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| # DeepCritical Documentation | |
| ## Medical Drug Repurposing Research Agent | |
| AI-powered deep research system for accelerating drug repurposing discovery. | |
| --- | |
| ## Quick Links | |
| ### Architecture | |
| - **[Overview](architecture/overview.md)** - Project overview, use case, architecture | |
| - **[Design Patterns](architecture/design-patterns.md)** - Technical patterns, data models | |
| ### Implementation | |
| - **[Roadmap](implementation/roadmap.md)** - Phased execution plan with TDD | |
| - **[Phase 1: Foundation](implementation/01_phase_foundation.md)** ✅ - Tooling, config, first tests | |
| - **[Phase 2: Search](implementation/02_phase_search.md)** ✅ - PubMed search | |
| - **[Phase 3: Judge](implementation/03_phase_judge.md)** ✅ - LLM evidence assessment | |
| - **[Phase 4: UI](implementation/04_phase_ui.md)** ✅ - Orchestrator + Gradio | |
| - **[Phase 5: Magentic](implementation/05_phase_magentic.md)** ✅ - Multi-agent orchestration | |
| - **[Phase 6: Embeddings](implementation/06_phase_embeddings.md)** ✅ - Semantic search + dedup | |
| - **[Phase 7: Hypothesis](implementation/07_phase_hypothesis.md)** ✅ - Mechanistic reasoning | |
| - **[Phase 8: Report](implementation/08_phase_report.md)** ✅ - Structured scientific reports | |
| - **[Phase 9: Source Cleanup](implementation/09_phase_source_cleanup.md)** ✅ - Remove DuckDuckGo | |
| - **[Phase 10: ClinicalTrials](implementation/10_phase_clinicaltrials.md)** ✅ - Clinical trials API | |
| - **[Phase 11: bioRxiv](implementation/11_phase_biorxiv.md)** ✅ - Preprint search | |
| - **[Phase 12: MCP Server](implementation/12_phase_mcp_server.md)** ✅ - Claude Desktop integration | |
| - **[Phase 13: Modal Integration](implementation/13_phase_modal_integration.md)** ✅ - Secure code execution | |
| - **[Phase 14: Demo Submission](implementation/14_phase_demo_submission.md)** ✅ - Hackathon submission | |
| ### Guides | |
| - **[Deployment Guide](guides/deployment.md)** - Gradio, MCP, and Modal launch steps | |
| ### Development | |
| - **[Testing Strategy](development/testing.md)** - Unit, Integration, and E2E testing patterns | |
| --- | |
| ## What We're Building | |
| **One-liner**: AI agent that searches medical literature to find existing drugs that might treat new diseases. | |
| **Example Query**: | |
| > "What existing drugs might help treat long COVID fatigue?" | |
| **Output**: Research report with drug candidates, mechanisms, evidence quality, and citations. | |
| --- | |
| ## Architecture Summary | |
| ``` | |
| User Question → Research Agent (Orchestrator) | |
| ↓ | |
| Search Loop: | |
| → Tools (PubMed, ClinicalTrials, bioRxiv) | |
| → Judge (Quality + Budget) | |
| → Repeat or Synthesize | |
| ↓ | |
| Research Report with Citations | |
| ``` | |
| --- | |
| ## Features | |
| | Feature | Status | Description | | |
| |---------|--------|-------------| | |
| | **Gradio UI** | ✅ Complete | Streaming chat interface | | |
| | **MCP Server** | ✅ Complete | Tools accessible from Claude Desktop | | |
| | **Modal Sandbox** | ✅ Complete | Secure statistical analysis | | |
| | **Multi-Source Search** | ✅ Complete | PubMed, ClinicalTrials, bioRxiv | | |
| --- | |
| ## Team | |
| - The-Obstacle-Is-The-Way | |
| - MarioAderman | |
| - Josephrp | |
| --- | |
| ## Status | |
| | Phase | Status | | |
| |-------|--------| | |
| | Phases 1-14 | ✅ COMPLETE | | |
| **Test Coverage**: 65% (96 tests passing) | |
| **Architecture Review**: PASSED (98-99/100) | |