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

arXiv: https://arxiv.org/abs/2508.15849 · HTML: https://mlsanity.com/paper/2508.15849/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 16 of its 19 references that are in the map.
- First posted on arXiv 20 Aug 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 16 of 16)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [LinkBERT: Pretraining Language Models with Document Links](https://mlsanity.com/paper/2203.15827/) (2022)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [Med-HALT: Medical Domain Hallucination Test for Large Language Models](https://mlsanity.com/paper/2307.15343/) (2023)
- [Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation](https://mlsanity.com/paper/2408.04187/) (2024)
- [MedRAG: Enhancing Retrieval-augmented Generation with Knowledge Graph-Elicited Reasoning for Healthcare Copilot](https://mlsanity.com/paper/2502.04413/) (2025)
- [Rationale-Guided Retrieval Augmented Generation for Medical Question Answering](https://mlsanity.com/paper/2411.00300/) (2024)
- [Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHRs](https://mlsanity.com/paper/2412.16178/) (2024)
- [HealthQ: Unveiling Questioning Capabilities of LLM Chains in Healthcare Conversations](https://mlsanity.com/paper/2409.19487/) (2024)
- [CDF-RAG: Causal Dynamic Feedback for Adaptive Retrieval-Augmented Generation](https://mlsanity.com/paper/2504.12560/) (2025)
- [RGAR: Recurrence Generation-augmented Retrieval for Factual-aware Medical Question Answering](https://mlsanity.com/paper/2502.13361/) (2025)
- [K-COMP: Retrieval-Augmented Medical Domain Question Answering With Knowledge-Injected Compressor](https://mlsanity.com/paper/2501.13567/) (2025)

## Built on by (most cited first, 5 of 5)

- [CARE-ECG: Causal Agent-based Reasoning for Explainable and Counterfactual ECG Interpretation](https://mlsanity.com/paper/2604.10420/) (2026)
- [Contradictions in Context: Challenges for Retrieval-Augmented Generation in Healthcare](https://mlsanity.com/paper/2511.06668/) (2025)
- [Foundation Models for Medical Imaging: Status, Challenges, and Directions](https://mlsanity.com/paper/2602.15913/) (2026)
- [To Reason or Not to: Selective Chain-of-Thought in Medical Question Answering](https://mlsanity.com/paper/2602.20130/) (2026)
- [PerCaM-Health: Personalized Dynamic Causal Graphs for Healthcare Reasoning](https://mlsanity.com/paper/2605.07267/) (2026)

## Abstract (arXiv)

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.