Clinical Reasoning

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Latest papers 133

24 papers in the last four weeks, up 14% on the four weeks before. 0.2% of all new papers.

Jul 9, 2026cs.AI

MentalHospital: A Virtual Environment for Evaluating Psychiatric Clinical Encounters

Large language models (LLMs) have shown strong performance on isolated psychiatric tasks, including dialogue, diagnosis, and treatment planning, yet existing benchmarks rarely simulate complete psychiatric clinical encounters. We introduce

\textbf{MentalHospital}

, a virtual evaluation environment for LLM-based psychiatric clinical encounters. MentalHospital instantiates the Subjective Interviewing, Objective Examination, Diagnostic Assessment, and Treatment Planning (S.O.A.P.) workflow, using skill-augmented standardized patients constructed from 1,193 de-identified psychiatric electronic health record (EHR) cases spanning all major ICD-11 categories and 76 disorders. Each encounter is assessed through a dual-track protocol that combines objective comparison against EHR-derived references with subjective assessment of clinical process quality. To scale specialist judgment, we develop

\textbf{MentalEval}

, five domain-specific evaluators covering communication empathy, interviewing professionalism, clinical-note quality, diagnostic rigor, and treatment appropriateness, trained with rubric-grounded SFT and expert-guided DPO. Survey responses from 22 clinicians support MentalHospital's clinical fidelity (3.88/5), while MentalEval achieves strong expert alignment with an average QWK of 0.944. Benchmarking shows that even the strongest LLM trails clinicians by 37.28 percentage points in objective psychiatric competence, with mental status assessment as a key bottleneck.

Yuming Yang, Xiao Sun, Yuanwei Zou +6

School of Computer Science, Chongqing University, Chongqing, China · School of Computer Science, Hunan University, Changsha, China

Mental Health Clinical Reasoning Clinical Language Model Evaluation Medical LLMs

Jul 9, 2026cs.AI

A safety-oriented hypothetico-deductive framework for AI-assisted differential diagnosis

Diagnostic error is a major threat to patient safety, yet current large language model (LLM) systems often treat diagnosis as a one-shot prediction task, lacking safeguards against missed high-risk alternatives or rigorous verification of their reasoning. Here, we present AegisDx, a safety-oriented framework for hypothetico-deductive clinical reasoning. AegisDx coordinates specialized LLM components through role-specific contracts, structured intermediate outputs, evidence-retrieval interfaces, and verification gates to generate broad differential diagnoses, enforce explicit screening for dangerous "must-not-miss" conditions, verify reasoning against grounded medical evidence, and structure actionable next steps. We evaluated AegisDx across three layers. On literature-derived case reports from NEJM and JAMA, with GPT-oss-120B as the shared backbone, Top-3 diagnostic accuracy was 59.9% versus 52.1% for the standalone LLM on JAMA cases and 62.7% versus 51.4% on NEJM cases. On cases from Annals of Emergency Medicine, Top-3 accuracy was 85.7% versus 68.6%; against physician-consensus must-not-miss diagnosis sets, AegisDx captured at least one such condition among its top three diagnoses in 78.0% of cases versus 52.0%. In a blinded physician evaluation of 43 real-world emergency department notes from the Yale New Haven Health System compared against GPT-5, AegisDx improved the physician-rated composite safety score from 4.31 to 4.55 on a 5-point scale (adjusted p = 2.1x10^-4), with qualitative gains in must-not-miss identification and reasoning safety. Our findings suggest that engineering diagnostic AI as a safety-oriented reasoning framework, rather than optimizing raw predictive accuracy alone, can provide a safer, more transparent, and clinically meaningful layer of bedside decision support for acute care workflows.

Fan Ma, Mauro Giuffrè, Donald Wright +12

Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, USA · Department of Medical, Surgical and Health Sciences, Università degli Studi di Trieste, Trieste, Italy · Department of Emergency Medicine, Yale School of Medicine, Yale University, New Haven, USA +3

Scientific Reasoning Medical Diagnosis Clinical Decision Support LLM Safety Clinical Reasoning Differential Diagnosis+1

Jul 8, 2026cs.AI

Aligning Clinical Needs and AI Capabilities: A Survey on LLMs for Medical Reasoning

Large language models (LLMs) have emerged as important tools in healthcare, showing growing potential for clinical reasoning and patient care. This survey examines recent progress in medical LLMs, focusing on reasoning applications and requirements. We present a dual-view approach that connects clinical practice with computational methods. On the clinical side, we establish a five-level competency scheme following Miller's Pyramid, progressing from knowledge recall to dynamic case management. On the computational side, we link deductive, inductive, and abductive reasoning patterns to common medical goals and tasks. We also introduce a benchmark dataset spanning five levels of medical reasoning capability and report results on 18 state-of-the-art models, revealing that medical specialist models excel in diagnosis-centric tasks while general models lead in decision support and dialogue. We conclude by discussing current progress and open challenges, including data limitations, hallucination, and grounding issues, and outline directions toward safer, more reliable, and workflow-ready systems.

Qi Peng, Jiatong Li, Sirui Huang +10

1The Hong Kong Polytechnic University, Hong Kong, China. · 2Hong Kong University, Hong Kong, China. · 3South China University of Technology, Guangzhou, China. +3

Clinical Reasoning Clinical Language Model Evaluation Medical LLMs

Jul 6, 2026cs.AI

Medi-Gemma: A Hybrid Clinical Decision Support System Integrating Deterministic EMR Analytics and Retrieval-Augmented Generation

Deploying Large Language Models (LLMs) in high-stakes clinical settings remains limited by structural hallucinations, weak deterministic reasoning over tabular patient data, and omissions in vector retrieval. This paper presents the architecture and validation of Medi-Gemma, a Clinical Decision Support System (CDSS) for wound pathology triage and workflow automation. The platform introduces a decoupled framework that separates clinical perception from data orchestration while preserving traceable reasoning. Medi-Gemma uses a multi-stage pipeline coordinated by a centralized ClinicalOrchestrator. Data requests are handled without generative inference by a DataManager that cleans unstructured Electronic Medical Record (EMR) files through type coercion. Natural language queries are processed by a hierarchical IntentRouter, which routes requests to deterministic analytics paths executed by a PandasQueryEngine or to patient-specific reasoning managed by a ClinicalRAGEngine using a CPU-optimized vector store. A key contribution is the Ground Truth Injection Module, which intercepts patient-specific queries, extracts numeric identification tokens, queries the structured dataframe via Pandas, retrieves the latest validated clinical state, and embeds this snapshot as an overriding context block in the LLM prompt before generation. Safety compliance is enforced by a deterministic ProtocolManager that maps clinical terminology to fixed evidence-based risk pathways, while a SafetyVerifier phrase filter prevents output rule violations. Validation shows that this architecture eliminates semantic context drift, prevents database compilation crashes, and improves factual adherence to backend clinical repositories. These results support Medi-Gemma as a safer pattern for LLM-based clinical decision support where structured data fidelity, retrieval grounding, and deterministic safeguards are essential.

Mohammed Saim Ahmed Quadri, Yunzhe Xue, Justin W. Ady +1

Department of Computer Science, New Jersey Institute of Technology Newark, NJ, USA · Department of Data Science, New Jersey Institute of Technology Newark, NJ, USA · Vascular and Endovascular Surgery, Robert Wood Johnson Hospital New Brunswick, NJ, USA

Retrieval-Augmented Generation LLM Hallucination Mitigation Clinical Decision Support Clinical Reasoning Medical LLMs

Jul 3, 2026cs.AI

Reinforcement Learning for Evidence-Seeking Diagnostic Reasoning with Large Language Models

Recent reasoning-centric Large Language Models (LLMs) have made significant strides, yet they predominantly operate on a passive-inference pattern that assumes complete information. In contrast, real-world clinical intelligence is inherently an iterative investigative process requiring strategic evidence acquisition. To bridge this gap, we formalize medical diagnosis as an Iterative Evidence-Seeking Task. We leverage Reinforcement Learning with Verifiable Rewards (RLVR) to elicit intrinsic reasoning within a closed-loop environment, guided by a novel suite of rewards that enforce diagnostic precision and examination consistency. To facilitate this, we introduce the Retrieval-Augmented Generation-based Examination Simulator (RAGES), a high-fidelity clinical oracle that provides realistic, knowledge-grounded follow-up evidence. Empirical results across diverse datasets demonstrate that our framework enables LLMs to transition from passive responders to autonomous assistants. Notably, our model demonstrates comparable performance to larger and reasoning-enhanced baselines, while RAGES proves superior to vanilla LLMs in generating biologically plausible clinical feedback.

Shengyi Hua, Kangzhe Hu, Conghui He +2

Qing Yuan Research Institute, Shanghai Jiao Tong University · Shanghai AI Laboratoty · Shanghai Innovation Institute

Medical Diagnosis RL for Language Model Reasoning Active Information Gathering Clinical Reasoning Medical LLMs

Jul 2, 2026cs.AI

A rubric-based controlled comparison of frontier language models on expert-authored clinical reasoning tasks

Multiple-choice medical benchmarks are increasingly saturated, and recent rubric-based evaluations such as HealthBench have shown that open-ended clinical performance is far from solved - its "Hard" subset top score remains 32%. We present a small, deliberately difficult evaluation dataset of five clinician-authored clinical scenarios spanning four specialties (anaesthesia, internal/family medicine, emergency medicine, and obstetrics), each accompanied by an atomic, weighted, MECE rubric (25-62 criteria per task; 184 criteria total) authored from a clinician-drafted golden answer. We evaluate three frontier models: GPT 5.4, Claude Opus 4.7, and Gemini 3.1 Pro. Mean rubric pass rates were 0.47 (Claude), 0.38 (GPT), and 0.37 (Gemini). The central finding is an inversion of clinical priority: the highest-weighted (weight-5, critical) criteria passed at only 32.4-41.7%, while low-stakes weight-1 criteria passed at 80-90%. 55 of 108 critical (weight-5) criteria (51%) were satisfied by no model. Three LLM autoraters reproduced expert met/not-met labels on 92.8-94.6% of 552 graded criteria. We position this as a methods-and-preliminary-findings contribution: the five tasks demonstrate a scalable, defensible pipeline ready to develop into a large-scale benchmark.

Samiha A. Ismail, Fan X. Chen, Ali Merali

Prime Analytics Consulting Limited · Talbert House; Thomas More University · MAKZ

Clinical Decision-Making Clinical Reasoning Rubric-Based Evaluation Clinical Language Model Evaluation

Jun 30, 2026cs.AI

RareDxR1: Autonomous Medical Reasoning for Rare Disease Diagnosis Beyond Human Annotation

Rare disease differential diagnosis is a critical yet arduous clinical task, requiring physicians to identify precise phenotypes from complex, unstructured patient symptoms and execute intricate reasoning within a vast search space. However, existing AI approaches typically rely on pipeline-based phenotype extraction or retrieval-augmented generation, which suffer from critical information loss due to predefined ontologies, retrieval bottlenecks, and a lack of diagnostic logic. To address these challenges, we introduce RareDxR1, an end-to-end reasoning-centric large language model designed for open-domain rare disease diagnosis directly from unstructured clinical notes. We design a progressive end-to-end training framework by synergizing knowledge internalization with autonomous evolutionary learning, thereby bypassing reliance on structured phenotypes and closed-set decision-making. To overcome the limitations of RAG and phenotype restriction, we enabled the deep internalization of fragmented rare-disease knowledge directly into the model's parameters. Moreover, to bridge the gap between model generation and expert reasoning, we propose Reflection-Enhanced Reasoning Sampling (RERS), a strategy that synthesizes expert-level diagnostic trajectories by learning from failures without human annotation. Additionally, we propose a dual-level curriculum reinforcement learning approach for gradually mastering rare disease diagnosis. Experimental results demonstrate that RareDxR1 achieves state-of-the-art accuracy across different benchmarks, marking a significant breakthrough in open-domain rare disease diagnosis. Our code and dataset will be publicly available.

Deyang Jiang, Haoran Wu, Ziyi Wang +4

The Key Laboratory of Cognition and Decision Intelligence for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China · Peking Union Medical College Hospital, Beijing, China · School of Future Technology, University of Chinese Academy of Sciences, Beijing, China

Rare Disease Diagnosis RL for Language Model Reasoning Clinical Reasoning Medical LLMs

Jun 30, 2026cs.CL

CLExEval: A Human-in-the-Loop Framework for Qualitative Evaluation of LLM Clinical Reasoning

Large Language Models (LLMs) achieve strong results on many medical benchmarks, but their clinical reasoning remains difficult to evaluate reliably. A central risk is an evaluation illusion: fluent and well-structured explanations can appear clinically convincing even when the final diagnosis is incorrect. We introduce CLExEval, a human-in-the-loop framework for evaluating LLM clinical reasoning under progressive information masking. CLExEval combines 5,600 expert-physician annotations with 200 clinical reasoning traces derived from 40 rare diagnostic cases. Our analysis identifies three recurring failure patterns: (i) verbosity bias, where GPT-4o-mini's diagnostic accuracy drops from 95.0% to 32.5% under information scarcity; (ii) a hidden knowledge paradox, where a specialist model reaches 92.5% maximum diagnostic potential but fails to retrieve that knowledge reliably in verbose contexts; and (iii) a 68.6% reasoning-to-output mismatch, where correct diagnoses appear in reasoning traces but are not reflected in final answers. We further evaluate the LLM-as-a-Judge paradigm on a human-verified failure set (n = 142). GPT-4o-mini approved 47.9% of clinically incorrect outputs, while HuatuoGPT-o1 approved all validly scored failures and showed a positive self-preference bias. These results suggest that standalone automated clinical evaluations can substantially overestimate clinical reliability without expert-grounded validation.

Ajmal M., Abin Roy, Afthab Salam Kanniyan +4

1MBZUAI · 2IIT Madras · 3Calicut Medical College

LLM-as-a-Judge Human-in-the-Loop Evaluation LLM Reliability Clinical Reasoning Clinical Language Model Evaluation

Jun 29, 2026cs.CL

Clinical Reasoning Graphs: Structured Evaluation of LLM Diagnostic Reasoning Reveals Competence Without Consistency

Modern large language models (LLMs) reach 60-70% diagnostic accuracy on complex clinical case benchmarks, but accuracy alone cannot distinguish stable clinically-grounded reasoning from pattern matching. We introduce clinical reasoning graphs, structured graph representations extracted from free-text LLM diagnostic traces using a domain-grounded ontology with 5 node types and 7 edge types. We apply this pipeline to 750 traces from five LLMs across 50 New England Journal of Medicine Clinicopathological Conference cases and three prompt conditions, and test whether diagnostic traces show stable structured reasoning patterns, or diagnostic schemas, for clinically similar cases. We operationalize this as higher graph similarity among clinically similar cases than among clinically dissimilar ones. Across 15 model-condition comparisons, within-cluster and between-cluster composite similarity are nearly equal, and no comparison survives multiple-testing correction; a component-level analysis finds any residual content signal far below schema scale. Graph similarity is also nearly identical for pairs of models that are both correct (0.488) and both incorrect (0.484), suggesting that graph structure captures a dimension not reflected in diagnostic accuracy. Structured reflection prompting increases explicit discriminating-feature analysis within traces (+33%) but does not increase cross-case consistency. These results show diagnostic competence without schema-scale reasoning consistency, and indicate that final-answer accuracy should be complemented by process-level evaluation. We release the ontology, extraction pipeline, validation protocol, and the extracted reasoning graphs and similarity artifacts as resources for structured evaluation of LLM clinical reasoning.

Nisarg A. Patel

University of California, San Francisco · Department of Oral and Maxillofacial Surgery, University of California, San Francisco, CA, USA · Department of Medicine, Division of Clinical Informatics and Digital Transformation, University of California, San Francisco, CA, USA

LLM Evaluation Reasoning Consistency in Language Models Clinical Reasoning Clinical Language Model Evaluation Medical LLMs

Jun 22, 2026cs.AI

EHR-Complex: Benchmarking Medical Agents for Complex Clinical Reasoning

Clinical agents promise to democratize access to electronic health records (EHRs), yet existing benchmarks fail to reflect the complexity of practical EHR analysis, e.g., often operating on idealized, clean EHRs via static SQL generation rather than interactive execution. In this work, we introduce EHR-Complex, a large-scale benchmark designed for interactive clinical database reasoning. Built on the large MIMIC-IV substrate (365K patients, 31 tables, 500M+ records), EHR-Complex comprises about 52K tasks spanning six clinical intents, supporting both patient-level and population-level queries, where each task requires an agent to interact with a sandboxed environment by executing SQL queries or Python code. Notably, EHR-Complex considers the real-world SQL task complexity for longitudinal multi-table aggregation and compositional reasoning, resulting in 31.93 SQL structural components per query on average. Evaluation results on EHR-Complex reveal the clinical difficulty of these EHR reasoning scenarios, with the top-performing model achieving only 62.3% exact-match accuracy. Pass^k consistency drops below 50% for nearly all evaluated models at k=4, exposing broad stochastic fragility. A fine-grained analysis of more than 3,800 failed trajectories for representative LLMs reveals three dominant failure modes: SQL logic errors, medical-code lookup failures, and semantic misunderstandings. EHR-Complex provides a rigorous testbed for clinical agents and highlights remaining gaps in robust reasoning for large-scale EHR analysis.

Yitong Qiao, Lei Liu, Yue Shen +4

1Zhejiang University · †Work done during an internship at Ant Group. · 2Ant Group

AI Agent Benchmarks Clinical Reasoning Electronic Health Records

Jun 16, 2026cs.AI

Agentic AI-based Framework for Mitigating Premature Diagnostic Handoff and Silent Hallucination in Healthcare Applications

Recent advances in Large Language Models (LLMs) and multi-agent systems have driven the rise of Agentic AI, showing promise for medical reasoning. However, open-ended conversational agents remain prone to two critical failure modes: premature diagnostic handoff and silent clinical hallucinations that may go undetected before reaching the patient. In this work, we propose a multi-agent framework that addresses both issues by replacing ``LLM-as-a-judge'' routing with deterministic orchestration constraints. The framework incorporates two safety mechanisms. First, a neuro-symbolic state-tracking gate enforces completeness of the OLDCARTS clinical protocol (Onset, Location, Duration, Character, Aggravating/Alleviating factors, Radiation, Timing, and Severity) by blocking diagnostic transitions until all required dimensions are collected. Second, an epistemic uncertainty quantification (UQ) gate computes semantic entropy (H) across K=5 independent diagnostic samples to identify and intercept divergent outputs before delivery. We evaluate the system using simulated patient agents powered by the llama-3.1-70b-instruct model on 150 test cases. The full architecture achieves 49.3% diagnostic precision, representing an absolute improvement of 11.3 percentage points over an unconstrained baseline. Additionally, we observe a statistically significant negative correlation (r = -0.181, p < 0.05) between OLDCARTS completeness (σ) and semantic entropy (H), suggesting that structured information gathering is associated with reduced diagnostic uncertainty.

Divyansh Srivastava, Shreya Ghosh, Anshul Verma +1

Quantum Cloud Computing and Distributed Systems (qCLOUDS) Lab, School of Computing and Information Systems, The University of Melbourne, Australia · Department of Computer Science and Engineering, School of Electrical and Computer Sciences (SECS), Indian Institute of Technology Bhubaneswar, India · Department of Computer Science2026 Banaras Hindu University, Varanasi, India

Multi-Agent LLM Systems LLM Hallucination Mitigation LLM Agent Orchestration Semantic Entropy Clinical Reasoning LLM Agent Safety

Jun 16, 2026cs.CL

AIPatient Arena: EHR-grounded evaluation of large language models in end-to-end clinical consultation workflows

Large language models (LLMs) are increasingly considered for use in clinical consultation tasks, yet most medical evaluations remain static, single-turn, or narrowly outcome-based, limiting their ability to reflect the sequential, uncertain, and interactive nature of real-world care. Here, we propose AIPatient Arena, an EHRs-grounded evaluation framework for assessing the clinical utility of LLMs across eight dimensions of clinical competence. The framework integrates EHR data into patient-specific knowledge graphs, enabling multi-turn physician-patient interactions. We applied AIPatient Arena on a primary cohort of 437 patients and two out-of-distribution validation cohorts of 119 and 67 patients. We observe that LLMs performed well in medical interview questioning skills (QS; mean scores, 4.43-4.99/5), ethical and professional conduct (ET; 4.38-4.93/5), and clarity and transparency of clinical explanations (EX; 3.80-4.72/5). Performance was moderate in information integration (II; 3.19-4.21/5) and medication safety and justification (MS; 3.13-3.78/5), but persistent weaknesses were observed in handling of ambiguous patient responses (HR; 2.57-3.32/5), information coverage (IC; 2.08-3.02/5), and diagnostic accuracy and reasoning (Dx; 2.63-3.55/5). Process-based evaluation revealed recurrent interaction failures, including repetitive questioning, omission of past medical history, and inadequate handling of uncertainty. Richer conversational context improved diagnostic reasoning but yielded limited gains in treatment planning. These findings indicate that final-answer accuracy alone is insufficient for evaluating clinical readiness and highlight the importance of assessing how models gather, interpret, and communicate information throughout a consultation. AIPatient Arena provides an EHR-grounded framework for workflow-oriented pre-deployment evaluation of medical LLMs.

Jiahui Niu, Huizi Yu, Wenkong Wang +11

School of Control Science and Engineering, Shandong University, Ji’nan, Shandong, China · Key Laboratory of Machine Intelligence and System Control, Shandong University, Ji’nan, Shandong, China · Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China +5

Clinical Reasoning Clinical Language Model Evaluation Medical LLMs

Jun 15, 2026cs.AI

Teaching agentic AI to generalize expert diagnostic reasoning in rare diseases

Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer. Large language models rank the correct disease first in only 35.4% of benchmark cases and often rely on learned phenotype-disease associations rather than reusable diagnostic reasoning strategies. We developed liteOdyssey through Policy Iteration with Human Feedback, a process in which model failures and expert corrections are iteratively consolidated into a clinician-gated, natural-language policy executed by a language model. Across 1,243 public benchmark cases spanning 722 rare diseases, liteOdyssey ranked the correct disease first in 59.3% of cases versus 26.5% without the policy, with comparable gains in cases involving diseases excluded from policy development. The same policy transferred across model families and sizes without retraining. Adaptation of the policy to the Undiagnosed Diseases Network (UDN) improved diagnostic accuracy among 515 UDN patients, with gains confirmed by blinded physician adjudication. These results show that expert reasoning can be externalized into an inspectable and revisable natural-language policy that generalizes across rare diseases, transfers across model backbones, and adapts to a real-world patient cohort.

Minh-Ha Nguyen, Erica Gray, Bryce A. Schuler +16

Department of Epidemiology, Vanderbilt University, Nashville, TN, USA · Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA · Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA +4

RL for Language Models Rare Disease Diagnosis Human-in-the-Loop AI Clinical Reasoning Medical LLMs

Jun 12, 2026cs.CV

ClinHallu: A Benchmark for Diagnosing Stage-Wise Hallucinations in Medical MLLM Reasoning

Building trustworthy medical multimodal large language models (MLLMs) is critical for reliable clinical decision support. Existing medical hallucination benchmarks mainly focus on data collection, but often ignore where hallucinations originate within the reasoning process. We find that hallucination sources vary across samples: errors may arise from visual misrecognition, incorrect medical knowledge recall, or flawed reasoning integration. To enable source-level hallucination diagnosis, we introduce ClinHallu, a benchmark for stage-wise hallucination diagnosis in medical MLLM reasoning. ClinHallu contains 7,031 validated instances, where each instance is augmented with a structured reasoning trace decomposed into Visual Recognition, Knowledge Recall, and Reasoning Integration. We also use stage-replacement interventions to measure how correcting specific stages affects the final answer. Beyond evaluation, we show that trace-supervised fine-tuning reduces stage-wise hallucinations. ClinHallu provides a fine-grained hallucination testbed for diagnosing and mitigating reasoning failures in medical MLLMs. The benchmark is publicly available at https://github.com/alibaba-damo-academy/ClinHallu.

Sicheng Yang, Hangjie Yuan, Wenjun Zhang +5

The Hong Kong University of Science and Technology (Guangzhou) · DAMO Academy, Alibaba Group · Hupan Lab +1

Multimodal Hallucination Clinical Reasoning Multimodal Model Evaluation Medical LLMs

Jun 10, 2026cs.AI

Lung-R1: A Knowledge Graph-Guided LLM for Pulmonary Diagnostic Reasoning

Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.

Haoyang Zeng, Yuanxi Fu, Rongzhen Li +11

School of Computer Science, Chongqing University, Chongqing, China · AI Research Institution, Mashang Financial Institution · Department of Information, Third Military Medical University

Medical Diagnosis Clinical Reasoning Medical LLMs

Jun 9, 2026cs.CL

Dep-LLM: Training-Free Depression Diagnosis via Evidence-Guided Structured Multi-factor with Reliable LLM Reasoning

Automatic Depression Detection (ADD) from clinical interviews is a pivotal task in computational mental health, yet it remains challenging due to two critical obstacles: 1) difficulty in modeling complex but sparsely distributed depression clues within lengthy, multi-topic clinical interviews, leading to superficial and unreliable reasoning; 2) scarcity of labeled data due to clinical privacy, together with high cost of training and fine-tuning, limiting the deployment of supervised ADD systems. To jointly address these challenges, we propose Dep-LLM, a training-free framework that mirrors the step-by-step reasoning of clinical psychiatrists and operates entirely on frozen off-the-shelf foundation LLMs. Dep-LLM comprises three stages. First, a Chain-of-Thought (CoT) Depression Multi-factor Analysis module structurally decomposes the long dialogue into five clinically aligned themes and produces evidence-grounded rationales, effectively handling long-context dependencies. Second, we introduce Confidence Analysis and Modulation module that quantifies the epistemic reliability from token-level entropy of each rationale and applies an intra-label and inter-theme modulation that amplifies trustworthy signals while suppressing uncertain ones without extra training. Third, a Collaborative Multi-factor Prediction module dynamically integrates multi-factor signals weighted by confidence into the final diagnosis. Extensive experiments on the DAIC-WOZ and E-DAIC datasets demonstrate the effectiveness and generalizability of Dep-LLM: it surpasses zero-shot baseline on nearly all 21 foundation LLMs across 9 metrics such as accuracy, macro F1 and weighted-average F1, and further outperforms state-of-the-art supervised domain-specific LLMs as well as the latest closed-source commercial LLMs, while requiring no extra training.

Yiqing Lyu, Xianbing Zhao, Buzhou Tang +1

LLM Inference Depression Detection Mental Health Clinical Reasoning Clinical NLP

Jun 8, 2026cs.AI

Experience Makes Skillful: Enabling Generalizable Medical Agent Reasoning via Self-Evolving Skill Memory

Medical agent systems are increasingly expected to support interactive clinical decision making rather than only static question answering. In such settings, effective agents must reuse prior experience across evolving cases, yet existing memory mechanisms often retain raw historical traces that are redundant, noisy, and difficult to govern. More importantly, they rarely distinguish which memories are truly useful for future reasoning. This limits their ability to accumulate compact and reliable experience for long-horizon clinical reasoning. To close this gap, we propose SkeMex, a post-deployment self-evolution framework that improves medical agents through a skill-based memory without updating model weights. SkeMex distills informative interaction trajectories into structured skills that encode reusable procedural knowledge, and organizes them into a multi-branch repository spanning general, task-specific, and action-level experience. To determine which memories should be reused and retained, SkeMex estimates context-dependent utility from environment feedback and uses it to guide value-aware retrieval and repository governance. A closed-loop ``Read--Write--Assess--Govern" lifecycle further supports continual evolution by writing new skills, updating utilities, promoting useful memories, and removing harmful entries. Experiments across diverse clinical tasks show that SkeMex consistently outperforms representative memory-based agents in both offline and online settings. It also generalizes across model backbones and supports transferable skill memory. All data and code will be released publicly.

Haoran Sun, Wenjie Li, Yujie Zhang +8

Fudan University · Shanghai Artificial Intelligence Laboratory · University of Science and Technology of China +1

Continual Learning for LLM Agents LLM Agent Memory LLM Agent Skill Learning LLM Agent Skill Retrieval Clinical Reasoning Self-Evolving Agents

Jun 8, 2026cs.LG

TRIAGE: Dialectical LLM Reasoning for Explainable Risk Prediction on Irregularly Sampled Medical Time Series

Clinical early warning systems built on irregularly sampled medical time series (ISMTS) from electronic health records must deliver continuous risk scores for patient triage as well as interpretable rationales that clinicians can verify. Large language models (LLMs) are uniquely positioned for both, deriving risk from their output probabilities and rationales from their medical knowledge. However, we find that conventional LLM reasoning collapses graded risk into overconfident predictions and thereby undermines the cross-patient comparability on which triage depends. We refer to this failure mode as risk polarization and identify two underlying behaviors: early commitment to a single outcome, and one-sided reasoning that focuses only on the evidence for that outcome. To address this, we propose TRIAGE, a framework that trains an LLM to reason dialectically over competing clinical outcomes by eliciting outcome-specific rationales. This dialectical formulation mitigates risk polarization, enabling a single LLM to jointly provide explicit clinical rationales and risk scores comparable across patients. Across five ISMTS benchmarks, TRIAGE improves mean AUPRC by 17.0% and reduces mean calibration error by 82.8% relative to the competitive LLM-based baseline, while surpassing the strongest ISMTS baseline by 3.5% in mean AUPRC.

Hyeongwon Jang, Gyouk Chu, Changhun Kim +4

KAIST · AITRICS · University of Wisconsin-Madison

Irregular Time-Series Modeling Logical Reasoning Clinical Triage Language Model Calibration Clinical Reasoning Clinical Risk Prediction

Jun 8, 2026cs.AI

Baichuan-M4: A Clinical-Grade Medical Agent System for Continuous Care

Baichuan-M4 is Baichuan Intelligence's clinical-grade medical large model, designed for continuous care rather than single-turn medical question answering. It is built as a coordinated medical agent system around three pillars: Baichuan-Harness, a unified runtime that keeps reinforcement-learning training and real-world deployment consistent while enforcing action constraints, tool use, long-term patient memory, and multi-agent coordination; a core reasoning model trained with a continuous-care reinforcement-learning framework that integrates span-level reward modeling (SPAR++), reasoning-path compression, curriculum learning, and stabilized policy optimization; and a clinical tool layer for patient-memory management, authoritative evidence-based retrieval, and multimodal medical perception across documents, X-rays, and dermatology. On a cross-dimensional medical evaluation suite, Baichuan-M4 attains leading results in static medical knowledge and safety, dynamic OSCE-style consultation, long-context clinical memory, evidence-based retrieval, medical document OCR, and multimodal image understanding, while lowering the hallucination rate to 3.3%.

Aiyuan Yang, Canbin Piao, Chengfeng Dou +25

Baichuan AI and THUBPM Group, Tsinghua University

RL for Language Models Healthcare Clinical Reasoning LLM Agent Training Medical LLMs Memory-Augmented Language Model Agents

Jun 8, 2026cs.CL

PACT: Learning Diverse Diagnostic Strategies via Privileged Synthesis and Branch Consensus

Clinical diagnosis requires flexible use of multiple reasoning paradigms under incomplete patient information. Existing LLM-based medical agents show strong medical reasoning ability, but single-paradigm or naively mixed dialogue supervision makes these paradigms difficult to learn without interference. We propose \textbf{PACT} (Periodic Anchor Consensus Training), a framework that couples supervised multi-paradigm dialogue synthesis with consensus-based Branch training. At the data level, \textbf{DPS} (Doctor-Patient-Supervisor) uses complete electronic medical records (EMRs) for quality control while keeping the doctor agent restricted to patient-visible information. This produces validated dialogues under four diagnostic reasoning paradigms without leaking hidden clinical answers. At the training level, PACT trains one paradigm-specific LoRA Branch per paradigm and periodically aggregates Branches into a shared Anchor through sign consensus. We further construct a dynamic multi-turn Chinese medical diagnosis benchmark for interactive consultation. Experiments show that PACT achieves state-of-the-art performance among compared proprietary, medical-specialized, and task-adapted baselines on diagnostic outcome and consultation-process metrics.

Gen Li, Yuanze Hu, Zhichao Yang +10

Beihang University · Baidu · ByteDance +2

Medical Diagnosis Clinical Reasoning LLM Agent Training Medical LLMs Text Generation

Jun 5, 2026cs.CL

Beyond English benchmarks: clinical llm evaluation in Brazilian Portuguese

Large Language Models are transforming the support for clinical decision and their application in real scenarios. Yet, most benchmarks are conducted in English, and cross-lingual evaluation is needed to tackle the language gaps in global access. We introduce ClinicalBr, the first bilingual benchmark for clinical decision built from real Brazilian case reports. The corpus contains 2,892 cases drawn from 28 SciELO medical journals, spanning 18 specialties, and is structured as parallel Portuguese-English pairs. Each case supports four evaluation tasks: diagnosis retrieval, differential diagnosis, exam recommendation, and treatment planning. We evaluate four models: MedGemma-27B, Sabiá-4, DeepSeek-R1, and o3-mini, across both languages. The central finding is that the Portuguese-English performance gap is task-dependent, not general. In diagnosis retrieval, English yields a consistent advantage across all models, with +7.5-12.1 accuracy points. This advantage disappears in differential diagnosis, exam recommendation, and treatment planning, where confidence intervals cross zero for most models and Portuguese completeness scores are marginally higher. Brazilian-endemic conditions proved easier than the full corpus, not harder, indicating that tropical presentations are adequately represented in current pre-training. Exam recommendation was the hardest task across all models and both languages, with F1 scores below 0.10, well below the differential diagnosis ceiling of 0.20-0.27.

Giordano de Pinho Souza, Glaucia Melo, Josefino Cabral Melo Lima +1

Federal University of Rio de Janeiro · Toronto Metropolitan University Toronto, CA

Multilingual Language Model Evaluation Clinical Decision-Making Clinical Reasoning Clinical Language Model Evaluation

Jun 2, 2026cs.MA

D2MDT: Department-aware Multidisciplinary Team Consultation with Deliberation for Efficient Clinical Prediction

Electronic health records (EHRs) are central to clinical prediction, but existing methods either rely on correlation-driven deep models or use single large language models (LLMs), making it difficult to support multidisciplinary clinical reasoning. Recent multi-agent systems (MAS) provide a promising alternative, yet current EHR-grounded MAS methods still suffer from weak evidence differentiation across agents and redundant multi-round interaction. We propose D2MDT, a Department-aware MultiDisciplinary Team Consultation with Deliberation for Efficient clinical prediction. D2MDT first constructs structured EHR evidence and consultation-ready semantic evidence for multi-agent consultation. It then assigns patient-specific department perspectives to doctor agents and retrieves complementary evidence for collaborative consultation. To improve efficiency, D2MDT further introduces residual deliberation, which updates only unresolved consensus rather than replaying the full discussion history. Finally, D2MDT fuses the refined consensus report with structured EHR representations for prediction. Experiments on mortality prediction show that D2MDT improves both predictive performance and consultation efficiency. We release the code online to ease the reproducibility of this paper.

Yongqi Liang, Qidong Liu, Chunze Yang +4

Xi’an Jiaotong University, Xi’an, China

Clinical Outcome Prediction Multi-Agent Collaboration Clinical Reasoning Electronic Health Records Mortality Prediction

Jun 2, 2026cs.MA

MeDxAgent: Multi-Agent Consultation for Interactive Medical Diagnosis

Large language models (LLMs) are increasingly used for health-related decision support. Yet most evaluations treat diagnosis as a single-shot task with complete information provided upfront, often as a multiple-choice selection. This diverges from clinical practice, where diagnosis is interactive and open-ended, involving sequential hypothesis refinement through targeted questioning. We address this gap. We build MeDxBench, a large-scale benchmark of 4,421 clinical cases across 20 specialties. We further propose MeDxAgent, a multi-agent consultation system for interactive diagnosis, and systematically study its prompt-, flow- and agent-level design choices. MeDxAgent achieves a 10.3% accuracy gain over the baseline on MeDxBench, closing 52.3% of the gap to a full-information oracle. We find that specific design choices: collecting demographics first, passing summarized dialogue for diagnosis, and feeding candidate diagnoses for targeted questioning, improve accuracy, mirroring how physicians reason, though their effect emerges fully only in combination. Code and dataset will be released upon publication.

Akshat Sanghvi, Naren Akash, Raza Imam +2

Microsoft Research India · Institute of AI and Innovation, AIG Hospitals · Mohamed bin Zayed University of Artificial Intelligence

Multi-Agent LLM Systems Medical Diagnosis AI Agent Benchmarks Clinical Reasoning

Jun 1, 2026cs.AI

ChatHealthAI: Aligning Electronic Health Record Representations with Large Language Models for Grounded Clinical Reasoning

Large language models (LLMs) exhibit strong natural-language reasoning abilities for clinical decision support, but struggle to effectively model structured longitudinal electronic health records (EHRs). In contrast, EHR foundation models can learn predictive patient representations, yet lack interpretable language-based reasoning. To bridge this gap, we propose ChatHealthAI, a multimodal reasoning framework that aligns structured EHR representations from a pretrained EHR foundation model with the semantic space of a frozen LLM through a task-aware resampler. By integrating longitudinal patient representations with refined clinical event descriptions, ChatHealthAI enables clinically grounded natural-language reasoning while maintaining accurate patient prediction. We evaluated ChatHealthAI on three clinical predictive tasks from the EHRSHOT benchmark. Results show that ChatHealthAI improves reasoning quality and interpretability while preserving competitive predictive performance. These findings highlight the potential of integrating EHR foundation models with pretrained LLMs for interpretable clinical prediction.

Bo-Hong Wang, Baicheng Peng, Ruilin Wang +3

School of Computer Science, McGill University, Montreal, QC, Canada · Mila - Quebec AI Institute, Montreal, QC, Canada

LLM Grounding LLM Alignment Clinical Outcome Prediction Clinical Reasoning Longitudinal EHR Modeling

May 31, 2026cs.AI

CAREAgent: Clinical Agent with Structured Reasoning and Tool-Integrated for Order Generation

Clinical order generation serves as a critical bridge between clinical decision-making and real-world practice, translating medical decisions into concrete and executable orders. Existing agents mainly focus on coarse-grained decisions and overlook the fine-grained, executable information required for clinical orders. To address this gap, we propose CAREAgent, an agent for clinical order generation. To support its training, we introduce a two-stage agentic reasoning data construction method. First, we design an agent framework that constructs verifiable reasoning trajectories aligned with realistic clinical tool usage. Second, we filter reasoning trajectories by format compliance, order validity, and clinical plausibility. Building on the constructed data, the model is first trained via supervised fine-tuning to acquire fundamental reasoning formats and medical knowledge, and is subsequently optimized through reinforcement learning with multi-dimensional reward functions to enhance complex clinical reasoning capabilities. Experiments on multiple benchmarks demonstrate the effectiveness of CAREAgent. On ClinicalBench (unseen during training), CAREAgent improves the F1 score by 5.05%, 2.09%, and 0.86% over the single-agent, multi-agent, and agentic reasoning methods, respectively.

Ruihui Hou, Ziyue Huai, Chennuo Zhang +5

East China University of Science and Technology, Shanghai, China · Zhongshan Hospital, Fudan University, Shanghai, China

Tool-Using Agents Clinical Reasoning LLM Agent Training

May 28, 2026cs.CL

MedCase-Structured: A Text-to-FHIR Dataset for Benchmarking Diagnostic Reasoning in Clinically Realistic EHR Settings

Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited. Existing benchmarks often rely on static datasets or unstructured inputs that do not reflect the interoperable data formats used in clinical systems. We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs. The pipeline combines staged LLM generation with terminology-grounded validation and repair to eliminate hallucinated codes and enforce structural and semantic consistency. Applying this approach to MedCaseReasoning, we construct MedCase-Structured, a synthetic dataset of 1,732 FHIR bundles derived from clinician-authored diagnostic cases, producing complete, valid bundles for 97.1% of attempted cases. Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Valentina Bui Muti, Eugénie Dulout, Ziquan Fu

System Inc., New York, NY, USA.

Healthcare Clinical Decision Support Synthetic Benchmark Generation Clinical Reasoning Clinical Language Model Evaluation Electronic Health Records

May 27, 2026cs.AI

C-MIG: Multi-view Information Gain-based Retrieval-Augmented Generation for Clinical Diagnosis Reasoning

Retrieval-augmented generation combined with reinforcement learning has shown promise for grounding large language models in trustworthy medical evidence. However, existing methods rely on exact-match binary rewards, which in clinical diagnosis cause two issues: (i) semantically relevant but non-verbatim steps receive zero signal, discarding valuable learning signals; and (ii) uni-dimensional rewards cannot effectively supervise heterogeneous reasoning capabilities. To address these issues, we propose C-MIG, a Multi-view Information Gain-based retrieval-augmented generation framework for Clinical diagnosis. C-MIG estimates information gain under a frozen reference model from two complementary views, retrieved-document and document-refinement, to jointly guide what to retrieve and how to refine, alleviating the issues of valuable reward signal loss and credit assignment. We further design a multi-subquery retrieval augmentation strategy that improves knowledge recall coverage in clinical diagnostic scenarios. Comprehensive experiments on four medical benchmarks demonstrate that C-MIG achieves the best performance among all RAG-RL methods on both in-domain and out-of-domain sets, and outperforms state-of-the-art general-purpose LLMs for clinical diagnosis.

Yuwei Miao, Gen Li, Yunsheng Zeng +8

1Baidu Inc.

Retrieval-Augmented Generation Healthcare RL for Language Model Reasoning Clinical Reasoning Information Retrieval Medical LLMs

May 26, 2026cs.AI

MedGuideX: Internalizing Decision Logic from Executable Guidelines into Large Language Models for Clinical Reasoning

Clinical practice guidelines (CPGs) encode evidence-based decision logic that clinicians apply by evaluating patient variables, conditional criteria, and recommendation rules. However, existing methods often use CPGs as free-text training data or retrieval sources, underutilizing their procedural decision structure. To better exploit this structure, we introduce a guideline-derived training pipeline that transforms CPG recommendations into executable clinical decision logic and uses it to generate factual and counterfactual question-answering data. Theses data teach models both guideline-supported decisions and how decisions change under different patient conditions. Post-training a medical LLM on the generated data yields MedGuideX. Across four clinical reasoning benchmarks, MedGuideX achieves a 10.28% relative improvement in average accuracy. Physician evaluation further shows that MedGuideX better recovers clinician authored reasoning steps and produces physician-preferred rationales in faithfulness, validity, completeness, and clarity. Overall, our results show that executable decision logic from CPGs can be transformed into scalable supervision for building reliable medical LLMs.

Yuhao Shen, Lang Cao, Simo Du +4

University of Illinois Urbana-Champaign · 2The Chinese University of Hong Kong, Shenzhen · 3Albert Einstein College of Medicine

Healthcare Clinical Decision Support Clinical Reasoning Medical LLMs

May 26, 2026cs.CV

Clinically-Grounded Counterfactual Reasoning for Medical Video Diagnosis

Medical video diagnosis involves inferring clinical decisions from dynamic tissue responses throughout examination processes. Existing methods rely on an end-to-end learning paradigm that i) focuses on appearance rather than pathology, ii) lacks clinical priors, and iii) reasons solely from observations without counterfactual comparison. This work introduces MedVCR, a counterfactual reasoning framework that mimics clinical diagnostic thinking. MedVCR comprises three components: a Counterfactual Generator that synthesizes tissue evolution under specified pathological states via a diffusion-based manner; a Counterfactual Representation Learning module that encodes diagnostic knowledge through clinical rules (i.e., temporal consistency, pathological separability, and counterfactual alignment); and a Dual Diagnostic Prediction strategy that integrates video-level assessment with frame-level counterfactual analysis. MedVCR is evaluated under both fully supervised (e.g., colposcopy) and weakly supervised (e.g., colonoscopy) video diagnosis settings, yielding 2.6%-10.2% performance gains compared with leading baselines. Comprehensive ablation studies further validate the effectiveness of each component. The code will be released.

Jianzhe Gao, Churan Wang, Weiyi Zhang +5

Healthcare Medical Diagnosis Clinical Reasoning Counterfactual Reasoning

May 26, 2026cs.CL

Towards Error-Free EHRs: Reasoning-Intensive Consistency Verification Between Clinical Notes and Structured Tables in Electronic Health Records

Data consistency between unstructured clinical notes and structured tables in Electronic Health Records (EHRs) is essential for patient safety and clinical decision-making. However, existing work on note-table consistency verification mainly relies on surface-level matching of numeric values or simple events. Such approaches fail to capture the reasoning underlying real-world EHR documentation, including clinical interpretation, event relations, and temporal changes. To address this gap, we introduce EHR-ReasonCon, a reasoning-intensive benchmark for note-table consistency verification. Built on MIMIC-III with expert-guided annotations, it comprises 8,048 entities derived from clinical notes and provides high-quality ground-truth labels. The annotation protocol is supported by specialized table-exploration tools to ensure systematic evidence retrieval and reliable consistency assessment. We also propose EHR-Inspector, an LLM-based framework that segments notes, extracts anchor entities and temporal references, and uses table-exploration tools to verify consistency against structured tables. Evaluated using expert-validated LLM-as-a-judge metrics under harsh and lenient criteria, EHR-Inspector achieves state-of-the-art performance across multiple model backbones. Analyses further demonstrate the effectiveness of its components and highlight differences from human verification.

Yeonsu Kwon, Jiho Kim, Junseong Choi +10

1KAIST · 2Ghent University · 3Samsung Medical Center +2

Factual Consistency Evaluation Clinical Reasoning Electronic Health Records