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Your AI coding agent already reads code and writes code. DrBrain gives it a structured knowledge graph of academic papers — so it can search literature, trace causal chains, find research gaps, and infer new relationships through rule-based reasoning.

• 📚 Your paper library becomes a queryable knowledge graph with concept-level granularity.
• 🧩 Reasoning is symbol-driven: closure rules, confidence propagation, counterfactuals — not just embedding similarity.
• ⚡ Corpus-scale hybrid retrieval: BM25 + dense vectors + RAPTOR tree summaries + graph traversal, fused by RRF and reranked — over hundreds of thousands of full-text papers, with vectors on semantically-complete tree nodes rather than arbitrary chunks.
• 🤖 Built for AI agents: every feature is accessible through the CLI that your agent already uses.

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✨ Highlights

• Incremental by default — add one paper to an N-paper library and only that paper builds; closure scans its neighborhood; embeddings micro-adjust.
• 7 reasoning workflows — review, gap-analysis, impact, compare, frontier, lineage, paradigm.
• OKF export — emit the entire knowledge graph as an OKF v0.1 markdown bundle that humans and agents can read with cat.
• 27 agent skills following the open AgentSkills.io standard.

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🚀 Quick Start

git clone https://github.com/UynajGI/DrBrain.git
cd DrBrain
uv sync && uv pip install -e .
drbrain setup          # interactive wizard (bilingual EN / 中文)

This creates ~/DrBrain/ as your library root (%USERPROFILE%/DrBrain on Windows).

# Ingest → build → embed → closure (all incremental)
drbrain fetch "10.1038/nature14539"     # grab a paper by DOI
drbrain build                           # 5-stage LLM extraction
drbrain embed                           # TransE graph embeddings
drbrain closure                         # rule-based inference
drbrain ask "What gaps remain in deep learning?"

# Or chain everything at once
drbrain pipeline --preset full

pipx install drbrain and uv tool install drbrain are coming in beta.

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📖 What It Does

All commands

setup ingest ingest-link fetch batch-fetch build embed closure query search hybrid ask reason graph analyze survey evolve landscape frontier paradigm citations check-citations export export-okf import translate session ws cg rag pipeline repair enrich audit backup restore metrics document fsearch patent-search proceedings explore report seed list stats show index queue delete lineage style check clean webui

Run drbrain --help for the full list, or see the CLI Reference.

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🤖 Works With Your Agent

Install DrBrain skills so your coding agent can use them:

npx skills add https://github.com/UynajGI/DrBrain/skills

Skills follow the open AgentSkills.io standard and work with Claude Code, Codex, Cline, Cursor, Windsurf, Qwen Code, GitHub Copilot, and other AI coding tools.

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⚙️ Configuration

drbrain setup walks you through the basics interactively (bilingual EN / 中文):

• LLM API key (any litellm provider: OpenAI, Anthropic, Ollama, DeepSeek, …)
• MinerU token (optional; PyMuPDF fallback for PDF parsing)
• Semantic Scholar / CrossRef / OpenAlex API keys (optional; higher rate limits)

drbrain check verifies your environment end-to-end. See Configuration for every setting.

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📚 Documentation

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🙏 Inspired By

DrBrain's agent-first design is inspired by ScholarAIO — the pioneering "research infrastructure for AI agents." DrBrain takes a different technical path: symbol-driven knowledge graph reasoning on top of a corpus-scale hybrid retriever (BM25 + vector + tree + graph, RRF-fused) whose vectors live on semantically-complete tree nodes rather than full-text chunks. Tree-structured retrieval is inspired by PageIndex and RAPTOR.

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🤝 Contributing

Contributions are welcome — bug reports, feature requests, docs, and code all help. See CONTRIBUTING.md for the full guide.

Quick start for contributors:

git clone https://github.com/UynajGI/DrBrain.git && cd DrBrain
uv sync && uv pip install -e .
pre-commit install                      # optional: auto-lint on commit
uv run pytest -m "not integration"      # fast tests

Before opening a PR, make sure these pass:

uv run ruff check . && uv run ruff format --check .
uv run mypy src/drbrain
uv run pytest -m "not integration"

We follow Conventional Commits (feat:, fix:, docs:, refactor:, test:, chore:).

Have a question or idea? Open a discussion. Found a bug? File an issue.

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📄 License

MIT — see LICENSE.