Skeleton Indexing + VectorCypher + Agentic Router with Self-Correction + Mangle Reasoning + Typed API

A production-ready Graph RAG system combining four cutting-edge techniques from recent research into a unified retrieval pipeline with declarative reasoning, full pipeline provenance, and a typed API contract (FastAPI REST + MCP).

Evaluated on 30 bilingual questions (15 Doc1 Russian + 15 Doc2 English) across 6 retrieval modes = 180 evaluations:

Accuracy by query type (across all modes):

3 modes at 100% (vector, hybrid, agent_mangle). Zero persistent failures — every question passes in at least 4/6 modes.

Ingestion:
  Document -> Docling -> Chunker -> Enricher -> Embedder
           -> Skeleton Indexer (PageRank top-B)
           -> Dual Node Builder (phrase + passage nodes)
           -> Neo4j (Vector Index + Knowledge Graph)

Retrieval:
  Query -> Router (simple/relation/multi_hop/global/temporal)
           Router cascade: Mangle -> LLM -> Pattern fallback
        -> Tool Selection (vector/cypher/hybrid/comprehensive/full_read/temporal)
        -> Self-Correction Loop (evaluate relevance -> escalate if <2.0)
        -> Graph Verifier (contradiction detection)
        -> Generator (GPT-4o synthesis + dynamic confidence + citations)

agentic-graph-rag/
├── packages/rag-core/        # Shared pip package (models, config, ingestion, retrieval)
│   └── rag_core/
│       ├── models.py          # Chunk, Entity, SearchResult, QAResult, QueryType
│       ├── config.py          # Pydantic Settings (nested: Neo4j, OpenAI, Indexing, Agent)
│       ├── loader.py          # Docling: PDF/DOCX/PPTX + GPU
│       ├── chunker.py         # Table-aware chunking
│       ├── enricher.py        # Contextual enrichment (OpenAI)
│       ├── embedder.py        # text-embedding-3-small batch processing
│       ├── vector_store.py    # Neo4j Vector Index CRUD
│       ├── kg_client.py       # Graphiti wrapper + Cypher
│       ├── generator.py       # LLM answer synthesis + dynamic confidence
│       ├── reflector.py       # Relevance evaluation (1-5 scale) + completeness check
│       └── i18n.py            # RU/EN localization (~50 keys)
│
├── agentic_graph_rag/         # Graph RAG components
│   ├── indexing/
│   │   ├── skeleton.py        # KET-RAG: KNN -> PageRank -> skeletal extraction
│   │   └── dual_node.py       # HippoRAG 2: phrase + passage nodes + PPR
│   ├── retrieval/
│   │   └── vector_cypher.py   # Vector entry -> Cypher traversal -> context
│   ├── agent/
│   │   ├── router.py          # Query classifier (pattern + LLM + Mangle)
│   │   ├── retrieval_agent.py # Orchestrator + self-correction loop + provenance
│   │   └── tools.py           # 7 tools: vector, cypher, community, hybrid, temporal, full_read, comprehensive
│   ├── generation/
│   │   └── graph_verifier.py  # Contradiction detection + claim verification
│   ├── reasoning/
│   │   ├── reasoning_engine.py # PyMangle Datalog engine wrapper
│   │   └── rules/             # Mangle rules: routing.mg, access.mg, graph.mg
│   ├── optimization/
│   │   ├── cache.py           # LRU SubgraphCache + CommunityCache
│   │   └── monitor.py         # QueryMonitor + PageRank tuning suggestions
│   └── service.py             # PipelineService — typed internal contract
│
├── api/                       # v6: Typed API contract
│   ├── app.py                 # FastAPI factory with lifespan
│   ├── routes.py              # REST endpoints (query, trace, health, graph_stats)
│   ├── deps.py                # Dependency injection (PipelineService singleton)
│   └── mcp_server.py          # MCP tools (resolve_intent, search_graph, explain_trace)
│
├── pymangle/                  # PyMangle Datalog engine (~5K lines)
│
├── ui/
│   └── streamlit_app.py       # 7-tab Streamlit UI (port 8506, httpx thin client)
│
├── benchmark/
│   ├── questions.json         # 30 test questions (5 types, EN/RU, 2 documents)
│   ├── runner.py              # 6-mode benchmark runner
│   └── compare.py             # Comparison table generator
│
├── scripts/
│   └── ingest.py              # CLI ingestion: python scripts/ingest.py <file>
│
├── data/
│   ├── sample_graph_rag.txt                # Doc1 (RU benchmark Q1-Q15): Graph RAG overview
│   └── sample_semantic_companion_layer.txt # Doc2 (EN benchmark Q16-Q30): SCL / MeaningHub architecture
│
├── docker-compose.yml         # Neo4j 5.x (docker compose up -d)
├── run_api.py                 # API launcher (uvicorn, port 8507)
└── tests/                     # 454 unit tests (346 core + 108 pymangle)

• Python 3.12+
• Docker — Docker Desktop for Windows/Mac, or docker-ce for Linux (install guide)
• OpenAI API key (get one here)

git clone https://github.com/vpakspace/agentic-graph-rag.git
cd agentic-graph-rag

pip install -e packages/rag-core --no-deps
pip install -r requirements.txt

Note on Docling: The first time you load a PDF or DOCX document, Docling will download its ML models (~1-2 GB). This is a one-time download. If you only plan to ingest .txt files, no model download is needed.

cp .env.example .env

Edit .env — at minimum set these two values:

• OPENAI_API_KEY — your OpenAI API key
• NEO4J_PASSWORD — password you want for the Neo4j database

Using Docker Compose (recommended):

docker compose up -d

Or manually:

docker run -d \
  --name agentic-graph-rag-neo4j \
  -p 7474:7474 -p 7687:7687 \
  -e NEO4J_AUTH=neo4j/your_password \
  neo4j:5

Two sample documents are included for testing (both needed for the full 30-question benchmark):

# Ingest both documents (required for benchmark reproducibility)
PYTHONPATH=.:pymangle python scripts/ingest.py data/

Or ingest individually:

PYTHONPATH=.:pymangle python scripts/ingest.py data/sample_graph_rag.txt                # Doc1: Graph RAG (RU, Q1-Q15)
PYTHONPATH=.:pymangle python scripts/ingest.py data/sample_semantic_companion_layer.txt # Doc2: SCL (EN, Q16-Q30)

This runs the full pipeline: load → chunk → enrich → embed → store → skeleton indexing → dual-node graph.

Options:

• --skip-enrichment — skip LLM contextual enrichment (faster, fewer OpenAI calls)
• --skip-skeleton — skip skeleton indexing (vector store only, no knowledge graph)
• --use-gpu — enable GPU acceleration for Docling

You can also ingest your own documents (PDF, DOCX, TXT):

PYTHONPATH=.:pymangle python scripts/ingest.py /path/to/your/document.pdf
PYTHONPATH=.:pymangle python scripts/ingest.py /path/to/documents/  # entire directory

Or use the Streamlit UI Ingest tab (see below).

The simplest way to try it — run Streamlit standalone (no API server needed):

PYTHONPATH=.:pymangle streamlit run ui/streamlit_app.py --server.port 8506

Open http://localhost:8506 in your browser. You'll see 7 tabs: Ingest, Search & Q&A, Graph Explorer, Agent Trace, Benchmark, Reasoning, Settings.

Optional: API Server (for programmatic access or MCP):

# Terminal 1: start API
PYTHONPATH=.:pymangle python run_api.py  # http://localhost:8507

# Terminal 2: start Streamlit with API backend
AGR_API_URL=http://localhost:8507 PYTHONPATH=.:pymangle streamlit run ui/streamlit_app.py --server.port 8506

When AGR_API_URL is set, Streamlit routes queries through the API. Without it, Streamlit calls Python directly — both modes work identically.

Why PYTHONPATH? The project uses two source roots: the main project directory and pymangle/ (the Datalog engine). Setting PYTHONPATH=.:pymangle makes both importable. Alternatively, you can export PYTHONPATH=.:pymangle in your shell profile.

PYTHONPATH=.:pymangle pytest tests/ packages/rag-core/tests/ pymangle/tests/ -x -q  # 586 tests, ~4 seconds

REST (port 8507):

• POST /api/v1/query — Query the pipeline (returns answer + trace)
• GET /api/v1/trace/{id} — Retrieve a pipeline trace by ID
• GET /api/v1/health — Health check (Neo4j connectivity)
• GET /api/v1/graph/stats — Graph node/edge statistics

MCP tools (SSE at /mcp):

• resolve_intent — Classify query type and select tool
• search_graph — Execute full pipeline search
• explain_trace — Explain a pipeline trace

from benchmark.runner import run_benchmark
from benchmark.compare import compare_modes

# Requires Neo4j running + documents ingested
results = run_benchmark(driver, openai_client)  # lang="ru" by default
print(compare_modes(results))

Every query produces a PipelineTrace — a structured record of the full pipeline execution:

{
  "trace_id": "tr_abc123def456",
  "timestamp": "2026-02-17T12:00:00Z",
  "query": "Какие методы используются?",
  "router_step": {"method": "mangle", "decision": {"query_type": "simple", "suggested_tool": "vector_search"}},
  "tool_steps": [{"tool_name": "vector_search", "results_count": 10, "relevance_score": 3.2, "duration_ms": 150}],
  "escalation_steps": [],
  "generator_step": {"model": "gpt-4o-mini", "prompt_tokens": 1200, "completion_tokens": 350, "confidence": 0.82},
  "total_duration_ms": 1800
}

Traces are cached (LRU, 100 entries) and retrievable via GET /api/v1/trace/{id} or the MCP explain_trace tool.

The agent evaluates retrieval quality (1-5 scale) and escalates through the tool chain when results are insufficient:

vector_search -> cypher_traverse -> hybrid_search -> comprehensive_search -> full_document_read

Each retry rephrases the query via LLM and uses a different tool with expanded search scope. For GLOBAL queries, a completeness check triggers additional retrieval if the answer is incomplete. Max 2 retries by default. Best results tracked across attempts.

Declarative routing via PyMangle (Python Datalog engine):

• 65 bilingual keywords (Russian + English) in routing.mg
• Router cascade: Mangle (confidence 0.7) -> LLM (0.85) -> Pattern (0.5)
• UI: "Mangle Router" checkbox in sidebar, Reasoning tab for rule testing
• Rules: agentic_graph_rag/reasoning/rules/ — routing, access control, graph traversal

All settings via .env or environment variables:

• LLM: OpenAI GPT-4o / GPT-4o-mini
• Embeddings: text-embedding-3-small (1536 dim)
• Graph DB: Neo4j 5.x (Vector Index + Cypher)
• Reasoning: PyMangle (Datalog engine)
• Doc Parsing: Docling (PDF/DOCX/PPTX + GPU)
• Graph Algorithms: NetworkX (PageRank, KNN, PPR)
• API: FastAPI (REST + MCP via FastMCP)
• UI: Streamlit (7 tabs, httpx thin client)
• Testing: pytest (586 tests) + ruff

1. Ingest — Upload documents, skeleton indexing with progress
2. Search & Q&A — Mode selector (vector/hybrid/agent), confidence bar, sources
3. Graph Explorer — Phrase + passage node visualization (Graphviz)
4. Agent Trace — Routing decision, self-correction steps, raw trace
5. Benchmark — Run 6 modes, PASS/FAIL table, comparison metrics
6. Reasoning — Mangle rule testing, query classification preview
7. Settings — Config display, cache stats, monitor analytics, clear DB

• KET-RAG: Cost-Efficient Graph RAG (KDD 2025)
• HippoRAG 2: Agentic Retrieval (ICML 2025)
• VectorCypher: Neo4j Graph Retrieval
• Agentic RAG: Self-Correcting Retrieval
• Mangle: Datalog Dialect (Google Research)

MIT