| # DeepCritical Documentation |
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| ## Medical Drug Repurposing Research Agent |
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| AI-powered deep research system for accelerating drug repurposing discovery. |
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| ## Quick Links |
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| ### Architecture |
| - **[Overview](architecture/overview.md)** - Project overview, use case, architecture |
| - **[Design Patterns](architecture/design-patterns.md)** - Technical patterns, data models |
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| ### 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 |
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| ### Guides |
| - **[Deployment Guide](guides/deployment.md)** - Gradio, MCP, and Modal launch steps |
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| ### Development |
| - **[Testing Strategy](development/testing.md)** - Unit, Integration, and E2E testing patterns |
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| ## What We're Building |
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| **One-liner**: AI agent that searches medical literature to find existing drugs that might treat new diseases. |
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| **Example Query**: |
| > "What existing drugs might help treat long COVID fatigue?" |
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| **Output**: Research report with drug candidates, mechanisms, evidence quality, and citations. |
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| ## Architecture Summary |
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| ``` |
| User Question → Research Agent (Orchestrator) |
| ↓ |
| Search Loop: |
| → Tools (PubMed, ClinicalTrials, bioRxiv) |
| → Judge (Quality + Budget) |
| → Repeat or Synthesize |
| ↓ |
| Research Report with Citations |
| ``` |
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| --- |
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| ## Features |
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| | 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 | |
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| --- |
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| ## Team |
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| - The-Obstacle-Is-The-Way |
| - MarioAderman |
| - Josephrp |
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| --- |
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| ## Status |
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| | Phase | Status | |
| |-------|--------| |
| | Phases 1-14 | ✅ COMPLETE | |
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| **Test Coverage**: 65% (96 tests passing) |
| **Architecture Review**: PASSED (98-99/100) |
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