polymath

Polymath

A Polymathic Research Intelligence System

Polymath is a self-growing research intelligence system designed for polymathic discovery—finding unexpected connections across disparate scientific domains. Unlike traditional literature databases that organize knowledge in silos, Polymath explicitly models cross-domain bridges: the fertile intersections where spatial transcriptomics meets information theory, where thermodynamics informs deep learning, where cybernetics illuminates biological systems.

Key Features

• 807K+ Searchable Items: 395K paper passages + 411K code chunks
• Cross-Domain Concept Graph: 222 concepts linked across 31K+ papers
• Hybrid Search: Combines semantic (ChromaDB), lexical (Postgres FTS), and graph (Neo4j) search
• Evidence-Bound Citations: Claims traced to page-level source text
• Self-Improving: Identifies coverage gaps and proposes expansions

Architecture

┌─────────────────────────────────────────────────────┐
│                    USER QUERY                        │
└─────────────────────┬───────────────────────────────┘
                      │
                      ▼
┌─────────────────────────────────────────────────────┐
│           HYBRID SEARCH (RRF Fusion)                │
└─────────────────────┬───────────────────────────────┘
                      │
        ┌─────────────┼─────────────┐
        ▼             ▼             ▼
┌─────────────┐ ┌──────────┐ ┌────────────┐
│  ChromaDB   │ │ Postgres │ │   Neo4j    │
│  807K vecs  │ │  (FTS)   │ │  (graph)   │
│  2 colls    │ │  SoR     │ │ 32K nodes  │
└─────────────┘ └──────────┘ └────────────┘

Installation

Prerequisites

• Python 3.10+
• PostgreSQL 14+
• Neo4j 5.x
• CUDA-capable GPU (recommended for embeddings)

Setup

# Clone the repository
git clone https://github.com/vanbelkummax/polymath.git
cd polymath

# Create virtual environment
python -m venv venv
source venv/bin/activate

# Install dependencies
pip install -e .

# Copy and configure environment
cp .env.example .env
# Edit .env with your database credentials

# Initialize databases
python scripts/init_databases.py

Database Setup

PostgreSQL

createdb polymath
psql -d polymath -f schema/postgres_schema.sql

Neo4j

# Start Neo4j and set password
neo4j start
cypher-shell -u neo4j -p neo4j "ALTER CURRENT USER SET PASSWORD FROM 'neo4j' TO 'your_password'"

ChromaDB

ChromaDB is file-based and will be created automatically on first run.

Quick Start

Search Papers

from lib.hybrid_search_v2 import HybridSearcherV2

hs = HybridSearcherV2()

# Semantic search
results = hs.search_papers("attention mechanism in pathology", n=10)

# With filters
results = hs.search_papers(
    "spatial transcriptomics",
    n=10,
    year_min=2023,
    concepts=["transformer"]
)

Search Code

# Find implementations
results = hs.search_code(
    "multiple instance learning",
    n=10,
    org_filter="mahmoodlab",
    language="python"
)

Hybrid Search (Papers + Code)

results = hs.hybrid_search(
    "predict gene expression from H&E",
    n=20,
    rerank=True  # Cross-encoder reranking
)

CLI

# System stats
python polymath_cli.py stats

# Semantic search
python polymath_cli.py search "compressed sensing spatial transcriptomics" -n 10

# Neo4j graph query
python polymath_cli.py graph "MATCH (p:Paper)-[:MENTIONS]->(c:CONCEPT) RETURN c.name, count(p) ORDER BY count(p) DESC LIMIT 10"

# Generate hypotheses
python polymath_cli.py hypothesis

MCP Server Tools

Polymath exposes tools via the Model Context Protocol (MCP):

Discovery Tools

Tool	Description
deep_hunt	Multi-source literature search
find_gaps	Detect research gaps
trend_radar	Analyze publication trends
find_datasets	Hunt for datasets

Reasoning Tools

Tool	Description
generate_hypothesis	Cross-domain hypothesis generation
validate_hypothesis	Validate claims against corpus
find_analogy	Find analogous solutions
serendipity	Surface unexpected connections

Self-Improvement Tools

Tool	Description
collection_health	Assess corpus health
expand_collection	Propose expansion targets

Ingestion

Papers

# Single PDF
python lib/unified_ingest.py path/to/paper.pdf

# Batch ingestion
python lib/unified_ingest.py path/to/pdfs/ --move

# With enhanced parsing
python lib/unified_ingest.py paper.pdf --enhanced-parser

Code Repositories

# Ingest a GitHub repo
python lib/code_ingest.py https://github.com/org/repo

# Batch ingest
python scripts/ingest_github_batch.py

Literature Sentry (Autonomous Curator)

# Full polymathic sweep
python -m lib.sentry.cli "spatial transcriptomics visium" --max 15

# GitHub only
python -m lib.sentry.cli "attention mechanism" --source github --min-stars 100

# Show paywalled items
python -m lib.sentry.cli --show-tickets

Project Structure

polymath/
├── lib/                    # Core libraries
│   ├── hybrid_search_v2.py # Hybrid search engine
│   ├── evidence_extractor.py # NLI-based verification
│   ├── code_ingest.py      # Code repository ingestion
│   ├── unified_ingest.py   # Paper ingestion
│   └── sentry/             # Literature Sentry
├── mcp/                    # MCP servers
│   └── polymath_v11/       # Main MCP server
├── scripts/                # Utility scripts
├── tests/                  # Integration tests
├── docs/                   # Documentation
├── schema/                 # Database schemas
└── skills/                 # Skill definitions

Cross-Domain Concepts

Polymath automatically detects and links these concepts:

Signal Processing: compressed_sensing, sparse_coding, wavelet, fourier Physics: entropy, free_energy, thermodynamics, diffusion Causality: causal_inference, counterfactual Systems: feedback, control_theory, emergence, cybernetics Cognitive: predictive_coding, bayesian, active_inference ML/AI: transformer, attention, contrastive_learning, graph_neural_network Biology: spatial_transcriptomics, single_cell, gene_expression

Testing

# Run integration tests
pytest tests/test_integration.py -v

# Run all tests
pytest tests/ -v

Configuration

Environment Variables

Variable	Description
POSTGRES_URL	PostgreSQL connection string
NEO4J_URI	Neo4j bolt URI
NEO4J_PASSWORD	Neo4j password
CHROMADB_PATH	Path to ChromaDB directory
BRAVE_API_KEY	Brave Search API key (optional)

Documentation

• User Manual - Comprehensive guide
• Academic Playbook - Academic use cases and optimization guide
• Hackathon Playbook - Spatial multimodal hackathon workflow
• Literature Sentry Design
• Code Ingestion Design

Author

Max Van Belkum

• Vanderbilt University
• MD-PhD Student

License

MIT License - See LICENSE for details.

Citation

If you use Polymath in your research, please cite:

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*"The test of a first-rate intelligence is the ability to hold two opposed ideas in mind at the same time and still retain the ability to function."* — F. Scott Fitzgerald