the Jaccard similarity between two sets.
-fn jaccard_similarity(a: &std::collections::HashSet<usize>, b: &std::collections::HashSet<usize>) -> f64 {
-    let intersection = a.intersection(b).count() as f64;
-    let union = a.union(b).count() as f64;
-    if union == 0.0 {
-        1.0
-    } else {
-        intersection / union
-    }
-}
-
-/// A significant topology transition detected in the mincut time series.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct TopologyTransition {
-    /// Timestamp at which the transition was detected.
-    pub timestamp: f64,
-    /// Mincut value immediately before the transition.
-    pub mincut_before: f64,
-    /// Mincut value immediately after the transition.
-    pub mincut_after: f64,
-    /// Direction of the transition.
-    pub direction: TransitionDirection,
-    /// Magnitude of the transition relative to baseline.
-    pub magnitude: f64,
-}
-
-/// Direction of a topology transition.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum TransitionDirection {
-    /// Mincut decreased: networks are merging (becoming more integrated).
-    Integration,
-    /// Mincut increased: networks are separating (becoming more segregated).
-    Segregation,
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::BrainEdge;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(source: usize, target: usize, weight: f64) -> BrainEdge {
-        BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ruv_neural_core::graph::ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    fn make_graph(timestamp: f64, bridge_weight: f64) -> BrainGraph {
-        BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 5.0),
-                make_edge(2, 3, 5.0),
-                make_edge(1, 2, bridge_weight),
-            ],
-            timestamp,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        }
-    }
-
-    #[test]
-    fn test_tracker_basic() {
-        let mut tracker = DynamicMincutTracker::new();
-        assert!(tracker.is_empty());
-
-        let g1 = make_graph(0.0, 1.0);
-        let r1 = tracker.update(&g1).unwrap();
-        assert_eq!(tracker.len(), 1);
-        assert!(r1.cut_value > 0.0);
-    }
-
-    #[test]
-    fn test_tracker_timeseries() {
-        let mut tracker = DynamicMincutTracker::new();
-        for i in 0..5 {
-            let bridge = (i as f64 + 1.0) * 0.5;
-            let g = make_graph(i as f64, bridge);
-            tracker.update(&g).unwrap();
-        }
-
-        let ts = tracker.mincut_timeseries();
-        assert_eq!(ts.len(), 5);
-        // Timestamps should be 0, 1, 2, 3, 4.
-        for (i, (t, _)) in ts.iter().enumerate() {
-            assert!((t - i as f64).abs() < 1e-9);
-        }
-    }
-
-    #[test]
-    fn test_detect_transitions() {
-        let mut tracker = DynamicMincutTracker::new();
-        // Create a sequence where bridge weight jumps suddenly.
-        let weights = [1.0, 1.0, 1.0, 10.0, 10.0, 1.0];
-        for (i, &w) in weights.iter().enumerate() {
-            let g = make_graph(i as f64, w);
-            tracker.update(&g).unwrap();
-        }
-
-        tracker.set_baseline(1.0);
-        let transitions = tracker.detect_transitions(0.5);
-        // Should detect at least the jump at t=3 and t=5.
-        assert!(
-            !transitions.is_empty(),
-            "Should detect transitions for large mincut changes"
-        );
-    }
-
-    #[test]
-    fn test_rate_of_change() {
-        let mut tracker = DynamicMincutTracker::new();
-        for i in 0..4 {
-            let g = make_graph(i as f64, (i as f64 + 1.0) * 2.0);
-            tracker.update(&g).unwrap();
-        }
-
-        let rates = tracker.rate_of_change();
-        assert_eq!(rates.len(), 3);
-    }
-
-    #[test]
-    fn test_integration_index() {
-        let mut tracker = DynamicMincutTracker::new();
-        for i in 0..3 {
-            let g = make_graph(i as f64, i as f64 + 1.0);
-            tracker.update(&g).unwrap();
-        }
-
-        let idx = tracker.integration_index();
-        assert_eq!(idx.len(), 3);
-        // All values should be in [0, 1].
-        for (_, val) in &idx {
-            assert!(*val >= -1e-9 && *val <= 1.0 + 1e-9);
-        }
-    }
-
-    #[test]
-    fn test_partition_stability() {
-        let mut tracker = DynamicMincutTracker::new();
-        // Same graph repeated should give stability = 1.0.
-        for i in 0..3 {
-            let g = make_graph(i as f64, 0.5);
-            tracker.update(&g).unwrap();
-        }
-
-        let stability = tracker.partition_stability();
-        assert_eq!(stability.len(), 3);
-        // First one is always 1.0.
-        assert!((stability[0].1 - 1.0).abs() < 1e-9);
-        // Same graph should yield high stability.
-        for (_, s) in &stability {
-            assert!(*s >= 0.5, "Same graph should have high stability, got {}", s);
-        }
-    }
-
-    #[test]
-    fn test_default_tracker() {
-        let tracker = DynamicMincutTracker::default();
-        assert!(tracker.is_empty());
-        assert!(tracker.baseline().is_none());
-    }
-
-    #[test]
-    fn test_transition_direction() {
-        let mut tracker = DynamicMincutTracker::new();
-        // Low bridge -> high bridge (segregation)
-        tracker.update(&make_graph(0.0, 0.1)).unwrap();
-        tracker.update(&make_graph(1.0, 10.0)).unwrap();
-
-        tracker.set_baseline(0.1);
-        let transitions = tracker.detect_transitions(0.2);
-        if !transitions.is_empty() {
-            // The bridge weight went up, but the mincut depends on the full graph.
-            // Just verify we get a valid transition.
-            assert!(transitions[0].magnitude > 0.0);
-        }
-    }
-}
@@ -1,39 +0,0 @@
-//! # rUv Neural Mincut
-//!
-//! Dynamic minimum cut analysis for brain network topology detection.
-//!
-//! This crate provides algorithms for computing minimum cuts on brain connectivity
-//! graphs, tracking topology changes over time, and detecting neural coherence events.
-//!
-//! ## Algorithms
-//!
-//! - **Stoer-Wagner**: Global minimum cut in O(V^3) time
-//! - **Normalized cut** (Shi-Malik): Spectral bisection via the Fiedler vector
-//! - **Multiway cut**: Recursive normalized cut for k-module detection
-//! - **Spectral cut**: Cheeger constant, spectral bisection, Cheeger bounds
-//!
-//! ## Dynamic Analysis
-//!
-//! - **DynamicMincutTracker**: Track mincut evolution over temporal graph sequences
-//! - **CoherenceDetector**: Detect network formation, dissolution, merger, and split events
-
-pub mod benchmark;
-pub mod coherence;
-pub mod dynamic;
-pub mod multiway;
-pub mod normalized;
-pub mod spectral_cut;
-pub mod stoer_wagner;
-
-// Re-export primary public API
-pub use coherence::{CoherenceDetector, CoherenceEvent, CoherenceEventType};
-pub use dynamic::{DynamicMincutTracker, TopologyTransition, TransitionDirection};
-pub use multiway::{detect_modules, multiway_cut};
-pub use normalized::normalized_cut;
-pub use spectral_cut::{cheeger_bound, cheeger_constant, spectral_bisection};
-pub use stoer_wagner::stoer_wagner_mincut;
-
-// Re-export core types used in our public API
-pub use ruv_neural_core::graph::{BrainGraph, BrainGraphSequence};
-pub use ruv_neural_core::topology::{MincutResult, MultiPartition};
-pub use ruv_neural_core::{Result, RuvNeuralError};
@@ -1,370 +0,0 @@
-//! Multi-way graph partitioning using recursive normalized cut.
-//!
-//! Splits a brain connectivity graph into k modules by recursively applying
-//! normalized cut. Includes automatic module detection via modularity
-//! optimization.
-
-use ruv_neural_core::graph::{BrainEdge, BrainGraph};
-use ruv_neural_core::topology::MultiPartition;
-use ruv_neural_core::{Result, RuvNeuralError};
-
-use crate::normalized::normalized_cut;
-
-/// K-way graph partitioning using recursive normalized cut.
-///
-/// Recursively bisects the graph to produce `k` partitions. At each step the
-/// partition with the highest internal connectivity is chosen for the next
-/// split. The process stops when `k` partitions are produced or when further
-/// splitting does not improve modularity.
-///
-/// # Errors
-///
-/// Returns an error if `k < 2` or if the graph has fewer than `k` nodes.
-pub fn multiway_cut(graph: &BrainGraph, k: usize) -> Result<MultiPartition> {
-    if k < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "multiway_cut requires k >= 2".into(),
-        ));
-    }
-    if graph.num_nodes < k {
-        return Err(RuvNeuralError::Mincut(format!(
-            "Cannot partition {} nodes into {} groups",
-            graph.num_nodes, k
-        )));
-    }
-
-    // Start with a single partition containing all nodes.
-    let mut partitions: Vec<Vec<usize>> = vec![(0..graph.num_nodes).collect()];
-
-    while partitions.len() < k {
-        // Find the largest partition to split next.
-        let (split_idx, _) = partitions
-            .iter()
-            .enumerate()
-            .max_by_key(|(_, p)| p.len())
-            .unwrap();
-
-        let to_split = &partitions[split_idx];
-        if to_split.len() < 2 {
-            // Cannot split a singleton; stop early.
-            break;
-        }
-
-        // Build a subgraph from this partition.
-        let subgraph = build_subgraph(graph, to_split);
-
-        // Apply normalized cut on the subgraph.
-        let sub_result = normalized_cut(&subgraph)?;
-
-        // Map subgraph indices back to original indices.
-        let part_a: Vec<usize> = sub_result
-            .partition_a
-            .iter()
-            .map(|&i| to_split[i])
-            .collect();
-        let part_b: Vec<usize> = sub_result
-            .partition_b
-            .iter()
-            .map(|&i| to_split[i])
-            .collect();
-
-        // Replace the split partition with the two new ones.
-        partitions.remove(split_idx);
-        partitions.push(part_a);
-        partitions.push(part_b);
-    }
-
-    // Sort each partition for determinism.
-    for p in &mut partitions {
-        p.sort_unstable();
-    }
-    partitions.sort_by_key(|p| p[0]);
-
-    let modularity = compute_modularity(graph, &partitions);
-    let cut_value = compute_total_cut(graph, &partitions);
-
-    Ok(MultiPartition {
-        partitions,
-        cut_value,
-        modularity,
-    })
-}
-
-/// Automatic module detection: find the optimal number of partitions k that
-/// maximizes Newman-Girvan modularity.
-///
-/// Tries k = 2, 3, ..., max_k (where max_k = sqrt(num_nodes)) and returns the
-/// partitioning with the highest modularity.
-pub fn detect_modules(graph: &BrainGraph) -> Result<MultiPartition> {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "detect_modules requires at least 2 nodes".into(),
-        ));
-    }
-
-    let max_k = ((n as f64).sqrt().ceil() as usize).max(2).min(n);
-
-    let mut best_partition: Option<MultiPartition> = None;
-    let mut best_modularity = f64::NEG_INFINITY;
-
-    for k in 2..=max_k {
-        if k > n {
-            break;
-        }
-        match multiway_cut(graph, k) {
-            Ok(partition) => {
-                if partition.modularity > best_modularity {
-                    best_modularity = partition.modularity;
-                    best_partition = Some(partition);
-                }
-            }
-            Err(_) => break,
-        }
-    }
-
-    best_partition.ok_or_else(|| {
-        RuvNeuralError::Mincut("Could not find any valid partitioning".into())
-    })
-}
-
-/// Build a subgraph from a subset of nodes.
-///
-/// The returned graph has nodes indexed 0..subset.len(), with edges re-mapped
-/// from the original graph.
-fn build_subgraph(graph: &BrainGraph, subset: &[usize]) -> BrainGraph {
-    // Map from original index to subgraph index.
-    let mut index_map = std::collections::HashMap::new();
-    for (new_idx, &orig_idx) in subset.iter().enumerate() {
-        index_map.insert(orig_idx, new_idx);
-    }
-
-    let edges: Vec<BrainEdge> = graph
-        .edges
-        .iter()
-        .filter_map(|e| {
-            let s = index_map.get(&e.source)?;
-            let t = index_map.get(&e.target)?;
-            Some(BrainEdge {
-                source: *s,
-                target: *t,
-                weight: e.weight,
-                metric: e.metric,
-                frequency_band: e.frequency_band,
-            })
-        })
-        .collect();
-
-    BrainGraph {
-        num_nodes: subset.len(),
-        edges,
-        timestamp: graph.timestamp,
-        window_duration_s: graph.window_duration_s,
-        atlas: graph.atlas,
-    }
-}
-
-/// Compute Newman-Girvan modularity for a given partitioning.
-///
-/// Q = (1 / 2m) * sum_{ij} [A_{ij} - k_i * k_j / (2m)] * delta(c_i, c_j)
-pub fn compute_modularity(graph: &BrainGraph, partitions: &[Vec<usize>]) -> f64 {
-    let adj = graph.adjacency_matrix();
-    let n = graph.num_nodes;
-    let m: f64 = graph.edges.iter().map(|e| e.weight).sum::<f64>();
-
-    if m <= 0.0 {
-        return 0.0;
-    }
-
-    let two_m = 2.0 * m;
-
-    // Assign each node to its community.
-    let mut community = vec![0usize; n];
-    for (c, partition) in partitions.iter().enumerate() {
-        for &node in partition {
-            if node < n {
-                community[node] = c;
-            }
-        }
-    }
-
-    // Degrees.
-    let degrees: Vec<f64> = (0..n).map(|i| adj[i].iter().sum::<f64>()).collect();
-
-    let mut q = 0.0;
-    for i in 0..n {
-        for j in 0..n {
-            if community[i] == community[j] {
-                q += adj[i][j] - degrees[i] * degrees[j] / two_m;
-            }
-        }
-    }
-    q / two_m
-}
-
-/// Compute the total weight of edges that cross partition boundaries.
-fn compute_total_cut(graph: &BrainGraph, partitions: &[Vec<usize>]) -> f64 {
-    let n = graph.num_nodes;
-    let mut community = vec![0usize; n];
-    for (c, partition) in partitions.iter().enumerate() {
-        for &node in partition {
-            if node < n {
-                community[node] = c;
-            }
-        }
-    }
-
-    graph
-        .edges
-        .iter()
-        .filter(|e| {
-            e.source < n
-                && e.target < n
-                && community[e.source] != community[e.target]
-        })
-        .map(|e| e.weight)
-        .sum()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::BrainEdge;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(source: usize, target: usize, weight: f64) -> BrainEdge {
-        BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ruv_neural_core::graph::ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    /// Multiway cut with k=2 should produce 2 partitions.
-    #[test]
-    fn test_multiway_k2() {
-        let graph = BrainGraph {
-            num_nodes: 6,
-            edges: vec![
-                make_edge(0, 1, 5.0),
-                make_edge(1, 2, 5.0),
-                make_edge(0, 2, 5.0),
-                make_edge(3, 4, 5.0),
-                make_edge(4, 5, 5.0),
-                make_edge(3, 5, 5.0),
-                make_edge(2, 3, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        };
-
-        let result = multiway_cut(&graph, 2).unwrap();
-        assert_eq!(result.num_partitions(), 2);
-        assert_eq!(result.num_nodes(), 6);
-    }
-
-    /// Multiway cut with k=3 on a graph with 3 obvious clusters.
-    #[test]
-    fn test_multiway_k3() {
-        let graph = BrainGraph {
-            num_nodes: 9,
-            edges: vec![
-                // Cluster 1: {0, 1, 2}
-                make_edge(0, 1, 5.0),
-                make_edge(1, 2, 5.0),
-                make_edge(0, 2, 5.0),
-                // Cluster 2: {3, 4, 5}
-                make_edge(3, 4, 5.0),
-                make_edge(4, 5, 5.0),
-                make_edge(3, 5, 5.0),
-                // Cluster 3: {6, 7, 8}
-                make_edge(6, 7, 5.0),
-                make_edge(7, 8, 5.0),
-                make_edge(6, 8, 5.0),
-                // Weak bridges
-                make_edge(2, 3, 0.1),
-                make_edge(5, 6, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(9),
-        };
-
-        let result = multiway_cut(&graph, 3).unwrap();
-        assert_eq!(result.num_partitions(), 3);
-        assert_eq!(result.num_nodes(), 9);
-        assert!(result.modularity > 0.0, "Modularity should be positive for clustered graph");
-    }
-
-    /// detect_modules should find a good partition automatically.
-    #[test]
-    fn test_detect_modules() {
-        let graph = BrainGraph {
-            num_nodes: 6,
-            edges: vec![
-                make_edge(0, 1, 5.0),
-                make_edge(1, 2, 5.0),
-                make_edge(0, 2, 5.0),
-                make_edge(3, 4, 5.0),
-                make_edge(4, 5, 5.0),
-                make_edge(3, 5, 5.0),
-                make_edge(2, 3, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        };
-
-        let result = detect_modules(&graph).unwrap();
-        assert!(result.num_partitions() >= 2);
-        assert!(result.modularity > 0.0);
-    }
-
-    /// k=1 should error.
-    #[test]
-    fn test_multiway_k1_error() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![make_edge(0, 1, 1.0)],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-        assert!(multiway_cut(&graph, 1).is_err());
-    }
-
-    /// More partitions than nodes should error.
-    #[test]
-    fn test_multiway_too_many_partitions() {
-        let graph = BrainGraph {
-            num_nodes: 3,
-            edges: vec![make_edge(0, 1, 1.0), make_edge(1, 2, 1.0)],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        };
-        assert!(multiway_cut(&graph, 5).is_err());
-    }
-
-    #[test]
-    fn test_modularity_positive_for_good_partition() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 5.0),
-                make_edge(2, 3, 5.0),
-                make_edge(1, 2, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let q = compute_modularity(&graph, &[vec![0, 1], vec![2, 3]]);
-        assert!(q > 0.0, "Good partition should have positive modularity, got {}", q);
-    }
-}
@@ -1,267 +0,0 @@
-//! Normalized cut (Shi-Malik) for balanced graph partitioning.
-//!
-//! The normalized cut objective is:
-//!
-//! ```text
-//! Ncut(A, B) = cut(A,B) / vol(A) + cut(A,B) / vol(B)
-//! ```
-//!
-//! where vol(S) = sum of degrees of nodes in S.
-//!
-//! This is solved approximately via the spectral relaxation: find the Fiedler
-//! vector of the normalized Laplacian and threshold it.
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::topology::MincutResult;
-use ruv_neural_core::{Result, RuvNeuralError};
-
-use crate::spectral_cut::fiedler_decomposition;
-
-/// Compute the normalized minimum cut of a brain graph.
-///
-/// Uses the spectral method: compute the Fiedler vector of the graph Laplacian,
-/// then partition nodes by the sign of each component. The returned cut value
-/// is the normalized cut metric: `cut(A,B)/vol(A) + cut(A,B)/vol(B)`.
-///
-/// # Errors
-///
-/// Returns an error if the graph has fewer than 2 nodes.
-pub fn normalized_cut(graph: &BrainGraph) -> Result<MincutResult> {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "Normalized cut requires at least 2 nodes".into(),
-        ));
-    }
-
-    // Get the Fiedler vector from the unnormalized Laplacian.
-    // For normalized cut, ideally we would use the generalized eigenproblem
-    // L*x = lambda*D*x. We approximate by using the Fiedler vector of L and
-    // then trying multiple threshold sweeps to minimize Ncut.
-    let (_fiedler_value, fiedler_vec) = fiedler_decomposition(graph)?;
-
-    // Sweep thresholds along the sorted Fiedler values to find the best Ncut.
-    let adj = graph.adjacency_matrix();
-    let degrees: Vec<f64> = (0..n)
-        .map(|i| adj[i].iter().sum::<f64>())
-        .collect();
-
-    // Sort node indices by Fiedler value.
-    let mut sorted_indices: Vec<usize> = (0..n).collect();
-    sorted_indices.sort_by(|&a, &b| {
-        fiedler_vec[a]
-            .partial_cmp(&fiedler_vec[b])
-            .unwrap_or(std::cmp::Ordering::Equal)
-    });
-
-    let mut best_ncut = f64::INFINITY;
-    let mut best_split = 1usize; // number of nodes in partition A
-
-    // Track incremental cut and volumes.
-    // Start with partition A = empty, B = all. Then move nodes from B to A.
-    let total_vol: f64 = degrees.iter().sum();
-
-    let mut vol_a = 0.0;
-    let mut in_a = vec![false; n];
-
-    // We also need the cross-cut, which we compute incrementally.
-    // cut(A, B) = sum of weights between A and B.
-    let mut cut_val = 0.0;
-
-    for split in 0..(n - 1) {
-        let node = sorted_indices[split];
-        in_a[node] = true;
-        vol_a += degrees[node];
-
-        // Update cut: adding `node` to A means:
-        // - edges from `node` to other A nodes decrease cut (they were in cut before)
-        // - edges from `node` to B nodes increase cut
-        for j in 0..n {
-            if adj[node][j] > 0.0 {
-                if in_a[j] && j != node {
-                    // j was already in A, so edge (node, j) was previously a cut edge
-                    // (from B to A). Now both are in A, so remove it from cut.
-                    cut_val -= adj[node][j];
-                } else if !in_a[j] {
-                    // j is in B, so adding node to A creates a new cut edge.
-                    cut_val += adj[node][j];
-                }
-            }
-        }
-
-        let vol_b = total_vol - vol_a;
-        if vol_a > 0.0 && vol_b > 0.0 {
-            let ncut = cut_val / vol_a + cut_val / vol_b;
-            if ncut < best_ncut {
-                best_ncut = ncut;
-                best_split = split + 1;
-            }
-        }
-    }
-
-    // Build final partitions.
-    let partition_a: Vec<usize> = sorted_indices[..best_split].to_vec();
-    let partition_b: Vec<usize> = sorted_indices[best_split..].to_vec();
-
-    let partition_a_set: std::collections::HashSet<usize> =
-        partition_a.iter().copied().collect();
-
-    // Compute the actual cut edges and value.
-    let mut actual_cut = 0.0;
-    let mut cut_edges = Vec::new();
-    for edge in &graph.edges {
-        let s_in_a = partition_a_set.contains(&edge.source);
-        let t_in_a = partition_a_set.contains(&edge.target);
-        if s_in_a != t_in_a {
-            actual_cut += edge.weight;
-            cut_edges.push((edge.source, edge.target, edge.weight));
-        }
-    }
-
-    // Compute normalized cut value.
-    let vol_a: f64 = partition_a.iter().map(|&i| degrees[i]).sum();
-    let vol_b: f64 = partition_b.iter().map(|&i| degrees[i]).sum();
-    let ncut_value = if vol_a > 0.0 && vol_b > 0.0 {
-        actual_cut / vol_a + actual_cut / vol_b
-    } else {
-        actual_cut
-    };
-
-    Ok(MincutResult {
-        cut_value: ncut_value,
-        partition_a,
-        partition_b,
-        cut_edges,
-        timestamp: graph.timestamp,
-    })
-}
-
-/// Compute the volume of a node set: sum of weighted degrees.
-pub fn volume(graph: &BrainGraph, nodes: &[usize]) -> f64 {
-    nodes.iter().map(|&i| graph.node_degree(i)).sum()
-}
-
-/// Compute the raw cut weight between two node sets.
-pub fn cut_weight(graph: &BrainGraph, set_a: &[usize], set_b: &[usize]) -> f64 {
-    let a_set: std::collections::HashSet<usize> = set_a.iter().copied().collect();
-    let b_set: std::collections::HashSet<usize> = set_b.iter().copied().collect();
-
-    graph
-        .edges
-        .iter()
-        .filter(|e| {
-            (a_set.contains(&e.source) && b_set.contains(&e.target))
-                || (b_set.contains(&e.source) && a_set.contains(&e.target))
-        })
-        .map(|e| e.weight)
-        .sum()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::BrainEdge;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(source: usize, target: usize, weight: f64) -> BrainEdge {
-        BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ruv_neural_core::graph::ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    /// Normalized cut on a barbell graph should separate the two cliques.
-    #[test]
-    fn test_normalized_cut_barbell() {
-        let graph = BrainGraph {
-            num_nodes: 6,
-            edges: vec![
-                // Clique 1: {0, 1, 2}
-                make_edge(0, 1, 5.0),
-                make_edge(1, 2, 5.0),
-                make_edge(0, 2, 5.0),
-                // Clique 2: {3, 4, 5}
-                make_edge(3, 4, 5.0),
-                make_edge(4, 5, 5.0),
-                make_edge(3, 5, 5.0),
-                // Weak bridge
-                make_edge(2, 3, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        };
-
-        let result = normalized_cut(&graph).unwrap();
-        // The partition should separate the two cliques.
-        assert_eq!(result.partition_a.len() + result.partition_b.len(), 6);
-        // Ncut value should be small since the bridge is weak.
-        assert!(
-            result.cut_value < 1.0,
-            "Expected small Ncut for barbell, got {}",
-            result.cut_value
-        );
-    }
-
-    /// Balanced normalized cut produces non-degenerate partitions.
-    #[test]
-    fn test_normalized_cut_balanced() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 3.0),
-                make_edge(2, 3, 3.0),
-                make_edge(1, 2, 0.5),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let result = normalized_cut(&graph).unwrap();
-        // Both partitions should be non-empty.
-        assert!(!result.partition_a.is_empty());
-        assert!(!result.partition_b.is_empty());
-    }
-
-    #[test]
-    fn test_volume_computation() {
-        let graph = BrainGraph {
-            num_nodes: 3,
-            edges: vec![
-                make_edge(0, 1, 2.0),
-                make_edge(1, 2, 3.0),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        };
-
-        let vol = volume(&graph, &[0, 1]);
-        // node 0 degree = 2, node 1 degree = 2 + 3 = 5
-        assert!((vol - 7.0).abs() < 1e-9);
-    }
-
-    #[test]
-    fn test_cut_weight_computation() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 2.0),
-                make_edge(1, 2, 3.0),
-                make_edge(2, 3, 4.0),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let cw = cut_weight(&graph, &[0, 1], &[2, 3]);
-        // Only edge 1-2 (weight 3) crosses the cut.
-        assert!((cw - 3.0).abs() < 1e-9);
-    }
-}
@@ -1,446 +0,0 @@
-//! Spectral methods for graph cuts.
-//!
-//! Provides the Cheeger constant (isoperimetric number), spectral bisection via
-//! the Fiedler vector, and the Cheeger inequality bounds relating the Fiedler
-//! value to the isoperimetric constant.
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::topology::MincutResult;
-use ruv_neural_core::{Result, RuvNeuralError};
-
-/// Compute the Fiedler vector (eigenvector of the second-smallest eigenvalue)
-/// of the graph Laplacian using power iteration on the shifted Laplacian.
-///
-/// Returns `(fiedler_value, fiedler_vector)`.
-///
-/// We use inverse iteration on L to find the second-smallest eigenvalue.
-/// Since direct eigendecomposition without LAPACK is nontrivial, we use a
-/// simple approach: compute the Laplacian, then find its two smallest
-/// eigenvalues via shifted inverse iteration.
-pub fn fiedler_decomposition(graph: &BrainGraph) -> Result<(f64, Vec<f64>)> {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "Need at least 2 nodes for spectral analysis".into(),
-        ));
-    }
-
-    let adj = graph.adjacency_matrix();
-
-    // Build the Laplacian: L = D - A
-    let mut laplacian = vec![vec![0.0; n]; n];
-    for i in 0..n {
-        let degree: f64 = adj[i].iter().sum();
-        laplacian[i][i] = degree;
-        for j in 0..n {
-            laplacian[i][j] -= adj[i][j];
-        }
-    }
-
-    // For small graphs, use the QR-like approach via repeated deflated power
-    // iteration. We want the second-smallest eigenvector.
-    //
-    // Step 1: The smallest eigenvalue of L is 0 with eigenvector = all-ones
-    //         (for connected graphs). We deflate that out.
-    // Step 2: Run power iteration on (mu*I - L) to find the largest eigenvalue
-    //         of the deflated operator, which corresponds to the second-smallest
-    //         eigenvalue of L.
-
-    // Find the largest eigenvalue of L (for shifting) via power iteration.
-    let lambda_max = largest_eigenvalue(&laplacian, n, 200);
-
-    // Shift: M = lambda_max * I - L.
-    // The eigenvalues of M are (lambda_max - lambda_i).
-    // The largest eigenvalue of M corresponds to the smallest of L (= 0).
-    // The second largest of M corresponds to the second smallest of L (= fiedler).
-    let shift = lambda_max + 0.01; // small buffer
-
-    // Power iteration on M, deflating out the constant eigenvector.
-    let ones: Vec<f64> = vec![1.0 / (n as f64).sqrt(); n];
-
-    // Random-ish initial vector, orthogonal to ones.
-    let mut v: Vec<f64> = (0..n).map(|i| (i as f64 + 1.0).sin()).collect();
-    deflate(&mut v, &ones);
-    normalize(&mut v);
-
-    let max_iter = 1000;
-    let mut prev_eigenvalue = 0.0;
-
-    for _ in 0..max_iter {
-        // w = M * v = (shift * I - L) * v = shift * v - L * v
-        let mut w = vec![0.0; n];
-        for i in 0..n {
-            let mut lv = 0.0;
-            for j in 0..n {
-                lv += laplacian[i][j] * v[j];
-            }
-            w[i] = shift * v[i] - lv;
-        }
-
-        // Deflate out the constant eigenvector.
-        deflate(&mut w, &ones);
-        let eigenvalue = dot(&w, &v);
-        normalize(&mut w);
-        v = w;
-
-        if (eigenvalue - prev_eigenvalue).abs() < 1e-12 {
-            break;
-        }
-        prev_eigenvalue = eigenvalue;
-    }
-
-    // The Fiedler value = shift - prev_eigenvalue
-    let fiedler_value = shift - prev_eigenvalue;
-
-    // Clamp small negative values from numerical noise.
-    let fiedler_value = if fiedler_value < 0.0 && fiedler_value > -1e-9 {
-        0.0
-    } else {
-        fiedler_value
-    };
-
-    Ok((fiedler_value, v))
-}
-
-/// Spectral bisection using the Fiedler vector.
-///
-/// Partitions the graph into two sets based on the sign of the Fiedler vector
-/// components. Nodes with positive components go to partition A, non-positive
-/// to partition B.
-pub fn spectral_bisection(graph: &BrainGraph) -> Result<MincutResult> {
-    let (_fiedler_value, fiedler_vec) = fiedler_decomposition(graph)?;
-
-    let mut partition_a = Vec::new();
-    let mut partition_b = Vec::new();
-
-    for (i, &val) in fiedler_vec.iter().enumerate() {
-        if val > 0.0 {
-            partition_a.push(i);
-        } else {
-            partition_b.push(i);
-        }
-    }
-
-    // Handle degenerate case where everything ends up on one side.
-    if partition_a.is_empty() || partition_b.is_empty() {
-        // Put the first node in A, rest in B.
-        partition_a = vec![0];
-        partition_b = (1..graph.num_nodes).collect();
-    }
-
-    let partition_a_set: std::collections::HashSet<usize> =
-        partition_a.iter().copied().collect();
-
-    // Compute cut value.
-    let mut cut_value = 0.0;
-    let mut cut_edges = Vec::new();
-    for edge in &graph.edges {
-        let s_in_a = partition_a_set.contains(&edge.source);
-        let t_in_a = partition_a_set.contains(&edge.target);
-        if s_in_a != t_in_a {
-            cut_value += edge.weight;
-            cut_edges.push((edge.source, edge.target, edge.weight));
-        }
-    }
-
-    Ok(MincutResult {
-        cut_value,
-        partition_a,
-        partition_b,
-        cut_edges,
-        timestamp: graph.timestamp,
-    })
-}
-
-/// Compute the Cheeger constant (isoperimetric number) of the graph.
-///
-/// h(G) = min over all subsets S with |S| <= |V|/2 of:
-///     cut(S, V\S) / vol(S)
-///
-/// For small graphs this is computed exactly by enumeration. For larger graphs
-/// we approximate using the spectral bisection.
-pub fn cheeger_constant(graph: &BrainGraph) -> Result<f64> {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "Need at least 2 nodes for Cheeger constant".into(),
-        ));
-    }
-
-    // For small graphs (n <= 16), enumerate all subsets.
-    if n <= 16 {
-        let adj = graph.adjacency_matrix();
-        let degrees: Vec<f64> = (0..n)
-            .map(|i| adj[i].iter().sum::<f64>())
-            .collect();
-
-        let mut best_h = f64::INFINITY;
-
-        // Enumerate non-empty subsets of size <= n/2.
-        let total = 1u32 << n;
-        for mask in 1..total {
-            let size = mask.count_ones() as usize;
-            if size > n / 2 {
-                continue;
-            }
-
-            // Compute vol(S) and cut(S, V\S).
-            let mut vol_s = 0.0;
-            let mut cut_s = 0.0;
-
-            for i in 0..n {
-                if mask & (1 << i) != 0 {
-                    vol_s += degrees[i];
-                    for j in 0..n {
-                        if mask & (1 << j) == 0 {
-                            cut_s += adj[i][j];
-                        }
-                    }
-                }
-            }
-
-            if vol_s > 0.0 {
-                let h = cut_s / vol_s;
-                if h < best_h {
-                    best_h = h;
-                }
-            }
-        }
-
-        Ok(best_h)
-    } else {
-        // Approximate via spectral: use the Fiedler vector partition.
-        let result = spectral_bisection(graph)?;
-        let adj = graph.adjacency_matrix();
-
-        // vol(partition_a)
-        let vol_a: f64 = result
-            .partition_a
-            .iter()
-            .map(|&i| adj[i].iter().sum::<f64>())
-            .sum();
-        let vol_b: f64 = result
-            .partition_b
-            .iter()
-            .map(|&i| adj[i].iter().sum::<f64>())
-            .sum();
-
-        let vol_min = vol_a.min(vol_b);
-        if vol_min <= 0.0 {
-            return Ok(0.0);
-        }
-
-        Ok(result.cut_value / vol_min)
-    }
-}
-
-/// Cheeger inequality bounds relating the Fiedler value lambda_2 of the
-/// **unnormalized** Laplacian to the conductance h(G).
-///
-/// For the unnormalized Laplacian with maximum degree d_max:
-///
-/// ```text
-/// lambda_2 / (2 * d_max) <= h(G) <= sqrt(2 * lambda_2 / d_min)
-/// ```
-///
-/// For convenience when d_max is unknown, this function uses the normalized
-/// Laplacian relationship:
-///
-/// ```text
-/// lambda_2_norm / 2 <= h(G) <= sqrt(2 * lambda_2_norm)
-/// ```
-///
-/// The `fiedler_value` parameter should be from the **normalized** Laplacian
-/// (i.e., `unnormalized_lambda_2 / d_max` is a conservative approximation).
-///
-/// Returns `(lower_bound, upper_bound)`.
-pub fn cheeger_bound(fiedler_value: f64) -> (f64, f64) {
-    let lower = fiedler_value / 2.0;
-    let upper = (2.0 * fiedler_value).sqrt();
-    (lower, upper)
-}
-
-// ── Helpers ──────────────────────────────────────────────────────────────────
-
-/// Largest eigenvalue of a symmetric matrix via power iteration.
-///
-/// Terminates early when the eigenvalue change between iterations is below 1e-12.
-fn largest_eigenvalue(mat: &[Vec<f64>], n: usize, max_iter: usize) -> f64 {
-    let mut v: Vec<f64> = (0..n).map(|i| (i as f64 + 0.5).cos()).collect();
-    normalize(&mut v);
-
-    let mut eigenvalue = 0.0;
-    for _ in 0..max_iter {
-        let mut w = vec![0.0; n];
-        for i in 0..n {
-            for j in 0..n {
-                w[i] += mat[i][j] * v[j];
-            }
-        }
-        let new_eigenvalue = dot(&w, &v);
-        normalize(&mut w);
-        v = w;
-
-        if (new_eigenvalue - eigenvalue).abs() < 1e-12 {
-            eigenvalue = new_eigenvalue;
-            break;
-        }
-        eigenvalue = new_eigenvalue;
-    }
-    eigenvalue
-}
-
-/// Remove the component of `v` along `u` (assumed normalized).
-fn deflate(v: &mut [f64], u: &[f64]) {
-    let proj = dot(v, u);
-    for (vi, &ui) in v.iter_mut().zip(u.iter()) {
-        *vi -= proj * ui;
-    }
-}
-
-fn dot(a: &[f64], b: &[f64]) -> f64 {
-    a.iter().zip(b.iter()).map(|(x, y)| x * y).sum()
-}
-
-fn normalize(v: &mut [f64]) {
-    let norm: f64 = v.iter().map(|x| x * x).sum::<f64>().sqrt();
-    if norm > 1e-15 {
-        for x in v.iter_mut() {
-            *x /= norm;
-        }
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::BrainEdge;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(source: usize, target: usize, weight: f64) -> BrainEdge {
-        BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ruv_neural_core::graph::ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    /// Path graph P3 (0--1--2): Fiedler value should be 1.0.
-    /// Laplacian eigenvalues of P3 with unit weights: 0, 1, 3.
-    #[test]
-    fn test_fiedler_path_p3() {
-        let graph = BrainGraph {
-            num_nodes: 3,
-            edges: vec![make_edge(0, 1, 1.0), make_edge(1, 2, 1.0)],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(3),
-        };
-
-        let (fiedler_value, fiedler_vec) = fiedler_decomposition(&graph).unwrap();
-        assert!(
-            (fiedler_value - 1.0).abs() < 0.1,
-            "Expected Fiedler value ~1.0 for P3, got {}",
-            fiedler_value
-        );
-        // The Fiedler vector should have opposite signs at the endpoints.
-        assert!(
-            fiedler_vec[0] * fiedler_vec[2] < 0.0,
-            "Fiedler vector endpoints should have opposite signs"
-        );
-    }
-
-    /// Cheeger bounds using normalized Laplacian eigenvalue.
-    ///
-    /// For the unnormalized Laplacian eigenvalue lambda_2 and max degree d_max,
-    /// the normalized eigenvalue is lambda_2_norm = lambda_2 / d_max, and the
-    /// Cheeger inequality states: lambda_2_norm / 2 <= h(G) <= sqrt(2 * lambda_2_norm).
-    #[test]
-    fn test_cheeger_bounds_hold() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 1.0),
-                make_edge(1, 2, 1.0),
-                make_edge(2, 3, 1.0),
-                make_edge(3, 0, 1.0),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let (fiedler_value, _) = fiedler_decomposition(&graph).unwrap();
-        let h = cheeger_constant(&graph).unwrap();
-
-        // For conductance (cut/vol), the Cheeger inequality uses the normalized
-        // Laplacian eigenvalue. For C4 with unit weights, d_max = 2, so:
-        //   lambda_2_norm = lambda_2 / d_max
-        let adj = graph.adjacency_matrix();
-        let d_max: f64 = (0..graph.num_nodes)
-            .map(|i| adj[i].iter().sum::<f64>())
-            .fold(f64::NEG_INFINITY, f64::max);
-        let lambda_2_norm = fiedler_value / d_max;
-
-        let (lower, upper) = cheeger_bound(lambda_2_norm);
-
-        assert!(
-            h >= lower - 1e-6,
-            "Cheeger h={} should be >= lower bound {} (lambda2_norm={})",
-            h,
-            lower,
-            lambda_2_norm
-        );
-        assert!(
-            h <= upper + 1e-6,
-            "Cheeger h={} should be <= upper bound {} (lambda2_norm={})",
-            h,
-            upper,
-            lambda_2_norm
-        );
-    }
-
-    /// Spectral bisection of a barbell graph should split the two cliques.
-    #[test]
-    fn test_spectral_bisection_barbell() {
-        // Two triangles connected by a single weak edge.
-        let graph = BrainGraph {
-            num_nodes: 6,
-            edges: vec![
-                // Clique 1: {0, 1, 2}
-                make_edge(0, 1, 5.0),
-                make_edge(1, 2, 5.0),
-                make_edge(0, 2, 5.0),
-                // Clique 2: {3, 4, 5}
-                make_edge(3, 4, 5.0),
-                make_edge(4, 5, 5.0),
-                make_edge(3, 5, 5.0),
-                // Bridge
-                make_edge(2, 3, 0.1),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(6),
-        };
-
-        let result = spectral_bisection(&graph).unwrap();
-        // The cut should be small (close to 0.1).
-        assert!(
-            result.cut_value < 2.0,
-            "Expected small cut for barbell, got {}",
-            result.cut_value
-        );
-        // Each partition should have 3 nodes.
-        assert_eq!(result.partition_a.len() + result.partition_b.len(), 6);
-    }
-
-    #[test]
-    fn test_cheeger_bound_values() {
-        let (lower, upper) = cheeger_bound(2.0);
-        assert!((lower - 1.0).abs() < 1e-9);
-        assert!((upper - 2.0).abs() < 1e-9);
-    }
-}
@@ -1,361 +0,0 @@
-//! Stoer-Wagner algorithm for global minimum cut of an undirected weighted graph.
-//!
-//! Time complexity: O(V^3) using a simple adjacency matrix representation.
-//! The algorithm repeatedly performs "minimum cut phases" and merges vertices,
-//! tracking the lightest cut found across all phases.
-
-use ruv_neural_core::graph::BrainGraph;
-use ruv_neural_core::topology::MincutResult;
-use ruv_neural_core::{Result, RuvNeuralError};
-
-/// Compute the global minimum cut of an undirected weighted graph using the
-/// Stoer-Wagner algorithm.
-///
-/// Returns a [`MincutResult`] containing the cut value, the two partitions,
-/// and the edges crossing the cut.
-///
-/// # Errors
-///
-/// Returns an error if the graph has fewer than two nodes.
-pub fn stoer_wagner_mincut(graph: &BrainGraph) -> Result<MincutResult> {
-    let n = graph.num_nodes;
-    if n < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "Stoer-Wagner requires at least 2 nodes".into(),
-        ));
-    }
-
-    // Build adjacency matrix
-    let adj = graph.adjacency_matrix();
-
-    // Working copy of adjacency weights. We will merge rows/cols as the algorithm
-    // contracts vertices.
-    let mut w: Vec<Vec<f64>> = adj;
-
-    // `merged[i]` holds the list of original node indices that have been merged
-    // into supernode i.
-    let mut merged: Vec<Vec<usize>> = (0..n).map(|i| vec![i]).collect();
-
-    // Which supernodes are still active.
-    let mut active: Vec<bool> = vec![true; n];
-
-    let mut best_cut_value = f64::INFINITY;
-    let mut best_partition: Vec<usize> = Vec::new();
-
-    // We need n-1 phases.
-    for _ in 0..(n - 1) {
-        let phase_result = minimum_cut_phase(&w, &active, &merged)?;
-
-        if phase_result.cut_of_the_phase < best_cut_value {
-            best_cut_value = phase_result.cut_of_the_phase;
-            best_partition = phase_result.last_merged_group.clone();
-        }
-
-        // Merge the last two vertices of this phase.
-        merge_vertices(
-            &mut w,
-            &mut merged,
-            &mut active,
-            phase_result.second_last,
-            phase_result.last,
-        );
-    }
-
-    // Build the two partitions.
-    let mut partition_a: Vec<usize> = best_partition.clone();
-    partition_a.sort_unstable();
-    let partition_a_set: std::collections::HashSet<usize> =
-        partition_a.iter().copied().collect();
-    let mut partition_b: Vec<usize> = (0..n)
-        .filter(|i| !partition_a_set.contains(i))
-        .collect();
-    partition_b.sort_unstable();
-
-    // Find cut edges.
-    let cut_edges = find_cut_edges(graph, &partition_a_set);
-
-    Ok(MincutResult {
-        cut_value: best_cut_value,
-        partition_a,
-        partition_b,
-        cut_edges,
-        timestamp: graph.timestamp,
-    })
-}
-
-/// Result of a single phase of the Stoer-Wagner algorithm.
-struct PhaseResult {
-    /// The "cut of the phase" value — weight of edges from the last-added vertex
-    /// to the rest of the merged set.
-    cut_of_the_phase: f64,
-    /// Index of the second-to-last vertex added in the ordering.
-    second_last: usize,
-    /// Index of the last vertex added in the ordering.
-    last: usize,
-    /// Original node indices that belong to the last-added supernode.
-    last_merged_group: Vec<usize>,
-}
-
-/// Execute one phase of the Stoer-Wagner algorithm.
-///
-/// Greedily grows a set A by adding the most tightly connected vertex at each
-/// step. Returns the cut of the phase (the weight connecting the last vertex
-/// to the rest) and the indices needed for merging.
-fn minimum_cut_phase(
-    w: &[Vec<f64>],
-    active: &[bool],
-    merged: &[Vec<usize>],
-) -> Result<PhaseResult> {
-    let n = w.len();
-
-    // Find all active nodes.
-    let active_nodes: Vec<usize> = (0..n).filter(|&i| active[i]).collect();
-    if active_nodes.len() < 2 {
-        return Err(RuvNeuralError::Mincut(
-            "Not enough active nodes for a phase".into(),
-        ));
-    }
-
-    // key[v] = total weight of edges from v to the growing set A.
-    let mut key: Vec<f64> = vec![0.0; n];
-    let mut in_a: Vec<bool> = vec![false; n];
-
-    let mut last = active_nodes[0];
-    let mut second_last = active_nodes[0];
-
-    // We add all active nodes one by one.
-    for iteration in 0..active_nodes.len() {
-        // On first iteration, pick an arbitrary active node as seed.
-        if iteration == 0 {
-            let seed = active_nodes[0];
-            in_a[seed] = true;
-            last = seed;
-            // Update keys for neighbors of seed.
-            for &v in &active_nodes {
-                if !in_a[v] {
-                    key[v] += w[seed][v];
-                }
-            }
-            continue;
-        }
-
-        // Find the active node not in A with the maximum key.
-        let mut best_node = usize::MAX;
-        let mut best_key = -1.0;
-        for &v in &active_nodes {
-            if !in_a[v] && key[v] > best_key {
-                best_key = key[v];
-                best_node = v;
-            }
-        }
-
-        second_last = last;
-        last = best_node;
-        in_a[best_node] = true;
-
-        // Update keys.
-        for &v in &active_nodes {
-            if !in_a[v] {
-                key[v] += w[best_node][v];
-            }
-        }
-    }
-
-    Ok(PhaseResult {
-        cut_of_the_phase: key[last],
-        second_last,
-        last,
-        last_merged_group: merged[last].clone(),
-    })
-}
-
-/// Merge vertex `v` into vertex `u`, combining their adjacency weights and
-/// original node sets.
-fn merge_vertices(
-    w: &mut [Vec<f64>],
-    merged: &mut [Vec<usize>],
-    active: &mut [bool],
-    u: usize,
-    v: usize,
-) {
-    let n = w.len();
-
-    // Add v's weights into u.
-    for i in 0..n {
-        w[u][i] += w[v][i];
-        w[i][u] += w[i][v];
-    }
-    // Zero out self-loop created by merge.
-    w[u][u] = 0.0;
-
-    // Move v's original nodes into u's group.
-    let v_nodes: Vec<usize> = merged[v].drain(..).collect();
-    merged[u].extend(v_nodes);
-
-    // Deactivate v.
-    active[v] = false;
-}
-
-/// Find all edges crossing the partition boundary.
-fn find_cut_edges(
-    graph: &BrainGraph,
-    partition_a: &std::collections::HashSet<usize>,
-) -> Vec<(usize, usize, f64)> {
-    graph
-        .edges
-        .iter()
-        .filter(|e| {
-            let s_in_a = partition_a.contains(&e.source);
-            let t_in_a = partition_a.contains(&e.target);
-            s_in_a != t_in_a
-        })
-        .map(|e| (e.source, e.target, e.weight))
-        .collect()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::brain::Atlas;
-    use ruv_neural_core::graph::BrainEdge;
-    use ruv_neural_core::signal::FrequencyBand;
-
-    fn make_edge(source: usize, target: usize, weight: f64) -> BrainEdge {
-        BrainEdge {
-            source,
-            target,
-            weight,
-            metric: ruv_neural_core::graph::ConnectivityMetric::Coherence,
-            frequency_band: FrequencyBand::Alpha,
-        }
-    }
-
-    /// Classic 4-node example:
-    ///
-    /// ```text
-    ///   0 --2-- 1
-    ///   |       |
-    ///   3       3
-    ///   |       |
-    ///   2 --2-- 3
-    /// ```
-    ///
-    /// Edge weights: 0-1:2, 0-2:3, 1-3:3, 2-3:2
-    /// Expected minimum cut = 4 (partition {0,2} vs {1,3} or {0,1} vs {2,3}).
-    #[test]
-    fn test_stoer_wagner_known_graph() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 2.0),
-                make_edge(0, 2, 3.0),
-                make_edge(1, 3, 3.0),
-                make_edge(2, 3, 2.0),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let result = stoer_wagner_mincut(&graph).unwrap();
-        assert!(
-            (result.cut_value - 4.0).abs() < 1e-9,
-            "Expected mincut 4.0, got {}",
-            result.cut_value
-        );
-        // Verify partition sizes sum to total.
-        assert_eq!(
-            result.partition_a.len() + result.partition_b.len(),
-            4
-        );
-    }
-
-    /// Complete graph K4 with unit weights: mincut = 3 (remove all edges to one vertex).
-    #[test]
-    fn test_stoer_wagner_complete_k4() {
-        let mut edges = Vec::new();
-        for i in 0..4 {
-            for j in (i + 1)..4 {
-                edges.push(make_edge(i, j, 1.0));
-            }
-        }
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges,
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let result = stoer_wagner_mincut(&graph).unwrap();
-        assert!(
-            (result.cut_value - 3.0).abs() < 1e-9,
-            "Expected mincut 3.0 for K4, got {}",
-            result.cut_value
-        );
-    }
-
-    /// Two disconnected components: mincut = 0.
-    #[test]
-    fn test_stoer_wagner_disconnected() {
-        let graph = BrainGraph {
-            num_nodes: 4,
-            edges: vec![
-                make_edge(0, 1, 5.0),
-                make_edge(2, 3, 5.0),
-            ],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(4),
-        };
-
-        let result = stoer_wagner_mincut(&graph).unwrap();
-        assert!(
-            result.cut_value.abs() < 1e-9,
-            "Expected mincut 0.0 for disconnected graph, got {}",
-            result.cut_value
-        );
-    }
-
-    /// Graph with a single node should return an error.
-    #[test]
-    fn test_stoer_wagner_single_node() {
-        let graph = BrainGraph {
-            num_nodes: 1,
-            edges: vec![],
-            timestamp: 0.0,
-            window_duration_s: 1.0,
-            atlas: Atlas::Custom(1),
-        };
-        assert!(stoer_wagner_mincut(&graph).is_err());
-    }
-
-    /// Complete graph K_n: mincut = n - 1 (unit weights).
-    #[test]
-    fn test_stoer_wagner_complete_kn() {
-        for n in 3..=6 {
-            let mut edges = Vec::new();
-            for i in 0..n {
-                for j in (i + 1)..n {
-                    edges.push(make_edge(i, j, 1.0));
-                }
-            }
-            let graph = BrainGraph {
-                num_nodes: n,
-                edges,
-                timestamp: 0.0,
-                window_duration_s: 1.0,
-                atlas: Atlas::Custom(n),
-            };
-            let result = stoer_wagner_mincut(&graph).unwrap();
-            let expected = (n - 1) as f64;
-            assert!(
-                (result.cut_value - expected).abs() < 1e-9,
-                "K{}: expected mincut {}, got {}",
-                n,
-                expected,
-                result.cut_value
-            );
-        }
-    }
-}
@@ -1,25 +0,0 @@
-[package]
-name = "ruv-neural-sensor"
-description = "rUv Neural — Sensor data acquisition for NV diamond, OPM, EEG, and simulated sources"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["simulator"]
-simulator = []
-nv_diamond = []
-opm = []
-eeg = []
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-serde = { workspace = true }
-serde_json = { workspace = true }
-tracing = { workspace = true }
-rand = { workspace = true }
-num-traits = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
@@ -1,92 +0,0 @@
-# ruv-neural-sensor
-
-Sensor data acquisition for NV diamond, OPM, EEG, and simulated sources.
-
-## Overview
-
-`ruv-neural-sensor` provides uniform sensor interfaces for multiple neural
-magnetometry and electrophysiology sensor types. Each sensor backend implements
-the `SensorSource` trait from `ruv-neural-core`, producing `MultiChannelTimeSeries`
-data. The crate also includes calibration utilities and real-time signal quality
-monitoring.
-
-## Features
-
- **Simulated sensor** (`simulator` feature, default): Synthetic multi-channel data
-  generation with configurable alpha rhythm injection, noise floor control, and
-  event injection (spikes, artifacts)
- **NV diamond** (`nv_diamond` feature): Nitrogen-vacancy diamond magnetometer
-  interface with configurable sensitivity and channel layout
- **OPM** (`opm` feature): Optically pumped magnetometer array with configurable
-  geometry
- **EEG** (`eeg` feature): Electroencephalography sensor interface
- **Calibration**: Gain/offset correction, noise floor estimation, and cross-calibration
-  between reference and target channels
- **Quality monitoring**: Real-time SNR estimation, artifact probability scoring,
-  and saturation detection with configurable alert thresholds
-
-## Usage
-
-```rust
-use ruv_neural_sensor::simulator::{SimulatedSensorArray, SensorEvent};
-use ruv_neural_sensor::{SensorSource, SensorType};
-
-// Create a simulated 16-channel array at 1000 Hz
-let mut sim = SimulatedSensorArray::new(16, 1000.0);
-sim.inject_alpha(100.0); // 100 fT alpha rhythm
-
-// Read 500 samples via the SensorSource trait
-let data = sim.read_chunk(500).unwrap();
-assert_eq!(data.num_channels, 16);
-assert_eq!(data.num_samples, 500);
-
-// Inject a spike event
-sim.inject_event(SensorEvent::Spike {
-    channel: 0,
-    amplitude_ft: 500.0,
-    sample_offset: 100,
-});
-
-// Calibrate channels
-use ruv_neural_sensor::calibration::{CalibrationData, calibrate_channel};
-let cal = CalibrationData {
-    gains: vec![2.0],
-    offsets: vec![10.0],
-    noise_floors: vec![1.0],
-};
-let corrected = calibrate_channel(100.0, 0, &cal); // (100 - 10) * 2 = 180
-
-// Monitor signal quality
-use ruv_neural_sensor::quality::QualityMonitor;
-let mut monitor = QualityMonitor::new(2);
-let qualities = monitor.check_quality(&[&data.data[0], &data.data[1]]);
-```
-
-## API Reference
-
-| Module        | Key Types / Functions                                        |
-|---------------|--------------------------------------------------------------|
-| `simulator`   | `SimulatedSensorArray`, `SensorEvent`                        |
-| `nv_diamond`  | `NvDiamondArray`, `NvDiamondConfig`                          |
-| `opm`         | `OpmArray`, `OpmConfig`                                      |
-| `eeg`         | `EegArray`, `EegConfig`                                      |
-| `calibration` | `CalibrationData`, `calibrate_channel`, `cross_calibrate`    |
-| `quality`     | `QualityMonitor`, `SignalQuality`                            |
-
-## Feature Flags
-
-| Feature     | Default | Description                          |
-|-------------|---------|--------------------------------------|
-| `simulator` | Yes     | Synthetic test data generator        |
-| `nv_diamond`| No      | NV diamond magnetometer backend      |
-| `opm`       | No      | Optically pumped magnetometer backend|
-| `eeg`       | No      | EEG sensor backend                   |
-
-## Integration
-
-Depends on `ruv-neural-core` for the `SensorSource` trait and `MultiChannelTimeSeries`
-type. Produced data feeds into `ruv-neural-signal` for preprocessing and filtering.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,60 +0,0 @@
-//! Sensor calibration utilities for gain/offset correction and cross-calibration.
-
-/// Calibration data for a sensor array.
-pub struct CalibrationData {
-    /// Per-channel gain factors.
-    pub gains: Vec<f64>,
-    /// Per-channel DC offsets to subtract.
-    pub offsets: Vec<f64>,
-    /// Per-channel noise floor estimates (fT RMS).
-    pub noise_floors: Vec<f64>,
-}
-
-/// Apply gain and offset correction to a single sample on a given channel.
-///
-/// `corrected = (raw - offset) * gain`
-pub fn calibrate_channel(raw: f64, channel: usize, cal: &CalibrationData) -> f64 {
-    let offset = cal.offsets.get(channel).copied().unwrap_or(0.0);
-    let gain = cal.gains.get(channel).copied().unwrap_or(1.0);
-    (raw - offset) * gain
-}
-
-/// Estimate the noise floor (RMS) of a quiet signal segment.
-pub fn estimate_noise_floor(signal: &[f64]) -> f64 {
-    if signal.is_empty() {
-        return 0.0;
-    }
-    let mean_sq = signal.iter().map(|x| x * x).sum::<f64>() / signal.len() as f64;
-    mean_sq.sqrt()
-}
-
-/// Cross-calibrate a target channel against a reference channel.
-///
-/// Returns `(gain, offset)` such that `target * gain + offset ~ reference`.
-/// Uses simple linear regression.
-pub fn cross_calibrate(reference: &[f64], target: &[f64]) -> (f64, f64) {
-    let n = reference.len().min(target.len());
-    if n == 0 {
-        return (1.0, 0.0);
-    }
-
-    let mean_r = reference[..n].iter().sum::<f64>() / n as f64;
-    let mean_t = target[..n].iter().sum::<f64>() / n as f64;
-
-    let mut num = 0.0;
-    let mut den = 0.0;
-    for i in 0..n {
-        let dr = reference[i] - mean_r;
-        let dt = target[i] - mean_t;
-        num += dr * dt;
-        den += dt * dt;
-    }
-
-    if den.abs() < 1e-15 {
-        return (1.0, mean_r - mean_t);
-    }
-
-    let gain = num / den;
-    let offset = mean_r - gain * mean_t;
-    (gain, offset)
-}
@@ -1,375 +0,0 @@
-//! EEG (Electroencephalography) interface.
-//!
-//! Provides a sensor interface for standard EEG systems using the 10-20
-//! international electrode placement system. Generates physically realistic
-//! EEG signals in microvolts including delta, theta, alpha, beta, and gamma
-//! rhythms, spatial coherence between nearby electrodes, eye blink artifacts,
-//! muscle artifacts, and powerline noise. Included as a comparison/fallback
-//! modality alongside higher-sensitivity magnetometer arrays.
-
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::sensor::{SensorArray, SensorChannel, SensorType};
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::traits::SensorSource;
-use serde::{Deserialize, Serialize};
-use std::f64::consts::PI;
-
-/// Standard 10-20 system electrode labels (21 channels).
-pub const STANDARD_10_20_LABELS: &[&str] = &[
-    "Fp1", "Fp2", "F7", "F3", "Fz", "F4", "F8", "T3", "C3", "Cz", "C4", "T4", "T5", "P3",
-    "Pz", "P4", "T6", "O1", "Oz", "O2", "A1",
-];
-
-/// Standard 10-20 system approximate positions on a unit sphere (nasion-inion axis = Y).
-fn standard_10_20_positions() -> Vec<[f64; 3]> {
-    // Simplified spherical positions for the 21-channel 10-20 montage.
-    let r = 0.09; // ~9 cm radius
-    STANDARD_10_20_LABELS
-        .iter()
-        .enumerate()
-        .map(|(i, _)| {
-            let phi = 2.0 * PI * i as f64 / STANDARD_10_20_LABELS.len() as f64;
-            let theta = PI / 3.0 + (i as f64 / STANDARD_10_20_LABELS.len() as f64) * PI / 3.0;
-            [
-                r * theta.sin() * phi.cos(),
-                r * theta.sin() * phi.sin(),
-                r * theta.cos(),
-            ]
-        })
-        .collect()
-}
-
-/// Configuration for an EEG sensor array.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct EegConfig {
-    /// Number of EEG channels.
-    pub num_channels: usize,
-    /// Sample rate in Hz.
-    pub sample_rate_hz: f64,
-    /// Channel labels (e.g., "Fp1", "Fz", etc.).
-    pub labels: Vec<String>,
-    /// Channel positions in head-frame coordinates.
-    pub positions: Vec<[f64; 3]>,
-    /// Reference electrode label (e.g., "A1" for linked ears).
-    pub reference: String,
-    /// Per-channel impedance in kOhm (None = not measured yet).
-    pub impedances_kohm: Vec<Option<f64>>,
-}
-
-impl Default for EegConfig {
-    fn default() -> Self {
-        let labels: Vec<String> = STANDARD_10_20_LABELS.iter().map(|s| s.to_string()).collect();
-        let num_channels = labels.len();
-        let positions = standard_10_20_positions();
-        Self {
-            num_channels,
-            sample_rate_hz: 256.0,
-            labels,
-            positions,
-            reference: "A1".to_string(),
-            impedances_kohm: vec![None; num_channels],
-        }
-    }
-}
-
-/// EEG sensor array.
-///
-/// Provides the [`SensorSource`] interface for EEG acquisition. Generates
-/// physiologically realistic EEG signals in microvolts with proper frequency
-/// band amplitudes, spatial coherence, and characteristic artifacts (eye
-/// blinks, muscle, powerline).
-#[derive(Debug)]
-pub struct EegArray {
-    config: EegConfig,
-    array: SensorArray,
-    sample_counter: u64,
-    /// Shared-source oscillator phases per frequency band, used to create
-    /// spatial coherence between nearby electrodes. Each band has one
-    /// "source" phase that all channels mix in proportionally.
-    source_phases: BrainSources,
-}
-
-/// Internal state for spatially coherent brain rhythm generation.
-#[derive(Debug, Clone)]
-struct BrainSources {
-    /// Delta (1-4 Hz): deep sleep, ~50 uV
-    delta_phase: f64,
-    /// Theta (4-8 Hz): drowsiness, ~30 uV
-    theta_phase: f64,
-    /// Alpha (8-13 Hz): relaxed wakefulness, ~40 uV
-    alpha_phase: f64,
-    /// Beta (13-30 Hz): active thinking, ~10 uV
-    beta_phase: f64,
-    /// Gamma (30-100 Hz): cognitive binding, ~3 uV
-    gamma_phase: f64,
-    /// Time of next eye blink event (in seconds from start).
-    next_blink_time: f64,
-}
-
-impl BrainSources {
-    fn new() -> Self {
-        Self {
-            delta_phase: 0.0,
-            theta_phase: 0.0,
-            alpha_phase: 0.0,
-            beta_phase: 0.0,
-            gamma_phase: 0.0,
-            next_blink_time: 4.0, // first blink around 4 seconds
-        }
-    }
-}
-
-/// Generate a single Gaussian sample using Box-Muller transform.
-fn box_muller_single(rng: &mut impl rand::Rng) -> f64 {
-    let u1: f64 = rand::Rng::gen::<f64>(rng).max(1e-15);
-    let u2: f64 = rand::Rng::gen(rng);
-    (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos()
-}
-
-/// Compute Euclidean distance between two 3D points.
-fn distance(a: &[f64; 3], b: &[f64; 3]) -> f64 {
-    ((a[0] - b[0]).powi(2) + (a[1] - b[1]).powi(2) + (a[2] - b[2]).powi(2)).sqrt()
-}
-
-/// Check if a channel label is a frontal-polar electrode (eye blink target).
-fn is_frontal_polar(label: &str) -> bool {
-    label == "Fp1" || label == "Fp2"
-}
-
-/// Check if a channel label is a temporal electrode (muscle artifact target).
-fn is_temporal(label: &str) -> bool {
-    label == "T3" || label == "T4" || label == "T5" || label == "T6"
-}
-
-impl EegArray {
-    /// Create a new EEG array from configuration.
-    pub fn new(config: EegConfig) -> Self {
-        let channels = (0..config.num_channels)
-            .map(|i| {
-                let pos = config.positions.get(i).copied().unwrap_or([0.0, 0.0, 0.0]);
-                let label = config
-                    .labels
-                    .get(i)
-                    .cloned()
-                    .unwrap_or_else(|| format!("EEG-{}", i));
-                SensorChannel {
-                    id: i,
-                    sensor_type: SensorType::Eeg,
-                    position: pos,
-                    orientation: [0.0, 0.0, 1.0],
-                    // EEG sensitivity is much lower than magnetometers.
-                    sensitivity_ft_sqrt_hz: 1000.0,
-                    sample_rate_hz: config.sample_rate_hz,
-                    label,
-                }
-            })
-            .collect();
-
-        let array = SensorArray {
-            channels,
-            sensor_type: SensorType::Eeg,
-            name: "EegArray".to_string(),
-        };
-
-        Self {
-            config,
-            array,
-            sample_counter: 0,
-            source_phases: BrainSources::new(),
-        }
-    }
-
-    /// Returns the sensor array metadata.
-    pub fn sensor_array(&self) -> &SensorArray {
-        &self.array
-    }
-
-    /// Update impedance measurement for a channel.
-    pub fn set_impedance(&mut self, channel: usize, impedance_kohm: f64) -> Result<()> {
-        if channel >= self.config.num_channels {
-            return Err(RuvNeuralError::ChannelOutOfRange {
-                channel,
-                max: self.config.num_channels - 1,
-            });
-        }
-        self.config.impedances_kohm[channel] = Some(impedance_kohm);
-        Ok(())
-    }
-
-    /// Check if all channels have acceptable impedance (< 5 kOhm).
-    pub fn impedance_ok(&self) -> bool {
-        self.config.impedances_kohm.iter().all(|imp| {
-            imp.map_or(false, |v| v < 5.0)
-        })
-    }
-
-    /// Get channels with high impedance (> threshold kOhm).
-    pub fn high_impedance_channels(&self, threshold_kohm: f64) -> Vec<usize> {
-        self.config
-            .impedances_kohm
-            .iter()
-            .enumerate()
-            .filter_map(|(i, imp)| {
-                imp.and_then(|v| if v > threshold_kohm { Some(i) } else { None })
-            })
-            .collect()
-    }
-
-    /// Get the reference electrode label.
-    pub fn reference(&self) -> &str {
-        &self.config.reference
-    }
-
-    /// Re-reference data to average reference.
-    ///
-    /// Subtracts the mean across channels at each time point.
-    pub fn average_reference(data: &mut [Vec<f64>]) {
-        if data.is_empty() {
-            return;
-        }
-        let num_samples = data[0].len();
-        let num_channels = data.len();
-        for s in 0..num_samples {
-            let mean: f64 = data.iter().map(|ch| ch[s]).sum::<f64>() / num_channels as f64;
-            for ch in data.iter_mut() {
-                ch[s] -= mean;
-            }
-        }
-    }
-
-    /// Compute spatial correlation factor between two electrodes.
-    /// Returns a value in [0, 1] where 1 = same location, decaying with distance.
-    fn spatial_correlation(&self, ch_a: usize, ch_b: usize) -> f64 {
-        let pos_a = self.config.positions.get(ch_a).unwrap_or(&[0.0, 0.0, 0.0]);
-        let pos_b = self.config.positions.get(ch_b).unwrap_or(&[0.0, 0.0, 0.0]);
-        let d = distance(pos_a, pos_b);
-        // Exponential decay with length constant ~5 cm.
-        (-d / 0.05).exp()
-    }
-
-    /// Generate an eye blink artifact waveform at a given time relative to
-    /// blink onset. Returns amplitude in microvolts. Blink duration ~0.3s.
-    fn blink_waveform(t_since_onset: f64) -> f64 {
-        let duration = 0.3;
-        if t_since_onset < 0.0 || t_since_onset > duration {
-            return 0.0;
-        }
-        // Smooth half-sinusoidal shape, peak ~100 uV
-        let phase = PI * t_since_onset / duration;
-        100.0 * phase.sin()
-    }
-}
-
-impl SensorSource for EegArray {
-    fn sensor_type(&self) -> SensorType {
-        SensorType::Eeg
-    }
-
-    fn num_channels(&self) -> usize {
-        self.config.num_channels
-    }
-
-    fn sample_rate_hz(&self) -> f64 {
-        self.config.sample_rate_hz
-    }
-
-    fn read_chunk(&mut self, num_samples: usize) -> Result<MultiChannelTimeSeries> {
-        let timestamp = self.sample_counter as f64 / self.config.sample_rate_hz;
-        let dt = 1.0 / self.config.sample_rate_hz;
-        let powerline_freq = 60.0; // Hz
-
-        let mut rng = rand::thread_rng();
-
-        // Pre-compute channel properties.
-        let labels: Vec<String> = (0..self.config.num_channels)
-            .map(|i| {
-                self.config
-                    .labels
-                    .get(i)
-                    .cloned()
-                    .unwrap_or_default()
-            })
-            .collect();
-
-        // Generate per-sample shared source oscillations first, then mix
-        // into each channel with spatial coherence.
-        // Frequencies: delta=2Hz, theta=6Hz, alpha=10Hz, beta=20Hz, gamma=40Hz
-        let delta_freq = 2.0;
-        let theta_freq = 6.0;
-        let alpha_freq = 10.0;
-        let beta_freq = 20.0;
-        let gamma_freq = 40.0;
-
-        // Amplitudes in microvolts (peak)
-        let delta_amp = 50.0;
-        let theta_amp = 30.0;
-        let alpha_amp = 40.0;
-        let beta_amp = 10.0;
-        let gamma_amp = 3.0;
-
-        let data: Vec<Vec<f64>> = (0..self.config.num_channels)
-            .map(|ch| {
-                let label = &labels[ch];
-                let frontal = is_frontal_polar(label);
-                let temporal = is_temporal(label);
-
-                // Noise floor based on impedance. Higher impedance = more noise.
-                let impedance = self.config.impedances_kohm[ch].unwrap_or(5.0);
-                // Thermal noise: ~0.5 uV per sqrt(kOhm) as a rough model
-                let noise_sigma = 0.5 * impedance.sqrt();
-
-                // Per-channel phase offset for spatial variation
-                let ch_phase = 0.5 * ch as f64;
-
-                (0..num_samples)
-                    .map(|s| {
-                        let t = timestamp + s as f64 * dt;
-
-                        // 1. Brain rhythms with per-channel phase offsets
-                        let delta = delta_amp * (2.0 * PI * delta_freq * t + ch_phase * 0.2).sin();
-                        let theta = theta_amp * (2.0 * PI * theta_freq * t + ch_phase * 0.3).sin();
-                        let alpha = alpha_amp * (2.0 * PI * alpha_freq * t + ch_phase * 0.4).sin();
-                        let beta = beta_amp * (2.0 * PI * beta_freq * t + ch_phase * 0.6).sin();
-                        let gamma = gamma_amp * (2.0 * PI * gamma_freq * t + ch_phase * 0.8).sin();
-                        let brain = delta + theta + alpha + beta + gamma;
-
-                        // 2. Eye blink artifact on frontal-polar channels
-                        let blink = if frontal {
-                            let t_since_blink = t - self.source_phases.next_blink_time;
-                            Self::blink_waveform(t_since_blink)
-                        } else {
-                            0.0
-                        };
-
-                        // 3. Muscle artifact on temporal channels (broadband high-frequency)
-                        let muscle = if temporal {
-                            // Simulate as burst of high-frequency activity (~5 uV RMS)
-                            5.0 * box_muller_single(&mut rng)
-                        } else {
-                            0.0
-                        };
-
-                        // 4. Powerline noise (small, ~1-2 uV)
-                        let line_noise = 1.5 * (2.0 * PI * powerline_freq * t).sin();
-
-                        // 5. White noise floor (electrode thermal noise)
-                        let white = noise_sigma * box_muller_single(&mut rng);
-
-                        brain + blink + muscle + line_noise + white
-                    })
-                    .collect()
-            })
-            .collect();
-
-        // Schedule next blink if current chunk passed the blink time.
-        let chunk_end_time = timestamp + num_samples as f64 * dt;
-        if chunk_end_time > self.source_phases.next_blink_time + 0.3 {
-            // Next blink in 4-6 seconds (deterministic offset from current time).
-            let interval = 4.0 + (self.sample_counter as f64 * 0.618).sin().abs() * 2.0;
-            self.source_phases.next_blink_time = chunk_end_time + interval;
-        }
-
-        self.sample_counter += num_samples as u64;
-        MultiChannelTimeSeries::new(data, self.config.sample_rate_hz, timestamp)
-    }
-}
@@ -1,261 +0,0 @@
-//! rUv Neural Sensor -- sensor data acquisition for NV diamond, OPM, EEG,
-//! and simulated sources.
-//!
-//! This crate provides uniform sensor interfaces via the [`SensorSource`] trait
-//! from `ruv-neural-core`. Each sensor backend is feature-gated:
-//!
-//! | Feature       | Module         | Sensor Type                        |
-//! |---------------|----------------|------------------------------------|
-//! | `simulator`   | [`simulator`]  | Synthetic test data                |
-//! | `nv_diamond`  | [`nv_diamond`] | Nitrogen-vacancy diamond magnetometer |
-//! | `opm`         | [`opm`]        | Optically pumped magnetometer      |
-//! | `eeg`         | [`eeg`]        | Electroencephalography             |
-//!
-//! The [`calibration`] and [`quality`] modules are always available.
-
-#[cfg(feature = "simulator")]
-pub mod simulator;
-
-#[cfg(feature = "nv_diamond")]
-pub mod nv_diamond;
-
-#[cfg(feature = "opm")]
-pub mod opm;
-
-#[cfg(feature = "eeg")]
-pub mod eeg;
-
-pub mod calibration;
-pub mod quality;
-
-// Re-exports from core for convenience.
-pub use ruv_neural_core::signal::MultiChannelTimeSeries;
-pub use ruv_neural_core::traits::SensorSource;
-pub use ruv_neural_core::{SensorArray, SensorChannel, SensorType};
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn simulator_produces_correct_shape() {
-        let mut sim = simulator::SimulatedSensorArray::new(16, 1000.0);
-        let data = sim.read_chunk(500).expect("read_chunk failed");
-        assert_eq!(data.num_channels, 16);
-        assert_eq!(data.num_samples, 500);
-        assert_eq!(data.sample_rate_hz, 1000.0);
-    }
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn simulator_sensor_type() {
-        let sim = simulator::SimulatedSensorArray::new(8, 500.0);
-        assert_eq!(sim.sensor_type(), SensorType::NvDiamond);
-    }
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn simulator_alpha_rhythm_frequency() {
-        // Generate 2 seconds of data at 1000 Hz to verify alpha peak near 10 Hz.
-        let mut sim = simulator::SimulatedSensorArray::new(1, 1000.0);
-        sim.inject_alpha(100.0); // 100 fT amplitude
-        let data = sim.read_chunk(2000).expect("read_chunk failed");
-        let ch = &data.data[0];
-
-        // Simple DFT at the alpha frequency bin.
-        let n = ch.len();
-        let sample_rate = 1000.0_f64;
-        let target_freq = 10.0_f64;
-        let bin = (target_freq * n as f64 / sample_rate).round() as usize;
-
-        let power_at = |freq_bin: usize| -> f64 {
-            let mut re = 0.0_f64;
-            let mut im = 0.0_f64;
-            for (t, &val) in ch.iter().enumerate() {
-                let angle =
-                    -2.0 * std::f64::consts::PI * freq_bin as f64 * t as f64 / n as f64;
-                re += val * angle.cos();
-                im += val * angle.sin();
-            }
-            (re * re + im * im).sqrt() / n as f64
-        };
-
-        let alpha_power = power_at(bin);
-        let noise_bin = (37.0 * n as f64 / sample_rate).round() as usize;
-        let noise_power = power_at(noise_bin);
-
-        assert!(
-            alpha_power > noise_power * 3.0,
-            "Alpha power ({alpha_power}) should be >> noise power ({noise_power})"
-        );
-    }
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn simulator_noise_floor() {
-        let noise_density = 15.0; // fT/sqrt(Hz)
-        let sample_rate = 1000.0;
-        let mut sim = simulator::SimulatedSensorArray::new(1, sample_rate)
-            .with_noise(noise_density);
-        let data = sim.read_chunk(10000).expect("read_chunk failed");
-        let ch = &data.data[0];
-        let rms = (ch.iter().map(|x| x * x).sum::<f64>() / ch.len() as f64).sqrt();
-
-        // Expected RMS = noise_density * sqrt(sample_rate / 2) for white noise.
-        let expected_rms = noise_density * (sample_rate / 2.0).sqrt();
-
-        // Allow generous tolerance due to randomness.
-        assert!(
-            rms > expected_rms * 0.4 && rms < expected_rms * 1.6,
-            "RMS {rms} not within tolerance of expected {expected_rms}"
-        );
-    }
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn simulator_inject_event() {
-        let mut sim = simulator::SimulatedSensorArray::new(4, 1000.0);
-        sim.inject_event(simulator::SensorEvent::Spike {
-            channel: 0,
-            amplitude_ft: 500.0,
-            sample_offset: 100,
-        });
-        let data = sim.read_chunk(200).expect("read_chunk failed");
-        // The spike should cause a large value near sample 100 in channel 0.
-        let ch0 = &data.data[0];
-        let max_val = ch0.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
-        assert!(
-            max_val > 400.0,
-            "Spike amplitude should be visible, got max {max_val}"
-        );
-    }
-
-    #[test]
-    fn calibration_apply_gain_offset() {
-        let cal = calibration::CalibrationData {
-            gains: vec![2.0, 0.5],
-            offsets: vec![10.0, -5.0],
-            noise_floors: vec![1.0, 2.0],
-        };
-        let corrected = calibration::calibrate_channel(100.0, 0, &cal);
-        // (100.0 - 10.0) * 2.0 = 180.0
-        assert!((corrected - 180.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn calibration_noise_floor_estimate() {
-        let quiet = vec![1.0, -1.0, 1.0, -1.0, 1.0, -1.0];
-        let nf = calibration::estimate_noise_floor(&quiet);
-        // RMS of alternating +/-1 = 1.0
-        assert!((nf - 1.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn calibration_cross_calibrate() {
-        let reference = vec![10.0, 20.0, 30.0, 40.0];
-        let target = vec![5.0, 10.0, 15.0, 20.0];
-        let (gain, offset) = calibration::cross_calibrate(&reference, &target);
-        // target * gain + offset should approximate reference.
-        // 5*2+0=10, 10*2+0=20, etc.
-        assert!((gain - 2.0).abs() < 1e-10);
-        assert!(offset.abs() < 1e-10);
-    }
-
-    #[test]
-    fn quality_detects_low_snr() {
-        let mut monitor = quality::QualityMonitor::new(2);
-
-        // Channel 0: strong signal.
-        let good_signal: Vec<f64> = (0..1000)
-            .map(|i| 100.0 * (2.0 * std::f64::consts::PI * 10.0 * i as f64 / 1000.0).sin())
-            .collect();
-
-        // Channel 1: high-frequency noise (alternating values = maximum first-difference noise).
-        let bad_signal: Vec<f64> = (0..1000)
-            .map(|i| if i % 2 == 0 { 1.0 } else { -1.0 })
-            .collect();
-
-        let qualities = monitor.check_quality(&[&good_signal, &bad_signal]);
-        assert_eq!(qualities.len(), 2);
-        // Smooth sinusoid should have higher SNR than alternating noise.
-        assert!(
-            qualities[0].snr_db > qualities[1].snr_db,
-            "Good SNR ({}) should be > bad SNR ({})",
-            qualities[0].snr_db,
-            qualities[1].snr_db,
-        );
-    }
-
-    #[test]
-    fn quality_saturation_detection() {
-        let mut monitor = quality::QualityMonitor::new(1);
-
-        // A signal that clips at max value for many samples.
-        let saturated: Vec<f64> = (0..1000)
-            .map(|i| if i % 2 == 0 { 1e6 } else { -1e6 })
-            .collect();
-
-        let qualities = monitor.check_quality(&[&saturated]);
-        assert!(qualities[0].saturated);
-    }
-
-    #[test]
-    fn quality_alert_thresholds() {
-        let q_good = quality::SignalQuality {
-            snr_db: 10.0,
-            artifact_probability: 0.1,
-            saturated: false,
-        };
-        assert!(!q_good.below_threshold());
-
-        let q_bad = quality::SignalQuality {
-            snr_db: 2.0,
-            artifact_probability: 0.6,
-            saturated: false,
-        };
-        assert!(q_bad.below_threshold());
-    }
-
-    #[cfg(feature = "simulator")]
-    #[test]
-    fn sensor_source_trait_works() {
-        let mut sim = simulator::SimulatedSensorArray::new(4, 500.0);
-        let source: &mut dyn SensorSource = &mut sim;
-        assert_eq!(source.num_channels(), 4);
-        assert_eq!(source.sample_rate_hz(), 500.0);
-        let data = source.read_chunk(100).expect("read_chunk failed");
-        assert_eq!(data.num_channels, 4);
-        assert_eq!(data.num_samples, 100);
-    }
-
-    #[cfg(feature = "nv_diamond")]
-    #[test]
-    fn nv_diamond_sensor_source() {
-        let config = nv_diamond::NvDiamondConfig::default();
-        let mut nv = nv_diamond::NvDiamondArray::new(config);
-        assert_eq!(nv.sensor_type(), SensorType::NvDiamond);
-        let data = nv.read_chunk(100).expect("read_chunk failed");
-        assert_eq!(data.num_channels, nv.num_channels());
-    }
-
-    #[cfg(feature = "opm")]
-    #[test]
-    fn opm_sensor_source() {
-        let config = opm::OpmConfig::default();
-        let mut opm_arr = opm::OpmArray::new(config);
-        assert_eq!(opm_arr.sensor_type(), SensorType::Opm);
-        let data = opm_arr.read_chunk(100).expect("read_chunk failed");
-        assert_eq!(data.num_channels, opm_arr.num_channels());
-    }
-
-    #[cfg(feature = "eeg")]
-    #[test]
-    fn eeg_sensor_source() {
-        let config = eeg::EegConfig::default();
-        let mut eeg_arr = eeg::EegArray::new(config);
-        assert_eq!(eeg_arr.sensor_type(), SensorType::Eeg);
-        let data = eeg_arr.read_chunk(100).expect("read_chunk failed");
-        assert_eq!(data.num_channels, eeg_arr.num_channels());
-    }
-}
@@ -1,294 +0,0 @@
-//! NV Diamond magnetometer interface.
-//!
-//! Nitrogen-vacancy (NV) centers in diamond provide room-temperature quantum
-//! magnetometry with ~10 fT/sqrt(Hz) sensitivity. This module implements the
-//! acquisition interface, calibration structures, and ODMR-based signal model
-//! for NV diamond arrays.
-
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::sensor::{SensorArray, SensorChannel, SensorType};
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::traits::SensorSource;
-use serde::{Deserialize, Serialize};
-use std::f64::consts::PI;
-
-/// NV center gyromagnetic ratio in GHz/T.
-const GAMMA_NV_GHZ_PER_T: f64 = 28.024;
-
-/// Configuration for an NV diamond magnetometer array.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct NvDiamondConfig {
-    /// Number of diamond sensor chips.
-    pub num_channels: usize,
-    /// Sample rate in Hz.
-    pub sample_rate_hz: f64,
-    /// Laser power in mW per chip.
-    pub laser_power_mw: f64,
-    /// Microwave drive frequency in GHz (near 2.87 GHz zero-field splitting).
-    pub microwave_freq_ghz: f64,
-    /// Positions of each diamond chip in head-frame coordinates (x, y, z in meters).
-    pub chip_positions: Vec<[f64; 3]>,
-}
-
-impl Default for NvDiamondConfig {
-    fn default() -> Self {
-        let num_channels = 16;
-        let positions: Vec<[f64; 3]> = (0..num_channels)
-            .map(|i| {
-                let angle = 2.0 * PI * i as f64 / num_channels as f64;
-                let r = 0.09;
-                [r * angle.cos(), r * angle.sin(), 0.0]
-            })
-            .collect();
-        Self {
-            num_channels,
-            sample_rate_hz: 1000.0,
-            laser_power_mw: 100.0,
-            microwave_freq_ghz: 2.87,
-            chip_positions: positions,
-        }
-    }
-}
-
-/// Per-channel calibration data for NV diamond sensors.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct NvCalibration {
-    /// Sensitivity in fT per fluorescence count, per channel.
-    pub sensitivity_ft_per_count: Vec<f64>,
-    /// Noise floor in fT/sqrt(Hz), per channel.
-    pub noise_floor_ft: Vec<f64>,
-    /// Zero-field splitting offset per channel in MHz.
-    pub zfs_offset_mhz: Vec<f64>,
-}
-
-impl NvCalibration {
-    /// Create default calibration for `n` channels.
-    pub fn default_for(n: usize) -> Self {
-        Self {
-            sensitivity_ft_per_count: vec![0.1; n],
-            noise_floor_ft: vec![10.0; n],
-            zfs_offset_mhz: vec![0.0; n],
-        }
-    }
-}
-
-/// NV Diamond magnetometer array.
-///
-/// Provides the [`SensorSource`] interface for NV diamond magnetometry.
-/// Generates physically realistic ODMR-based magnetic field signals including
-/// neural oscillation bands (alpha, beta, gamma) and sensor-characteristic
-/// noise (1/f pink noise + shot noise).
-#[derive(Debug)]
-pub struct NvDiamondArray {
-    config: NvDiamondConfig,
-    calibration: NvCalibration,
-    array: SensorArray,
-    sample_counter: u64,
-    /// Pink noise state per channel (1/f generator using Voss-McCartney algorithm).
-    pink_state: Vec<PinkNoiseGen>,
-}
-
-/// Voss-McCartney pink noise generator (8 octaves).
-#[derive(Debug, Clone)]
-struct PinkNoiseGen {
-    octaves: [f64; 8],
-    counter: u32,
-}
-
-impl PinkNoiseGen {
-    fn new() -> Self {
-        Self {
-            octaves: [0.0; 8],
-            counter: 0,
-        }
-    }
-
-    /// Generate the next pink noise sample using the Voss-McCartney algorithm.
-    /// Returns a value with approximate unit variance when averaged.
-    fn next(&mut self, rng: &mut impl rand::Rng) -> f64 {
-        self.counter = self.counter.wrapping_add(1);
-        let changed = self.counter;
-        // Update octave i when bit i flips from 0 to 1
-        for i in 0..8u32 {
-            if changed & (1 << i) != 0 {
-                self.octaves[i as usize] = box_muller_single(rng);
-                break; // Voss-McCartney: only update the lowest changed bit
-            }
-        }
-        // Sum all octaves and normalize
-        let sum: f64 = self.octaves.iter().sum();
-        sum / (8.0_f64).sqrt()
-    }
-}
-
-/// Generate a single Gaussian sample using Box-Muller transform.
-fn box_muller_single(rng: &mut impl rand::Rng) -> f64 {
-    let u1: f64 = rand::Rng::gen::<f64>(rng).max(1e-15);
-    let u2: f64 = rand::Rng::gen(rng);
-    (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos()
-}
-
-impl NvDiamondArray {
-    /// Create a new NV diamond array from configuration.
-    pub fn new(config: NvDiamondConfig) -> Self {
-        let calibration = NvCalibration::default_for(config.num_channels);
-        let channels = (0..config.num_channels)
-            .map(|i| {
-                let pos = config
-                    .chip_positions
-                    .get(i)
-                    .copied()
-                    .unwrap_or([0.0, 0.0, 0.0]);
-                SensorChannel {
-                    id: i,
-                    sensor_type: SensorType::NvDiamond,
-                    position: pos,
-                    orientation: [0.0, 0.0, 1.0],
-                    sensitivity_ft_sqrt_hz: calibration.noise_floor_ft[i],
-                    sample_rate_hz: config.sample_rate_hz,
-                    label: format!("NV-{:03}", i),
-                }
-            })
-            .collect();
-
-        let array = SensorArray {
-            channels,
-            sensor_type: SensorType::NvDiamond,
-            name: "NvDiamondArray".to_string(),
-        };
-
-        let pink_state = (0..config.num_channels)
-            .map(|_| PinkNoiseGen::new())
-            .collect();
-
-        Self {
-            config,
-            calibration,
-            array,
-            sample_counter: 0,
-            pink_state,
-        }
-    }
-
-    /// Returns the sensor array metadata.
-    pub fn sensor_array(&self) -> &SensorArray {
-        &self.array
-    }
-
-    /// Set custom calibration data.
-    pub fn with_calibration(mut self, calibration: NvCalibration) -> Result<Self> {
-        if calibration.sensitivity_ft_per_count.len() != self.config.num_channels {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: self.config.num_channels,
-                got: calibration.sensitivity_ft_per_count.len(),
-            });
-        }
-        self.calibration = calibration;
-        Ok(self)
-    }
-
-    /// Get the current calibration data.
-    pub fn calibration(&self) -> &NvCalibration {
-        &self.calibration
-    }
-
-    /// Convert raw fluorescence counts to magnetic field (fT) via ODMR analysis.
-    ///
-    /// Models the ODMR dip as a Lorentzian centered at the zero-field splitting
-    /// frequency (2.87 GHz + channel offset). The fluorescence value represents
-    /// a deviation from the baseline ODMR dip depth, which is proportional to
-    /// the magnetic field via the NV gyromagnetic ratio (28.024 GHz/T).
-    ///
-    /// The conversion applies per-channel calibration sensitivity to translate
-    /// the fluorescence deviation into a field measurement in femtotesla.
-    pub fn odmr_to_field(&self, fluorescence: f64, channel: usize) -> Result<f64> {
-        if channel >= self.config.num_channels {
-            return Err(RuvNeuralError::ChannelOutOfRange {
-                channel,
-                max: self.config.num_channels - 1,
-            });
-        }
-        // The fluorescence deviation from baseline is proportional to the
-        // resonance frequency shift. Convert via calibrated sensitivity.
-        // field_ft = (fluorescence - baseline) * sensitivity_ft_per_count
-        // The baseline is implicitly zero in our convention (deviation from it).
-        let field_ft = fluorescence * self.calibration.sensitivity_ft_per_count[channel];
-        Ok(field_ft)
-    }
-
-    /// Generate the brain signal component at a given time (in seconds) for
-    /// a given channel, returning the value in femtotesla.
-    ///
-    /// Models superimposed neural oscillation bands:
-    /// - Alpha (8-13 Hz): ~50 fT
-    /// - Beta (13-30 Hz): ~20 fT
-    /// - Gamma (30-100 Hz): ~5 fT
-    fn brain_signal_ft(&self, t: f64, ch: usize) -> f64 {
-        let sens = self.calibration.sensitivity_ft_per_count[ch];
-        // Scale amplitudes by channel sensitivity (higher sensitivity = larger signal)
-        let scale = sens / 0.1; // normalized to default sensitivity
-
-        // Alpha band: 10 Hz representative frequency
-        let alpha = 50.0 * scale * (2.0 * PI * 10.0 * t + 0.3 * ch as f64).sin();
-        // Beta band: 20 Hz representative frequency
-        let beta = 20.0 * scale * (2.0 * PI * 20.0 * t + 0.7 * ch as f64).sin();
-        // Gamma band: 40 Hz representative frequency
-        let gamma = 5.0 * scale * (2.0 * PI * 40.0 * t + 1.1 * ch as f64).sin();
-
-        alpha + beta + gamma
-    }
-}
-
-impl SensorSource for NvDiamondArray {
-    fn sensor_type(&self) -> SensorType {
-        SensorType::NvDiamond
-    }
-
-    fn num_channels(&self) -> usize {
-        self.config.num_channels
-    }
-
-    fn sample_rate_hz(&self) -> f64 {
-        self.config.sample_rate_hz
-    }
-
-    fn read_chunk(&mut self, num_samples: usize) -> Result<MultiChannelTimeSeries> {
-        let timestamp = self.sample_counter as f64 / self.config.sample_rate_hz;
-        let dt = 1.0 / self.config.sample_rate_hz;
-
-        let mut rng = rand::thread_rng();
-        let data: Vec<Vec<f64>> = (0..self.config.num_channels)
-            .map(|ch| {
-                let noise_floor = self.calibration.noise_floor_ft[ch];
-                // White noise (shot noise) scaled to noise floor.
-                // noise_floor is in fT/sqrt(Hz), convert to per-sample sigma.
-                let white_sigma = noise_floor * (self.config.sample_rate_hz / 2.0).sqrt();
-
-                // 1/f (pink) noise amplitude: comparable to white noise floor
-                // but spectrally shaped to dominate at low frequencies.
-                let pink_amplitude = noise_floor * 2.0;
-
-                (0..num_samples)
-                    .map(|s| {
-                        let t = timestamp + s as f64 * dt;
-
-                        // 1. Brain signal: alpha + beta + gamma oscillations
-                        let brain = self.brain_signal_ft(t, ch);
-
-                        // 2. 1/f (pink) noise from Voss-McCartney generator
-                        let pink = pink_amplitude * self.pink_state[ch].next(&mut rng);
-
-                        // 3. White (shot) noise floor
-                        let white = white_sigma * box_muller_single(&mut rng);
-
-                        // Sum all components
-                        brain + pink + white
-                    })
-                    .collect()
-            })
-            .collect();
-
-        self.sample_counter += num_samples as u64;
-        MultiChannelTimeSeries::new(data, self.config.sample_rate_hz, timestamp)
-    }
-}
@@ -1,500 +0,0 @@
-//! OPM (Optically Pumped Magnetometer) interface.
-//!
-//! OPMs operating in SERF (Spin-Exchange Relaxation Free) mode provide
-//! ~7 fT/sqrt(Hz) sensitivity in a compact, cryogen-free package suitable
-//! for wearable MEG systems. This module implements the acquisition interface,
-//! cross-talk compensation via Gaussian elimination, active shielding, and a
-//! physically realistic signal model with neural oscillations and powerline
-//! interference.
-
-use ruv_neural_core::error::{Result, RuvNeuralError};
-use ruv_neural_core::sensor::{SensorArray, SensorChannel, SensorType};
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::traits::SensorSource;
-use serde::{Deserialize, Serialize};
-use std::f64::consts::PI;
-
-/// Configuration for an OPM sensor array.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct OpmConfig {
-    /// Number of OPM sensors.
-    pub num_channels: usize,
-    /// Sample rate in Hz.
-    pub sample_rate_hz: f64,
-    /// Whether SERF mode is enabled (spin-exchange relaxation free).
-    pub serf_mode: bool,
-    /// Helmet geometry: channel positions in head-frame coordinates.
-    pub channel_positions: Vec<[f64; 3]>,
-    /// Per-channel sensitivity in fT/sqrt(Hz).
-    pub sensitivities: Vec<f64>,
-    /// Cross-talk matrix (num_channels x num_channels).
-    /// `cross_talk[i][j]` is the coupling from channel j into channel i.
-    pub cross_talk: Vec<Vec<f64>>,
-    /// Active shielding compensation coefficients per channel.
-    pub active_shielding_coeffs: Vec<f64>,
-}
-
-impl Default for OpmConfig {
-    fn default() -> Self {
-        let num_channels = 32;
-        let positions: Vec<[f64; 3]> = (0..num_channels)
-            .map(|i| {
-                let phi = 2.0 * PI * i as f64 / num_channels as f64;
-                let theta = PI / 4.0 + (i as f64 / num_channels as f64) * PI / 2.0;
-                let r = 0.1;
-                [
-                    r * theta.sin() * phi.cos(),
-                    r * theta.sin() * phi.sin(),
-                    r * theta.cos(),
-                ]
-            })
-            .collect();
-        let sensitivities = vec![7.0; num_channels];
-        // Identity cross-talk (no coupling).
-        let cross_talk = (0..num_channels)
-            .map(|i| {
-                (0..num_channels)
-                    .map(|j| if i == j { 1.0 } else { 0.0 })
-                    .collect()
-            })
-            .collect();
-        let active_shielding_coeffs = vec![1.0; num_channels];
-
-        Self {
-            num_channels,
-            sample_rate_hz: 1000.0,
-            serf_mode: true,
-            channel_positions: positions,
-            sensitivities,
-            cross_talk,
-            active_shielding_coeffs,
-        }
-    }
-}
-
-/// OPM sensor array.
-///
-/// Provides the [`SensorSource`] interface for optically pumped magnetometry.
-/// Generates SERF-mode magnetometer signals with realistic bandwidth (DC to
-/// ~200 Hz), neural oscillations (alpha/beta/gamma), powerline harmonics,
-/// and applies full cross-talk compensation and active shielding.
-#[derive(Debug)]
-pub struct OpmArray {
-    config: OpmConfig,
-    array: SensorArray,
-    sample_counter: u64,
-}
-
-impl OpmArray {
-    /// Create a new OPM array from configuration.
-    pub fn new(config: OpmConfig) -> Self {
-        let channels = (0..config.num_channels)
-            .map(|i| {
-                let pos = config
-                    .channel_positions
-                    .get(i)
-                    .copied()
-                    .unwrap_or([0.0, 0.0, 0.0]);
-                let sens = config.sensitivities.get(i).copied().unwrap_or(7.0);
-                SensorChannel {
-                    id: i,
-                    sensor_type: SensorType::Opm,
-                    position: pos,
-                    orientation: [0.0, 0.0, 1.0],
-                    sensitivity_ft_sqrt_hz: sens,
-                    sample_rate_hz: config.sample_rate_hz,
-                    label: format!("OPM-{:03}", i),
-                }
-            })
-            .collect();
-
-        let array = SensorArray {
-            channels,
-            sensor_type: SensorType::Opm,
-            name: "OpmArray".to_string(),
-        };
-
-        Self {
-            config,
-            array,
-            sample_counter: 0,
-        }
-    }
-
-    /// Returns the sensor array metadata.
-    pub fn sensor_array(&self) -> &SensorArray {
-        &self.array
-    }
-
-    /// Apply cross-talk compensation to raw channel data.
-    ///
-    /// Solves the linear system `cross_talk * corrected = raw` to obtain
-    /// `corrected = inv(cross_talk) * raw`. Falls back to diagonal-only
-    /// correction if the cross-talk matrix is singular.
-    pub fn compensate_cross_talk(&self, raw: &mut [f64]) -> Result<()> {
-        if raw.len() != self.config.num_channels {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: self.config.num_channels,
-                got: raw.len(),
-            });
-        }
-        if let Some(corrected) = solve_linear_system(&self.config.cross_talk, raw) {
-            raw.copy_from_slice(&corrected);
-        } else {
-            // Fallback: diagonal scaling when the matrix is singular.
-            for (i, val) in raw.iter_mut().enumerate() {
-                let diag = self.config.cross_talk[i][i];
-                if diag.abs() > 1e-15 {
-                    *val /= diag;
-                }
-            }
-        }
-        Ok(())
-    }
-
-    /// Apply full cross-talk compensation to an entire time-series matrix.
-    ///
-    /// `data` is laid out as channels x samples. The cross-talk system is
-    /// solved independently for each time point (column).
-    pub fn full_cross_talk_compensation(&self, data: &mut Vec<Vec<f64>>) -> Result<()> {
-        let n = self.config.num_channels;
-        if data.len() != n {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: n,
-                got: data.len(),
-            });
-        }
-        if n == 0 {
-            return Ok(());
-        }
-        let num_samples = data[0].len();
-        for ch_data in data.iter() {
-            if ch_data.len() != num_samples {
-                return Err(RuvNeuralError::Sensor(
-                    "all channels must have the same number of samples".to_string(),
-                ));
-            }
-        }
-
-        for t in 0..num_samples {
-            let mut col: Vec<f64> = data.iter().map(|ch| ch[t]).collect();
-            self.compensate_cross_talk(&mut col)?;
-            for (ch, val) in col.into_iter().enumerate() {
-                data[ch][t] = val;
-            }
-        }
-        Ok(())
-    }
-
-    /// Apply active shielding compensation.
-    pub fn apply_active_shielding(&self, data: &mut [f64]) -> Result<()> {
-        if data.len() != self.config.num_channels {
-            return Err(RuvNeuralError::DimensionMismatch {
-                expected: self.config.num_channels,
-                got: data.len(),
-            });
-        }
-        for (i, val) in data.iter_mut().enumerate() {
-            *val *= self.config.active_shielding_coeffs[i];
-        }
-        Ok(())
-    }
-}
-
-/// Solve the linear system `matrix * x = rhs` using Gaussian elimination
-/// with partial pivoting.
-///
-/// Returns `None` if the matrix is singular (any pivot magnitude < 1e-12).
-fn solve_linear_system(matrix: &[Vec<f64>], rhs: &[f64]) -> Option<Vec<f64>> {
-    let n = rhs.len();
-    if matrix.len() != n {
-        return None;
-    }
-    for row in matrix.iter() {
-        if row.len() != n {
-            return None;
-        }
-    }
-
-    // Build augmented matrix [A | b].
-    let mut aug: Vec<Vec<f64>> = matrix
-        .iter()
-        .enumerate()
-        .map(|(i, row)| {
-            let mut r = row.clone();
-            r.push(rhs[i]);
-            r
-        })
-        .collect();
-
-    // Forward elimination with partial pivoting.
-    for col in 0..n {
-        // Find pivot row.
-        let mut max_abs = aug[col][col].abs();
-        let mut max_row = col;
-        for row in (col + 1)..n {
-            let a = aug[row][col].abs();
-            if a > max_abs {
-                max_abs = a;
-                max_row = row;
-            }
-        }
-        if max_abs < 1e-12 {
-            return None; // Singular.
-        }
-        if max_row != col {
-            aug.swap(col, max_row);
-        }
-
-        let pivot = aug[col][col];
-        for row in (col + 1)..n {
-            let factor = aug[row][col] / pivot;
-            for j in col..=n {
-                let above = aug[col][j];
-                aug[row][j] -= factor * above;
-            }
-        }
-    }
-
-    // Back-substitution.
-    let mut x = vec![0.0; n];
-    for i in (0..n).rev() {
-        let mut sum = aug[i][n];
-        for j in (i + 1)..n {
-            sum -= aug[i][j] * x[j];
-        }
-        if aug[i][i].abs() < 1e-12 {
-            return None;
-        }
-        x[i] = sum / aug[i][i];
-    }
-    Some(x)
-}
-
-impl SensorSource for OpmArray {
-    fn sensor_type(&self) -> SensorType {
-        SensorType::Opm
-    }
-
-    fn num_channels(&self) -> usize {
-        self.config.num_channels
-    }
-
-    fn sample_rate_hz(&self) -> f64 {
-        self.config.sample_rate_hz
-    }
-
-    fn read_chunk(&mut self, num_samples: usize) -> Result<MultiChannelTimeSeries> {
-        let timestamp = self.sample_counter as f64 / self.config.sample_rate_hz;
-        let dt = 1.0 / self.config.sample_rate_hz;
-        let powerline_freq = 60.0; // Hz (could be made configurable)
-
-        let mut rng = rand::thread_rng();
-        let data: Vec<Vec<f64>> = (0..self.config.num_channels)
-            .map(|ch| {
-                let sens = self.config.sensitivities.get(ch).copied().unwrap_or(7.0);
-                // White noise: sensitivity in fT/sqrt(Hz) -> per-sample sigma
-                let white_sigma = sens * (self.config.sample_rate_hz / 2.0).sqrt();
-                let scale = sens / 7.0; // normalized to default sensitivity
-                let shielding = self.config.active_shielding_coeffs
-                    .get(ch).copied().unwrap_or(1.0);
-
-                (0..num_samples)
-                    .map(|s| {
-                        let t = timestamp + s as f64 * dt;
-
-                        // 1. Brain signal: alpha + beta + gamma neural oscillations
-                        let alpha = 50.0 * scale * (2.0 * PI * 10.0 * t + 0.3 * ch as f64).sin();
-                        let beta = 20.0 * scale * (2.0 * PI * 20.0 * t + 0.7 * ch as f64).sin();
-                        let gamma = 5.0 * scale * (2.0 * PI * 40.0 * t + 1.1 * ch as f64).sin();
-                        let brain = alpha + beta + gamma;
-
-                        // 2. Powerline harmonics (50/60 Hz + 2nd/3rd harmonics)
-                        // Active shielding attenuates environmental interference.
-                        // A shielding coeff of 1.0 means "fully compensated" (no residual).
-                        // Values < 1.0 leave residual interference.
-                        let residual = (1.0 - shielding.clamp(0.0, 1.0)).max(0.0);
-                        let powerline = 500.0 * residual
-                            * ((2.0 * PI * powerline_freq * t).sin()
-                                + 0.3 * (2.0 * PI * 2.0 * powerline_freq * t).sin()
-                                + 0.1 * (2.0 * PI * 3.0 * powerline_freq * t).sin());
-
-                        // 3. White noise floor (SERF-mode thermal noise)
-                        let u1: f64 = rand::Rng::gen::<f64>(&mut rng).max(1e-15);
-                        let u2: f64 = rand::Rng::gen(&mut rng);
-                        let white = white_sigma * (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos();
-
-                        brain + powerline + white
-                    })
-                    .collect()
-            })
-            .collect();
-
-        self.sample_counter += num_samples as u64;
-        MultiChannelTimeSeries::new(data, self.config.sample_rate_hz, timestamp)
-    }
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-
-    /// Helper: build a small OpmArray with a given cross-talk matrix.
-    fn make_opm(cross_talk: Vec<Vec<f64>>) -> OpmArray {
-        let n = cross_talk.len();
-        let config = OpmConfig {
-            num_channels: n,
-            sample_rate_hz: 1000.0,
-            serf_mode: true,
-            channel_positions: vec![[0.0, 0.0, 0.0]; n],
-            sensitivities: vec![7.0; n],
-            cross_talk,
-            active_shielding_coeffs: vec![1.0; n],
-        };
-        OpmArray::new(config)
-    }
-
-    #[test]
-    fn identity_cross_talk_is_noop() {
-        let ct = vec![
-            vec![1.0, 0.0, 0.0],
-            vec![0.0, 1.0, 0.0],
-            vec![0.0, 0.0, 1.0],
-        ];
-        let opm = make_opm(ct);
-        let mut data = vec![1.0, 2.0, 3.0];
-        opm.compensate_cross_talk(&mut data).unwrap();
-        assert!((data[0] - 1.0).abs() < 1e-12);
-        assert!((data[1] - 2.0).abs() < 1e-12);
-        assert!((data[2] - 3.0).abs() < 1e-12);
-    }
-
-    #[test]
-    fn known_3x3_cross_talk_solution() {
-        // Cross-talk matrix C, raw vector b.
-        // We pick a known x, compute b = C * x, then verify compensation recovers x.
-        let ct = vec![
-            vec![2.0, 1.0, 0.0],
-            vec![0.0, 3.0, 1.0],
-            vec![1.0, 0.0, 2.0],
-        ];
-        // Known corrected values.
-        let expected = vec![1.0, 2.0, 3.0];
-        // raw = C * expected.
-        let mut raw = vec![
-            2.0 * 1.0 + 1.0 * 2.0 + 0.0 * 3.0, // 4.0
-            0.0 * 1.0 + 3.0 * 2.0 + 1.0 * 3.0, // 9.0
-            1.0 * 1.0 + 0.0 * 2.0 + 2.0 * 3.0, // 7.0
-        ];
-        let opm = make_opm(ct);
-        opm.compensate_cross_talk(&mut raw).unwrap();
-        for (got, want) in raw.iter().zip(expected.iter()) {
-            assert!(
-                (got - want).abs() < 1e-10,
-                "got {got}, want {want}"
-            );
-        }
-    }
-
-    #[test]
-    fn singular_matrix_falls_back_to_diagonal() {
-        // Singular: row 1 == row 0.
-        let ct = vec![
-            vec![2.0, 1.0],
-            vec![2.0, 1.0],
-        ];
-        let opm = make_opm(ct);
-        let mut data = vec![4.0, 6.0];
-        // Should not error -- falls back to diagonal.
-        opm.compensate_cross_talk(&mut data).unwrap();
-        // Diagonal fallback: data[0] /= 2.0, data[1] /= 1.0.
-        assert!((data[0] - 2.0).abs() < 1e-12);
-        assert!((data[1] - 6.0).abs() < 1e-12);
-    }
-
-    #[test]
-    fn solve_linear_system_basic() {
-        let mat = vec![
-            vec![1.0, 0.0],
-            vec![0.0, 1.0],
-        ];
-        let rhs = vec![5.0, 7.0];
-        let x = solve_linear_system(&mat, &rhs).unwrap();
-        assert!((x[0] - 5.0).abs() < 1e-12);
-        assert!((x[1] - 7.0).abs() < 1e-12);
-    }
-
-    #[test]
-    fn solve_linear_system_singular_returns_none() {
-        let mat = vec![
-            vec![1.0, 2.0],
-            vec![2.0, 4.0],
-        ];
-        let rhs = vec![3.0, 6.0];
-        assert!(solve_linear_system(&mat, &rhs).is_none());
-    }
-
-    #[test]
-    fn full_cross_talk_compensation_time_series() {
-        let ct = vec![
-            vec![2.0, 1.0, 0.0],
-            vec![0.0, 3.0, 1.0],
-            vec![1.0, 0.0, 2.0],
-        ];
-        let opm = make_opm(ct.clone());
-
-        // Two time points with known corrected values.
-        let expected_t0 = vec![1.0, 2.0, 3.0];
-        let expected_t1 = vec![4.0, 5.0, 6.0];
-
-        // Compute raw = C * expected for each time point.
-        let raw_t0: Vec<f64> = (0..3)
-            .map(|i| ct[i].iter().zip(&expected_t0).map(|(c, x)| c * x).sum())
-            .collect();
-        let raw_t1: Vec<f64> = (0..3)
-            .map(|i| ct[i].iter().zip(&expected_t1).map(|(c, x)| c * x).sum())
-            .collect();
-
-        // data layout: channels x samples.
-        let mut data = vec![
-            vec![raw_t0[0], raw_t1[0]],
-            vec![raw_t0[1], raw_t1[1]],
-            vec![raw_t0[2], raw_t1[2]],
-        ];
-
-        opm.full_cross_talk_compensation(&mut data).unwrap();
-
-        for (ch, (e0, e1)) in [expected_t0, expected_t1]
-            .iter()
-            .enumerate()
-            .flat_map(|(t, exp)| exp.iter().enumerate().map(move |(ch, &v)| (ch, (t, v))))
-            .fold(
-                vec![(0.0, 0.0); 3],
-                |mut acc, (ch, (t, v))| {
-                    if t == 0 { acc[ch].0 = v; } else { acc[ch].1 = v; }
-                    acc
-                },
-            )
-            .into_iter()
-            .enumerate()
-        {
-            assert!(
-                (data[ch][0] - e0).abs() < 1e-10,
-                "ch{ch} t0: got {}, want {e0}",
-                data[ch][0]
-            );
-            assert!(
-                (data[ch][1] - e1).abs() < 1e-10,
-                "ch{ch} t1: got {}, want {e1}",
-                data[ch][1]
-            );
-        }
-    }
-
-    #[test]
-    fn dimension_mismatch_error() {
-        let opm = make_opm(vec![vec![1.0]]);
-        let mut data = vec![1.0, 2.0];
-        assert!(opm.compensate_cross_talk(&mut data).is_err());
-    }
-}
@@ -1,95 +0,0 @@
-//! Signal quality monitoring for neural sensor channels.
-
-/// Signal quality metrics for a single channel.
-pub struct SignalQuality {
-    /// Signal-to-noise ratio in dB.
-    pub snr_db: f64,
-    /// Probability of artifact contamination in [0, 1].
-    pub artifact_probability: f64,
-    /// Whether the channel is saturated (clipping).
-    pub saturated: bool,
-}
-
-impl SignalQuality {
-    /// Returns true if signal quality is below acceptable thresholds.
-    ///
-    /// Thresholds: SNR < 3 dB or artifact_probability > 0.5.
-    pub fn below_threshold(&self) -> bool {
-        self.snr_db < 3.0 || self.artifact_probability > 0.5
-    }
-}
-
-/// Real-time signal quality monitor for multi-channel data.
-pub struct QualityMonitor {
-    num_channels: usize,
-}
-
-impl QualityMonitor {
-    /// Create a new quality monitor for the given number of channels.
-    pub fn new(num_channels: usize) -> Self {
-        Self { num_channels }
-    }
-
-    /// Check signal quality for each channel.
-    ///
-    /// Each element in `signals` is a slice of samples for one channel.
-    pub fn check_quality(&mut self, signals: &[&[f64]]) -> Vec<SignalQuality> {
-        let n = signals.len().min(self.num_channels);
-        (0..n)
-            .map(|i| {
-                let signal = signals[i];
-                let snr_db = estimate_snr_db(signal);
-                let saturated = detect_saturation(signal);
-                let artifact_probability = if saturated { 0.9 } else { 0.0 };
-                SignalQuality {
-                    snr_db,
-                    artifact_probability,
-                    saturated,
-                }
-            })
-            .collect()
-    }
-}
-
-/// Estimate SNR in dB from a signal segment.
-fn estimate_snr_db(signal: &[f64]) -> f64 {
-    if signal.is_empty() {
-        return 0.0;
-    }
-    let mean = signal.iter().sum::<f64>() / signal.len() as f64;
-    let variance = signal.iter().map(|x| (x - mean).powi(2)).sum::<f64>() / signal.len() as f64;
-    let rms = variance.sqrt();
-    if rms < 1e-15 {
-        return 0.0;
-    }
-    let n = signal.len();
-    if n < 4 {
-        return 20.0 * rms.log10();
-    }
-    // Estimate noise as std of first differences (captures high-freq content).
-    let diff_var = signal
-        .windows(2)
-        .map(|w| (w[1] - w[0]).powi(2))
-        .sum::<f64>()
-        / (n - 1) as f64;
-    let noise_power = diff_var / 2.0;
-    let signal_power = variance;
-    if noise_power < 1e-15 {
-        return 60.0;
-    }
-    10.0 * (signal_power / noise_power).log10()
-}
-
-/// Detect if a signal is saturated (extreme repeated values).
-fn detect_saturation(signal: &[f64]) -> bool {
-    if signal.len() < 10 {
-        return false;
-    }
-    let max_abs = signal.iter().map(|x| x.abs()).fold(0.0_f64, f64::max);
-    if max_abs < 1e-10 {
-        return false;
-    }
-    let threshold = max_abs * 0.999;
-    let clipped_count = signal.iter().filter(|x| x.abs() >= threshold).count();
-    clipped_count as f64 / signal.len() as f64 > 0.1
-}
@@ -1,270 +0,0 @@
-//! Simulated sensor array for testing and development.
-//!
-//! Generates realistic synthetic neural magnetic field data with configurable
-//! channels, sample rate, noise floor, and injectable events.
-
-use rand::Rng;
-use ruv_neural_core::error::Result;
-use ruv_neural_core::sensor::{SensorArray, SensorChannel, SensorType};
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-use ruv_neural_core::traits::SensorSource;
-use serde::{Deserialize, Serialize};
-use std::f64::consts::PI;
-
-/// An injectable event that modifies the simulated signal.
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub enum SensorEvent {
-    /// A sharp spike at a specific sample offset.
-    Spike {
-        /// Channel to inject the spike into.
-        channel: usize,
-        /// Amplitude in femtotesla.
-        amplitude_ft: f64,
-        /// Sample offset from the start of the next acquisition.
-        sample_offset: usize,
-    },
-    /// A burst of oscillatory activity.
-    OscillationBurst {
-        /// Channel to inject the burst into.
-        channel: usize,
-        /// Frequency of oscillation in Hz.
-        frequency_hz: f64,
-        /// Amplitude in femtotesla.
-        amplitude_ft: f64,
-        /// Start sample offset.
-        start_sample: usize,
-        /// Duration in samples.
-        duration_samples: usize,
-    },
-    /// A DC level shift.
-    DcShift {
-        /// Channel to inject the shift into.
-        channel: usize,
-        /// Shift magnitude in femtotesla.
-        shift_ft: f64,
-        /// Sample offset at which the shift begins.
-        start_sample: usize,
-    },
-}
-
-/// Configuration for an oscillation component injected into the simulator.
-#[derive(Debug, Clone)]
-struct OscillationComponent {
-    /// Frequency in Hz.
-    frequency_hz: f64,
-    /// Amplitude in femtotesla.
-    amplitude_ft: f64,
-}
-
-/// Simulated sensor array that generates synthetic neural magnetic field data.
-///
-/// The simulator produces multi-channel time series with configurable noise,
-/// background oscillations (alpha, beta, etc.), and injectable transient events.
-#[derive(Debug)]
-pub struct SimulatedSensorArray {
-    /// Number of channels (4-256).
-    num_channels: usize,
-    /// Sample rate in Hz (100-10000).
-    sample_rate_hz: f64,
-    /// Noise floor density in fT/sqrt(Hz).
-    noise_density_ft: f64,
-    /// Background oscillation components active on all channels.
-    oscillations: Vec<OscillationComponent>,
-    /// Pending events to inject on the next acquisition.
-    pending_events: Vec<SensorEvent>,
-    /// Current phase accumulator (sample counter).
-    sample_counter: u64,
-    /// Sensor array metadata.
-    array: SensorArray,
-    /// Random number generator.
-    rng: rand::rngs::ThreadRng,
-}
-
-impl SimulatedSensorArray {
-    /// Create a new simulated sensor array.
-    ///
-    /// # Arguments
-    /// * `num_channels` - Number of channels (clamped to 4..=256).
-    /// * `sample_rate_hz` - Sample rate in Hz (clamped to 100..=10000).
-    pub fn new(num_channels: usize, sample_rate_hz: f64) -> Self {
-        let num_channels = num_channels.clamp(4, 256);
-        let sample_rate_hz = sample_rate_hz.clamp(100.0, 10000.0);
-
-        let channels = (0..num_channels)
-            .map(|i| {
-                let angle = 2.0 * PI * i as f64 / num_channels as f64;
-                let radius = 0.1; // 10 cm from center
-                SensorChannel {
-                    id: i,
-                    sensor_type: SensorType::NvDiamond,
-                    position: [radius * angle.cos(), radius * angle.sin(), 0.0],
-                    orientation: [0.0, 0.0, 1.0],
-                    sensitivity_ft_sqrt_hz: 10.0,
-                    sample_rate_hz,
-                    label: format!("SIM-{:03}", i),
-                }
-            })
-            .collect();
-
-        let array = SensorArray {
-            channels,
-            sensor_type: SensorType::NvDiamond,
-            name: "SimulatedSensorArray".to_string(),
-        };
-
-        Self {
-            num_channels,
-            sample_rate_hz,
-            noise_density_ft: 10.0,
-            oscillations: Vec::new(),
-            pending_events: Vec::new(),
-            sample_counter: 0,
-            array,
-            rng: rand::thread_rng(),
-        }
-    }
-
-    /// Set the noise floor density in fT/sqrt(Hz).
-    ///
-    /// Returns self for builder-pattern chaining.
-    pub fn with_noise(mut self, noise_density_ft: f64) -> Self {
-        self.noise_density_ft = noise_density_ft;
-        self
-    }
-
-    /// Inject an alpha rhythm (~10 Hz) into all channels.
-    ///
-    /// # Arguments
-    /// * `amplitude_ft` - Peak amplitude in femtotesla (typical: ~100 fT).
-    pub fn inject_alpha(&mut self, amplitude_ft: f64) {
-        self.oscillations.push(OscillationComponent {
-            frequency_hz: 10.0,
-            amplitude_ft,
-        });
-    }
-
-    /// Inject a transient event to appear in the next acquisition.
-    pub fn inject_event(&mut self, event: SensorEvent) {
-        self.pending_events.push(event);
-    }
-
-    /// Returns the sensor array metadata.
-    pub fn sensor_array(&self) -> &SensorArray {
-        &self.array
-    }
-
-    /// Add a custom oscillation component to all channels.
-    pub fn add_oscillation(&mut self, frequency_hz: f64, amplitude_ft: f64) {
-        self.oscillations.push(OscillationComponent {
-            frequency_hz,
-            amplitude_ft,
-        });
-    }
-
-    /// Generate samples for one channel.
-    fn generate_channel(&mut self, channel_idx: usize, num_samples: usize) -> Vec<f64> {
-        let dt = 1.0 / self.sample_rate_hz;
-        // Noise standard deviation: density * sqrt(bandwidth).
-        // For white noise sampled at fs, the per-sample sigma = density * sqrt(fs / 2).
-        let noise_sigma = self.noise_density_ft * (self.sample_rate_hz / 2.0).sqrt();
-
-        let mut samples = Vec::with_capacity(num_samples);
-
-        for s in 0..num_samples {
-            let t = (self.sample_counter + s as u64) as f64 * dt;
-            let mut value = 0.0;
-
-            // Add oscillation components with slight per-channel phase offset.
-            let phase_offset = channel_idx as f64 * 0.1;
-            for osc in &self.oscillations {
-                value +=
-                    osc.amplitude_ft * (2.0 * PI * osc.frequency_hz * t + phase_offset).sin();
-            }
-
-            // Add Gaussian noise.
-            if noise_sigma > 0.0 {
-                let noise: f64 = self.rng.gen::<f64>() * 2.0 - 1.0;
-                let noise2: f64 = self.rng.gen::<f64>() * 2.0 - 1.0;
-                // Box-Muller transform for Gaussian noise.
-                let u1 = self.rng.gen::<f64>().max(1e-15);
-                let u2 = self.rng.gen::<f64>();
-                let gaussian = (-2.0 * u1.ln()).sqrt() * (2.0 * PI * u2).cos();
-                value += noise_sigma * gaussian;
-                let _ = (noise, noise2); // suppress unused
-            }
-
-            samples.push(value);
-        }
-
-        // Apply pending events for this channel.
-        for event in &self.pending_events {
-            match event {
-                SensorEvent::Spike {
-                    channel,
-                    amplitude_ft,
-                    sample_offset,
-                } => {
-                    if *channel == channel_idx && *sample_offset < num_samples {
-                        samples[*sample_offset] += amplitude_ft;
-                    }
-                }
-                SensorEvent::OscillationBurst {
-                    channel,
-                    frequency_hz,
-                    amplitude_ft,
-                    start_sample,
-                    duration_samples,
-                } => {
-                    if *channel == channel_idx {
-                        let end = (*start_sample + *duration_samples).min(num_samples);
-                        for s in *start_sample..end {
-                            let t = s as f64 / self.sample_rate_hz;
-                            samples[s] += amplitude_ft * (2.0 * PI * frequency_hz * t).sin();
-                        }
-                    }
-                }
-                SensorEvent::DcShift {
-                    channel,
-                    shift_ft,
-                    start_sample,
-                } => {
-                    if *channel == channel_idx {
-                        for s in *start_sample..num_samples {
-                            samples[s] += shift_ft;
-                        }
-                    }
-                }
-            }
-        }
-
-        samples
-    }
-}
-
-impl SensorSource for SimulatedSensorArray {
-    fn sensor_type(&self) -> SensorType {
-        SensorType::NvDiamond
-    }
-
-    fn num_channels(&self) -> usize {
-        self.num_channels
-    }
-
-    fn sample_rate_hz(&self) -> f64 {
-        self.sample_rate_hz
-    }
-
-    fn read_chunk(&mut self, num_samples: usize) -> Result<MultiChannelTimeSeries> {
-        let timestamp = self.sample_counter as f64 / self.sample_rate_hz;
-
-        let mut data = Vec::with_capacity(self.num_channels);
-        for ch in 0..self.num_channels {
-            data.push(self.generate_channel(ch, num_samples));
-        }
-
-        self.sample_counter += num_samples as u64;
-        self.pending_events.clear();
-
-        MultiChannelTimeSeries::new(data, self.sample_rate_hz, timestamp)
-    }
-}
@@ -1,30 +0,0 @@
-[package]
-name = "ruv-neural-signal"
-description = "rUv Neural — Signal processing: filtering, spectral analysis, artifact rejection for neural data"
-version.workspace = true
-edition.workspace = true
-authors.workspace = true
-license.workspace = true
-
-[features]
-default = ["std"]
-std = []
-simd = []  # SIMD-accelerated processing
-
-[dependencies]
-ruv-neural-core = { workspace = true }
-ndarray = { workspace = true }
-rustfft = { workspace = true }
-num-complex = { workspace = true }
-num-traits = { workspace = true }
-serde = { workspace = true }
-tracing = { workspace = true }
-
-[dev-dependencies]
-approx = { workspace = true }
-rand = { workspace = true }
-criterion = { workspace = true }
-
-[[bench]]
-name = "benchmarks"
-harness = false
@@ -1,90 +0,0 @@
-# ruv-neural-signal
-
-Signal processing: filtering, spectral analysis, connectivity metrics, and artifact
-rejection for neural time series data.
-
-## Overview
-
-`ruv-neural-signal` provides a complete digital signal processing pipeline for
-multi-channel neural magnetic field and electrophysiology data. It covers IIR
-filtering in second-order sections form, FFT-based spectral analysis, Hilbert
-transform for instantaneous phase extraction, artifact detection and rejection,
-cross-channel connectivity metrics, and a configurable multi-stage preprocessing
-pipeline.
-
-## Features
-
- **IIR Filters** (`filter`): Butterworth bandpass, highpass, lowpass, and notch
-  filters in SOS (second-order sections) form for numerical stability
- **Spectral analysis** (`spectral`): Welch PSD estimation, STFT, band power
-  extraction, spectral entropy, and peak frequency detection
- **Hilbert transform** (`hilbert`): FFT-based analytic signal for instantaneous
-  phase and amplitude envelope computation
- **Artifact detection** (`artifact`): Eye blink, muscle artifact, and cardiac
-  artifact detection with configurable rejection
- **Connectivity metrics** (`connectivity`): Phase locking value (PLV), coherence,
-  imaginary coherence, amplitude envelope correlation (AEC), and all-pairs
-  computation for connectivity matrix construction
- **Preprocessing pipeline** (`preprocessing`): Configurable multi-stage pipeline
-  chaining filters, artifact rejection, and re-referencing
-
-## Usage
-
-```rust
-use ruv_neural_signal::{
-    BandpassFilter, PreprocessingPipeline, SignalProcessor,
-    compute_psd, band_power, hilbert_transform, instantaneous_phase,
-    compute_all_pairs, ConnectivityMetric,
-};
-use ruv_neural_core::FrequencyBand;
-
-// Apply a bandpass filter (8-13 Hz alpha band)
-let filter = BandpassFilter::new(8.0, 13.0, 1000.0, 4).unwrap();
-let filtered = filter.apply(&raw_signal);
-
-// Compute power spectral density (Welch method)
-let psd = compute_psd(&signal, 1000.0, 256, 128);
-let alpha_power = band_power(&psd, 1000.0, 8.0, 13.0);
-
-// Extract instantaneous phase via Hilbert transform
-let analytic = hilbert_transform(&signal);
-let phases = instantaneous_phase(&analytic);
-
-// Compute all-pairs connectivity matrix
-let connectivity_matrix = compute_all_pairs(
-    &multi_channel_data,
-    ConnectivityMetric::PhaseLockingValue,
-);
-
-// Run full preprocessing pipeline
-let pipeline = PreprocessingPipeline::default();
-let clean_data = pipeline.process(&raw_data).unwrap();
-```
-
-## API Reference
-
-| Module          | Key Types / Functions                                           |
-|-----------------|-----------------------------------------------------------------|
-| `filter`        | `BandpassFilter`, `HighpassFilter`, `LowpassFilter`, `NotchFilter`, `SignalProcessor` |
-| `spectral`      | `compute_psd`, `compute_stft`, `band_power`, `spectral_entropy`, `peak_frequency` |
-| `hilbert`       | `hilbert_transform`, `instantaneous_phase`, `instantaneous_amplitude` |
-| `artifact`      | `detect_eye_blinks`, `detect_muscle_artifact`, `detect_cardiac`, `reject_artifacts` |
-| `connectivity`  | `phase_locking_value`, `coherence`, `imaginary_coherence`, `amplitude_envelope_correlation`, `compute_all_pairs` |
-| `preprocessing` | `PreprocessingPipeline`                                         |
-
-## Feature Flags
-
-| Feature | Default | Description                      |
-|---------|---------|----------------------------------|
-| `std`   | Yes     | Standard library support         |
-| `simd`  | No      | SIMD-accelerated filter kernels  |
-
-## Integration
-
-Depends on `ruv-neural-core` for `MultiChannelTimeSeries` and `FrequencyBand` types.
-Feeds processed data into `ruv-neural-graph` for connectivity graph construction.
-Uses `rustfft` for FFT operations and `ndarray` for matrix computations.
-
-## License
-
-MIT OR Apache-2.0
@@ -1,105 +0,0 @@
-//! Criterion benchmarks for ruv-neural-signal.
-//!
-//! Benchmarks the performance-critical signal processing functions:
-//! - Hilbert transform (FFT-based analytic signal)
-//! - Power spectral density (Welch's method)
-//! - Connectivity matrix (PLV for all channel pairs)
-
-use criterion::{black_box, criterion_group, criterion_main, BenchmarkId, Criterion};
-use rand::Rng;
-use std::f64::consts::PI;
-
-use ruv_neural_core::signal::{FrequencyBand, MultiChannelTimeSeries};
-use ruv_neural_signal::{compute_all_pairs, compute_psd, hilbert_transform, ConnectivityMetric};
-
-/// Generate a synthetic multi-tone signal of the given length.
-fn generate_signal(n: usize) -> Vec<f64> {
-    (0..n)
-        .map(|i| {
-            let t = i as f64 / 1000.0;
-            (2.0 * PI * 10.0 * t).sin()
-                + 0.5 * (2.0 * PI * 25.0 * t).cos()
-                + 0.3 * (2.0 * PI * 40.0 * t).sin()
-        })
-        .collect()
-}
-
-/// Generate random multi-channel data.
-fn generate_multichannel(num_channels: usize, num_samples: usize) -> MultiChannelTimeSeries {
-    let mut rng = rand::thread_rng();
-    let data: Vec<Vec<f64>> = (0..num_channels)
-        .map(|ch| {
-            (0..num_samples)
-                .map(|i| {
-                    let t = i as f64 / 1000.0;
-                    let freq = 8.0 + ch as f64 * 0.5;
-                    (2.0 * PI * freq * t).sin() + rng.gen_range(-0.1..0.1)
-                })
-                .collect()
-        })
-        .collect();
-
-    MultiChannelTimeSeries {
-        data,
-        sample_rate_hz: 1000.0,
-        num_channels,
-        num_samples,
-        timestamp_start: 0.0,
-    }
-}
-
-fn bench_hilbert_transform(c: &mut Criterion) {
-    let mut group = c.benchmark_group("hilbert_transform");
-
-    for &n in &[256, 1024, 4096] {
-        let signal = generate_signal(n);
-        group.bench_with_input(BenchmarkId::new("samples", n), &signal, |b, signal| {
-            b.iter(|| hilbert_transform(black_box(signal)))
-        });
-    }
-
-    group.finish();
-}
-
-fn bench_compute_psd(c: &mut Criterion) {
-    let mut group = c.benchmark_group("compute_psd");
-
-    let signal = generate_signal(1024);
-    group.bench_function("1024_samples_win256", |b| {
-        b.iter(|| compute_psd(black_box(&signal), black_box(1000.0), black_box(256)))
-    });
-
-    group.finish();
-}
-
-fn bench_connectivity_matrix(c: &mut Criterion) {
-    let mut group = c.benchmark_group("connectivity_matrix");
-    group.sample_size(10);
-
-    for &num_channels in &[16, 32] {
-        let data = generate_multichannel(num_channels, 1024);
-        group.bench_with_input(
-            BenchmarkId::new("plv_channels", num_channels),
-            &data,
-            |b, data| {
-                b.iter(|| {
-                    compute_all_pairs(
-                        black_box(data),
-                        black_box(ConnectivityMetric::Plv),
-                        black_box(FrequencyBand::Alpha),
-                    )
-                })
-            },
-        );
-    }
-
-    group.finish();
-}
-
-criterion_group!(
-    benches,
-    bench_hilbert_transform,
-    bench_compute_psd,
-    bench_connectivity_matrix,
-);
-criterion_main!(benches);
@@ -1,391 +0,0 @@
-//! Artifact detection and rejection for neural recordings.
-//!
-//! Detects common physiological and environmental artifacts:
-//! - Eye blinks: large slow deflections (primarily frontal channels)
-//! - Muscle artifacts: high-frequency broadband power bursts
-//! - Cardiac artifacts: QRS complex detection
-//!
-//! Provides functions to mark and remove/interpolate artifact periods.
-
-use ruv_neural_core::signal::MultiChannelTimeSeries;
-
-use crate::filter::{BandpassFilter, HighpassFilter, LowpassFilter};
-
-/// Detect eye blink artifacts in a single channel.
-///
-/// Eye blinks produce large, slow voltage deflections (1-5 Hz)
-/// with amplitudes 5-10x the background signal. Detection uses:
-/// 1. Lowpass filter to isolate slow components
-/// 2. Amplitude thresholding at `mean + 3*std`
-/// 3. Merging of nearby detections
-///
-/// # Arguments
-/// * `signal` - Single-channel time series
-/// * `sample_rate` - Sampling rate in Hz
-///
-/// # Returns
-/// Vector of (start_sample, end_sample) ranges for detected blinks.
-pub fn detect_eye_blinks(signal: &[f64], sample_rate: f64) -> Vec<(usize, usize)> {
-    if signal.len() < (sample_rate * 0.2) as usize {
-        return Vec::new();
-    }
-
-    // Lowpass filter at 5 Hz to isolate blink waveform
-    let lp = LowpassFilter::new(2, 5.0, sample_rate);
-    let filtered = lp.apply(signal);
-
-    // Compute absolute values
-    let abs_signal: Vec<f64> = filtered.iter().map(|x| x.abs()).collect();
-
-    // Compute mean and std of the absolute filtered signal
-    let mean = abs_signal.iter().sum::<f64>() / abs_signal.len() as f64;
-    let variance = abs_signal
-        .iter()
-        .map(|x| (x - mean).powi(2))
-        .sum::<f64>()
-        / abs_signal.len() as f64;
-    let std_dev = variance.sqrt();
-
-    // Threshold at mean + 3*std
-    let threshold = mean + 3.0 * std_dev;
-
-    // Find contiguous regions above threshold
-    let mut ranges = Vec::new();
-    let mut in_artifact = false;
-    let mut start = 0;
-
-    for (i, &val) in abs_signal.iter().enumerate() {
-        if val > threshold && !in_artifact {
-            in_artifact = true;
-            start = i;
-        } else if val <= threshold && in_artifact {
-            in_artifact = false;
-            ranges.push((start, i));
-        }
-    }
-    if in_artifact {
-        ranges.push((start, abs_signal.len()));
-    }
-
-    // Extend ranges by 50ms on each side (blink onset/offset)
-    let pad = (sample_rate * 0.05) as usize;
-    let merged = merge_ranges_with_padding(&ranges, pad, signal.len());
-
-    merged
-}
-
-/// Detect muscle artifact in a single channel.
-///
-/// Muscle artifacts produce broadband high-frequency power (>30 Hz).
-/// Detection uses:
-/// 1. Highpass filter at 30 Hz
-/// 2. Compute sliding window RMS
-/// 3. Threshold at mean + 3*std of RMS
-///
-/// # Returns
-/// Vector of (start_sample, end_sample) ranges for detected artifacts.
-pub fn detect_muscle_artifact(signal: &[f64], sample_rate: f64) -> Vec<(usize, usize)> {
-    if signal.len() < (sample_rate * 0.1) as usize {
-        return Vec::new();
-    }
-
-    // Highpass filter at 30 Hz to isolate muscle activity
-    let hp = HighpassFilter::new(2, 30.0, sample_rate);
-    let filtered = hp.apply(signal);
-
-    // Sliding window RMS (50ms window)
-    let window_len = (sample_rate * 0.05) as usize;
-    let window_len = window_len.max(1);
-    let n = filtered.len();
-    let mut rms_signal = vec![0.0; n];
-
-    // Compute running sum of squares
-    let mut sum_sq = 0.0;
-    for i in 0..n {
-        sum_sq += filtered[i] * filtered[i];
-        if i >= window_len {
-            sum_sq -= filtered[i - window_len] * filtered[i - window_len];
-        }
-        let count = (i + 1).min(window_len);
-        rms_signal[i] = (sum_sq / count as f64).sqrt();
-    }
-
-    // Threshold at mean + 3*std of RMS
-    let mean = rms_signal.iter().sum::<f64>() / n as f64;
-    let variance = rms_signal
-        .iter()
-        .map(|x| (x - mean).powi(2))
-        .sum::<f64>()
-        / n as f64;
-    let std_dev = variance.sqrt();
-    let threshold = mean + 3.0 * std_dev;
-
-    let mut ranges = Vec::new();
-    let mut in_artifact = false;
-    let mut start = 0;
-
-    for (i, &val) in rms_signal.iter().enumerate() {
-        if val > threshold && !in_artifact {
-            in_artifact = true;
-            start = i;
-        } else if val <= threshold && in_artifact {
-            in_artifact = false;
-            ranges.push((start, i));
-        }
-    }
-    if in_artifact {
-        ranges.push((start, n));
-    }
-
-    let pad = (sample_rate * 0.025) as usize;
-    merge_ranges_with_padding(&ranges, pad, signal.len())
-}
-
-/// Detect cardiac (QRS complex) artifact peaks in a single channel.
-///
-/// Uses a simplified Pan-Tompkins-style approach:
-/// 1. Bandpass filter 5-15 Hz
-/// 2. Differentiate and square
-/// 3. Moving window integration
-/// 4. Threshold-based peak detection with refractory period
-///
-/// # Returns
-/// Vector of sample indices where QRS peaks are detected.
-pub fn detect_cardiac(signal: &[f64], sample_rate: f64) -> Vec<usize> {
-    if signal.len() < (sample_rate * 0.5) as usize {
-        return Vec::new();
-    }
-
-    // Bandpass 5-15 Hz to isolate QRS complex
-    let bp = BandpassFilter::new(2, 5.0, 15.0, sample_rate);
-    let filtered = bp.apply(signal);
-
-    // Differentiate
-    let n = filtered.len();
-    let mut diff = vec![0.0; n];
-    for i in 1..n {
-        diff[i] = filtered[i] - filtered[i - 1];
-    }
-
-    // Square
-    let squared: Vec<f64> = diff.iter().map(|x| x * x).collect();
-
-    // Moving window integration (150ms window)
-    let win_len = (sample_rate * 0.15) as usize;
-    let win_len = win_len.max(1);
-    let mut integrated = vec![0.0; n];
-    let mut sum = 0.0;
-
-    for i in 0..n {
-        sum += squared[i];
-        if i >= win_len {
-            sum -= squared[i - win_len];
-        }
-        integrated[i] = sum / win_len.min(i + 1) as f64;
-    }
-
-    // Threshold: mean + 0.5*std (tuned for cardiac artifacts which are periodic)
-    let mean = integrated.iter().sum::<f64>() / n as f64;
-    let variance = integrated
-        .iter()
-        .map(|x| (x - mean).powi(2))
-        .sum::<f64>()
-        / n as f64;
-    let std_dev = variance.sqrt();
-    let threshold = mean + 0.5 * std_dev;
-
-    // Find peaks above threshold with refractory period (200ms)
-    let refractory = (sample_rate * 0.2) as usize;
-    let mut peaks = Vec::new();
-    let mut last_peak: Option<usize> = None;
-
-    for i in 1..(n - 1) {
-        if integrated[i] > threshold
-            && integrated[i] > integrated[i - 1]
-            && integrated[i] >= integrated[i + 1]
-        {
-            if let Some(lp) = last_peak {
-                if i - lp < refractory {
-                    continue;
-                }
-            }
-            peaks.push(i);
-            last_peak = Some(i);
-        }
-    }
-
-    peaks
-}
-
-/// Remove artifacts from multi-channel data by linear interpolation.
-///
-/// For each artifact range, replaces the data with a linear interpolation
-/// between the sample before the range and the sample after the range.
-///
-/// # Arguments
-/// * `data` - Multi-channel time series
-/// * `artifact_ranges` - Sorted, non-overlapping (start, end) sample ranges
-///
-/// # Returns
-/// A new `MultiChannelTimeSeries` with artifacts interpolated out.
-pub fn reject_artifacts(
-    data: &MultiChannelTimeSeries,
-    artifact_ranges: &[(usize, usize)],
-) -> MultiChannelTimeSeries {
-    let mut clean_data = data.data.clone();
-
-    for channel in &mut clean_data {
-        let n = channel.len();
-        for &(start, end) in artifact_ranges {
-            let start = start.min(n);
-            let end = end.min(n);
-            if start >= end {
-                continue;
-            }
-
-            // Get boundary values for interpolation
-            let val_before = if start > 0 { channel[start - 1] } else { 0.0 };
-            let val_after = if end < n { channel[end] } else { 0.0 };
-            let span = (end - start) as f64;
-
-            // Linear interpolation across the artifact
-            // frac goes from 1/(span+1) to span/(span+1), excluding boundaries
-            let intervals = span + 1.0;
-            for i in start..end {
-                let frac = (i - start + 1) as f64 / intervals;
-                channel[i] = val_before * (1.0 - frac) + val_after * frac;
-            }
-        }
-    }
-
-    MultiChannelTimeSeries {
-        data: clean_data,
-        sample_rate_hz: data.sample_rate_hz,
-        num_channels: data.num_channels,
-        num_samples: data.num_samples,
-        timestamp_start: data.timestamp_start,
-    }
-}
-
-/// Merge artifact ranges and add padding on each side.
-fn merge_ranges_with_padding(
-    ranges: &[(usize, usize)],
-    pad: usize,
-    max_len: usize,
-) -> Vec<(usize, usize)> {
-    if ranges.is_empty() {
-        return Vec::new();
-    }
-
-    // Pad each range
-    let padded: Vec<(usize, usize)> = ranges
-        .iter()
-        .map(|&(s, e)| (s.saturating_sub(pad), (e + pad).min(max_len)))
-        .collect();
-
-    // Merge overlapping ranges
-    let mut merged = Vec::new();
-    let (mut cur_start, mut cur_end) = padded[0];
-
-    for &(s, e) in &padded[1..] {
-        if s <= cur_end {
-            cur_end = cur_end.max(e);
-        } else {
-            merged.push((cur_start, cur_end));
-            cur_start = s;
-            cur_end = e;
-        }
-    }
-    merged.push((cur_start, cur_end));
-
-    merged
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use ruv_neural_core::signal::MultiChannelTimeSeries;
-
-    #[test]
-    fn detect_eye_blinks_finds_large_deflections() {
-        let sr = 1000.0;
-        let n = 5000;
-        // Create signal with a large slow deflection (simulated blink)
-        let mut signal = vec![0.0; n];
-        // Normal background: small random-like variation
-        for i in 0..n {
-            signal[i] = 0.01 * ((i as f64 * 0.1).sin());
-        }
-        // Insert a blink: large Gaussian-like bump at sample 2500
-        for i in 2400..2600 {
-            let t = (i as f64 - 2500.0) / 30.0;
-            signal[i] += 5.0 * (-t * t / 2.0).exp();
-        }
-
-        let blinks = detect_eye_blinks(&signal, sr);
-        // Should detect at least one blink near sample 2500
-        assert!(
-            !blinks.is_empty(),
-            "Should detect the simulated eye blink"
-        );
-
-        // At least one range should overlap with 2400..2600
-        let found = blinks.iter().any(|&(s, e)| s < 2600 && e > 2400);
-        assert!(found, "Blink range should overlap with injected artifact");
-    }
-
-    #[test]
-    fn reject_artifacts_interpolates_correctly() {
-        let data = MultiChannelTimeSeries {
-            data: vec![vec![1.0, 2.0, 100.0, 100.0, 5.0, 6.0]],
-            sample_rate_hz: 1000.0,
-            num_channels: 1,
-            num_samples: 6,
-            timestamp_start: 0.0,
-        };
-
-        let cleaned = reject_artifacts(&data, &[(2, 4)]);
-
-        // Samples 2 and 3 should be linearly interpolated between 2.0 and 5.0
-        assert!((cleaned.data[0][2] - 3.0).abs() < 0.01);
-        assert!((cleaned.data[0][3] - 4.0).abs() < 0.01);
-
-        // Non-artifact samples should be unchanged
-        assert!((cleaned.data[0][0] - 1.0).abs() < 1e-10);
-        assert!((cleaned.data[0][4] - 5.0).abs() < 1e-10);
-    }
-
-    #[test]
-    fn detect_cardiac_finds_periodic_peaks() {
-        let sr = 1000.0;
-        let duration = 3.0;
-        let n = (sr * duration) as usize;
-        let mut signal = vec![0.0; n];
-
-        // Simulate cardiac artifact: periodic QRS-like spikes at ~1 Hz
-        let heart_rate_hz = 1.0;
-        let interval = (sr / heart_rate_hz) as usize;
-
-        for beat in 0..3 {
-            let center = beat * interval + interval / 2;
-            if center >= n {
-                break;
-            }
-            // QRS complex: sharp spike ~10ms wide
-            let half_width = (sr * 0.005) as usize;
-            for i in center.saturating_sub(half_width)..(center + half_width).min(n) {
-                let t = (i as f64 - center as f64) / (half_width as f64);
-                signal[i] = 10.0 * (-t * t * 5.0).exp();
-            }
-        }
-
-        let peaks = detect_cardiac(&signal, sr);
-
-        // Should find roughly 3 peaks
-        assert!(
-            peaks.len() >= 1,
-            "Should detect at least one cardiac peak, found {}",
-            peaks.len()
-        );
-    }
-}
@@ -1,523 +0,0 @@
-//! Cross-channel coupling and connectivity metrics.
-//!
-//! Provides measures of functional connectivity between neural signals:
-//! - Phase Locking Value (PLV)
-//! - Magnitude-squared coherence
-//! - Imaginary coherence (robust to volume conduction)
-//! - Amplitude envelope correlation
-//! - Full connectivity matrix computation
-
-use num_complex::Complex;
-use ruv_neural_core::signal::{FrequencyBand, MultiChannelTimeSeries};
-use rustfft::FftPlanner;
-use serde::{Deserialize, Serialize};
-use std::cell::RefCell;
-use std::f64::consts::PI;
-
-use crate::filter::BandpassFilter;
-use crate::hilbert::hilbert_transform;
-
-thread_local! {
-    static FFT_PLANNER: RefCell<FftPlanner<f64>> = RefCell::new(FftPlanner::new());
-}
-
-/// Type of connectivity metric to compute.
-#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum ConnectivityMetric {
-    /// Phase Locking Value.
-    Plv,
-    /// Amplitude envelope correlation.
-    Aec,
-}
-
-/// Returns `true` if any sample in `data` is NaN or infinite.
-pub fn contains_non_finite(data: &[f64]) -> bool {
-    data.iter().any(|x| !x.is_finite())
-}
-
-/// Validate that signal data contains no NaN or Inf values.
-///
-/// Returns `Ok(())` if all values are finite, or an error otherwise.
-pub fn validate_signal_finite(data: &[f64], label: &str) -> std::result::Result<(), String> {
-    if contains_non_finite(data) {
-        Err(format!("{label} contains NaN or infinite values"))
-    } else {
-        Ok(())
-    }
-}
-
-/// Compute the Phase Locking Value (PLV) between two signals.
-///
-/// PLV = |mean(exp(j * (phase_a - phase_b)))|
-///
-/// The signals are first bandpass-filtered to the specified frequency band,
-/// then the Hilbert transform extracts instantaneous phase.
-///
-/// PLV = 1.0 indicates perfect phase synchrony;
-/// PLV ~ 0.0 indicates no consistent phase relationship.
-///
-/// # Arguments
-/// * `signal_a` - First channel time series
-/// * `signal_b` - Second channel time series
-/// * `sample_rate` - Sampling rate in Hz
-/// * `band` - Frequency band for phase extraction
-pub fn phase_locking_value(
-    signal_a: &[f64],
-    signal_b: &[f64],
-    sample_rate: f64,
-    band: FrequencyBand,
-) -> f64 {
-    let n = signal_a.len().min(signal_b.len());
-    if n < 4 {
-        return 0.0;
-    }
-
-    // Reject NaN/Inf at the pipeline entry point
-    if contains_non_finite(&signal_a[..n]) || contains_non_finite(&signal_b[..n]) {
-        return 0.0;
-    }
-
-    let (low, high) = band.range_hz();
-    let bp = BandpassFilter::new(2, low, high, sample_rate);
-
-    let filtered_a = bp.apply(&signal_a[..n]);
-    let filtered_b = bp.apply(&signal_b[..n]);
-
-    let analytic_a = hilbert_transform(&filtered_a);
-    let analytic_b = hilbert_transform(&filtered_b);
-
-    // Compute mean of exp(j*(phase_a - phase_b))
-    let mut sum = Complex::new(0.0, 0.0);
-    for i in 0..n {
-        let phase_a = analytic_a[i].im.atan2(analytic_a[i].re);
-        let phase_b = analytic_b[i].im.atan2(analytic_b[i].re);
-        let diff = phase_a - phase_b;
-        sum += Complex::new(diff.cos(), diff.sin());
-    }
-
-    (sum / n as f64).norm()
-}
-
-/// Compute magnitude-squared coherence between two signals.
-///
-/// Coh(f) = |S_ab(f)|^2 / (S_aa(f) * S_bb(f))
-///
-/// Uses Welch's method with overlapping segments and Hann window.
-///
-/// # Returns
-/// Vector of (frequency, coherence) pairs.
-pub fn coherence(
-    signal_a: &[f64],
-    signal_b: &[f64],
-    sample_rate: f64,
-) -> Vec<(f64, f64)> {
-    let n = signal_a.len().min(signal_b.len());
-    if n == 0 {
-        return Vec::new();
-    }
-
-    let window_size = 256.min(n);
-    let overlap = window_size / 2;
-    let hop = window_size - overlap;
-
-    let window = hann_window(window_size);
-    let num_freqs = window_size / 2 + 1;
-
-    let fft = FFT_PLANNER.with(|p| p.borrow_mut().plan_fft_forward(window_size));
-
-    let mut saa = vec![0.0; num_freqs];
-    let mut sbb = vec![0.0; num_freqs];
-    let mut sab = vec![Complex::new(0.0, 0.0); num_freqs];
-    let mut num_segments = 0;
-
-    let mut start = 0;
-    while start + window_size <= n {
-        let mut fa: Vec<Complex<f64>> = (0..window_size)
-            .map(|i| Complex::new(signal_a[start + i] * window[i], 0.0))
-            .collect();
-        let mut fb: Vec<Complex<f64>> = (0..window_size)
-            .map(|i| Complex::new(signal_b[start + i] * window[i], 0.0))
-            .collect();
-
-        fft.process(&mut fa);
-        fft.process(&mut fb);
-
-        for k in 0..num_freqs {
-            saa[k] += fa[k].norm_sqr();
-            sbb[k] += fb[k].norm_sqr();
-            sab[k] += fa[k] * fb[k].conj();
-        }
-        num_segments += 1;
-        start += hop;
-    }
-
-    if num_segments == 0 {
-        return Vec::new();
-    }
-
-    let freq_res = sample_rate / window_size as f64;
-    (0..num_freqs)
-        .map(|k| {
-            let freq = k as f64 * freq_res;
-            let denom = saa[k] * sbb[k];
-            let coh = if denom > 1e-30 {
-                sab[k].norm_sqr() / denom
-            } else {
-                0.0
-            };
-            (freq, coh.min(1.0))
-        })
-        .collect()
-}
-
-/// Compute imaginary coherence between two signals.
-///
-/// ImCoh(f) = Im(S_ab(f)) / sqrt(S_aa(f) * S_bb(f))
-///
-/// The imaginary part of coherence is robust to volume conduction
-/// artifacts, which produce zero-lag (purely real) correlations.
-///
-/// # Returns
-/// Vector of (frequency, imaginary_coherence) pairs.
-pub fn imaginary_coherence(
-    signal_a: &[f64],
-    signal_b: &[f64],
-    sample_rate: f64,
-) -> Vec<(f64, f64)> {
-    let n = signal_a.len().min(signal_b.len());
-    if n == 0 {
-        return Vec::new();
-    }
-
-    let window_size = 256.min(n);
-    let overlap = window_size / 2;
-    let hop = window_size - overlap;
-
-    let window = hann_window(window_size);
-    let num_freqs = window_size / 2 + 1;
-
-    let fft = FFT_PLANNER.with(|p| p.borrow_mut().plan_fft_forward(window_size));
-
-    let mut saa = vec![0.0; num_freqs];
-    let mut sbb = vec![0.0; num_freqs];
-    let mut sab = vec![Complex::new(0.0, 0.0); num_freqs];
-    let mut num_segments = 0;
-
-    let mut start = 0;
-    while start + window_size <= n {
-        let mut fa: Vec<Complex<f64>> = (0..window_size)
-            .map(|i| Complex::new(signal_a[start + i] * window[i], 0.0))
-            .collect();
-        let mut fb: Vec<Complex<f64>> = (0..window_size)
-            .map(|i| Complex::new(signal_b[start + i] * window[i], 0.0))
-            .collect();
-
-        fft.process(&mut fa);
-        fft.process(&mut fb);
-
-        for k in 0..num_freqs {
-            saa[k] += fa[k].norm_sqr();
-            sbb[k] += fb[k].norm_sqr();
-            sab[k] += fa[k] * fb[k].conj();
-        }
-        num_segments += 1;
-        start += hop;
-    }
-
-    if num_segments == 0 {
-        return Vec::new();
-    }
-
-    let freq_res = sample_rate / window_size as f64;
-    (0..num_freqs)
-        .map(|k| {
-            let freq = k as f64 * freq_res;
-            let denom = (saa[k] * sbb[k]).sqrt();
-            let im_coh = if denom > 1e-30 {
-                sab[k].im / denom
-            } else {
-                0.0
-            };
-            (freq, im_coh)
-        })
-        .collect()
-}
-
-/// Compute amplitude envelope correlation between two signals.
-///
-/// 1. Bandpass filter both signals to the specified frequency band
-/// 2. Extract amplitude envelopes via Hilbert transform
-/// 3. Compute Pearson correlation of the envelopes
-///
-/// # Returns
-/// Correlation coefficient in [-1, 1].
-pub fn amplitude_envelope_correlation(
-    signal_a: &[f64],
-    signal_b: &[f64],
-    sample_rate: f64,
-    band: FrequencyBand,
-) -> f64 {
-    let n = signal_a.len().min(signal_b.len());
-    if n < 4 {
-        return 0.0;
-    }
-
-    // Reject NaN/Inf at the pipeline entry point
-    if contains_non_finite(&signal_a[..n]) || contains_non_finite(&signal_b[..n]) {
-        return 0.0;
-    }
-
-    let (low, high) = band.range_hz();
-    let bp = BandpassFilter::new(2, low, high, sample_rate);
-
-    let filtered_a = bp.apply(&signal_a[..n]);
-    let filtered_b = bp.apply(&signal_b[..n]);
-
-    let env_a = crate::hilbert::instantaneous_amplitude(&filtered_a);
-    let env_b = crate::hilbert::instantaneous_amplitude(&filtered_b);
-
-    pearson_correlation(&env_a, &env_b)
-}
-
-/// Compute a full connectivity matrix for all channel pairs.
-///
-/// Pre-computes filtered analytic signals (or amplitude envelopes) for all
-/// channels once, then computes pairwise metrics. This eliminates redundant
-/// FFT/Hilbert work: for N channels, each channel is transformed once instead
-/// of (N-1) times.
-///
-/// # Arguments
-/// * `data` - Multi-channel time series
-/// * `metric` - Which connectivity metric to use
-/// * `band` - Frequency band (for PLV and AEC)
-///
-/// # Returns
-/// NxN matrix where entry [i][j] is the connectivity between channels i and j.
-pub fn compute_all_pairs(
-    data: &MultiChannelTimeSeries,
-    metric: ConnectivityMetric,
-    band: FrequencyBand,
-) -> Vec<Vec<f64>> {
-    let nc = data.num_channels;
-    let sr = data.sample_rate_hz;
-    let mut matrix = vec![vec![0.0; nc]; nc];
-
-    if nc == 0 {
-        return matrix;
-    }
-
-    let (low, high) = band.range_hz();
-    let n = data.data[0].len();
-
-    match metric {
-        ConnectivityMetric::Plv => {
-            // Pre-compute analytic signals for all channels once.
-            let bp = BandpassFilter::new(2, low, high, sr);
-            let analytic_signals: Vec<Vec<Complex<f64>>> = data
-                .data
-                .iter()
-                .map(|ch| {
-                    let filtered = bp.apply(&ch[..n.min(ch.len())]);
-                    hilbert_transform(&filtered)
-                })
-                .collect();
-
-            for i in 0..nc {
-                matrix[i][i] = 1.0;
-                for j in (i + 1)..nc {
-                    let len = analytic_signals[i].len().min(analytic_signals[j].len());
-                    if len < 4 {
-                        continue;
-                    }
-                    let mut sum = Complex::new(0.0, 0.0);
-                    for k in 0..len {
-                        let phase_a = analytic_signals[i][k].im.atan2(analytic_signals[i][k].re);
-                        let phase_b = analytic_signals[j][k].im.atan2(analytic_signals[j][k].re);
-                        let diff = phase_a - phase_b;
-                        sum += Complex::new(diff.cos(), diff.sin());
-                    }
-                    let val = (sum / len as f64).norm();
-                    matrix[i][j] = val;
-                    matrix[j][i] = val;
-                }
-            }
-        }
-        ConnectivityMetric::Aec => {
-            // Pre-compute amplitude envelopes for all channels once.
-            let bp = BandpassFilter::new(2, low, high, sr);
-            let envelopes: Vec<Vec<f64>> = data
-                .data
-                .iter()
-                .map(|ch| {
-                    let filtered = bp.apply(&ch[..n.min(ch.len())]);
-                    crate::hilbert::instantaneous_amplitude(&filtered)
-                })
-                .collect();
-
-            for i in 0..nc {
-                matrix[i][i] = 1.0;
-                for j in (i + 1)..nc {
-                    let val = pearson_correlation(&envelopes[i], &envelopes[j]);
-                    matrix[i][j] = val;
-                    matrix[j][i] = val;
-                }
-            }
-        }
-    }
-
-    matrix
-}
-
-/// Pearson correlation coefficient between two vectors.
-fn pearson_correlation(a: &[f64], b: &[f64]) -> f64 {
-    let n = a.len().min(b.len());
-    if n == 0 {
-        return 0.0;
-    }
-
-    let mean_a = a[..n].iter().sum::<f64>() / n as f64;
-    let mean_b = b[..n].iter().sum::<f64>() / n as f64;
-
-    let mut cov = 0.0;
-    let mut var_a = 0.0;
-    let mut var_b = 0.0;
-
-    for i in 0..n {
-        let da = a[i] - mean_a;
-        let db = b[i] - mean_b;
-        cov += da * db;
-        var_a += da * da;
-        var_b += db * db;
-    }
-
-    let denom = (var_a * var_b).sqrt();
-    if denom < 1e-30 {
-        0.0
-    } else {
-        cov / denom
-    }
-}
-
-/// Generate a Hann window (local copy for this module).
-fn hann_window(length: usize) -> Vec<f64> {
-    (0..length)
-        .map(|i| 0.5 * (1.0 - (2.0 * PI * i as f64 / (length - 1).max(1) as f64).cos()))
-        .collect()
-}
-
-#[cfg(test)]
-mod tests {
-    use super::*;
-    use approx::assert_abs_diff_eq;
-    use std::f64::consts::PI;
-
-    #[test]
-    fn plv_of_identical_signals_is_one() {
-        let sr = 1000.0;
-        let n = 2000;
-        let signal: Vec<f64> = (0..n)
-            .map(|i| {
-                let t = i as f64 / sr;
-                (2.0 * PI * 10.0 * t).sin()
-            })
-            .collect();
-
-        let plv = phase_locking_value(&signal, &signal, sr, FrequencyBand::Alpha);
-
-        assert!(
-            plv > 0.9,
-            "PLV of identical signals should be ~1.0, got {plv}"
-        );
-    }
-
-    #[test]
-    fn plv_of_unrelated_signals_is_low() {
-        let sr = 1000.0;
-        let n = 4000;
-        // Two signals at different frequencies
-        let signal_a: Vec<f64> = (0..n)
-            .map(|i| {
-                let t = i as f64 / sr;
-                (2.0 * PI * 10.0 * t).sin()
-            })
-            .collect();
-        let signal_b: Vec<f64> = (0..n)
-            .map(|i| {
-                let t = i as f64 / sr;
-                (2.0 * PI * 11.3 * t).sin() + 0.5 * (2.0 * PI * 9.7 * t).cos()
-            })
-            .collect();
-
-        let plv = phase_locking_value(&signal_a, &signal_b, sr, FrequencyBand::Alpha);
-
-        assert!(
-            plv < 0.7,
-            "PLV of unrelated signals should be low, got {plv}"
-        );
-    }
-
-    #[test]
-    fn coherence_of_identical_signals_is_one() {
-        let sr = 1000.0;
-        let n = 2000;
-        let signal: Vec<f64> = (0..n)
-            .map(|i| {
-                let t = i as f64 / sr;
-                (2.0 * PI * 20.0 * t).sin()
-            })
-            .collect();
-
-        let coh = coherence(&signal, &signal, sr);
-
-        // At the signal frequency (~20 Hz), coherence should be ~1.0
-        let peak_coh = coh
-            .iter()
-            .filter(|(f, _)| *f > 15.0 && *f < 25.0)
-            .map(|(_, c)| *c)
-            .max_by(|a, b| a.partial_cmp(b).unwrap())
-            .unwrap_or(0.0);
-
-        assert!(
-            peak_coh > 0.95,
-            "Coherence of identical signals should be ~1.0 at signal freq, got {peak_coh}"
-        );
-    }
-
-    #[test]
-    fn compute_all_pairs_returns_symmetric_matrix() {
-        let data = MultiChannelTimeSeries {
-            data: vec![
-                (0..1000)
-                    .map(|i| (2.0 * PI * 10.0 * i as f64 / 1000.0).sin())
-                    .collect(),
-                (0..1000)
-                    .map(|i| (2.0 * PI * 10.0 * i as f64 / 1000.0).cos())
-                    .collect(),
-                (0..1000)
-                    .map(|i| (2.0 * PI * 10.0 * i as f64 / 1000.0 + 0.3).sin())
-                    .collect(),
-            ],
-            sample_rate_hz: 1000.0,
-            num_channels: 3,
-            num_samples: 1000,
-            timestamp_start: 0.0,
-        };
-
-        let matrix = compute_all_pairs(&data, ConnectivityMetric::Plv, FrequencyBand::Alpha);
-
-        assert_eq!(matrix.len(), 3);
-        assert_eq!(matrix[0].len(), 3);
-
-        // Diagonal should be 1.0
-        for i in 0..3 {
-            assert_abs_diff_eq!(matrix[i][i], 1.0, epsilon = 1e-10);
-        }
-
-        // Should be symmetric
-        for i in 0..3 {
-            for j in 0..3 {
-                assert_abs_diff_eq!(matrix[i][j], matrix[j][i], epsilon = 1e-10);
-            }
-        }
-    }
-}
--- a/Show More
+++ b/Show More