phago-rag

Biological RAG — query interface on self-organizing Hebbian knowledge graph.

Overview

This crate provides retrieval-augmented generation capabilities:

• Hybrid Query: Combines TF-IDF with graph-based re-ranking
• Structural Queries: Shortest path, centrality, bridges, components
• MCP Adapter: Model Context Protocol integration for external LLMs
• Scoring: Precision, MRR, NDCG metrics

Benchmark Results

The graph's value is in re-ranking TF-IDF candidates using structural context.

Usage

use phago_rag::prelude::*;

// Hybrid query (TF-IDF + graph re-ranking)
let results = hybrid_query(&colony, "membrane transport", &HybridConfig {
    alpha: 0.5,              // 50% TF-IDF, 50% graph
    max_results: 10,
    candidate_multiplier: 3,
});

for r in results {
    println!("{}: {:.3}", r.label, r.final_score);
}

MCP Integration

use phago_rag::mcp::*;

// Remember a document
phago_remember(&mut colony, &RememberRequest {
    title: "Doc".into(),
    content: "Content".into(),
    ticks: Some(15),
});

// Recall with hybrid scoring
let results = phago_recall(&colony, &RecallRequest {
    query: "search".into(),
    max_results: 5,
    alpha: 0.5,
});

// Explore graph structure
let stats = phago_explore(&colony, &ExploreRequest::Stats);

Part of Phago

This is a subcrate of phago. For most use cases, depend on the main phago crate instead.

License

MIT