MedCoT-RAG: Causal Chain-of-Thought RAG for Medical Question Answering

Abstract

Large language models (LLMs) have shown promise in medical question answering but often struggle with hallucinations and shallow reasoning, particularly in tasks requiring nuanced clinical understanding. Retrieval-augmented generation (RAG) offers a practical and privacy-preserving way to enhance LLMs with external medical knowledge. However, most existing approaches rely on surface-level semantic retrieval and lack the structured reasoning needed for clinical decision support. We introduce MedCoT-RAG, a domain-specific framework that combines causal-aware document retrieval with structured chain-of-thought prompting tailored to medical workflows. This design enables models to retrieve evidence aligned with diagnostic logic and generate step-by-step causal reasoning reflective of real-world clinical practice. Experiments on three diverse medical QA benchmarks show that MedCoT-RAG outperforms strong baselines by up to 10.3% over vanilla RAG and 6.4% over advanced domain-adapted methods, improving accuracy, interpretability, and consistency in complex medical tasks.