RAG-X: Systematic Diagnosis of Retrieval-Augmented Generation for Medical Question Answering

Retrieval-Augmented Generation (RAG) is widely employed to mitigate risks such as hallucinations and knowledge obsolescence in medical question answering, yet its predominantly single-round, static retrieval paradigm misaligns with the multi-stage process of clinical reasoning. This compressed workflow induces two structural deficiencies: question-to-query translation often lacks clinically grounded semantic interpretation, and retrieval lacks iterative sufficiency feedback, making it difficult to form reliable evidence chains. We argue that both issues stem from a deeper cause: overloading a single reasoning chain with heterogeneous tasks of interpretation, exploration, and adjudication. The remedy is to reconstruct the workflow via task decoupling and dynamic multi-round exploration. To this end, we propose SEMA-RAG, a Self-Evolving Multi-Agent RAG framework for medical question answering, which assigns these roles to three specialist agents: the Interpreter Agent for clinical schema interpretation, the Explorer Agent for sufficiency-driven self-evolving retrieval, and the Arbiter Agent for evidence adjudication and answer selection. Across five benchmarks and five LLM backbones, SEMA-RAG improves the strongest baseline by +6.46 accuracy points on average, measured per backbone.

Large language models (LLMs) have demonstrated strong capabilities in medical question answering; however, purely parametric models often suffer from knowledge gaps and limited factual grounding. Retrieval-augmented generation (RAG) addresses this limitation by integrating external knowledge retrieval into the reasoning process. Despite increasing interest in RAG-based medical systems, the impact of individual retrieval components on performance remains insufficiently understood. This study presents a systematic evaluation of retrieval-augmented medical question answering using the MedQA USMLE benchmark and a structured textbook-based knowledge corpus. We analyze the interaction between language models, embedding models, retrieval strategies, query reformulation, and cross-encoder reranking within a unified experimental framework comprising forty configurations. Results show that retrieval augmentation significantly improves zero-shot medical question answering performance. The best-performing configuration was dense retrieval with query reformulation and reranking achieved 60.49% accuracy. Domain-specialized language models were also found to better utilize retrieved medical evidence than general-purpose models. The analysis further reveals a clear tradeoff between retrieval effectiveness and computational cost, with simpler dense retrieval configurations providing strong performance while maintaining higher throughput. All experiments were conducted on a single consumer-grade GPU, demonstrating that systematic evaluation of retrieval-augmented medical QA systems can be performed under modest computational resources.

Retrieval-Augmented Generation (RAG) significantly improves the factuality of Large Language Models (LLMs), yet standard pipelines often lack mechanisms to verify inter- mediate reasoning, leaving them vulnerable to hallucinations in high-stakes domains. To address this, we propose a domain-specific RAG framework that integrates explicit rea- soning and faithfulness verification. Our architecture augments standard retrieval with neural query rewriting, BGE-based cross-encoder reranking, and a rationale generation module that grounds sub-claims in specific evidence spans. We further introduce an eight-category verification taxonomy that enables fine-grained assessment of rationale faithfulness, distinguishing between explicit and implicit support patterns to facilitate structured error diagnosis. We evaluate this framework on the BioASQ and PubMedQA benchmarks, specifically analyzing the impact of dynamic in-context learning and rerank- ing under constrained token budgets. Experiments demonstrate that explicit rationale generation improves accuracy over vanilla RAG baselines, while dynamic demonstration selection combined with robust reranking yields further gains in few-shot settings. Using Llama-3-8B-Instruct, our approach achieves 89.1% on BioASQ-Y/N and 73.0% on Pub- MedQA, competitive with systems using significantly larger models. Additionally, we perform a pilot study combining human expert assessment with LLM-based verification to explore how explicit rationale generation improves system transparency and enables more detailed diagnosis of retrieval failures in biomedical question answering.