Taking the PULSE of Medical Reasoning: Step-Level Retrieval Timing for Knowledge-Grounded Inference

Large reasoning models such as DeepSeek-R1 and OpenAI o1 generate extended chains of thought spanning thousands of tokens, yet their integration with retrieval-augmented generation (RAG) remains fundamentally misaligned. Current RAG systems optimize for providing context before reasoning begins, while reasoning models require evidence injection during multi-step inference chains. We introduce ReaLM-Retrieve, a reasoning-aware retrieval framework that addresses this mismatch through three key innovations: (1) a step-level uncertainty detector that identifies knowledge gaps at reasoning-step granularity rather than token or sentence level; (2) a retrieval intervention policy that learns when external evidence maximally benefits ongoing reasoning; and (3) an efficiency-optimized integration mechanism that reduces per-retrieval overhead by 3.2x compared to naive integration. Experiments on MuSiQue, HotpotQA, and 2WikiMultiHopQA demonstrate that ReaLM-Retrieve achieves on average 10.1% absolute improvement in answer F1 over standard RAG (range: 9.0-11.8% across the three benchmarks) while reducing retrieval calls by 47% compared to fixed-interval approaches like IRCoT (all improvements significant at p<0.01, paired bootstrap). On the challenging MuSiQue benchmark requiring 2-4 hop reasoning, our method achieves 71.2% F1 with an average of only 1.8 retrieval calls per question. Analysis shows that ReaLM-Retrieve also improves retrieval quality itself, achieving 81.3% Recall@5 with consistently higher precision and MRR than fixed-interval baselines on supporting evidence, establishing new state-of-the-art efficiency-accuracy trade-offs for reasoning-intensive retrieval tasks.

Clinical reasoning LLMs need external medical knowledge, but retrieved evidence and reasoning chains can be outdated, poisoned, or hallucinated. Harmful knowledge can cause regression: changing a correct answer into an incorrect one. We construct a medical knowledge-poisoning benchmark covering retrieved evidence and reasoning chains, with seven attack families filtered by a three-judge "subtle-but-wrong" vote and paired clean exams that separate poisoning effects from question difficulty. No fixed knowledge-use strategy is robust across these settings: strong RAG methods trade robustness to poisoned evidence against accuracy when evidence is useful. We formulate knowledge use as per-instance routing and introduce Med-TrustRouter, a lightweight controller that keeps the solver frozen. From leakage-free runtime signals, it estimates each action's expected correctness gain and uncertainty, preserving the base answer unless another action is confidently better. Across seven medical reasoning settings, Med-TrustRouter achieves 78.9 macro and 69.2 worst-case accuracy, matching the strongest competitor on macro accuracy while substantially improving the worst-case floor. Its gains transfer across solvers and evidence judges, unlike a hand-coded router using the same signals. Similar performance across linear, tree, and neural action-value heads suggests that the benefit comes from routing rather than estimator complexity. These results support learning when to trust external knowledge for robust clinical reasoning.

Trustworthy biomedical question answering (QA) systems must not only provide accurate answers but also justify them with current, verifiable evidence. Retrieval-augmented approaches partially address this gap but lack mechanisms to iteratively refine poor queries, whereas self-reflection methods kick in only after full retrieval is completed. In this context, we introduce PubMed Reasoner, a biomedical QA agent composed of three stages: self-critic query refinement evaluates MeSH terms for coverage, alignment, and redundancy to enhance PubMed queries based on partial (metadata) retrieval; reflective retrieval processes articles in batches until sufficient evidence is gathered; and evidence-grounded response generation produces answers with explicit citations. PubMed Reasoner with a GPT-4o backbone achieves 78.32% accuracy on PubMedQA, slightly surpassing human experts, and showing consistent gains on MMLU Clinical Knowledge. Moreover, LLM-as-judge evaluations prefer our responses across: reasoning soundness, evidence grounding, clinical relevance, and trustworthiness. By orchestrating retrieval-first reasoning over authoritative sources, our approach provides practical assistance to clinicians and biomedical researchers while controlling compute and token costs.