Which Medical Questions Deserve Rationales? Perturbation-Sensitive Selection for Robust QA

Test-time reinforcement learning adapts a model on its own unlabeled test set using majority-vote pseudo-labels and has shown strong results in mathematics. We show that this recipe collapses on medical multiple-choice QA: accuracy stagnates while output diversity rapidly declines. Through a controlled experiment that keeps the questions, model, and optimizer fixed while changing only the answer space, we trace this failure to answer-space structure rather than domain difficulty. In small answer spaces, incorrect rollouts often collide on the same wrong pseudo-label and reinforce it; in large answer spaces, they disperse and receive little reward. This diagnosis motivates PROSE, Process Reward Guided Self-Training, which rewards reasoning quality instead of answer agreement. PROSE scores each reasoning step with a medical process reward model, assigns the trajectory reward as the minimum score across steps, and enforces answer-format constraints. Without labels, PROSE substantially improves a general Llama model, surpassing purpose-built medical models and matching much larger systems. Because the process signal is internalized into the policy, the adapted model requires no reward model at inference and transfers its gains to unseen datasets. We further show that the minimum aggregation is essential: mean aggregation can be exploited, saturating the proxy reward while degrading accuracy.

In medical multiple-choice question answering (MCQA), Retrieval-Augmented Generation (RAG) can supplement the domain knowledge of language models (LMs). However, since vanilla RAG indiscriminately utilizes retrieved documents, it can degrade LM performance. To address this, we propose MedJudgeRAG. Our framework represents retrieved documents as a dynamic knowledge graph (KG) composed of entities and relations. For each option, the model judges an evidence verdict from the retrieved documents and the KG. Based on the verdict combination, the model determines a knowledge utilization strategy to reason toward the final answer. These capabilities are trained via supervised fine-tuning using structured reasoning traces generated by a teacher LM. The training employs a weighted cross-entropy loss that differentially weights the KG and reasoning segments. Experiments on two medical MCQA benchmarks demonstrate that MedJudgeRAG consistently outperforms both vanilla RAG and parametric baselines. Furthermore, ablation analysis reveals that the dynamic KG is more effective as graph-conditioned supervision at training time than as an explicit output at inference time. Our code is available at https://github.com/hyu-amllab/medjudgerag, and the generated reasoning traces are released at https://huggingface.co/datasets/youarethewon/medjudgerag.

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.