docs/index.md

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 - Project overview, use case, architecture, timeline
• Design Patterns - 17 technical patterns, reference repos, judge prompts, data models

Implementation (Start Here!)

• Roadmap - Phased execution plan with TDD
• Phase 1: Foundation ✅ - Tooling, config, first tests
• Phase 2: Search ✅ - PubMed search
• Phase 3: Judge ✅ - LLM evidence assessment
• Phase 4: UI ✅ - Orchestrator + Gradio
• Phase 5: Magentic ✅ - Multi-agent orchestration
• Phase 6: Embeddings ✅ - Semantic search + dedup
• Phase 7: Hypothesis ✅ - Mechanistic reasoning
• Phase 8: Report ✅ - Structured scientific reports
• Phase 9: Source Cleanup 📝 - Remove DuckDuckGo
• Phase 10: ClinicalTrials 📝 - Clinical trials API
• Phase 11: bioRxiv 📝 - Preprint search

Guides

• Setup Guide (coming soon)
• Deployment Guide - Gradio, MCP, and Modal launch steps

Development

• Testing Strategy - Unit, Integration, and E2E testing patterns
• Contributing (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)