# DeepCritical Documentation

## Medical Drug Repurposing Research Agent

AI-powered deep research system for accelerating drug repurposing discovery.

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## Quick Links

### Architecture
- **[Overview](architecture/overview.md)** - Project overview, use case, architecture, timeline
- **[Design Patterns](architecture/design-patterns.md)** - 17 technical patterns, reference repos, judge prompts, data models

### Implementation (Start Here!)
- **[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

### Guides
- [Setup Guide](guides/setup.md) (coming soon)
- **[Deployment Guide](guides/deployment.md)** - Gradio, MCP, and Modal launch steps

### Development
- **[Testing Strategy](development/testing.md)** - Unit, Integration, and E2E testing patterns
- [Contributing](development/contributing.md) (coming soon)


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## 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.

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## Architecture Summary

```
User Question → Research Agent (Orchestrator)
                      ↓
              Search Loop:
                → Tools (PubMed, Web Search)
                → Judge (Quality + Budget)
                → Repeat or Synthesize
                      ↓
              Research Report with Citations
```

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## Hackathon Tracks

| Track | Status | Key Feature |
|-------|--------|-------------|
| **Gradio** | ✅ Planned | Streaming UI with progress |
| **MCP** | ✅ Planned | PubMed as MCP server |
| **Modal** | 🔄 Stretch | GPU inference option |

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## Team

- Physician (medical domain expert) ✅
- Software engineers ✅
- AI architecture validated by multiple agents ✅

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## Status

| Phase | Status |
|-------|--------|
| Phases 1-8 | ✅ COMPLETE |
| Phase 9: Remove DuckDuckGo | 📝 SPEC READY |
| Phase 10: ClinicalTrials.gov | 📝 SPEC READY |
| Phase 11: bioRxiv | 📝 SPEC READY |

**Architecture Review**: PASSED (98-99/100)
**Phases 1-8**: COMPLETE
**Next**: Phases 9-11 (Multi-Source Enhancement)