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class=md-nav__link> <span class=md-ellipsis> Graph Orchestration Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/graph_orchestration/ class=md-nav__link> <span class=md-ellipsis> Graph Orchestration Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/workflows/ class=md-nav__link> <span class=md-ellipsis> DeepCritical Workflow - Simplified Magentic Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/workflow-diagrams/ class=md-nav__link> <span class=md-ellipsis> DeepCritical Workflow - Simplified Magentic Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/agents/ class=md-nav__link> <span class=md-ellipsis> Agents Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/orchestrators/ class=md-nav__link> <span class=md-ellipsis> Orchestrators Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/tools/ class=md-nav__link> <span class=md-ellipsis> Tools Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/middleware/ class=md-nav__link> <span class=md-ellipsis> Middleware Architecture </span> </a> </li> <li class=md-nav__item> <a href=architecture/services/ class=md-nav__link> <span class=md-ellipsis> Services Architecture </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle md-toggle--indeterminate" type=checkbox id=__nav_6> <label class=md-nav__link for=__nav_6 id=__nav_6_label tabindex=0> <span class=md-ellipsis> API Reference </span> <span class="md-nav__icon md-icon"></span> </label> <nav class=md-nav data-md-level=1 aria-labelledby=__nav_6_label aria-expanded=false> <label class=md-nav__title for=__nav_6> <span class="md-nav__icon md-icon"></span> API Reference </label> <ul class=md-nav__list data-md-scrollfix> <li class=md-nav__item> <a href=api/agents/ class=md-nav__link> <span class=md-ellipsis> Agents API Reference </span> </a> </li> <li class=md-nav__item> <a href=api/tools/ class=md-nav__link> <span class=md-ellipsis> Tools API Reference </span> </a> </li> <li class=md-nav__item> <a href=api/orchestrators/ class=md-nav__link> <span class=md-ellipsis> Orchestrators API Reference </span> </a> </li> <li class=md-nav__item> <a href=api/services/ class=md-nav__link> <span class=md-ellipsis> Services API Reference </span> </a> </li> <li class=md-nav__item> <a href=api/models/ class=md-nav__link> <span class=md-ellipsis> Models API Reference </span> </a> </li> </ul> </nav> </li> <li class=md-nav__item> <a href=contributing/ class=md-nav__link> <span class=md-ellipsis> Contributing </span> </a> </li> <li class=md-nav__item> <a href=license/ class=md-nav__link> <span class=md-ellipsis> License </span> </a> </li> <li class=md-nav__item> <a href=team/ class=md-nav__link> <span class=md-ellipsis> Team </span> </a> </li> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component=sidebar data-md-type=toc> <div class=md-sidebar__scrollwrap> <div class=md-sidebar__inner> <nav class="md-nav md-nav--secondary" aria-label="Table of contents"> <label class=md-nav__title for=__toc> <span class="md-nav__icon md-icon"></span> Table of contents </label> <ul class=md-nav__list data-md-component=toc data-md-scrollfix> <li class=md-nav__item> <a href=#features class=md-nav__link> <span class=md-ellipsis> Features </span> </a> </li> <li class=md-nav__item> <a href=#quick-start class=md-nav__link> <span class=md-ellipsis> Quick Start </span> </a> </li> <li class=md-nav__item> <a href=#architecture class=md-nav__link> <span class=md-ellipsis> Architecture </span> </a> </li> <li class=md-nav__item> <a href=#documentation class=md-nav__link> <span class=md-ellipsis> Documentation </span> </a> </li> <li class=md-nav__item> <a href=#links class=md-nav__link> <span class=md-ellipsis> Links </span> </a> </li> </ul> </nav> </div> </div> </div> <div class=md-content data-md-component=content> <article class="md-content__inner md-typeset"> <h1 id=deepcritical>DeepCritical<a class=headerlink href=#deepcritical title="Permanent link">¶</a></h1> <p><strong>AI-Native Drug Repurposing Research Agent</strong></p> <p>DeepCritical is a deep research agent system that uses iterative search-and-judge loops to comprehensively answer research questions. The system supports multiple orchestration patterns, graph-based execution, parallel research workflows, and long-running task management with real-time streaming.</p> <h2 id=features>Features<a class=headerlink href=#features title="Permanent link">¶</a></h2> <ul> <li><strong>Multi-Source Search</strong>: PubMed, ClinicalTrials.gov, Europe PMC (includes bioRxiv/medRxiv)</li> <li><strong>MCP Integration</strong>: Use our tools from Claude Desktop or any MCP client</li> <li><strong>HuggingFace OAuth</strong>: Sign in with your HuggingFace account to automatically use your API token</li> <li><strong>Modal Sandbox</strong>: Secure execution of AI-generated statistical code</li> <li><strong>LlamaIndex RAG</strong>: Semantic search and evidence synthesis</li> <li><strong>HuggingFace Inference</strong>: Free tier support with automatic fallback</li> <li><strong>Strongly Typed Composable Graphs</strong>: Graph-based orchestration with Pydantic AI</li> <li><strong>Specialized Research Teams of Agents</strong>: Multi-agent coordination for complex research tasks</li> </ul> <h2 id=quick-start>Quick Start<a class=headerlink href=#quick-start title="Permanent link">¶</a></h2> <div class=highlight><pre><span></span><code><a id=__codelineno-0-1 name=__codelineno-0-1 href=#__codelineno-0-1></a><span class=c1># Install uv if you haven't already</span>
	<a id=__codelineno-0-2 name=__codelineno-0-2 href=#__codelineno-0-2></a>pip<span class=w> </span>install<span class=w> </span>uv
	<a id=__codelineno-0-3 name=__codelineno-0-3 href=#__codelineno-0-3></a>
	<a id=__codelineno-0-4 name=__codelineno-0-4 href=#__codelineno-0-4></a><span class=c1># Sync dependencies</span>
	<a id=__codelineno-0-5 name=__codelineno-0-5 href=#__codelineno-0-5></a>uv<span class=w> </span>sync
	<a id=__codelineno-0-6 name=__codelineno-0-6 href=#__codelineno-0-6></a>
	<a id=__codelineno-0-7 name=__codelineno-0-7 href=#__codelineno-0-7></a><span class=c1># Start the Gradio app</span>
	<a id=__codelineno-0-8 name=__codelineno-0-8 href=#__codelineno-0-8></a>uv<span class=w> </span>run<span class=w> </span>gradio<span class=w> </span>run<span class=w> </span>src/app.py
	</code></pre></div> <p>Open your browser to <code>http://localhost:7860</code>.</p> <p>For detailed installation and setup instructions, see the <a href=getting-started/installation/ >Getting Started Guide</a>.</p> <h2 id=architecture>Architecture<a class=headerlink href=#architecture title="Permanent link">¶</a></h2> <p>DeepCritical uses a Vertical Slice Architecture:</p> <ol> <li><strong>Search Slice</strong>: Retrieving evidence from PubMed, ClinicalTrials.gov, and Europe PMC</li> <li><strong>Judge Slice</strong>: Evaluating evidence quality using LLMs</li> <li><strong>Orchestrator Slice</strong>: Managing the research loop and UI</li> </ol> <p>The system supports three main research patterns:</p> <ul> <li><strong>Iterative Research</strong>: Single research loop with search-judge-synthesize cycles</li> <li><strong>Deep Research</strong>: Multi-section parallel research with planning and synthesis</li> <li><strong>Research Team</strong>: Multi-agent coordination using Magentic framework</li> </ul> <p>Learn more about the <a href=overview/architecture/ >Architecture</a>.</p> <h2 id=documentation>Documentation<a class=headerlink href=#documentation title="Permanent link">¶</a></h2> <ul> <li><a href=overview/architecture/ >Overview</a> - System architecture and design</li> <li><a href=getting-started/installation/ >Getting Started</a> - Installation and setup</li> <li><a href=configuration/ >Configuration</a> - Configuration guide</li> <li><a href=api/agents/ >API Reference</a> - API documentation</li> <li><a href=contributing/ >Contributing</a> - Development guidelines</li> </ul> <h2 id=links>Links<a class=headerlink href=#links title="Permanent link">¶</a></h2> <ul> <li><a href=https://github.com/DeepCritical/GradioDemo>GitHub Repository</a></li> <li><a href=https://huggingface.co/spaces/DataQuests/DeepCritical>HuggingFace Space</a></li> </ul> </article> </div> <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script> </div> <button type=button class="md-top md-icon" data-md-component=top hidden> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8z"/></svg> Back to top </button> </main> <footer class=md-footer> <div class="md-footer-meta md-typeset"> <div class="md-footer-meta__inner md-grid"> <div class=md-copyright> <div class=md-copyright__highlight> Copyright © 2024 DeepCritical Team </div> Made with <a href=https://squidfunk.github.io/mkdocs-material/ target=_blank rel=noopener> Material for MkDocs </a> </div> <div class=md-social> <a href=https://github.com/DeepCritical/GradioDemo target=_blank rel=noopener title=github.com class=md-social__link> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 512 512"><!-- Font Awesome Free 7.1.0 by @fontawesome - 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