ruvector/examples/data/framework/docs/cut_aware_hnsw.md
rUv 38d93a6e8d feat: Add comprehensive dataset discovery framework for RuVector (#104)
* feat: Add comprehensive dataset discovery framework for RuVector

This commit introduces a powerful dataset discovery framework with
integrations for three high-impact public data sources:

## Core Framework (examples/data/framework/)
- DataIngester: Streaming ingestion with batching and deduplication
- CoherenceEngine: Min-cut based coherence signal computation
- DiscoveryEngine: Pattern detection for emerging structures

## OpenAlex Integration (examples/data/openalex/)
- Research frontier radar: Detect emerging fields via boundary motion
- Cross-domain bridge detection: Find connector subgraphs
- Topic graph construction from citation networks
- Full API client with cursor-based pagination

## Climate Integration (examples/data/climate/)
- NOAA GHCN and NASA Earthdata clients
- Sensor network graph construction
- Regime shift detection using min-cut coherence breaks
- Time series vectorization for similarity search
- Seasonal decomposition analysis

## SEC EDGAR Integration (examples/data/edgar/)
- XBRL financial statement parsing
- Peer network construction
- Coherence watch: Detect fundamental vs narrative divergence
- Filing analysis with sentiment and risk extraction
- Cross-company contagion detection

Each integration leverages RuVector's unique capabilities:
- Vector memory for semantic similarity
- Graph structures for relationship modeling
- Dynamic min-cut for coherence signal computation
- Time series embeddings for pattern matching

Discovery thesis: Detect emerging patterns before they have names,
find non-obvious cross-domain bridges, and map causality chains.

* feat: Add working discovery examples for climate and financial data

- Fix borrow checker issues in coherence analysis modules
- Create standalone workspace for data examples
- Add regime_detector.rs for climate network coherence analysis
- Add coherence_watch.rs for SEC EDGAR narrative-fundamental divergence
- Add frontier_radar.rs template for OpenAlex research discovery
- Update Cargo.toml dependencies for example executability
- Add rand dev-dependency for demo data generation

Examples successfully detect:
- Climate regime shifts via min-cut coherence analysis
- Cross-regional teleconnection patterns
- Fundamental vs narrative divergence in SEC filings
- Sector fragmentation signals in financial data

* feat: Add working discovery examples for climate and financial data

- Add RuVector-native discovery engine with Stoer-Wagner min-cut
- Implement cross-domain pattern detection (climate ↔ finance)
- Add cosine similarity for vector-based semantic matching
- Create cross_domain_discovery example demonstrating:
  - 42% cross-domain edge connectivity
  - Bridge formation detection with 0.73-0.76 confidence
  - Climate and finance correlation hypothesis generation

* perf: Add optimized discovery engine with SIMD and parallel processing

Performance improvements:
- 8.84x speedup for vector insertion via parallel batching
- 2.91x SIMD speedup for cosine similarity (chunked + AVX2)
- Incremental graph updates with adjacency caching
- Early termination in Stoer-Wagner min-cut

Statistical analysis features:
- P-value computation for pattern significance
- Effect size (Cohen's d) calculation
- 95% confidence intervals
- Granger-style temporal causality detection

Benchmark results (248 vectors, 3 domains):
- Cross-domain edges: 34.9% of total graph
- Domain coherence: Climate 0.74, Finance 0.94, Research 0.97
- Detected climate-finance temporal correlations

* feat: Add discovery hunter and comprehensive README tutorial

New features:
- Discovery hunter example with multi-phase pattern detection
- Climate extremes, financial stress, and research data generation
- Cross-domain hypothesis generation
- Anomaly injection testing

Documentation:
- Detailed README with step-by-step tutorial
- API reference for OptimizedConfig and patterns
- Performance benchmarks and best practices
- Troubleshooting guide

* feat: Complete discovery framework with all features

HNSW Indexing (754 lines):
- O(log n) approximate nearest neighbor search
- Configurable M, ef_construction parameters
- Cosine, Euclidean, Manhattan distance metrics
- Batch insertion support

API Clients (888 lines):
- OpenAlex: academic works, authors, topics
- NOAA: climate observations
- SEC EDGAR: company filings
- Rate limiting and retry logic

Persistence (638 lines):
- Save/load engine state and patterns
- Gzip compression (3-10x size reduction)
- Incremental pattern appending

CLI Tool (1,109 lines):
- discover, benchmark, analyze, export commands
- Colored terminal output
- JSON and human-readable formats

Streaming (570 lines):
- Async stream processing
- Sliding and tumbling windows
- Real-time pattern detection
- Backpressure handling

Tests (30 unit tests):
- Stoer-Wagner min-cut verification
- SIMD cosine similarity accuracy
- Statistical significance
- Granger causality
- Cross-domain patterns

Benchmarks:
- CLI: 176 vectors/sec @ 2000 vectors
- SIMD: 6.82M ops/sec (2.06x speedup)
- Vector insertion: 1.61x speedup
- Total: 44.74ms for 248 vectors

* feat: Add visualization, export, forecasting, and real data discovery

Visualization (555 lines):
- ASCII graph rendering with box-drawing characters
- Domain-based ANSI coloring (Climate=blue, Finance=green, Research=yellow)
- Coherence timeline sparklines
- Pattern summary dashboard
- Domain connectivity matrix

Export (650 lines):
- GraphML export for Gephi/Cytoscape
- DOT export for Graphviz
- CSV export for patterns and coherence history
- Filtered export by domain, weight, time range
- Batch export with README generation

Forecasting (525 lines):
- Holt's double exponential smoothing for trend
- CUSUM-based regime change detection (70.67% accuracy)
- Cross-domain correlation forecasting (r=1.000)
- Prediction intervals (95% CI)
- Anomaly probability scoring

Real Data Discovery:
- Fetched 80 actual papers from OpenAlex API
- Topics: climate risk, stranded assets, carbon pricing, physical risk, transition risk
- Built coherence graph: 592 nodes, 1049 edges
- Average min-cut: 185.76 (well-connected research cluster)

* feat: Add medical, real-time, and knowledge graph data sources

New API Clients:
- PubMed E-utilities for medical literature search (NCBI)
- ClinicalTrials.gov v2 API for clinical study data
- FDA OpenFDA for drug adverse events and recalls
- Wikipedia article search and extraction
- Wikidata SPARQL queries for structured knowledge

Real-time Features:
- RSS/Atom feed parsing with deduplication
- News aggregator with multiple source support
- WebSocket and REST polling infrastructure
- Event streaming with configurable windows

Examples:
- medical_discovery: PubMed + ClinicalTrials + FDA integration
- multi_domain_discovery: Climate-health-finance triangulation
- wiki_discovery: Wikipedia/Wikidata knowledge graph
- realtime_feeds: News feed aggregation demo

Tested across 70+ unit tests with all domains integrated.

* feat: Add economic, patent, and ArXiv data source clients

New API Clients:
- FredClient: Federal Reserve economic indicators (GDP, CPI, unemployment)
- WorldBankClient: Global development indicators and climate data
- AlphaVantageClient: Stock market daily prices
- ArxivClient: Scientific preprint search with category and date filters
- UsptoPatentClient: USPTO patent search by keyword, assignee, CPC class
- EpoClient: Placeholder for European patent search

New Domain:
- Domain::Economic for economic/financial indicator data

Updated Exports:
- Domain colors and shapes for Economic in visualization and export

Examples:
- economic_discovery: FRED + World Bank integration demo
- arxiv_discovery: AI/ML/Climate paper search demo
- patent_discovery: Climate tech and AI patent search demo

All 85 tests passing. APIs tested with live endpoints.

* feat: Add Semantic Scholar, bioRxiv/medRxiv, and CrossRef research clients

New Research API Clients:
- SemanticScholarClient: Citation graph analysis, paper search, author lookup
  - Methods: search_papers, get_citations, get_references, search_by_field
  - Builds citation networks for graph analysis

- BiorxivClient: Life sciences preprints
  - Methods: search_recent, search_by_category (neuroscience, genomics, etc.)
  - Automatic conversion to Domain::Research

- MedrxivClient: Medical preprints
  - Methods: search_covid, search_clinical, search_by_date_range
  - Automatic conversion to Domain::Medical

- CrossRefClient: DOI metadata and scholarly communication
  - Methods: search_works, get_work, search_by_funder, get_citations
  - Polite pool support for better rate limits

All clients include:
- Rate limiting respecting API guidelines
- Retry logic with exponential backoff
- SemanticVector conversion with rich metadata
- Comprehensive unit tests

Examples:
- biorxiv_discovery: Fetch neuroscience and clinical research
- crossref_demo: Search publications, funders, datasets

Total: 104 tests passing, ~2,500 new lines of code

* feat: Add MCP server with STDIO/SSE transport and optimized discovery

MCP Server Implementation (mcp_server.rs):
- JSON-RPC 2.0 protocol with MCP 2024-11-05 compliance
- Dual transport: STDIO for CLI, SSE for HTTP streaming
- 22 discovery tools exposing all data sources:
  - Research: OpenAlex, ArXiv, Semantic Scholar, CrossRef, bioRxiv, medRxiv
  - Medical: PubMed, ClinicalTrials.gov, FDA
  - Economic: FRED, World Bank
  - Climate: NOAA
  - Knowledge: Wikipedia, Wikidata SPARQL
  - Discovery: Multi-source, coherence analysis, pattern detection
- Resources: discovery://patterns, discovery://graph, discovery://history
- Pre-built prompts: cross_domain_discovery, citation_analysis, trend_detection

Binary Entry Point (bin/mcp_discovery.rs):
- CLI arguments with clap
- Configurable discovery parameters
- STDIO/SSE mode selection

Optimized Discovery Runner:
- Parallel data fetching with tokio::join!
- SIMD-accelerated vector operations (1.1M comparisons/sec)
- 6-phase discovery pipeline with benchmarking
- Statistical significance testing (p-values)
- Cross-domain correlation analysis
- CSV export and hypothesis report generation

Performance Results:
- 180 vectors from 3 sources in 7.5s
- 686 edges computed in 8ms
- SIMD throughput: 1,122,216 comparisons/sec

All 106 tests passing.

* feat: Add space, genomics, and physics data source clients

Add exotic data source integrations:
- Space clients: NASA (APOD, NEO, Mars, DONKI), Exoplanet Archive, SpaceX API, TNS Astronomy
- Genomics clients: NCBI (genes, proteins, SNPs), UniProt, Ensembl, GWAS Catalog
- Physics clients: USGS Earthquakes, CERN Open Data, Argo Ocean, Materials Project

New domains: Space, Genomics, Physics, Seismic, Ocean

All 106 tests passing, SIMD benchmark: 208k comparisons/sec

* chore: Update export/visualization and output files

* docs: Add API client inventory and reference documentation

* fix: Update API clients for 2025 endpoint changes

- ArXiv: Switch from HTTP to HTTPS (export.arxiv.org)
- USPTO: Migrate to PatentSearch API v2 (search.patentsview.org)
  - Legacy API (api.patentsview.org) discontinued May 2025
  - Updated query format from POST to GET
  - Note: May require API authentication
- FRED: Require API key (mandatory as of 2025)
  - Added error handling for missing API key
  - Added response error field parsing

All tests passing, ArXiv discovery confirmed working

* feat: Implement comprehensive 2025 API client library (11,810 lines)

Add 7 new API client modules implementing 35+ data sources:

Academic APIs (1,328 lines):
- OpenAlexClient, CoreClient, EricClient, UnpaywallClient

Finance APIs (1,517 lines):
- FinnhubClient, TwelveDataClient, CoinGeckoClient, EcbClient, BlsClient

Geospatial APIs (1,250 lines):
- NominatimClient, OverpassClient, GeonamesClient, OpenElevationClient

News & Social APIs (1,606 lines):
- HackerNewsClient, GuardianClient, NewsDataClient, RedditClient

Government APIs (2,354 lines):
- CensusClient, DataGovClient, EuOpenDataClient, UkGovClient
- WorldBankGovClient, UNDataClient

AI/ML APIs (2,035 lines):
- HuggingFaceClient, OllamaClient, ReplicateClient
- TogetherAiClient, PapersWithCodeClient

Transportation APIs (1,720 lines):
- GtfsClient, MobilityDatabaseClient
- OpenRouteServiceClient, OpenChargeMapClient

All clients include:
- Async/await with tokio and reqwest
- Mock data fallback for testing without API keys
- Rate limiting with configurable delays
- SemanticVector conversion for RuVector integration
- Comprehensive unit tests (252 total tests passing)
- Full error handling with FrameworkError

* docs: Add API client documentation for new implementations

Add documentation for:
- Geospatial clients (Nominatim, Overpass, Geonames, OpenElevation)
- ML clients (HuggingFace, Ollama, Replicate, Together, PapersWithCode)
- News clients (HackerNews, Guardian, NewsData, Reddit)
- Finance clients implementation notes

* feat: Implement dynamic min-cut tracking system (SODA 2026)

Based on El-Hayek, Henzinger, Li (SODA 2026) subpolynomial dynamic min-cut algorithm.

Core Components (2,626 lines):
- dynamic_mincut.rs (1,579 lines): EulerTourTree, DynamicCutWatcher, LocalMinCutProcedure
- cut_aware_hnsw.rs (1,047 lines): CutAwareHNSW, CoherenceZones, CutGatedSearch

Key Features:
- O(log n) connectivity queries via Euler-tour trees
- n^{o(1)} update time when λ ≤ 2^{(log n)^{3/4}} (vs O(n³) Stoer-Wagner)
- Cut-gated HNSW search that respects coherence boundaries
- Real-time cut monitoring with threshold-based deep evaluation
- Thread-safe structures with Arc<RwLock>

Performance (benchmarked):
- 75x speedup over periodic recomputation
- O(1) min-cut queries vs O(n³) recompute
- ~25µs per edge update

Tests & Benchmarks:
- 36+ unit tests across both modules
- 5 benchmark suites comparing periodic vs dynamic
- Integration with existing OptimizedDiscoveryEngine

This enables real-time coherence tracking in RuVector, transforming
min-cut from an expensive periodic computation to a maintained invariant.

---------

Co-authored-by: Claude <noreply@anthropic.com>
2026-01-04 14:36:41 -05:00

10 KiB
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Cut-Aware HNSW: Dynamic Min-Cut Integration with Vector Search

Overview

cut_aware_hnsw.rs implements a coherence-aware extension to HNSW (Hierarchical Navigable Small World) graphs that respects semantic boundaries in vector spaces. Traditional HNSW blindly follows similarity edges during search. Cut-aware HNSW adds "coherence gates" that halt expansion at weak cuts, keeping searches within semantically coherent regions.

Architecture

Core Components

  1. DynamicCutWatcher - Tracks minimum cuts and graph coherence

    • Implements Stoer-Wagner algorithm for global min-cut
    • Incremental updates with caching for efficiency
    • Identifies boundary edges crossing partitions
  2. CutAwareHNSW - Extended HNSW with coherence gating

    • Wraps standard HNSW index
    • Maintains cut watcher for edge weights
    • Supports both gated and ungated search modes
  3. CoherenceZone - Regions of strong internal connectivity

    • Computed from min-cut partitions
    • Tracked with coherence ratios
    • Used for zone-aware queries

Key Features

let config = CutAwareConfig {
    coherence_gate_threshold: 0.3,  // Cuts below this are "weak"
    max_cross_cut_hops: 2,           // Max boundary crossings
    ..Default::default()
};

let mut index = CutAwareHNSW::new(config);

// Insert vectors
index.insert(node_id, &vector)?;

// Gated search (respects boundaries)
let gated_results = index.search_gated(&query, k);

// Ungated search (baseline)
let ungated_results = index.search_ungated(&query, k);

Gated Search will:

  • Track cut crossings for each result
  • Gate expansion at weak cuts (below threshold)
  • Return coherence scores (1.0 = no cuts crossed)
  • Prune expansions exceeding max_cross_cut_hops

2. Coherent Neighborhoods

Find all nodes reachable without crossing weak cuts:

let neighbors = index.coherent_neighborhood(node_id, radius);
// Returns nodes within `radius` hops that don't cross weak cuts

3. Zone-Based Queries

Partition the graph into coherence zones and query specific regions:

// Compute zones
let zones = index.compute_zones();

// Search within specific zones
let results = index.cross_zone_search(&query, k, &[zone_0, zone_1]);

4. Dynamic Updates

Efficiently handle graph changes with incremental cut recomputation:

// Single edge update
index.add_edge(u, v, weight);
index.remove_edge(u, v);

// Batch updates
let updates = vec![
    EdgeUpdate { kind: UpdateKind::Insert, u: 0, v: 1, weight: Some(0.8) },
    EdgeUpdate { kind: UpdateKind::Delete, u: 2, v: 3, weight: None },
];
let stats = index.batch_update(updates);

5. Cut Pruning

Remove weak edges to improve coherence:

let pruned_count = index.prune_weak_edges(threshold);

Performance Characteristics

Time Complexity

Operation Complexity Notes
Insert O(log n × M) Same as HNSW
Search (ungated) O(log n) Same as HNSW
Search (gated) O(log n) Plus gate checks
Min-cut O(n³) Stoer-Wagner, cached
Zone computation O(n²) Periodic recomputation

Space Complexity

  • Base HNSW: O(n × M × L) where L is layer count
  • Cut tracking: O(n²) for adjacency (sparse in practice)
  • Total: O(n × M × L + e) where e is edge count

Optimizations

  1. Cached Min-Cut: Recomputes only when graph changes
  2. Incremental Updates: Version-tracked cache invalidation
  3. Sparse Adjacency: HashMap-based for efficiency
  4. Periodic Recomputation: Configurable via cut_recompute_interval

Use Cases

1. Multi-Domain Discovery

Search within specific research domains without crossing into others:

// Climate papers in one cluster, finance in another
// Query climate without getting finance results
let climate_results = index.search_gated(&climate_query, 10);

2. Anomaly Detection

Identify nodes that bridge disparate clusters:

let zones = index.compute_zones();
for zone in zones {
    if zone.coherence_ratio < threshold {
        // Low coherence = potential boundary/anomaly
    }
}

3. Hierarchical Exploration

Navigate from abstract to specific within a coherent region:

let l1_neighbors = index.coherent_neighborhood(root, 1);
let l2_neighbors = index.coherent_neighborhood(root, 2);
// Expand without crossing semantic boundaries

4. Cross-Domain Linking

Explicitly find connections between domains:

// Find papers that bridge climate and finance
let bridging_papers = index.cross_zone_search(
    &interdisciplinary_query,
    10,
    &[climate_zone, finance_zone]
);

Metrics and Monitoring

Track performance and behavior:

let metrics = index.metrics();
println!("Searches: {}", metrics.searches_performed.load(Ordering::Relaxed));
println!("Gates triggered: {}", metrics.cut_gates_triggered.load(Ordering::Relaxed));
println!("Expansions pruned: {}", metrics.expansions_pruned.load(Ordering::Relaxed));

// Export as JSON
let json = index.export_metrics();

// Get cut distribution
let dist = index.cut_distribution();
for layer_stats in dist {
    println!("Layer {}: avg_cut={:.3}", layer_stats.layer, layer_stats.avg_cut);
}

Configuration Guide

CutAwareConfig Parameters

pub struct CutAwareConfig {
    // Standard HNSW
    pub m: usize,                    // Max connections per node (default: 16)
    pub ef_construction: usize,      // Construction quality (default: 200)
    pub ef_search: usize,            // Search quality (default: 50)

    // Cut-aware
    pub coherence_gate_threshold: f64,    // Weak cut threshold (default: 0.3)
    pub max_cross_cut_hops: usize,        // Max boundary crossings (default: 2)
    pub enable_cut_pruning: bool,         // Auto-prune weak edges (default: false)
    pub cut_recompute_interval: usize,    // Recompute frequency (default: 100)
    pub min_zone_size: usize,             // Min nodes per zone (default: 5)
}

Tuning Guidelines

Workload coherence_gate_threshold max_cross_cut_hops Notes
Strict coherence 0.5-0.8 0-1 Stay within zones
Moderate 0.3-0.5 2-3 Some flexibility
Exploratory 0.1-0.3 3-5 Cross boundaries
No gating 0.0 Ungated search

Examples

Basic Usage

use ruvector_data_framework::cut_aware_hnsw::{CutAwareHNSW, CutAwareConfig};

let config = CutAwareConfig::default();
let mut index = CutAwareHNSW::new(config);

// Build index
for i in 0..100 {
    let vector = generate_vector(i);
    index.insert(i as u32, &vector)?;
}

// Query
let results = index.search_gated(&query, 10);
for result in results {
    println!("Node {}: distance={:.4}, coherence={:.3}",
        result.node_id, result.distance, result.coherence_score);
}

Advanced: Multi-Cluster Discovery

See examples/cut_aware_demo.rs for a complete example demonstrating:

  • Three distinct semantic clusters
  • Gated vs ungated search comparison
  • Coherent neighborhood exploration
  • Cross-zone queries
  • Metrics tracking

Testing

The implementation includes 16 comprehensive tests:

cargo test --lib cut_aware_hnsw

Test Coverage:

  • Dynamic cut watcher (basic, partition, triangle)
  • Cut-aware insert and search
  • Gated vs ungated comparison
  • Coherent neighborhoods
  • Zone computation
  • Cross-zone search
  • Edge updates (single and batch)
  • Weak edge pruning
  • Metrics tracking and export
  • Boundary edge identification

Benchmarks

Compare gated vs ungated search performance:

cargo bench --bench cut_aware_hnsw_bench

Benchmarks:

  • Gated vs ungated search (100, 500, 1000 nodes)
  • Coherent neighborhood (radius 2, 5)
  • Zone computation
  • Batch updates (10, 50, 100 edges)
  • Cross-zone search

Expected Results:

  • Ungated search: ~10-50 μs for 1000 nodes
  • Gated search: ~15-70 μs (overhead from gate checks)
  • Zone computation: ~1-5 ms for 1000 nodes

Integration with RuVector

With ruvector-core

// Use ruvector-core for production HNSW
use ruvector_core::hnsw::HnswIndex as RuvectorHNSW;

// Wrap with cut-awareness
let base_index = RuvectorHNSW::new(dimension);
let cut_aware = CutAwareHNSW::with_base(base_index, config);

With ruvector-mincut

// Use ruvector-mincut for production min-cut
use ruvector_mincut::StoerWagner;

// Replace DynamicCutWatcher backend
let mincut = StoerWagner::new();
let watcher = DynamicCutWatcher::with_backend(mincut);

Limitations

  1. Min-Cut Complexity: O(n³) Stoer-Wagner limits scalability to ~10k nodes
  2. Memory: Stores full adjacency (sparse) for cut computation
  3. Static Partitions: Zones recomputed periodically, not incrementally
  4. Threshold Sensitivity: Results depend on coherence_gate_threshold

Future Enhancements

Planned Features

  1. Euler Tour Trees - O(log n) dynamic connectivity for faster updates
  2. Hierarchical Cuts - Multi-level zone hierarchy
  3. Approximate Min-Cut - Karger's algorithm for large graphs
  4. Persistent Zones - Incremental zone maintenance
  5. SIMD Distance - Accelerated vector comparisons

Research Directions

  1. Learned Gates - ML-based coherence threshold prediction
  2. Temporal Coherence - Track coherence evolution over time
  3. Multi-Metric Cuts - Combine similarity, citation, correlation
  4. Distributed Cuts - Partition across machines

References

  1. Stoer-Wagner Algorithm

    • Stoer & Wagner (1997). "A simple min-cut algorithm"
  2. HNSW

    • Malkov & Yashunin (2018). "Efficient and robust approximate nearest neighbor search"
  3. Dynamic Connectivity

    • Holm et al. (2001). "Poly-logarithmic deterministic fully-dynamic algorithms"
  4. Applications

    • Cross-domain research discovery
    • Hierarchical document clustering
    • Anomaly detection in graphs

License

Same as RuVector (MIT/Apache-2.0)

Contributing

See CONTRIBUTING.md for guidelines on:

  • Adding new distance metrics
  • Optimizing cut algorithms
  • Improving zone computation
  • Adding tests and benchmarks