# Benchmarking Retrieval-Augmented Generation for Medicine

arXiv: https://arxiv.org/abs/2402.13178 · HTML: https://mlsanity.com/paper/2402.13178/

## Key facts

- Cited by 331 papers in the map (data through 14 Oct 2026).
- Placed in Medical and biomedical RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 40 of its 67 references that are in the map.
- First posted on arXiv 20 Feb 2024.

## Placed in

- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)

## Builds on (most cited first, 30 of 40)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Dense Passage Retrieval for Open-Domain Question Answering](https://mlsanity.com/paper/2004.04906/) (2020)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models](https://mlsanity.com/paper/2104.08663/) (2021)
- [Unsupervised Dense Information Retrieval with Contrastive Learning](https://mlsanity.com/paper/2112.09118/) (2021)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval](https://mlsanity.com/paper/2007.00808/) (2020)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [In-Context Retrieval-Augmented Language Models](https://mlsanity.com/paper/2302.00083/) (2023)
- [SummEval: Re-evaluating Summarization Evaluation](https://mlsanity.com/paper/2007.12626/) (2020)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [Fact or Fiction: Verifying Scientific Claims](https://mlsanity.com/paper/2004.14974/) (2020)
- [CCNet: Extracting High Quality Monolingual Datasets from Web Crawl Data](https://mlsanity.com/paper/1911.00359/) (2019)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [SPECTER: Document-level Representation Learning using Citation-informed Transformers](https://mlsanity.com/paper/2004.07180/) (2020)
- [Augmented Language Models: a Survey](https://mlsanity.com/paper/2302.07842/) (2023)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [Can large language models reason about medical questions?](https://mlsanity.com/paper/2207.08143/) (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)
- [Deep Bidirectional Language-Knowledge Graph Pretraining](https://mlsanity.com/paper/2210.09338/) (2022)
- [PaperQA: Retrieval-Augmented Generative Agent for Scientific Research](https://mlsanity.com/paper/2312.07559/) (2023)

## Built on by (most cited first, 30 of 331)

- [Retrieval-Augmented Generation for AI-Generated Content: A Survey](https://mlsanity.com/paper/2402.19473/) (2024)
- [AgentClinic: a multimodal agent benchmark to evaluate AI in simulated clinical environments](https://mlsanity.com/paper/2405.07960/) (2024)
- [RankRAG: Unifying Context Ranking with Retrieval-Augmented Generation in LLMs](https://mlsanity.com/paper/2407.02485/) (2024)
- [Retrieval-Augmented Generation with Graphs (GraphRAG)](https://mlsanity.com/paper/2501.00309/) (2024)
- [MDAgents: An Adaptive Collaboration of LLMs for Medical Decision-Making](https://mlsanity.com/paper/2404.15155/) (2024)
- [Evaluation of Retrieval-Augmented Generation: A Survey](https://mlsanity.com/paper/2405.07437/) (2024)
- [Long-Context LLMs Meet RAG: Overcoming Challenges for Long Inputs in RAG](https://mlsanity.com/paper/2410.05983/) (2024)
- [InstructRAG: Instructing Retrieval-Augmented Generation via Self-Synthesized Rationales](https://mlsanity.com/paper/2406.13629/) (2024)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation](https://mlsanity.com/paper/2408.04187/) (2024)
- [AgentInstruct: Toward Generative Teaching with Agentic Flows](https://mlsanity.com/paper/2407.03502/) (2024)
- [A Systematic Survey and Critical Review on Evaluating Large Language Models: Challenges, Limitations, and Recommendations](https://mlsanity.com/paper/2407.04069/) (2024)
- [MedTrinity-25M: A Large-scale Multimodal Dataset with Multigranular Annotations for Medicine](https://mlsanity.com/paper/2408.02900/) (2024)
- [A Survey on Retrieval-Augmented Text Generation for Large Language Models](https://mlsanity.com/paper/2404.10981/) (2024)
- [Retrieval-Augmented Generation for Natural Language Processing: A Survey](https://mlsanity.com/paper/2407.13193/) (2024)
- [Process vs. Outcome Reward: Which is Better for Agentic RAG Reinforcement Learning](https://mlsanity.com/paper/2505.14069/) (2025)
- [RAGChecker: A Fine-grained Framework for Diagnosing Retrieval-Augmented Generation](https://mlsanity.com/paper/2408.08067/) (2024)
- [Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions](https://mlsanity.com/paper/2408.00727/) (2024)
- [RAG vs. GraphRAG: A Systematic Evaluation and Key Insights](https://mlsanity.com/paper/2502.11371/) (2025)
- [From Tokens to Words: On the Inner Lexicon of LLMs](https://mlsanity.com/paper/2410.05864/) (2024)
- [MedExpQA: Multilingual Benchmarking of Large Language Models for Medical Question Answering](https://mlsanity.com/paper/2404.05590/) (2024)
- [s3: You Don't Need That Much Data to Train a Search Agent via RL](https://mlsanity.com/paper/2505.14146/) (2025)
- [What is the Role of Small Models in the LLM Era: A Survey](https://mlsanity.com/paper/2409.06857/) (2024)
- [Rationale-Guided Retrieval Augmented Generation for Medical Question Answering](https://mlsanity.com/paper/2411.00300/) (2024)
- [Knowledge Boundary of Large Language Models: A Survey](https://mlsanity.com/paper/2412.12472/) (2024)
- [MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks](https://mlsanity.com/paper/2503.07459/) (2025)
- [Self-Evolving Multi-Agent Simulations for Realistic Clinical Interactions](https://mlsanity.com/paper/2503.22678/) (2025)
- [BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers](https://mlsanity.com/paper/2404.18443/) (2024)
- [MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning](https://mlsanity.com/paper/2405.03000/) (2024)
- [A Survey on Medical Large Language Models: Technology, Application, Trustworthiness, and Future Directions](https://mlsanity.com/paper/2406.03712/) (2024)

## Abstract (arXiv)

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine.