Graph-of-Thoughts: structured reasoning over retrieved nodes.
Vector DB Integration: Combines graph data with vector embeddings for hybrid search.
Workflow
Input: Natural language question.
Retrieval: Fetch relevant sub-graph and similar text chunks.
Reasoning: LLM traverses the graph to find connecting paths.
Answer: Generate response with citation of graph nodes.
Example Usage
User: "Explain the mechanism connecting BRCA1 mutations to ovarian cancer."
Agent Action:
python -m kragen.solve --question "BRCA1 mutations to ovarian cancer mechanism"
1---2name: kragen-knowledge-graph3description: Graph-RAG Solver4license: MIT5---67<!--8# COPYRIGHT NOTICE9# This file is part of the "Universal Biomedical Skills" project.10# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>11# All Rights Reserved.12#13# This code is proprietary and confidential.14# Unauthorized copying of this file, via any medium is strictly prohibited.15#16# Provenance: Authenticated by MD BABU MIA1718-->192021# KRAGEN (Knowledge Graph Enhanced RAG)2223A knowledge graph-enhanced Retrieval-Augmented Generation system for biomedical problem solving, using Graph-of-Thoughts (GoT) reasoning.2425## When to Use2627* **Complex Reasoning**: Questions requiring multi-hop deduction (e.g., "How does gene A influence disease B via protein C?").28* **Hypothesis Verification**: Checking if a proposed mechanism is supported by existing knowledge graphs.29* **Literature Synthesis**: Combining facts from structured DBs and unstructured text.3031## Core Capabilities32331. **Graph Retrieval**: Query biomedical knowledge graphs (e.g., PrimeKG, SPOKE).342. **Graph-of-Thoughts**: structured reasoning over retrieved nodes.353. **Vector DB Integration**: Combines graph data with vector embeddings for hybrid search.3637## Workflow38391. **Input**: Natural language question.402. **Retrieval**: Fetch relevant sub-graph and similar text chunks.413. **Reasoning**: LLM traverses the graph to find connecting paths.424. **Answer**: Generate response with citation of graph nodes.4344## Example Usage4546**User**: "Explain the mechanism connecting BRCA1 mutations to ovarian cancer."4748**Agent Action**:49```bash50python -m kragen.solve --question "BRCA1 mutations to ovarian cancer mechanism"51```525354<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
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Graph-RAG Solver It is listed under AI & ML on SkillMD.
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