Daily Papers

Treatment reasoning underpins every therapeutic decision, integrating disease context, comorbidities, medications, contraindications, and evolving biomedical knowledge to select an appropriate therapy. It is inherently iterative: candidates are weighed against many constraints, revised as evidence emerges, and grounded in verifiable sources. Here we introduce ATHENA-R1, an AI agent for treatment reasoning across all FDA approved drugs since 1939, trained by reinforcement learning over a universe of 212 biomedical tools. At each step it identifies missing information, selects and runs relevant tools, and incorporates the evidence. To train it without human-annotated traces, we build a two-level self-learning framework: multi-agent systems construct the tools, tasks, and reasoning trajectories for supervised fine-tuning, then reinforcement learning with scientific feedback rewards reasoning quality (evidence gathering, grounded tool use, logical non-redundancy). Across five benchmarks of 3,168 drug reasoning tasks and 456 patient treatment cases, ATHENA-R1 outperforms language models and tool-use systems, reaching 94.7% accuracy on open-ended drug reasoning and 82.9% on treatment reasoning, 17.8 and 10.7 points above GPT-5. In blinded evaluations by experts from 28 rare disease organizations, it is preferred over reference models on all criteria, and physicians rated it favorably on complex hospitalized cardiovascular and infectious-disease cases. Adverse-event hypotheses it generated, tested in electronic health records from 5.4 million patients, reached adjusted odds ratios of 1.48-1.84, with no elevation among negative controls. Because it requires knowing what evidence to seek before concluding, treatment reasoning has long been hard for AI; we show it can be reframed as a learnable process of iterative evidence gathering that reinforcement learning can train AI to perform.

Lung cancer clinical decision support demands precise reasoning across complex, multi-stage oncological workflows. Existing multimodal large language models (MLLMs) fail to handle guideline-constrained staging and treatment reasoning. We formalize three oncological precision treatment (OPT) tasks for lung cancer, spanning TNM staging, treatment recommendation, and end-to-end clinical decision support. We introduce LungCURE, the first standardized multimodal benchmark built from 1,000 real-world, clinician-labeled cases across more than 10 hospitals. We further propose LCAgent, a multi-agent framework that ensures guideline-compliant lung cancer clinical decision-making by suppressing cascading reasoning errors across the clinical pathway. Experiments reveal large differences across various large language models (LLMs) in their capabilities for complex medical reasoning, when given precise treatment requirements. We further verify that LCAgent, as a simple yet effective plugin, enhances the reasoning performance of LLMs in real-world medical scenarios.

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code will be publicly available.

Epilepsy diagnosis and treatment require evidence-intensive reasoning across heterogeneous clinical knowledge, including biosignal patterns, genetic mechanisms, pharmacogenomics, treatment strategies, and patient outcomes. In this work, we present EpiGraph, a large-scale epilepsy knowledge graph and benchmark for evaluating knowledge-augmented clinical reasoning. EpiGraph integrates 48,166 peer-reviewed papers and seven clinical resources into a heterogeneous graph containing 24,324 entities and 32,009 evidence-grounded triplets across five clinical layers. Built upon this graph, EpiBench defines five clinically motivated tasks spanning clinical decision-making, EEG report generation, pharmacogenomic precision medicine, treatment recommendation, and deep research planning. We evaluate six LLMs under both standard and Graph-RAG settings. Results show that integrating EpiGraph consistently improves performance across all tasks, with the largest gains observed in pharmacogenomic reasoning (+30--41\%). Our findings demonstrate that structured epilepsy knowledge substantially enhances evidence-grounded clinical reasoning and provides a practical benchmark framework for evaluating knowledge-augmented LLMs in real-world neurological settings. Our code is available at: https://github.com/LabRAI/EEG-KG.

Dental image analysis plays a pivotal role in supporting accurate diagnosis and treatment planning in oral healthcare. Although recent advances have produced dental AI models for specific tasks and individual imaging modalities, their isolated designs limit practical use in real-world clinical workflows. In this paper, we present OralAgent, the first dental-specialized AI agent that unifies multimodal reasoning, tool-based decision-making, and knowledge-grounded retrieval within an end-to-end automated framework. It integrates 22 visual analysis tools and 368 widely-used classical dental textbooks, enabling autonomous reasoning, planning, tool use, knowledge retrieval, and multi-step workflow execution. Furthermore, we introduce OralCorpus, a large-scale, high-quality bilingual textual resource containing 134.8M tokens curated for dental retrieval-augmented generation (RAG). To evaluate models' multidisciplinary dental knowledge, we construct OralQA-ZH, a Chinese multiple-choice question benchmark consisting of 798 items across eleven oral subspecialties. Extensive experiments demonstrate that OralAgent achieves state-of-the-art performance on the MMOral-Uni, MMOral-OPG, and OralQA-ZH benchmarks, highlighting its effectiveness, interpretability, and adaptability in real-world clinical settings. The code and models are publicly available at https://github.com/isjinghao/OralAgent.

Accurately grounding regions of interest (ROIs) is critical for diagnosis and treatment planning in medical imaging. While multimodal large language models (MLLMs) combine visual perception with natural language, current medical-grounding pipelines still rely on supervised fine-tuning with explicit spatial hints, making them ill-equipped to handle the implicit queries common in clinical practice. This work makes three core contributions. We first define Unified Medical Reasoning Grounding (UMRG), a novel vision-language task that demands clinical reasoning and pixel-level grounding. Second, we release U-MRG-14K, a dataset of 14K samples featuring pixel-level masks alongside implicit clinical queries and reasoning traces, spanning 10 modalities, 15 super-categories, and 108 specific categories. Finally, we introduce MedReasoner, a modular framework that distinctly separates reasoning from segmentation: an MLLM reasoner is optimized with reinforcement learning, while a frozen segmentation expert converts spatial prompts into masks, with alignment achieved through format and accuracy rewards. MedReasoner achieves state-of-the-art performance on U-MRG-14K and demonstrates strong generalization to unseen clinical queries, underscoring the significant promise of reinforcement learning for interpretable medical grounding.

Causal reasoning and compositional reasoning are two core aspirations in generative AI. Measuring the extent of these behaviors requires principled evaluation methods. We explore a unified perspective that considers both behaviors simultaneously, termed compositional causal reasoning (CCR): the ability to infer how causal measures compose and, equivalently, how causal quantities propagate through graphs. We instantiate a framework for the systematic evaluation of CCR for the average treatment effect and the probability of necessity and sufficiency. As proof of concept, we demonstrate the design of CCR tasks for language models in the LLama, Phi, and GPT families. On a math word problem, our framework revealed a range of taxonomically distinct error patterns. Additionally, CCR errors increased with the complexity of causal paths for all models except o1.

Latent visual reasoning aims to mimic human's imagination process by meditating through hidden states of Multimodal Large Language Models. While recognized as a promising paradigm for visual reasoning, the underlying mechanisms driving its effectiveness remain unclear. Motivated to demystify the true source of its efficacy, we investigate the validity of latent reasoning using Causal Mediation Analysis. We model the process as a causal chain: the input as the treatment, the latent tokens as the mediator, and the final answer as the outcome. Our findings uncover two critical disconnections: (a) Input-Latent Disconnect: dramatic perturbations on the input result in negligible changes to the latent tokens, suggesting that latent tokens do not effectively attend to the input sequence. (b) Latent-Answer Disconnect: perturbations on the latent tokens yield minimal impact on the final answer, indicating the limited causal effect latent tokens imposing on the outcome. Furthermore, extensive probing analysis reveals that latent tokens encode limited visual information and exhibit high similarity. Consequently, we challenge the necessity of latent reasoning and propose a straightforward alternative named CapImagine, which teaches the model to explicitly imagine using text. Experiments on vision-centric benchmarks show that CapImagine significantly outperforms complex latent-space baselines, highlighting the superior potential of visual reasoning through explicit imagination.

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

Medical image segmentation plays a vital role in clinical decision-making, enabling precise localization of lesions and guiding interventions. Despite significant advances in segmentation accuracy, the black-box nature of most deep models has raised growing concerns about their trustworthiness in high-stakes medical scenarios. Current explanation techniques have primarily focused on classification tasks, leaving the segmentation domain relatively underexplored. We introduced an explanation model for segmentation task which employs the causal inference framework and backpropagates the average treatment effect (ATE) into a quantification metric to determine the influence of input regions, as well as network components, on target segmentation areas. Through comparison with recent segmentation explainability techniques on two representative medical imaging datasets, we demonstrated that our approach provides more faithful explanations than existing approaches. Furthermore, we carried out a systematic causal analysis of multiple foundational segmentation models using our method, which reveals significant heterogeneity in perceptual strategies across different models, and even between different inputs for the same model. Suggesting the potential of our method to provide notable insights for optimizing segmentation models. Our code can be found at https://github.com/lcmmai/PdCR.

The proliferation of Large Language Models (LLMs) in medicine has enabled impressive capabilities, yet a critical gap remains in their ability to perform systematic, transparent, and verifiable reasoning, a cornerstone of clinical practice. This has catalyzed a shift from single-step answer generation to the development of LLMs explicitly designed for medical reasoning. This paper provides the first systematic review of this emerging field. We propose a taxonomy of reasoning enhancement techniques, categorized into training-time strategies (e.g., supervised fine-tuning, reinforcement learning) and test-time mechanisms (e.g., prompt engineering, multi-agent systems). We analyze how these techniques are applied across different data modalities (text, image, code) and in key clinical applications such as diagnosis, education, and treatment planning. Furthermore, we survey the evolution of evaluation benchmarks from simple accuracy metrics to sophisticated assessments of reasoning quality and visual interpretability. Based on an analysis of 60 seminal studies from 2022-2025, we conclude by identifying critical challenges, including the faithfulness-plausibility gap and the need for native multimodal reasoning, and outlining future directions toward building efficient, robust, and sociotechnically responsible medical AI.

Integrating large language models (LLMs) like DeepSeek R1 into healthcare requires rigorous evaluation of their reasoning alignment with clinical expertise. This study assesses DeepSeek R1's medical reasoning against expert patterns using 100 MedQA clinical cases. The model achieved 93% diagnostic accuracy, demonstrating systematic clinical judgment through differential diagnosis, guideline-based treatment selection, and integration of patient-specific factors. However, error analysis of seven incorrect cases revealed persistent limitations: anchoring bias, challenges reconciling conflicting data, insufficient exploration of alternatives, overthinking, knowledge gaps, and premature prioritization of definitive treatment over intermediate care. Crucially, reasoning length correlated with accuracy - shorter responses (<5,000 characters) were more reliable, suggesting extended explanations may signal uncertainty or rationalization of errors. While DeepSeek R1 exhibits foundational clinical reasoning capabilities, recurring flaws highlight critical areas for refinement, including bias mitigation, knowledge updates, and structured reasoning frameworks. These findings underscore LLMs' potential to augment medical decision-making through artificial reasoning but emphasize the need for domain-specific validation, interpretability safeguards, and confidence metrics (e.g., response length thresholds) to ensure reliability in real-world applications.

Recent advancements in reasoning-enhanced large language models (LLMs), such as DeepSeek-R1 and OpenAI-o3, have demonstrated significant progress. However, their application in professional medical contexts remains underexplored, particularly in evaluating the quality of their reasoning processes alongside final outputs. Here, we introduce MedR-Bench, a benchmarking dataset of 1,453 structured patient cases, annotated with reasoning references derived from clinical case reports. Spanning 13 body systems and 10 specialties, it includes both common and rare diseases. To comprehensively evaluate LLM performance, we propose a framework encompassing three critical examination recommendation, diagnostic decision-making, and treatment planning, simulating the entire patient care journey. To assess reasoning quality, we present the Reasoning Evaluator, a novel automated system that objectively scores free-text reasoning responses based on efficiency, actuality, and completeness using dynamic cross-referencing and evidence checks. Using this benchmark, we evaluate five state-of-the-art reasoning LLMs, including DeepSeek-R1, OpenAI-o3-mini, and Gemini-2.0-Flash Thinking, etc. Our results show that current LLMs achieve over 85% accuracy in relatively simple diagnostic tasks when provided with sufficient examination results. However, performance declines in more complex tasks, such as examination recommendation and treatment planning. While reasoning outputs are generally reliable, with factuality scores exceeding 90%, critical reasoning steps are frequently missed. These findings underscore both the progress and limitations of clinical LLMs. Notably, open-source models like DeepSeek-R1 are narrowing the gap with proprietary systems, highlighting their potential to drive accessible and equitable advancements in healthcare.

Surprisal theory links human processing effort to the predictability of an upcoming linguistic unit, but empirical work often leaves the notion of a unit underspecified. In practice, experimental stimuli are segmented into linguistically motivated units (e.g., words), while pretrained language models assign probability mass to a fixed token alphabet that typically does not align with those units. As a result, surprisal-based predictors depend implicitly on ad hoc procedures that conflate two distinct modeling choices: the definition of the unit of analysis and the choice of regions of interest over which predictions are evaluated. In this paper, we disentangle these choices and give a unified framework for reasoning about surprisal over arbitrary unit inventories. We argue that surprisal-based analyses should make these choices explicit and treat tokenization as an implementation detail rather than a scientific primitive.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Recent advancements in large language models (LLMs) have shown promise in medical applications such as disease diagnosis and treatment planning. However, most existing medical LLMs struggle with the advanced reasoning required for complex clinical scenarios, such as differential diagnosis or personalized treatment suggestions. We proposed FineMedLM-o1, which leverages high-quality synthetic medical data and long-form reasoning data for Supervised Fine-Tuning (SFT) and Direct Preference Optimization (DPO), enabling advanced dialogue and deep reasoning capabilities. Additionally, we introduced Test-Time Training (TTT) in the medical domain for the first time, facilitating domain adaptation and ensuring reliable, accurate reasoning. Experimental results demonstrate that FineMedLM-o1 achieves a 23% average performance improvement over prior models on key medical benchmarks. Furthermore, the introduction of TTT provides an additional 14% performance boost, highlighting its effectiveness in enhancing medical reasoning capabilities. To support this process, we also proposed a novel method for synthesizing medical dialogue. Compared to other open-source datasets, our dataset stands out as superior in both quality and complexity. The project and data will be released on GitHub.

Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

Self-consistency (SC) is a widely used test-time inference technique for improving performance in chain-of-thought reasoning. It involves generating multiple responses, or samples from a large language model (LLM) and selecting the most frequent answer. This procedure can naturally be viewed as a majority vote or empirical mode estimation. Despite its effectiveness, SC is prohibitively expensive at scale when naively applied to datasets, and it lacks a unified theoretical treatment of sample efficiency and scaling behavior. In this paper, we provide the first comprehensive analysis of SC's scaling behavior and its variants, drawing on mode estimation and voting theory. We derive and empirically validate power law scaling for self-consistency across datasets, and analyze the sample efficiency for fixed-allocation and dynamic-allocation sampling schemes. From these insights, we introduce Blend-ASC, a novel variant of self-consistency that dynamically allocates samples to questions during inference, achieving state-of-the-art sample efficiency. Our approach uses 6.8x fewer samples than vanilla SC on average, outperforming both fixed- and dynamic-allocation SC baselines, thereby demonstrating the superiority of our approach in terms of efficiency. In contrast to existing variants, Blend-ASC is hyperparameter-free and can fit an arbitrary sample budget, ensuring it can be easily applied to any self-consistency application.

In psychotherapy, therapeutic outcome assessment, or treatment outcome evaluation, is essential for enhancing mental health care by systematically evaluating therapeutic processes and outcomes. Existing large language model approaches often focus on therapist-centered, single-session evaluations, neglecting the client's subjective experience and longitudinal progress across multiple sessions. To address these limitations, we propose IPAEval, a client-Informed Psychological Assessment-based Evaluation framework that automates treatment outcome evaluations from the client's perspective using clinical interviews. IPAEval integrates cross-session client-contextual assessment and session-focused client-dynamics assessment to provide a comprehensive understanding of therapeutic progress. Experiments on our newly developed TheraPhase dataset demonstrate that IPAEval effectively tracks symptom severity and treatment outcomes over multiple sessions, outperforming previous single-session models and validating the benefits of items-aware reasoning mechanisms.

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.

Multimodal large language models (MLLMs) have demonstrated promising prospects in healthcare, particularly for addressing complex medical tasks, supporting multidisciplinary treatment (MDT), and enabling personalized precision medicine. However, their practical deployment faces critical challenges in resource efficiency, diagnostic accuracy, clinical considerations, and ethical privacy. To address these limitations, we propose Infi-Med, a comprehensive framework for medical MLLMs that introduces three key innovations: (1) a resource-efficient approach through curating and constructing high-quality supervised fine-tuning (SFT) datasets with minimal sample requirements, with a forward-looking design that extends to both pretraining and posttraining phases; (2) enhanced multimodal reasoning capabilities for cross-modal integration and clinical task understanding; and (3) a systematic evaluation system that assesses model performance across medical modalities and task types. Our experiments demonstrate that Infi-Med achieves state-of-the-art (SOTA) performance in general medical reasoning while maintaining rapid adaptability to clinical scenarios. The framework establishes a solid foundation for deploying MLLMs in real-world healthcare settings by balancing model effectiveness with operational constraints.

Reinforcement learning with verifiable rewards (RLVR) has demonstrated superior performance in enhancing the reasoning capability of large language models (LLMs). However, this accuracy-oriented learning paradigm often suffers from entropy collapse, which reduces policy exploration and limits reasoning capabilities. To address this challenge, we propose an efficient reinforcement learning framework that leverages entropy signals at both the semantic and token levels to improve reasoning. From the data perspective, we introduce semantic entropy-guided curriculum learning, organizing training data from low to high semantic entropy to guide progressive optimization from easier to more challenging tasks. For the algorithmic design, we adopt non-uniform token treatment by imposing KL regularization on low-entropy tokens that critically impact policy exploration and applying stronger constraints on high-covariance portions within these tokens. By jointly optimizing data organization and algorithmic design, our method effectively mitigates entropy collapse and enhances LLM reasoning. Experimental results across 6 benchmarks with 3 different parameter-scale base models demonstrate that our method outperforms other entropy-based approaches in improving reasoning.

Medical imaging provides critical evidence for clinical diagnosis, treatment planning, and surgical decisions, yet most existing imaging models are narrowly focused and require multiple specialized networks, limiting their generalization. Although large-scale language and multimodal models exhibit strong reasoning and multi-task capabilities, real-world clinical applications demand precise visual grounding, multimodal integration, and chain-of-thought reasoning. We introduce Citrus-V, a multimodal medical foundation model that combines image analysis with textual reasoning. The model integrates detection, segmentation, and multimodal chain-of-thought reasoning, enabling pixel-level lesion localization, structured report generation, and physician-like diagnostic inference in a single framework. We propose a novel multimodal training approach and release a curated open-source data suite covering reasoning, detection, segmentation, and document understanding tasks. Evaluations demonstrate that Citrus-V outperforms existing open-source medical models and expert-level imaging systems across multiple benchmarks, delivering a unified pipeline from visual grounding to clinical reasoning and supporting precise lesion quantification, automated reporting, and reliable second opinions.

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

The integration of Large Language Models (LLMs) into healthcare holds significant potential to enhance diagnostic accuracy and support medical treatment planning. These AI-driven systems can analyze vast datasets, assisting clinicians in identifying diseases, recommending treatments, and predicting patient outcomes. This study evaluates the performance of a range of contemporary LLMs, including both open-source and closed-source models, on the 2024 Portuguese National Exam for medical specialty access (PNA), a standardized medical knowledge assessment. Our results highlight considerable variation in accuracy and cost-effectiveness, with several models demonstrating performance exceeding human benchmarks for medical students on this specific task. We identify leading models based on a combined score of accuracy and cost, discuss the implications of reasoning methodologies like Chain-of-Thought, and underscore the potential for LLMs to function as valuable complementary tools aiding medical professionals in complex clinical decision-making.

Building upon our previous investigations of O1 replication (Part 1: Journey Learning [Qin et al., 2024] and Part 2: Distillation [Huang et al., 2024]), this work explores the potential of inference-time scaling in large language models (LLMs) for medical reasoning tasks, ranging from diagnostic decision-making to treatment planning. Through extensive experiments on medical benchmarks of varying complexity (MedQA, Medbullets, and JAMA Clinical Challenges), our investigation reveals several key insights: (1) Increasing inference time does lead to improved performance. With a modest training set of 500 samples, our model yields substantial performance improvements of 6%-11%. (2) Task complexity directly correlates with the required length of reasoning chains, confirming the necessity of extended thought processes for challenging problems. (3) The differential diagnoses generated by our model adhere to the principles of the hypothetico-deductive method, producing a list of potential conditions that may explain a patient's symptoms and systematically narrowing these possibilities by evaluating the evidence. These findings demonstrate the promising synergy between inference-time scaling and journey learning in advancing LLMs' real-world clinical reasoning capabilities.

Large language models (LLMs) offer a promising pre-screening tool, improving early disease detection and providing enhanced healthcare access for underprivileged communities. The early diagnosis of various diseases continues to be a significant challenge in healthcare, primarily due to the nonspecific nature of early symptoms, the shortage of expert medical practitioners, and the need for prolonged clinical evaluations, all of which can delay treatment and adversely affect patient outcomes. With impressive accuracy in prediction across a range of diseases, LLMs have the potential to revolutionize clinical pre-screening and decision-making for various medical conditions. In this work, we study the diagnostic capability of LLMs for Rheumatoid Arthritis (RA) with real world patients data. Patient data was collected alongside diagnoses from medical experts, and the performance of LLMs was evaluated in comparison to expert diagnoses for RA disease prediction. We notice an interesting pattern in disease diagnosis and find an unexpected misalignment between prediction and explanation. We conduct a series of multi-round analyses using different LLM agents. The best-performing model accurately predicts rheumatoid arthritis (RA) diseases approximately 95\% of the time. However, when medical experts evaluated the reasoning generated by the model, they found that nearly 68\% of the reasoning was incorrect. This study highlights a clear misalignment between LLMs high prediction accuracy and its flawed reasoning, raising important questions about relying on LLM explanations in clinical settings. LLMs provide incorrect reasoning to arrive at the correct answer for RA disease diagnosis.

Visual grounding is essential for precise perception and reasoning in multimodal large language models (MLLMs), especially in medical imaging domains. While existing medical visual grounding benchmarks primarily focus on single-image scenarios, real-world clinical applications often involve sequential images, where accurate lesion localization across different modalities and temporal tracking of disease progression (e.g., pre- vs. post-treatment comparison) require fine-grained cross-image semantic alignment and context-aware reasoning. To remedy the underrepresentation of image sequences in existing medical visual grounding benchmarks, we propose MedSG-Bench, the first benchmark tailored for Medical Image Sequences Grounding. It comprises eight VQA-style tasks, formulated into two paradigms of the grounding tasks, including 1) Image Difference Grounding, which focuses on detecting change regions across images, and 2) Image Consistency Grounding, which emphasizes detection of consistent or shared semantics across sequential images. MedSG-Bench covers 76 public datasets, 10 medical imaging modalities, and a wide spectrum of anatomical structures and diseases, totaling 9,630 question-answer pairs. We benchmark both general-purpose MLLMs (e.g., Qwen2.5-VL) and medical-domain specialized MLLMs (e.g., HuatuoGPT-vision), observing that even the advanced models exhibit substantial limitations in medical sequential grounding tasks. To advance this field, we construct MedSG-188K, a large-scale instruction-tuning dataset tailored for sequential visual grounding, and further develop MedSeq-Grounder, an MLLM designed to facilitate future research on fine-grained understanding across medical sequential images. The benchmark, dataset, and model are available at https://huggingface.co/MedSG-Bench

Clinical reasoning demands multi-step interactions -- gathering patient history, ordering tests, interpreting results, and making safe treatment decisions -- yet a unified training environment provides the breadth of clinical domains and specialized tools to train generalizable medical AI agents through reinforcement learning remains elusive. We present a comprehensive empirical study of multi-turn agentic RL for medical AI, built on , a gymnasium-compatible environment spanning 10 clinical domains with 3.6K+ tasks, 135 domain-specific tools, and a knowledge base of 828K medical passages. Our analysis reveals that agentic multi-turn structure degrades into verbose single-turn monologues, characterized by monotonic length explosion and a simultaneous erosion of tool-use frequency. We characterize how this collapse, alongside distillation instability, stems from the misalignment of sparse terminal rewards with sequential clinical trajectories. We find that vanilla GRPO achieves strong final accuracy on some benchmarks but suffers from training instability, evidenced by significant oscillations in response length and prolonged convergence periods. To improve training efficiency and stability, we propose Turn-level Truncated On-Policy Distillation (TT-OPD), a self-distillation framework where a gradient-free EMA teacher leverages outcome-privileged information to provide dense, outcome-aware KL regularization at every conversation turn. TT-OPD achieves the best performance on 10 of 18 benchmarks with an average +3.9~pp improvement over the non-RL baseline with faster early convergence, controlled response length, and sustained multi-turn tool use.

Supervised fine-tuning (SFT) on long chain-of-thought (CoT) trajectories has emerged as a crucial technique for enhancing the reasoning abilities of large language models (LLMs). However, the standard cross-entropy loss treats all tokens equally, ignoring their heterogeneous contributions across a reasoning trajectory. This uniform treatment leads to misallocated supervision and weak generalization, especially in complex, long-form reasoning tasks. To address this, we introduce Variance-Controlled Optimization-based REweighting (VCORE), a principled framework that reformulates CoT supervision as a constrained optimization problem. By adopting an optimization-theoretic perspective, VCORE enables a principled and adaptive allocation of supervision across tokens, thereby aligning the training objective more closely with the goal of robust reasoning generalization. Empirical evaluations demonstrate that VCORE achieves the strongest overall average performance, with especially clear gains on lower-capacity models. Across both in-domain and out-of-domain settings, VCORE achieves substantial performance gains on mathematical and coding benchmarks, using models from the Qwen3 series (4B, 8B, 32B) and LLaMA-3.1-8B-Instruct. Moreover, we show that VCORE serves as a more effective initialization for subsequent reinforcement learning, establishing a stronger foundation for advancing the reasoning capabilities of LLMs. The Code will be released at https://github.com/coder-gx/VCORE.

While large language models (LLMs) have shown promise in diagnostic dialogue, their capabilities for effective management reasoning - including disease progression, therapeutic response, and safe medication prescription - remain under-explored. We advance the previously demonstrated diagnostic capabilities of the Articulate Medical Intelligence Explorer (AMIE) through a new LLM-based agentic system optimised for clinical management and dialogue, incorporating reasoning over the evolution of disease and multiple patient visit encounters, response to therapy, and professional competence in medication prescription. To ground its reasoning in authoritative clinical knowledge, AMIE leverages Gemini's long-context capabilities, combining in-context retrieval with structured reasoning to align its output with relevant and up-to-date clinical practice guidelines and drug formularies. In a randomized, blinded virtual Objective Structured Clinical Examination (OSCE) study, AMIE was compared to 21 primary care physicians (PCPs) across 100 multi-visit case scenarios designed to reflect UK NICE Guidance and BMJ Best Practice guidelines. AMIE was non-inferior to PCPs in management reasoning as assessed by specialist physicians and scored better in both preciseness of treatments and investigations, and in its alignment with and grounding of management plans in clinical guidelines. To benchmark medication reasoning, we developed RxQA, a multiple-choice question benchmark derived from two national drug formularies (US, UK) and validated by board-certified pharmacists. While AMIE and PCPs both benefited from the ability to access external drug information, AMIE outperformed PCPs on higher difficulty questions. While further research would be needed before real-world translation, AMIE's strong performance across evaluations marks a significant step towards conversational AI as a tool in disease management.

Large Language Models have demonstrated profound utility in the medical domain. However, their application to autonomous Electronic Health Records~(EHRs) navigation remains constrained by a reliance on curated inputs and simplified retrieval tasks. To bridge the gap between idealized experimental settings and realistic clinical environments, we present AgentEHR. This benchmark challenges agents to execute complex decision-making tasks, such as diagnosis and treatment planning, requiring long-range interactive reasoning directly within raw and high-noise databases. In tackling these tasks, we identify that existing summarization methods inevitably suffer from critical information loss and fractured reasoning continuity. To address this, we propose RetroSum, a novel framework that unifies a retrospective summarization mechanism with an evolving experience strategy. By dynamically re-evaluating interaction history, the retrospective mechanism prevents long-context information loss and ensures unbroken logical coherence. Additionally, the evolving strategy bridges the domain gap by retrieving accumulated experience from a memory bank. Extensive empirical evaluations demonstrate that RetroSum achieves performance gains of up to 29.16% over competitive baselines, while significantly decreasing total interaction errors by up to 92.3%.

Large language model (LLM) reinforcement learning has increasingly relied on group-based policy optimization frameworks, such as GRPO and GSPO, to achieve stable fine-tuning at scale. However, a fundamental trade-off persists between optimization granularity and training stability. While GSPO improves robustness via sequence-level optimization, its monolithic treatment of sequences introduces severe inefficiencies: its conservative clipping mechanism indiscriminately discards valid training samples-a phenomenon we term gradient underutilization-and its uniform credit assignment fails to capture the heterogeneous contributions of critical reasoning steps. In this work, we propose Entropy Importance Sampling Policy Optimization (ESPO), a novel framework that reconciles fine-grained control with training stability. ESPO decomposes sequences into groups based on predictive entropy, enabling (1) Entropy-driven Importance Sampling to capture intra-sequence heterogeneity, and (2) Entropy-adaptive Clipping to dynamically allocate trust regions based on model uncertainty. Extensive experiments on mathematical reasoning benchmarks demonstrate that ESPO not only accelerates convergence but also achieves state-of-the-art performance, notably improving accuracy on the challenging HMMT benchmark from 4.4% to 13.13%.

AI is undergoing a paradigm shift, with breakthroughs achieved by systems orchestrating multiple large language models (LLMs) and other complex components. As a result, developing principled and automated optimization methods for compound AI systems is one of the most important new challenges. Neural networks faced a similar challenge in its early days until backpropagation and automatic differentiation transformed the field by making optimization turn-key. Inspired by this, we introduce TextGrad, a powerful framework performing automatic ``differentiation'' via text. TextGrad backpropagates textual feedback provided by LLMs to improve individual components of a compound AI system. In our framework, LLMs provide rich, general, natural language suggestions to optimize variables in computation graphs, ranging from code snippets to molecular structures. TextGrad follows PyTorch's syntax and abstraction and is flexible and easy-to-use. It works out-of-the-box for a variety of tasks, where the users only provide the objective function without tuning components or prompts of the framework. We showcase TextGrad's effectiveness and generality across a diverse range of applications, from question answering and molecule optimization to radiotherapy treatment planning. Without modifying the framework, TextGrad improves the zero-shot accuracy of GPT-4o in Google-Proof Question Answering from 51% to 55%, yields 20% relative performance gain in optimizing LeetCode-Hard coding problem solutions, improves prompts for reasoning, designs new druglike small molecules with desirable in silico binding, and designs radiation oncology treatment plans with high specificity. TextGrad lays a foundation to accelerate the development of the next-generation of AI systems.

Reasoning is a fundamental cognitive process that enables logical inference, problem-solving, and decision-making. With the rapid advancement of large language models (LLMs), reasoning has emerged as a key capability that distinguishes advanced AI systems from conventional models that empower chatbots. In this survey, we categorize existing methods along two orthogonal dimensions: (1) Regimes, which define the stage at which reasoning is achieved (either at inference time or through dedicated training); and (2) Architectures, which determine the components involved in the reasoning process, distinguishing between standalone LLMs and agentic compound systems that incorporate external tools, and multi-agent collaborations. Within each dimension, we analyze two key perspectives: (1) Input level, which focuses on techniques that construct high-quality prompts that the LLM condition on; and (2) Output level, which methods that refine multiple sampled candidates to enhance reasoning quality. This categorization provides a systematic understanding of the evolving landscape of LLM reasoning, highlighting emerging trends such as the shift from inference-scaling to learning-to-reason (e.g., DeepSeek-R1), and the transition to agentic workflows (e.g., OpenAI Deep Research, Manus Agent). Additionally, we cover a broad spectrum of learning algorithms, from supervised fine-tuning to reinforcement learning such as PPO and GRPO, and the training of reasoners and verifiers. We also examine key designs of agentic workflows, from established patterns like generator-evaluator and LLM debate to recent innovations. ...

Reasoning is a fundamental aspect of human intelligence that plays a crucial role in activities such as problem solving, decision making, and critical thinking. In recent years, large language models (LLMs) have made significant progress in natural language processing, and there is observation that these models may exhibit reasoning abilities when they are sufficiently large. However, it is not yet clear to what extent LLMs are capable of reasoning. This paper provides a comprehensive overview of the current state of knowledge on reasoning in LLMs, including techniques for improving and eliciting reasoning in these models, methods and benchmarks for evaluating reasoning abilities, findings and implications of previous research in this field, and suggestions on future directions. Our aim is to provide a detailed and up-to-date review of this topic and stimulate meaningful discussion and future work.

Reasoning, as an essential ability for complex problem-solving, can provide back-end support for various real-world applications, such as medical diagnosis, negotiation, etc. This paper provides a comprehensive survey of cutting-edge research on reasoning with language model prompting. We introduce research works with comparisons and summaries and provide systematic resources to help beginners. We also discuss the potential reasons for emerging such reasoning abilities and highlight future research directions. Resources are available at https://github.com/zjunlp/Prompt4ReasoningPapers (updated periodically).

Although large language models (LLMs) have demonstrated impressive reasoning capabilities across general domains, their effectiveness in real-world clinical practice remains limited. This is likely due to their insufficient exposure to real-world clinical data during training, as such data is typically not included due to privacy concerns. To address this, we propose enhancing the clinical reasoning capabilities of LLMs by leveraging real-world clinical data. We constructed reasoning-intensive questions from a nationwide sepsis registry and fine-tuned Phi-4 on these questions using reinforcement learning, resulting in C-Reason. C-Reason exhibited strong clinical reasoning capabilities on the in-domain test set, as evidenced by both quantitative metrics and expert evaluations. Furthermore, its enhanced reasoning capabilities generalized to a sepsis dataset involving different tasks and patient cohorts, an open-ended consultations on antibiotics use task, and other diseases. Future research should focus on training LLMs with large-scale, multi-disease clinical datasets to develop more powerful, general-purpose clinical reasoning models.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, e.g., Large Language Models (LLMs), there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

Large Language Models (LLMs) are highly proficient in language-based tasks. Their language capabilities have positioned them at the forefront of the future AGI (Artificial General Intelligence) race. However, on closer inspection, Valmeekam et al. (2024); Zecevic et al. (2023); Wu et al. (2024) highlight a significant gap between their language proficiency and reasoning abilities. Reasoning in LLMs and Vision Language Models (VLMs) aims to bridge this gap by enabling these models to think and re-evaluate their actions and responses. Reasoning is an essential capability for complex problem-solving and a necessary step toward establishing trust in Artificial Intelligence (AI). This will make AI suitable for deployment in sensitive domains, such as healthcare, banking, law, defense, security etc. In recent times, with the advent of powerful reasoning models like OpenAI O1 and DeepSeek R1, reasoning endowment has become a critical research topic in LLMs. In this paper, we provide a detailed overview and comparison of existing reasoning techniques and present a systematic survey of reasoning-imbued language models. We also study current challenges and present our findings.

Reasoning is a cognitive process of using evidence to reach a sound conclusion. The reasoning capability is essential for large language models (LLMs) to serve as the brain of the artificial general intelligence agent. Recent studies reveal that fine-tuning LLMs on data with the chain of thought (COT) reasoning process can significantly enhance their reasoning capabilities. However, we find that the fine-tuned LLMs suffer from an Assessment Misalignment problem, i.e., they frequently assign higher scores to subpar COTs, leading to potential limitations in their reasoning abilities. To address this problem, we introduce an Alignment Fine-Tuning (AFT) paradigm, which involves three steps: 1) fine-tuning LLMs with COT training data; 2) generating multiple COT responses for each question, and categorizing them into positive and negative ones based on whether they achieve the correct answer; 3) calibrating the scores of positive and negative responses given by LLMs with a novel constraint alignment loss. Specifically, the constraint alignment loss has two objectives: a) Alignment, which guarantees that positive scores surpass negative scores to encourage answers with high-quality COTs; b) Constraint, which keeps the negative scores confined to a reasonable range to prevent the model degradation. Beyond just the binary positive and negative feedback, the constraint alignment loss can be seamlessly adapted to the ranking situations when ranking feedback is accessible. Furthermore, we also delve deeply into recent ranking-based alignment methods, such as DPO, RRHF, and PRO, and discover that the constraint, which has been overlooked by these approaches, is also crucial for their performance. Extensive experiments on four reasoning benchmarks with both binary and ranking feedback demonstrate the effectiveness of AFT.

There are two main barriers to using large language models (LLMs) in clinical reasoning. Firstly, while LLMs exhibit significant promise in Natural Language Processing (NLP) tasks, their performance in complex reasoning and planning falls short of expectations. Secondly, LLMs use uninterpretable methods to make clinical decisions that are fundamentally different from the clinician's cognitive processes. This leads to user distrust. In this paper, we present a multi-agent framework called ArgMed-Agents, which aims to enable LLM-based agents to make explainable clinical decision reasoning through interaction. ArgMed-Agents performs self-argumentation iterations via Argumentation Scheme for Clinical Discussion (a reasoning mechanism for modeling cognitive processes in clinical reasoning), and then constructs the argumentation process as a directed graph representing conflicting relationships. Ultimately, use symbolic solver to identify a series of rational and coherent arguments to support decision. We construct a formal model of ArgMed-Agents and present conjectures for theoretical guarantees. ArgMed-Agents enables LLMs to mimic the process of clinical argumentative reasoning by generating explanations of reasoning in a self-directed manner. The setup experiments show that ArgMed-Agents not only improves accuracy in complex clinical decision reasoning problems compared to other prompt methods, but more importantly, it provides users with decision explanations that increase their confidence.

Large language models (LLMs) have achieved strong performance on medical exam-style tasks, motivating growing interest in their deployment in real-world clinical settings. However, clinical decision-making is inherently safety-critical, context-dependent, and conducted under evolving evidence. In such situations, reliable LLM performance depends not on factual recall alone, but on robust medical reasoning. In this work, we present a comprehensive review of medical reasoning with LLMs. Grounded in cognitive theories of clinical reasoning, we conceptualize medical reasoning as an iterative process of abduction, deduction, and induction, and organize existing methods into seven major technical routes spanning training-based and training-free approaches. We further conduct a unified cross-benchmark evaluation of representative medical reasoning models under a consistent experimental setting, enabling a more systematic and comparable assessment of the empirical impact of existing methods. To better assess clinically grounded reasoning, we introduce MR-Bench, a benchmark derived from real-world hospital data. Evaluations on MR-Bench expose a pronounced gap between exam-level performance and accuracy on authentic clinical decision tasks. Overall, this survey provides a unified view of existing medical reasoning methods, benchmarks, and evaluation practices, and highlights key gaps between current model performance and the requirements of real-world clinical reasoning.

Reasoning is a fundamental cognitive process underlying inference, problem-solving, and decision-making. While large language models (LLMs) demonstrate strong reasoning capabilities in closed-world settings, they struggle in open-ended and dynamic environments. Agentic reasoning marks a paradigm shift by reframing LLMs as autonomous agents that plan, act, and learn through continual interaction. In this survey, we organize agentic reasoning along three complementary dimensions. First, we characterize environmental dynamics through three layers: foundational agentic reasoning, which establishes core single-agent capabilities including planning, tool use, and search in stable environments; self-evolving agentic reasoning, which studies how agents refine these capabilities through feedback, memory, and adaptation; and collective multi-agent reasoning, which extends intelligence to collaborative settings involving coordination, knowledge sharing, and shared goals. Across these layers, we distinguish in-context reasoning, which scales test-time interaction through structured orchestration, from post-training reasoning, which optimizes behaviors via reinforcement learning and supervised fine-tuning. We further review representative agentic reasoning frameworks across real-world applications and benchmarks, including science, robotics, healthcare, autonomous research, and mathematics. This survey synthesizes agentic reasoning methods into a unified roadmap bridging thought and action, and outlines open challenges and future directions, including personalization, long-horizon interaction, world modeling, scalable multi-agent training, and governance for real-world deployment.

Large Language Models (LLMs) have demonstrated significant potential in handling complex reasoning tasks through step-by-step rationale generation. However, recent studies have raised concerns regarding the hallucination and flaws in their reasoning process. Substantial efforts are being made to improve the reliability and faithfulness of the generated rationales. Some approaches model reasoning as planning, while others focus on annotating for process supervision. Nevertheless, the planning-based search process often results in high latency due to the frequent assessment of intermediate reasoning states and the extensive exploration space. Additionally, supervising the reasoning process with human annotation is costly and challenging to scale for LLM training. To address these issues, in this paper, we propose a framework to learn planning-based reasoning through direct preference optimization (DPO) on collected trajectories, which are ranked according to synthesized process rewards. Our results on challenging logical reasoning benchmarks demonstrate the effectiveness of our learning framework, showing that our 7B model can surpass the strong counterparts like GPT-3.5-Turbo.

Recently, slow-thinking reasoning systems, such as o1, have demonstrated remarkable capabilities in solving complex reasoning tasks. These systems typically engage in an extended thinking process before responding to a query, allowing them to generate more thorough, accurate, and well-reasoned solutions. These systems are primarily developed and maintained by industry, with their core techniques not publicly disclosed. In response, an increasing number of studies from the research community aim to explore the technical foundations underlying these powerful reasoning systems. Building on these prior efforts, this paper presents a reproduction report on implementing o1-like reasoning systems. We introduce an "imitate, explore, and self-improve" framework as our primary technical approach to train the reasoning model. In the initial phase, we use distilled long-form thought data to fine-tune the reasoning model, enabling it to invoke a slow-thinking mode. The model is then encouraged to explore challenging problems by generating multiple rollouts, which can result in increasingly more high-quality trajectories that lead to correct answers. Furthermore, the model undergoes self-improvement by iteratively refining its training dataset. To verify the effectiveness of this approach, we conduct extensive experiments on three challenging benchmarks. The experimental results demonstrate that our approach achieves competitive performance compared to industry-level reasoning systems on these benchmarks.

Large Language Models (LLMs) have succeeded remarkably in various natural language processing (NLP) tasks, yet their reasoning capabilities remain a fundamental challenge. While LLMs exhibit impressive fluency and factual recall, their ability to perform complex reasoning-spanning logical deduction, mathematical problem-solving, commonsense inference, and multi-step reasoning-often falls short of human expectations. This survey provides a comprehensive review of emerging techniques enhancing reasoning in LLMs. We categorize existing methods into key approaches, including prompting strategies (e.g., Chain-of-Thought reasoning, Self-Consistency, and Tree-of-Thought reasoning), architectural innovations (e.g., retrieval-augmented models, modular reasoning networks, and neuro-symbolic integration), and learning paradigms (e.g., fine-tuning with reasoning-specific datasets, reinforcement learning, and self-supervised reasoning objectives). Additionally, we explore evaluation frameworks used to assess reasoning in LLMs and highlight open challenges, such as hallucinations, robustness, and reasoning generalization across diverse tasks. By synthesizing recent advancements, this survey aims to provide insights into promising directions for future research and practical applications of reasoning-augmented LLMs.

Reasoning is an essential capacity for large language models (LLMs) to address complex tasks, where the identification of process errors is vital for improving this ability. Recently, process-level reward models (PRMs) were proposed to provide step-wise rewards that facilitate reinforcement learning and data production during training and guide LLMs toward correct steps during inference, thereby improving reasoning accuracy. However, existing benchmarks of PRMs are text-based and focus on error detection, neglecting other scenarios like reasoning search. To address this gap, we introduce MPBench, a comprehensive, multi-task, multimodal benchmark designed to systematically assess the effectiveness of PRMs in diverse scenarios. MPBench employs three evaluation paradigms, each targeting a specific role of PRMs in the reasoning process: (1) Step Correctness, which assesses the correctness of each intermediate reasoning step; (2) Answer Aggregation, which aggregates multiple solutions and selects the best one; and (3) Reasoning Process Search, which guides the search for optimal reasoning steps during inference. Through these paradigms, MPBench makes comprehensive evaluations and provides insights into the development of multimodal PRMs.

Though reasoning-based large language models (LLMs) have excelled in mathematics and programming, their capabilities in knowledge-intensive medical question answering remain underexplored. To address this, we introduce ReasonMed, the largest medical reasoning dataset, comprising 370k high-quality examples distilled from 1.7 million initial reasoning paths generated by various LLMs. ReasonMed is constructed through a multi-agent verification and refinement process, where we design an Error Refiner to enhance the reasoning paths by identifying and correcting error-prone steps flagged by a verifier. Leveraging ReasonMed, we systematically investigate best practices for training medical reasoning models and find that combining detailed Chain-of-Thought (CoT) reasoning with concise answer summaries yields the most effective fine-tuning strategy. Based on this strategy, we train ReasonMed-7B, which sets a new benchmark for sub-10B models, outperforming the prior best by 4.17\% and even exceeding LLaMA3.1-70B on PubMedQA by 4.60\%.

The breakthrough of OpenAI o1 highlights the potential of enhancing reasoning to improve LLM. Yet, most research in reasoning has focused on mathematical tasks, leaving domains like medicine underexplored. The medical domain, though distinct from mathematics, also demands robust reasoning to provide reliable answers, given the high standards of healthcare. However, verifying medical reasoning is challenging, unlike those in mathematics. To address this, we propose verifiable medical problems with a medical verifier to check the correctness of model outputs. This verifiable nature enables advancements in medical reasoning through a two-stage approach: (1) using the verifier to guide the search for a complex reasoning trajectory for fine-tuning LLMs, (2) applying reinforcement learning (RL) with verifier-based rewards to enhance complex reasoning further. Finally, we introduce HuatuoGPT-o1, a medical LLM capable of complex reasoning, which outperforms general and medical-specific baselines using only 40K verifiable problems. Experiments show complex reasoning improves medical problem-solving and benefits more from RL. We hope our approach inspires advancements in reasoning across medical and other specialized domains.

Reasoning-enhanced large language models (LLMs) explicitly generate intermediate reasoning steps prior to generating final answers, helping the model excel in complex problem-solving. In this paper, we demonstrate that this emerging generation framework offers a unique opportunity for more fine-grained control over model behavior. We propose Thinking Intervention, a novel paradigm designed to explicitly guide the internal reasoning processes of LLMs by strategically inserting or revising specific thinking tokens. We conduct comprehensive evaluations across multiple tasks, including instruction following on IFEval, instruction hierarchy on SEP, and safety alignment on XSTest and SORRY-Bench. Our results demonstrate that Thinking Intervention significantly outperforms baseline prompting approaches, achieving up to 6.7% accuracy gains in instruction-following scenarios, 15.4% improvements in reasoning about instruction hierarchies, and a 40.0% increase in refusal rates for unsafe prompts using open-source DeepSeek R1 models. Overall, our work opens a promising new research avenue for controlling reasoning LLMs.

Transparency in AI healthcare decision-making is crucial for building trust among AI and users. Incorporating reasoning capabilities enables Large Language Models (LLMs) to understand emotions in context, handle nuanced language, and infer unstated sentiments. In this work, we introduce a new task -- Sentiment Reasoning -- for both speech and text modalities, along with our proposed multimodal multitask framework and dataset. Sentiment Reasoning is an auxiliary task in sentiment analysis where the model predicts both the sentiment label and generates the rationale behind it based on the input transcript. Our study conducted on both human transcripts and Automatic Speech Recognition (ASR) transcripts shows that Sentiment Reasoning helps improve model transparency by providing rationale for model prediction with quality semantically comparable to humans while also improving model performance (1% increase in both accuracy and macro-F1) via rationale-augmented fine-tuning. Also, no significant difference in the semantic quality of generated rationales between human and ASR transcripts. All code, data (English-translated and Vietnamese) and models are published online: https://github.com/leduckhai/MultiMed.

Hierarchical reasoning model (HRM) achieves extraordinary performance on various reasoning tasks, significantly outperforming large language model-based reasoners. To understand the strengths and potential failure modes of HRM, we conduct a mechanistic study on its reasoning patterns and find three surprising facts: (a) Failure of extremely simple puzzles, e.g., HRM can fail on a puzzle with only one unknown cell. We attribute this failure to the violation of the fixed point property, a fundamental assumption of HRM. (b) "Grokking" dynamics in reasoning steps, i.e., the answer is not improved uniformly, but instead there is a critical reasoning step that suddenly makes the answer correct; (c) Existence of multiple fixed points. HRM "guesses" the first fixed point, which could be incorrect, and gets trapped there for a while or forever. All facts imply that HRM appears to be "guessing" instead of "reasoning". Leveraging this "guessing" picture, we propose three strategies to scale HRM's guesses: data augmentation (scaling the quality of guesses), input perturbation (scaling the number of guesses by leveraging inference randomness), and model bootstrapping (scaling the number of guesses by leveraging training randomness). On the practical side, by combining all methods, we develop Augmented HRM, boosting accuracy on Sudoku-Extreme from 54.5% to 96.9%. On the scientific side, our analysis provides new insights into how reasoning models "reason".

The ability of large language models (LLMs) to follow user instructions is central to their reliability, safety, and usefulness. While prior studies assess instruction adherence in the model's main responses, we argue that it is also critical for large reasoning models (LRMs) to follow user instructions throughout their reasoning process. Reasoning instruction following makes LRMs more controllable and transparent, while reducing risks of undesirable shortcuts, hallucinations, or reward hacking within reasoning traces. To evaluate this dimension, we introduce ReasonIF, a systematic benchmark for assessing reasoning instruction following. ReasonIF includes six categories of instruction prompts, spanning multilingual reasoning, formatting and length control. Across many open-source LRMs including GPT-OSS, Qwen3, and DeepSeek-R1, we find substantial failures in reasoning instruction adherence: the highest instruction following score (IFS) remains below 0.25, meaning that fewer than 25% of reasoning traces comply with the given instructions. Notably, as task difficulty increases, reasoning instruction following degrades further. We also explore two strategies to enhance reasoning instruction fidelity. (1) multi-turn reasoning and (2) Reasoning Instruction Finetuning (RIF) using synthetic data. RIF improves the IFS of GPT-OSS-20B from 0.11 to 0.27, indicating measurable progress but leaving ample room for improvement.

Language has long been conceived as an essential tool for human reasoning. The breakthrough of Large Language Models (LLMs) has sparked significant research interest in leveraging these models to tackle complex reasoning tasks. Researchers have moved beyond simple autoregressive token generation by introducing the concept of "thought" -- a sequence of tokens representing intermediate steps in the reasoning process. This innovative paradigm enables LLMs' to mimic complex human reasoning processes, such as tree search and reflective thinking. Recently, an emerging trend of learning to reason has applied reinforcement learning (RL) to train LLMs to master reasoning processes. This approach enables the automatic generation of high-quality reasoning trajectories through trial-and-error search algorithms, significantly expanding LLMs' reasoning capacity by providing substantially more training data. Furthermore, recent studies demonstrate that encouraging LLMs to "think" with more tokens during test-time inference can further significantly boost reasoning accuracy. Therefore, the train-time and test-time scaling combined to show a new research frontier -- a path toward Large Reasoning Model. The introduction of OpenAI's o1 series marks a significant milestone in this research direction. In this survey, we present a comprehensive review of recent progress in LLM reasoning. We begin by introducing the foundational background of LLMs and then explore the key technical components driving the development of large reasoning models, with a focus on automated data construction, learning-to-reason techniques, and test-time scaling. We also analyze popular open-source projects at building large reasoning models, and conclude with open challenges and future research directions.

Logical reasoning is a key task for artificial intelligence due to it's role in major downstream tasks such as Question Answering, Summarization. Recent methods in improving the reasoning ability of LLMs fall short in correctly converting a natural language reasoning problem to an equivalent logical formulation, which hinders the framework's overall ability to reason. Towards this, we propose to use finetuning on a preference optimization dataset to learn to parse and represent a natural language problem as a whole to a consistent logical program by 1) introducing a new supervised and preference optimization dataset LogicPO, and 2) adopting popular techniques such as Direct Preference Optimization (DPO), Kahneman-Tversky optimization (KTO) to finetune open-source LLMs. Our best model with Phi-3.5 consistently outperforms GPT-3.5-turbo's (8-shot) by producing 10% more logically correct and with 14% less syntax errors. Through the framework and our improved evaluation metrics, we offer a promising direction in improving the logical reasoning of LLMs by better representing them in their logical formulations.

The emergence of advanced reasoning capabilities in Large Language Models (LLMs) marks a transformative development in healthcare applications. Beyond merely expanding functional capabilities, these reasoning mechanisms enhance decision transparency and explainability-critical requirements in medical contexts. This survey examines the transformation of medical LLMs from basic information retrieval tools to sophisticated clinical reasoning systems capable of supporting complex healthcare decisions. We provide a thorough analysis of the enabling technological foundations, with a particular focus on specialized prompting techniques like Chain-of-Thought and recent breakthroughs in Reinforcement Learning exemplified by DeepSeek-R1. Our investigation evaluates purpose-built medical frameworks while also examining emerging paradigms such as multi-agent collaborative systems and innovative prompting architectures. The survey critically assesses current evaluation methodologies for medical validation and addresses persistent challenges in field interpretation limitations, bias mitigation strategies, patient safety frameworks, and integration of multimodal clinical data. Through this survey, we seek to establish a roadmap for developing reliable LLMs that can serve as effective partners in clinical practice and medical research.

Logical reasoning is a critical benchmark for evaluating the capabilities of large language models (LLMs), as it reflects their ability to derive valid conclusions from given premises. While the combination of test-time scaling with dedicated outcome or process reward models has opened up new avenues to enhance LLMs performance in complex reasoning tasks, this space is under-explored in deductive logical reasoning. We present a set of Outcome Reward Models (ORMs) for deductive reasoning. To train the ORMs we mainly generate data using Chain-of-Thought (CoT) with single and multiple samples. Additionally, we propose a novel tactic to further expand the type of errors covered in the training dataset of the ORM. In particular, we propose an echo generation technique that leverages LLMs' tendency to reflect incorrect assumptions made in prompts to extract additional training data, covering previously unexplored error types. While a standard CoT chain may contain errors likely to be made by the reasoner, the echo strategy deliberately steers the model toward incorrect reasoning. We show that ORMs trained on CoT and echo-augmented data demonstrate improved performance on the FOLIO, JustLogic, and ProverQA datasets across four different LLMs.

Deductive reasoning plays a pivotal role in the formulation of sound and cohesive arguments. It allows individuals to draw conclusions that logically follow, given the truth value of the information provided. Recent progress in the domain of large language models (LLMs) has showcased their capability in executing deductive reasoning tasks. Nonetheless, a significant portion of research primarily assesses the accuracy of LLMs in solving such tasks, often overlooking a deeper analysis of their reasoning behavior. In this study, we draw upon principles from cognitive psychology to examine inferential strategies employed by LLMs, through a detailed evaluation of their responses to propositional logic problems. Our findings indicate that LLMs display reasoning patterns akin to those observed in humans, including strategies like supposition following or chain construction. Moreover, our research demonstrates that the architecture and scale of the model significantly affect its preferred method of reasoning, with more advanced models tending to adopt strategies more frequently than less sophisticated ones. Importantly, we assert that a model's accuracy, that is the correctness of its final conclusion, does not necessarily reflect the validity of its reasoning process. This distinction underscores the necessity for more nuanced evaluation procedures in the field.

Recent proprietary models (e.g., o3) have begun to demonstrate strong multimodal reasoning capabilities. Yet, most existing open-source research concentrates on training text-only reasoning models, with evaluations limited to mainly mathematical and general-domain tasks. Therefore, it remains unclear how to effectively extend reasoning capabilities beyond text input and general domains. This paper explores a fundamental research question: Is reasoning generalizable across modalities and domains? Our findings support an affirmative answer: General-domain text-based post-training can enable such strong generalizable reasoning. Leveraging this finding, we introduce X-Reasoner, a vision-language model post-trained solely on general-domain text for generalizable reasoning, using a two-stage approach: an initial supervised fine-tuning phase with distilled long chain-of-thoughts, followed by reinforcement learning with verifiable rewards. Experiments show that X-Reasoner successfully transfers reasoning capabilities to both multimodal and out-of-domain settings, outperforming existing state-of-the-art models trained with in-domain and multimodal data across various general and medical benchmarks (Figure 1). Additionally, we find that X-Reasoner's performance in specialized domains can be further enhanced through continued training on domain-specific text-only data. Building upon this, we introduce X-Reasoner-Med, a medical-specialized variant that achieves new state of the art on numerous text-only and multimodal medical benchmarks.

While large language models show promise in medical applications, achieving expert-level clinical reasoning remains challenging due to the need for both accurate answers and transparent reasoning processes. To address this challenge, we introduce Fleming-R1, a model designed for verifiable medical reasoning through three complementary innovations. First, our Reasoning-Oriented Data Strategy (RODS) combines curated medical QA datasets with knowledge-graph-guided synthesis to improve coverage of underrepresented diseases, drugs, and multi-hop reasoning chains. Second, we employ Chain-of-Thought (CoT) cold start to distill high-quality reasoning trajectories from teacher models, establishing robust inference priors. Third, we implement a two-stage Reinforcement Learning from Verifiable Rewards (RLVR) framework using Group Relative Policy Optimization, which consolidates core reasoning skills while targeting persistent failure modes through adaptive hard-sample mining. Across diverse medical benchmarks, Fleming-R1 delivers substantial parameter-efficient improvements: the 7B variant surpasses much larger baselines, while the 32B model achieves near-parity with GPT-4o and consistently outperforms strong open-source alternatives. These results demonstrate that structured data design, reasoning-oriented initialization, and verifiable reinforcement learning can advance clinical reasoning beyond simple accuracy optimization. We release Fleming-R1 publicly to promote transparent, reproducible, and auditable progress in medical AI, enabling safer deployment in high-stakes clinical environments.

Large-scale high-quality training data is important for improving the performance of models. After trained with data that has rationales (reasoning steps), models gain reasoning capability. However, the dataset with high-quality rationales is relatively scarce due to the high annotation cost. To address this issue, we propose Self-motivated Learning framework. The framework motivates the model itself to automatically generate rationales on existing datasets. Based on the inherent rank from correctness across multiple rationales, the model learns to generate better rationales, leading to higher reasoning capability. Specifically, we train a reward model with the rank to evaluate the quality of rationales, and improve the performance of reasoning through reinforcement learning. Experiment results of Llama2 7B on multiple reasoning datasets show that our method significantly improves the reasoning ability of models, even outperforming text-davinci-002 in some datasets.

Outcome-reward reinforcement learning (RL) has proven effective at improving the reasoning capabilities of large language models (LLMs). However, standard RL assigns credit only at the level of the final answer, penalizing entire reasoning traces when the outcome is incorrect and uniformly reinforcing all steps when it is correct. As a result, correct intermediate steps may be discouraged in failed traces, while spurious steps may be reinforced in successful ones. We refer to this failure mode as the problem of credit assignment. While a natural remedy is to train a process reward model, accurately optimizing such models to identify corrective reasoning steps remains challenging. We introduce Intervention Training (InT), a training paradigm in which the model performs fine-grained credit assignment on its own reasoning traces by proposing short, targeted corrections that steer trajectories toward higher reward. Using reference solutions commonly available in mathematical reasoning datasets and exploiting the fact that verifying a model-generated solution is easier than generating a correct one from scratch, the model identifies the first error in its reasoning and proposes a single-step intervention to redirect the trajectory toward the correct solution. We then apply supervised fine-tuning (SFT) to the on-policy rollout up to the point of error concatenated with the intervention, localizing error to the specific step that caused failure. We show that the resulting model serves as a far better initialization for RL training. After running InT and subsequent fine-tuning with RL, we improve accuracy by nearly 14% over a 4B-parameter base model on IMO-AnswerBench, outperforming larger open-source models such as gpt-oss-20b.

Reinforcement Learning (RL) has proven to be an effective post-training strategy for enhancing reasoning in vision-language models (VLMs). Group Relative Policy Optimization (GRPO) is a recent prominent method that encourages models to generate complete reasoning traces before answering, leading to increased token usage and computational cost. Inspired by the human-like thinking process-where people skip reasoning for easy questions but think carefully when needed-we explore how to enable VLMs to first decide when reasoning is necessary. To realize this, we propose TON, a two-stage training strategy: (i) a supervised fine-tuning (SFT) stage with a simple yet effective 'thought dropout' operation, where reasoning traces are randomly replaced with empty thoughts. This introduces a think-or-not format that serves as a cold start for selective reasoning; (ii) a GRPO stage that enables the model to freely explore when to think or not, while maximizing task-aware outcome rewards. Experimental results show that TON can reduce the completion length by up to 90% compared to vanilla GRPO, without sacrificing performance or even improving it. Further evaluations across diverse vision-language tasks-covering a range of reasoning difficulties under both 3B and 7B models-consistently reveal that the model progressively learns to bypass unnecessary reasoning steps as training advances. These findings shed light on the path toward human-like reasoning patterns in reinforcement learning approaches. Our code is available at https://github.com/kokolerk/TON.

Enhancing the capability of large language models (LLMs) in reasoning has gained significant attention in recent years. Previous studies have demonstrated the effectiveness of various prompting strategies in aiding LLMs in reasoning (called "reasoning actions"), such as step-by-step thinking, reflecting before answering, solving with programs, and their combinations. However, these approaches often applied static, predefined reasoning actions uniformly to all questions, without considering the specific characteristics of each question or the capability of the task-solving LLM. In this paper, we propose DOTS, an approach enabling LLMs to reason dynamically via optimal reasoning trajectory search, tailored to the specific characteristics of each question and the inherent capability of the task-solving LLM. Our approach involves three key steps: i) defining atomic reasoning action modules that can be composed into various reasoning action trajectories; ii) searching for the optimal action trajectory for each training question through iterative exploration and evaluation for the specific task-solving LLM; and iii) using the collected optimal trajectories to train an LLM to plan for the reasoning trajectories of unseen questions. In particular, we propose two learning paradigms, i.e., fine-tuning an external LLM as a planner to guide the task-solving LLM, or directly fine-tuning the task-solving LLM with an internalized capability for reasoning actions planning. Our experiments across eight reasoning tasks show that our method consistently outperforms static reasoning techniques and the vanilla instruction tuning approach. Further analysis reveals that our method enables LLMs to adjust their computation based on problem complexity, allocating deeper thinking and reasoning to harder problems.

Exploiting large language models (LLMs) to tackle deductive reasoning has garnered growing attention. It still remains highly challenging to achieve satisfactory results in complex deductive problems, characterized by plenty of premises (i.e., facts or rules) entailing intricate relationships among entities and requiring multi-hop reasoning. One intuitive solution is to decompose the original task into smaller sub-tasks, and then chain the multiple casual reasoning steps together in a forward (e.g., Selection-Inference) or backward (e.g., LAMBADA) direction. However, these techniques inevitably necessitate a large number of overall stages, leading to computationally expensive operations and a higher possibility of making misleading steps. In addition to stage-by-stage decomposition, we draw inspiration from another aspect of human problem-solving. Humans tend to distill the most relevant information and organize their thoughts systematically (e.g., creating mind maps), which assists them in answering questions or drawing conclusions precisely and quickly. In light of this, we propose a novel reasoning approach named Concise and Organized Perception (COP). COP carefully analyzes the given statements to efficiently identify the most pertinent information while eliminating redundancy. It then prompts the LLMs in a more organized form that adapts to the model's inference process. By perceiving concise and organized proofs, the deductive reasoning abilities of LLMs can be better elicited, and the risk of acquiring errors caused by excessive reasoning stages is mitigated. Furthermore, our approach can be combined with the aforementioned ones to further boost their performance. Extensive experimental results on three popular deductive benchmarks (i.e., ProofWriter, PrOntoQA and PrOntoQA-OOD) show that COP significantly outperforms previous state-of-the-art methods.

As AI systems progress, we rely more on them to make decisions with us and for us. To ensure that such decisions are aligned with human values, it is imperative for us to understand not only what decisions they make but also how they come to those decisions. Reasoning language models, which provide both final responses and (partially transparent) intermediate thinking traces, present a timely opportunity to study AI procedural reasoning. Unlike math and code problems which often have objectively correct answers, moral dilemmas are an excellent testbed for process-focused evaluation because they allow for multiple defensible conclusions. To do so, we present MoReBench: 1,000 moral scenarios, each paired with a set of rubric criteria that experts consider essential to include (or avoid) when reasoning about the scenarios. MoReBench contains over 23 thousand criteria including identifying moral considerations, weighing trade-offs, and giving actionable recommendations to cover cases on AI advising humans moral decisions as well as making moral decisions autonomously. Separately, we curate MoReBench-Theory: 150 examples to test whether AI can reason under five major frameworks in normative ethics. Our results show that scaling laws and existing benchmarks on math, code, and scientific reasoning tasks fail to predict models' abilities to perform moral reasoning. Models also show partiality towards specific moral frameworks (e.g., Benthamite Act Utilitarianism and Kantian Deontology), which might be side effects of popular training paradigms. Together, these benchmarks advance process-focused reasoning evaluation towards safer and more transparent AI.

Improving performance on complex tasks and enabling interpretable decision making in large language models (LLMs), especially for clinical applications, requires effective reasoning. Yet this remains challenging without supervised fine-tuning (SFT) on costly chain-of-thought (CoT) data distilled from closed-source models (e.g., GPT-4o). In this work, we present AlphaMed, the first medical LLM to show that reasoning capability can emerge purely through reinforcement learning (RL), using minimalist rule-based rewards on public multiple-choice QA datasets, without relying on SFT or distilled CoT data. AlphaMed achieves state-of-the-art results on six medical QA benchmarks, outperforming models trained with conventional SFT+RL pipelines. On challenging benchmarks (e.g., MedXpert), AlphaMed even surpasses larger or closed-source models such as DeepSeek-V3-671B and Claude-3.5-Sonnet. To understand the factors behind this success, we conduct a comprehensive data-centric analysis guided by three questions: (i) Can minimalist rule-based RL incentivize reasoning without distilled CoT supervision? (ii) How do dataset quantity and diversity impact reasoning? (iii) How does question difficulty shape the emergence and generalization of reasoning? Our findings show that dataset informativeness is a key driver of reasoning performance, and that minimalist RL on informative, multiple-choice QA data is effective at inducing reasoning without CoT supervision. We also observe divergent trends across benchmarks, underscoring limitations in current evaluation and the need for more challenging, reasoning-oriented medical QA benchmarks.

Reasoning LLMs often spend substantial tokens on long intermediate reasoning traces (e.g., chain-of-thought) when solving new problems. We propose to summarize and store reusable reasoning skills distilled from extensive deliberation and trial-and-error exploration, and to retrieve these skills at inference time to guide future reasoning. Unlike the prevailing reasoning from scratch paradigm, our approach first recalls relevant skills for each query, helping the model avoid redundant detours and focus on effective solution paths. We evaluate our method on coding and mathematical reasoning tasks, and find that it significantly reduces reasoning tokens while improving overall performance. The resulting lower per-request cost indicates strong practical and economic potential for real-world deployment.

The reasoning abilities of large language models (LLMs) have improved with chain-of-thought (CoT) prompting, allowing models to solve complex tasks in a stepwise manner. However, training CoT capabilities requires detailed reasoning data, which is often scarce. The self-taught reasoner (STaR) framework addresses this by using reinforcement learning to automatically generate reasoning steps, reducing reliance on human-labeled data. Although STaR and its variants have demonstrated empirical success, a theoretical foundation explaining these improvements is lacking. This work provides a theoretical framework for understanding the effectiveness of reinforcement learning on CoT reasoning and STaR. Our contributions are: (1) an analysis of policy improvement, showing why LLM reasoning improves iteratively with STaR; (2) conditions for convergence to an optimal reasoning policy; (3) an examination of STaR's robustness, explaining how it can improve reasoning even when incorporating occasional incorrect steps; and (4) criteria for the quality of pre-trained models necessary to initiate effective reasoning improvement. This framework aims to bridge empirical findings with theoretical insights, advancing reinforcement learning approaches for reasoning in LLMs.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Reasoning is an essential component of human intelligence as it plays a fundamental role in our ability to think critically, support responsible decisions, and solve challenging problems. Traditionally, AI has addressed reasoning in the context of logic-based representations of knowledge. However, the recent leap forward in natural language processing, with the emergence of language models based on transformers, is hinting at the possibility that these models exhibit reasoning abilities, particularly as they grow in size and are trained on more data. Despite ongoing discussions about what reasoning is in language models, it is still not easy to pin down to what extent these models are actually capable of reasoning. The goal of this workshop is to create a platform for researchers from different disciplines and/or AI perspectives, to explore approaches and techniques with the aim to reconcile reasoning between language models using transformers and using logic-based representations. The specific objectives include analyzing the reasoning abilities of language models measured alongside KR methods, injecting KR-style reasoning abilities into language models (including by neuro-symbolic means), and formalizing the kind of reasoning language models carry out. This exploration aims to uncover how language models can effectively integrate and leverage knowledge and reasoning with it, thus improving their application and utility in areas where precision and reliability are a key requirement.

Studies have underscored how, regardless of the recent breakthrough and swift advances in AI research, even state-of-the-art Large Language models (LLMs) continue to struggle when performing logical and mathematical reasoning. The results seem to suggest that LLMs still work as (highly advanced) data pattern identifiers, scoring poorly when attempting to generalise and solve reasoning problems the models have never previously seen or that are not close to samples presented in their training data. To address this compelling concern, this paper makes use of the notion of critical questions from the literature on argumentation theory, focusing in particular on Toulmin's model of argumentation. We show that employing these critical questions can improve the reasoning capabilities of LLMs. By probing the rationale behind the models' reasoning process, the LLM can assess whether some logical mistake is occurring and correct it before providing the final reply to the user prompt. The underlying idea is drawn from the gold standard of any valid argumentative procedure: the conclusion is valid if it is entailed by accepted premises. Or, to paraphrase such Aristotelian principle in a real-world approximation, characterised by incomplete information and presumptive logic, the conclusion is valid if not proved otherwise. This approach successfully steers the models' output through a reasoning pipeline, resulting in better performance against the baseline and its Chain-of-Thought (CoT) implementation. To this end, an extensive evaluation of the proposed approach on the MT-Bench Reasoning and Math tasks across a range of LLMs is provided.

Recent advancements in the field of large language models, particularly through the Chain of Thought (CoT) approach, have demonstrated significant improvements in solving complex problems. However, existing models either tend to sacrifice detailed reasoning for brevity due to user preferences, or require extensive and expensive training data to learn complicated reasoning ability, limiting their potential in solving complex tasks. To bridge this gap, following the concept of scaling test-time, we propose a simple method by encouraging models to adopt a more patient reasoning style without the need of introducing new knowledge or skills. To employ a preference optimization approach, we generate detailed reasoning processes as positive examples and simple answers as negative examples, thereby training the model to favor thoroughness in its responses. Our results demonstrate a performance increase of up to 6.7% on GSM8k with training just on a lightweight dataset.

Supervised fine-tuning (SFT) has emerged as one of the most effective ways to improve the performance of large language models (LLMs) in downstream tasks. However, SFT can have difficulty generalizing when the underlying data distribution changes, even when the new data does not fall completely outside the training domain. Recent reasoning-focused models such as o1 and R1 have demonstrated consistent gains over their non-reasoning counterparts, highlighting the importance of reasoning for improved generalization and reliability. However, collecting high-quality reasoning traces for SFT remains challenging -- annotations are costly, subjective, and difficult to scale. To address this limitation, we leverage Reinforcement Learning (RL) to enable models to learn reasoning strategies directly from task outcomes. We propose a pipeline in which LLMs generate reasoning steps that guide both the invocation of tools (e.g., function calls) and the final answer generation for conversational agents. Our method employs Group Relative Policy Optimization (GRPO) with rewards designed around tool accuracy and answer correctness, allowing the model to iteratively refine its reasoning and actions. Experimental results demonstrate that our approach improves both the quality of reasoning and the precision of tool invocations, achieving a 1.5% relative improvement over the SFT model (trained without explicit thinking) and a 40% gain compared to the base of the vanilla Qwen3-1.7B model. These findings demonstrate the promise of unifying reasoning and action learning through RL to build more capable and generalizable conversational agents.

Training reasoning language models (LMs) with reinforcement learning (RL) for one-hot correctness inherently relies on the LM being able to explore and solve its task with some chance at initialization. Furthermore, a key use case of reasoning LMs is to act as teachers for distilling new students and cold-starting future RL iterations rather than being deployed themselves. From these considerations, we introduce a new framework that avoids RL's exploration challenge by training a new class of Reinforcement-Learned Teachers (RLTs) focused on yielding the most effective downstream distillation. RLTs are prompted with both the question and solution to each problem, and tasked to simply "connect-the-dots" with detailed explanations tailored for their students. We train RLTs with dense rewards obtained by feeding each explanation to the student and testing its understanding of the problem's solution. In practice, the raw outputs of a 7B RLT provide higher final performance on competition and graduate-level tasks than existing distillation and cold-starting pipelines that collect and postprocess the reasoning traces of orders of magnitude larger LMs. Furthermore, RLTs maintain their effectiveness when training larger students and when applied zero-shot to out-of-distribution tasks, unlocking new levels of efficiency and re-usability for the RL reasoning framework.

Reasoning-enhanced large language models (RLLMs), whether explicitly trained for reasoning or prompted via chain-of-thought (CoT), have achieved state-of-the-art performance on many complex reasoning tasks. However, we uncover a surprising and previously overlooked phenomenon: explicit CoT reasoning can significantly degrade instruction-following accuracy. Evaluating 15 models on two benchmarks: IFEval (with simple, rule-verifiable constraints) and ComplexBench (with complex, compositional constraints), we consistently observe performance drops when CoT prompting is applied. Through large-scale case studies and an attention-based analysis, we identify common patterns where reasoning either helps (e.g., with formatting or lexical precision) or hurts (e.g., by neglecting simple constraints or introducing unnecessary content). We propose a metric, constraint attention, to quantify model focus during generation and show that CoT reasoning often diverts attention away from instruction-relevant tokens. To mitigate these effects, we introduce and evaluate four strategies: in-context learning, self-reflection, self-selective reasoning, and classifier-selective reasoning. Our results demonstrate that selective reasoning strategies, particularly classifier-selective reasoning, can substantially recover lost performance. To our knowledge, this is the first work to systematically expose reasoning-induced failures in instruction-following and offer practical mitigation strategies.

The deployment of large language models (LLMs) in mental health and other sensitive domains raises urgent questions about ethical reasoning, fairness, and responsible alignment. Yet, existing benchmarks for moral and clinical decision-making do not adequately capture the unique ethical dilemmas encountered in mental health practice, where confidentiality, autonomy, beneficence, and bias frequently intersect. To address this gap, we introduce Ethical Reasoning in Mental Health (EthicsMH), a pilot dataset of 125 scenarios designed to evaluate how AI systems navigate ethically charged situations in therapeutic and psychiatric contexts. Each scenario is enriched with structured fields, including multiple decision options, expert-aligned reasoning, expected model behavior, real-world impact, and multi-stakeholder viewpoints. This structure enables evaluation not only of decision accuracy but also of explanation quality and alignment with professional norms. Although modest in scale and developed with model-assisted generation, EthicsMH establishes a task framework that bridges AI ethics and mental health decision-making. By releasing this dataset, we aim to provide a seed resource that can be expanded through community and expert contributions, fostering the development of AI systems capable of responsibly handling some of society's most delicate decisions.

Reasoning models enhance performance by tackling problems in a step-by-step manner, decomposing them into sub-problems and exploring long chains of thought before producing an answer. However, applying extended reasoning to every step introduces substantial redundancy, as sub-problems vary widely in difficulty and complexity: a small number of pivotal steps are genuinely challenging and decisive for the final answer, while many others only involve straightforward revisions or simple computations. Therefore, a natural idea is to endow reasoning models with the ability to adaptively respond to this variation, rather than treating all steps with the same level of elaboration. To this end, we propose MixReasoning, a framework that dynamically adjusts the depth of reasoning within a single response. The resulting chain of thought then becomes a mixture of detailed reasoning on difficult steps and concise inference on simpler ones. Experiments on GSM8K, MATH-500, and AIME show that MixReasoning shortens reasoning length and substantially improves efficiency without compromising accuracy.

Explaining Artificial Intelligence (AI) decisions is a major challenge nowadays in AI, in particular when applied to sensitive scenarios like medicine and law. However, the need to explain the rationale behind decisions is a main issue also for human-based deliberation as it is important to justify why a certain decision has been taken. Resident medical doctors for instance are required not only to provide a (possibly correct) diagnosis, but also to explain how they reached a certain conclusion. Developing new tools to aid residents to train their explanation skills is therefore a central objective of AI in education. In this paper, we follow this direction, and we present, to the best of our knowledge, the first multilingual dataset for Medical Question Answering where correct and incorrect diagnoses for a clinical case are enriched with a natural language explanation written by doctors. These explanations have been manually annotated with argument components (i.e., premise, claim) and argument relations (i.e., attack, support), resulting in the Multilingual CasiMedicos-Arg dataset which consists of 558 clinical cases in four languages (English, Spanish, French, Italian) with explanations, where we annotated 5021 claims, 2313 premises, 2431 support relations, and 1106 attack relations. We conclude by showing how competitive baselines perform over this challenging dataset for the argument mining task.

Multimodal large language models (MLLMs) have begun to demonstrate robust reasoning capabilities on general tasks, yet their application in the medical domain remains in its early stages. Constructing chain-of-thought (CoT) training data is essential for bolstering the reasoning abilities of medical MLLMs. However, existing approaches exhibit a deficiency in offering a comprehensive framework for searching and evaluating effective reasoning paths towards critical diagnosis. To address this challenge, we propose Mentor-Intern Collaborative Search (MICS), a novel reasoning-path searching scheme to generate rigorous and effective medical CoT data. MICS first leverages mentor models to initialize the reasoning, one step at a time, then prompts each intern model to continue the thinking along those initiated paths, and finally selects the optimal reasoning path according to the overall reasoning performance of multiple intern models. The reasoning performance is determined by an MICS-Score, which assesses the quality of generated reasoning paths. Eventually, we construct MMRP, a multi-task medical reasoning dataset with ranked difficulty, and Chiron-o1, a new medical MLLM devised via a curriculum learning strategy, with robust visual question-answering and generalizable reasoning capabilities. Extensive experiments demonstrate that Chiron-o1, trained on our CoT dataset constructed using MICS, achieves state-of-the-art performance across a list of medical visual question answering and reasoning benchmarks. Codes are available at GitHub - manglu097/Chiron-o1: Enhancing Step-by-Step and Verifiable Medical Reasoning in MLLMs

Logical reading comprehension is a challenging task that entails grasping the underlying semantics of text and applying reasoning to deduce the correct answer. Prior researches have primarily focused on enhancing logical reasoning capabilities through Chain-of-Thought (CoT) or data augmentation. However, previous work constructing chain-of-thought rationales concentrates solely on analyzing correct options, neglecting the incorrect alternatives. Addtionally, earlier efforts on data augmentation by altering contexts rely on rule-based methods, which result in generated contexts that lack diversity and coherence. To address these issues, we propose a Premise-Oriented Data Augmentation (PODA) framework. This framework can generate CoT rationales including analyses for both correct and incorrect options, while constructing diverse and high-quality counterfactual contexts from incorrect candidate options. We integrate summarizing premises and identifying premises for each option into rationales. Subsequently, we employ multi-step prompts with identified premises to construct counterfactual context. To facilitate the model's capabilities to better differentiate the reasoning process associated with each option, we introduce a novel thought-path contrastive learning method that compares reasoning paths between the original and counterfactual samples. Experimental results on three representative LLMs demonstrate that our method can improve the baselines substantially across two challenging logical reasoning benchmarks (ReClor and LogiQA 2.0). The data and code are released at https://github.com/lalalamdbf/TPReasoner.

Reasoning is central to a wide range of intellectual activities, and while the capabilities of large language models (LLMs) continue to advance, their performance in reasoning tasks remains limited. The processes and mechanisms underlying reasoning are not yet fully understood, but key elements include path exploration, selection of relevant knowledge, and multi-step inference. Problems are solved through the synthesis of these components. In this paper, we propose a benchmark that focuses on a specific aspect of reasoning ability: the direct evaluation of multi-step inference. To this end, we design a special reasoning task where multi-step inference is specifically focused by largely eliminating path exploration and implicit knowledge utilization. Our dataset comprises pairs of explicit instructions and corresponding questions, where the procedures necessary for solving the questions are entirely detailed within the instructions. This setup allows models to solve problems solely by following the provided directives. By constructing problems that require varying numbers of steps to solve and evaluating responses at each step, we enable a thorough assessment of state-of-the-art LLMs' ability to follow instructions. To ensure the robustness of our evaluation, we include multiple distinct tasks. Furthermore, by comparing accuracy across tasks, utilizing step-aware metrics, and applying separately defined measures of complexity, we conduct experiments that offer insights into the capabilities and limitations of LLMs in reasoning tasks. Our findings have significant implications for the development of LLMs and highlight areas for future research in advancing their reasoning abilities. Our dataset is available at https://huggingface.co/datasets/ifujisawa/procbench and code at https://github.com/ifujisawa/proc-bench.

Reasoning is central to human intelligence, enabling structured problem-solving across diverse tasks. Recent advances in large language models (LLMs) have greatly enhanced their reasoning abilities in arithmetic, commonsense, and symbolic domains. However, effectively extending these capabilities into multimodal contexts-where models must integrate both visual and textual inputs-continues to be a significant challenge. Multimodal reasoning introduces complexities, such as handling conflicting information across modalities, which require models to adopt advanced interpretative strategies. Addressing these challenges involves not only sophisticated algorithms but also robust methodologies for evaluating reasoning accuracy and coherence. This paper offers a concise yet insightful overview of reasoning techniques in both textual and multimodal LLMs. Through a thorough and up-to-date comparison, we clearly formulate core reasoning challenges and opportunities, highlighting practical methods for post-training optimization and test-time inference. Our work provides valuable insights and guidance, bridging theoretical frameworks and practical implementations, and sets clear directions for future research.

With the emergence of advanced reasoning models like OpenAI o3 and DeepSeek-R1, large language models (LLMs) have demonstrated remarkable reasoning capabilities. However, their ability to perform rigorous logical reasoning remains an open question. This survey synthesizes recent advancements in logical reasoning within LLMs, a critical area of AI research. It outlines the scope of logical reasoning in LLMs, its theoretical foundations, and the benchmarks used to evaluate reasoning proficiency. We analyze existing capabilities across different reasoning paradigms - deductive, inductive, abductive, and analogical - and assess strategies to enhance reasoning performance, including data-centric tuning, reinforcement learning, decoding strategies, and neuro-symbolic approaches. The review concludes with future directions, emphasizing the need for further exploration to strengthen logical reasoning in AI systems.

Post-training has become a primary driver of recent progress in large reasoning models, and reasoning data are often the key variable determining whether this stage succeeds. Work on post-training reasoning data has grown rapidly, yet this literature remains scattered across dataset papers, reinforcement-learning recipes, reward-model studies, benchmarks, and frontier system reports. This paper is the first primer to synthesize over 150 key public studies and system reports on post-training reasoning data. We organize the field around four questions: what data objects exist, what makes them useful, how they are constructed, and how they scale. Together, this organization provides an attribution framework for future reasoning-data releases and post-training recipes.

Rule-based reasoning, a fundamental type of legal reasoning, enables us to draw conclusions by accurately applying a rule to a set of facts. We explore causal language models as rule-based reasoners, specifically with respect to compositional rules - rules consisting of multiple elements which form a complex logical expression. Reasoning about compositional rules is challenging because it requires multiple reasoning steps, and attending to the logical relationships between elements. We introduce a new prompting method, Chain of Logic, which elicits rule-based reasoning through decomposition (solving elements as independent threads of logic), and recomposition (recombining these sub-answers to resolve the underlying logical expression). This method was inspired by the IRAC (Issue, Rule, Application, Conclusion) framework, a sequential reasoning approach used by lawyers. We evaluate chain of logic across eight rule-based reasoning tasks involving three distinct compositional rules from the LegalBench benchmark and demonstrate it consistently outperforms other prompting methods, including chain of thought and self-ask, using open-source and commercial language models.

Large language models have shown promise in clinical decision making, but current approaches struggle to localize and correct errors at specific steps of the reasoning process. This limitation is critical in medicine, where identifying and addressing reasoning errors is essential for accurate diagnosis and effective patient care. We introduce Med-PRM, a process reward modeling framework that leverages retrieval-augmented generation to verify each reasoning step against established medical knowledge bases. By verifying intermediate reasoning steps with evidence retrieved from clinical guidelines and literature, our model can precisely assess the reasoning quality in a fine-grained manner. Evaluations on five medical QA benchmarks and two open-ended diagnostic tasks demonstrate that Med-PRM achieves state-of-the-art performance, with improving the performance of base models by up to 13.50% using Med-PRM. Moreover, we demonstrate the generality of Med-PRM by integrating it in a plug-and-play fashion with strong policy models such as Meerkat, achieving over 80\% accuracy on MedQA for the first time using small-scale models of 8 billion parameters. Our code and data are available at: https://med-prm.github.io/

Machine learning has successfully framed many sequential decision making problems as either supervised prediction, or optimal decision-making policy identification via reinforcement learning. In data-constrained offline settings, both approaches may fail as they assume fully optimal behavior or rely on exploring alternatives that may not exist. We introduce an inherently different approach that identifies possible "dead-ends" of a state space. We focus on the condition of patients in the intensive care unit, where a "medical dead-end" indicates that a patient will expire, regardless of all potential future treatment sequences. We postulate "treatment security" as avoiding treatments with probability proportional to their chance of leading to dead-ends, present a formal proof, and frame discovery as an RL problem. We then train three independent deep neural models for automated state construction, dead-end discovery and confirmation. Our empirical results discover that dead-ends exist in real clinical data among septic patients, and further reveal gaps between secure treatments and those that were administered.

Reinforcement learning (RL) has become the dominant paradigm for endowing language models with advanced reasoning capabilities. Despite the substantial empirical gains demonstrated by RL-based training methods like GRPO, a granular understanding of their advantages is still lacking. To address this gap, we introduce a fine-grained analytic framework to dissect the impact of RL on reasoning. Our framework specifically investigates key elements that have been hypothesized to benefit from RL training: (1) plan-following and execution, (2) problem decomposition, and (3) improved reasoning and knowledge utilization. Using this framework, we gain insights beyond mere accuracy. For instance, providing models with explicit step-by-step plans surprisingly degrades performance on the most challenging benchmarks, yet RL-tuned models exhibit greater robustness, experiencing markedly smaller performance drops than their base counterparts. This suggests that RL may not primarily enhance the execution of external plans but rather empower models to formulate and follow internal strategies better suited to their reasoning processes. Conversely, we observe that RL enhances the model's capacity to integrate provided knowledge into its reasoning process, leading to performance improvements across diverse tasks. We also study difficulty, showing improved training by developing new ways to exploit hard problems. Our findings lay a foundation for more principled training and evaluation of reasoning models.

Deductive reasoning is a crucial logical capability that assists us in solving complex problems based on existing knowledge. Although augmented by Chain-of-Thought prompts, Large Language Models (LLMs) might not follow the correct reasoning paths. Enhancing the deductive reasoning abilities of LLMs, and leveraging their extensive built-in knowledge for various reasoning tasks, remains an open question. Attempting to mimic the human deductive reasoning paradigm, we propose a multi-stage Syllogistic-Reasoning Framework of Thought (SR-FoT) that enables LLMs to perform syllogistic deductive reasoning to handle complex knowledge-based reasoning tasks. Our SR-FoT begins by interpreting the question and then uses the interpretation and the original question to propose a suitable major premise. It proceeds by generating and answering minor premise questions in two stages to match the minor premises. Finally, it guides LLMs to use the previously generated major and minor premises to perform syllogistic deductive reasoning to derive the answer to the original question. Extensive and thorough experiments on knowledge-based reasoning tasks have demonstrated the effectiveness and advantages of our SR-FoT.

Although Large Language Models (LLMs) achieve remarkable performance across various tasks, they often struggle with complex reasoning tasks, such as answering mathematical questions. Recent efforts to address this issue have primarily focused on leveraging mathematical datasets through supervised fine-tuning or self-improvement techniques. However, these methods often depend on high-quality datasets that are difficult to prepare, or they require substantial computational resources for fine-tuning. Inspired by findings that LLMs know how to produce the right answer but struggle to select the correct reasoning path, we propose a purely inference-based searching method -- MindStar (M*). This method formulates reasoning tasks as searching problems and proposes two search ideas to identify the optimal reasoning paths. We evaluate the M* framework on both the GSM8K and MATH datasets, comparing its performance with existing open and closed-source LLMs. Our results demonstrate that M* significantly enhances the reasoning abilities of open-source models, such as Llama-2-13B and Mistral-7B, and achieves comparable performance to GPT-3.5 and Grok-1, but with substantially reduced model size and computational costs.

Reasoning models excel in complex problem solving but exhibit a concerning trade off between reasoning capabilities and instruction following abilities. Existing approaches for improving instruction following rely on stronger external models, creating methodological bottlenecks and practical limitations including increased costs and accessibility constraints. We propose a self-supervised RL framework that leverages reasoning models' own internal signals to improve instruction following capabilities without external supervision. Extensive experiments demonstrate that our framework significantly improves instruction following capabilities while maintaining reasoning performance, offering a scalable and cost-effective approach to enhance instruction following in reasoning models. The data and code are publicly available at https://github.com/Rainier-rq/verl-if.

Large Language Models (LLMs) have shown remarkable capabilities in reasoning, exemplified by the success of OpenAI-o1 and DeepSeek-R1. However, integrating reasoning with external search processes remains challenging, especially for complex multi-hop questions requiring multiple retrieval steps. We propose ReSearch, a novel framework that trains LLMs to Reason with Search via reinforcement learning without using any supervised data on reasoning steps. Our approach treats search operations as integral components of the reasoning chain, where when and how to perform searches is guided by text-based thinking, and search results subsequently influence further reasoning. We train ReSearch on Qwen2.5-7B(-Instruct) and Qwen2.5-32B(-Instruct) models and conduct extensive experiments. Despite being trained on only one dataset, our models demonstrate strong generalizability across various benchmarks. Analysis reveals that ReSearch naturally elicits advanced reasoning capabilities such as reflection and self-correction during the reinforcement learning process.

When people reason about cause and effect, they often consider many competing "what if" scenarios before deciding which explanation fits best. Analogously, advanced language models capable of causal inference can consider multiple interventions and counterfactuals to judge the validity of causal claims. Crucially, this type of reasoning is less like a single calculation and more like an internal dialogue between alternative hypotheses. In this paper, we make this dialogue explicit through a dual-agent debate framework where one model provides a structured causal inference, and the other critically examines this reasoning for logical flaws. When disagreements arise, agents attempt to persuade each other, challenging each other's logic and revising their conclusions until they converge on a mutually agreed answer. To take advantage of this deliberative process, we specifically use reasoning language models, whose strengths in both causal inference and adversarial debate remain under-explored relative to standard large language models. We evaluate our approach on the CLadder dataset, a benchmark linking natural language questions to formally defined causal graphs across all three rungs of Pearl's ladder of causation. With Qwen3 and DeepSeek-R1 as debater agents, we demonstrate that multi-agent debate improves DeepSeek-R1's overall accuracy in causal inference from 78.03% to 87.45%, with the counterfactual category specifically improving from 67.94% to 80.04% accuracy. Similarly, Qwen3's overall accuracy improves from 84.16% to 89.41%, and counterfactual questions from 71.53% to 80.35%, showing that strong models can still benefit greatly from debate with weaker agents. Our results highlight the potential of reasoning models as building blocks for multi-agent systems in causal inference, and demonstrate the importance of diverse perspectives in causal problem-solving.

What is reasoning? This question has driven centuries of philosophical inquiry, from Aristotle's syllogisms to modern computational complexity theory. In the age of large language models achieving superhuman performance on benchmarks like GSM8K (95\% accuracy) and HumanEval (90\% pass@1), we must ask: have these systems learned to reason, or have they learned to pattern-match over reasoning traces? This paper argues for a specific answer: reasoning is iterative operator application in state spaces, converging to fixed points. This definition is not merely philosophical -- it has concrete architectural implications that explain both the failures of current systems and the path to genuine reasoning capabilities. Our investigation begins with a puzzle (OpenXOR), progresses through theory (OpenOperator), and culminates in a working solution (OpenLM) that achieves 76\% accuracy where state-of-the-art LLMs achieve 0\%. This is not about criticizing existing systems, but about understanding what reasoning requires and building architectures that provide it.

Equipping agents with the capacity to justify made decisions using supporting evidence represents a cornerstone of accountable decision-making. Furthermore, ensuring that justifications are in line with human expectations and societal norms is vital, especially in high-stakes situations such as healthcare. In this work, we propose the use of a debate-based reward model for reinforcement learning agents, where the outcome of a zero-sum debate game quantifies the justifiability of a decision in a particular state. This reward model is then used to train a justifiable policy, whose decisions can be more easily corroborated with supporting evidence. In the debate game, two argumentative agents take turns providing supporting evidence for two competing decisions. Given the proposed evidence, a proxy of a human judge evaluates which decision is better justified. We demonstrate the potential of our approach in learning policies for prescribing and justifying treatment decisions of septic patients. We show that augmenting the reward with the feedback signal generated by the debate-based reward model yields policies highly favored by the judge when compared to the policy obtained solely from the environment rewards, while hardly sacrificing any performance. Moreover, in terms of the overall performance and justifiability of trained policies, the debate-based feedback is comparable to the feedback obtained from an ideal judge proxy that evaluates decisions using the full information encoded in the state. This suggests that the debate game outputs key information contained in states that is most relevant for evaluating decisions, which in turn substantiates the practicality of combining our approach with human-in-the-loop evaluations. Lastly, we showcase that agents trained via multi-agent debate learn to propose evidence that is resilient to refutations and closely aligns with human preferences.

Background Major depressive disorder (MDD) is a leading cause of global disability, yet current diagnostic approaches often rely on subjective assessments and lack the ability to integrate multimodal clinical information. Large language models (LLMs) hold promise for enhancing diagnostic accuracy through advanced reasoning but face challenges in interpretability, hallucination, and reliance on synthetic data. Methods We developed MDD-Thinker, an LLM-based diagnostic framework that integrates supervised fine-tuning (SFT) with reinforcement learning (RL) to strengthen reasoning ability and interpretability. Using the UK Biobank dataset, we generated 40,000 reasoning samples, supplemented with 10,000 samples from publicly available mental health datasets. The model was fine-tuned on these reasoning corpora, and its diagnostic and reasoning performance was evaluated against machine learning, deep learning, and state-of-the-art LLM baselines. Findings MDD-Thinker achieved an accuracy of 0.8268 and F1-score of 0.8081, significantly outperforming traditional baselines such as SVM and MLP, as well as general-purpose LLMs. Incorporating both SFT and RL yielded the greatest improvements, with relative gains of 29.0% in accuracy, 38.1% in F1-score, and 34.8% in AUC. Moreover, the model demonstrated comparable reasoning performance compared to much larger LLMs, while maintaining computational efficiency. Interpretation This study presents the first reasoning-enhanced LLM framework for MDD diagnosis trained on large-scale real-world clinical data. By integrating SFT and RL, MDD-Thinker balances accuracy, interpretability, and efficiency, offering a scalable approach for intelligent psychiatric diagnostics. These findings suggest that reasoning-oriented LLMs can provide clinically reliable support for MDD detection and may inform broader applications in mental health care.

Recent developments, particularly OpenAI's O1 model, have demonstrated the remarkable potential of Large Language Models (LLMs) for complex reasoning tasks. Through analysis of O1's outputs and provided sample Chain-of-Thought (CoT) demonstrations, we observe that it approaches problem-solving in a distinctly human-like manner, systematically brainstorming ideas, testing hypotheses, verifying results, and planning comprehensive solutions. These sophisticated reasoning capabilities remain notably absent in other state-of-the-art language models. In this paper, we hypothesize that this performance gap stems from the limited availability of high-quality reasoning process data in current training sets. We demonstrate that by constructing a specialized dataset focused on explicit problem-solving workflows ("worked solutions"), we can elicit substantially improved planning capabilities from existing models. Additionally, we propose the Reasoning Enhancement Loop (REL), a method for generating synthetic worked solutions.

Mental health disorders affect hundreds of millions globally, and the Web now serves as a primary medium for accessing support, information, and assessment. Large language models (LLMs) offer scalable and accessible assistance, yet their deployment in mental-health settings remains risky when their reasoning is incomplete, inconsistent, or ungrounded. Existing psychological LLMs emphasize emotional understanding or knowledge recall but overlook the step-wise, clinically aligned reasoning required for appraisal, diagnosis, intervention planning, abstraction, and verification. To address these issues, we introduce MentraSuite, a unified framework for advancing reliable mental-health reasoning. We propose MentraBench, a comprehensive benchmark spanning five core reasoning aspects, six tasks, and 13 datasets, evaluating both task performance and reasoning quality across five dimensions: conciseness, coherence, hallucination avoidance, task understanding, and internal consistency. We further present Mindora, a post-trained model optimized through a hybrid SFT-RL framework with an inconsistency-detection reward to enforce faithful and coherent reasoning. To support training, we construct high-quality trajectories using a novel reasoning trajectory generation strategy, that strategically filters difficult samples and applies a structured, consistency-oriented rewriting process to produce concise, readable, and well-balanced trajectories. Across 20 evaluated LLMs, Mindora achieves the highest average performance on MentraBench and shows remarkable performances in reasoning reliability, demonstrating its effectiveness for complex mental-health scenarios.

Reasoning models have demonstrated remarkable progress in solving complex and logic-intensive tasks by generating extended Chain-of-Thoughts (CoTs) prior to arriving at a final answer. Yet, the emergence of this "slow-thinking" paradigm, with numerous tokens generated in sequence, inevitably introduces substantial computational overhead. To this end, it highlights an urgent need for effective acceleration. This survey aims to provide a comprehensive overview of recent advances in efficient reasoning. It categorizes existing works into three key directions: (1) shorter - compressing lengthy CoTs into concise yet effective reasoning chains; (2) smaller - developing compact language models with strong reasoning capabilities through techniques such as knowledge distillation, other model compression techniques, and reinforcement learning; and (3) faster - designing efficient decoding strategies to accelerate inference. A curated collection of papers discussed in this survey is available in our GitHub repository.

Medical Vision-Language Models (VLMs) are prone to hallucinations, compromising clinical reliability. While reinforcement learning methods like Group Relative Policy Optimization (GRPO) offer a low-cost alignment solution, their reliance on sparse, outcome-based rewards inadvertently encourages models to "overthink" -- generating verbose, convoluted, and unverifiable Chain-of-Thought reasoning to justify answers. This focus on outcomes obscures factual errors and poses significant safety risks. To address this, we propose CheXPO-v2, a novel alignment framework that shifts from outcome to process supervision. Our core innovation is a Knowledge Graph Consistency Reward mechanism driven by Entity-Relation Matching. By explicitly parsing reasoning steps into structured "Disease, Relation, Anatomy" triplets, we provide fine-grained supervision that penalizes incoherent logic and hallucinations at the atomic level. Integrating this with a hard-example mining strategy, our approach significantly outperforms GRPO and state-of-the-art models on benchmarks like MIMIC-CXR-VQA. Crucially, CheXPO-v2 achieves new state-of-the-art accuracy using only 5k samples, demonstrating exceptional data efficiency while producing clinically sound and verifiable reasoning. The project source code is publicly available at: https://github.com/ecoxial2007/CheX-Phi4MM.

Large Reasoning Models (LRMs) have significantly enhanced their capabilities in complex problem-solving by introducing a thinking draft that enables multi-path Chain-of-Thought explorations before producing final answers. Ensuring the faithfulness of these intermediate reasoning processes is crucial for reliable monitoring, interpretation, and effective control. In this paper, we propose a systematic counterfactual intervention framework to rigorously evaluate thinking draft faithfulness. Our approach focuses on two complementary dimensions: (1) Intra-Draft Faithfulness, which assesses whether individual reasoning steps causally influence subsequent steps and the final draft conclusion through counterfactual step insertions; and (2) Draft-to-Answer Faithfulness, which evaluates whether final answers are logically consistent with and dependent on the thinking draft, by perturbing the draft's concluding logic. We conduct extensive experiments across six state-of-the-art LRMs. Our findings show that current LRMs demonstrate selective faithfulness to intermediate reasoning steps and frequently fail to faithfully align with the draft conclusions. These results underscore the need for more faithful and interpretable reasoning in advanced LRMs.

Reasoning models are large language models that emit a long chain-of-thought before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained for chemistry without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models. We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 640,730 experimentally-grounded chemistry problems across 375 tasks ranging from synthesizability, to blood-brain barrier permeability, to human receptor activity, to scent. Our model exceeds general-purpose chemistry models, frontier models, and human experts on molecular design tasks. It is also more data efficient relative to specialized models. We anticipate that this method can be applied to train data-efficient language models specialized for tasks across a wide variety of scientific domains.

Recent advancements in large language models (LLMs) have resulted in increasingly anthropomorphic language concerning the ability of LLMs to reason. Whether reasoning in LLMs should be understood to be inherently different is, however, widely debated. We propose utilizing a representation engineering approach wherein model activations are read from the residual stream of an LLM when processing a reasoning task. The activations are used to derive a control vector that is applied to the model as an inference-time intervention, modulating the representational space of the model, to improve performance on the specified task. We publish the code for deriving control vectors and analyzing model representations. The method allows us to improve performance on reasoning benchmarks and assess how control vectors influence the final logit distribution of a model via metrics such as KL divergence and entropy. We apply control vectors to Mistral-7B-Instruct and a range of Pythia models on an inductive, a deductive and mathematical reasoning task. We show that an LLM can, to a certain degree, be controlled to improve its perceived reasoning ability by modulating activations. The intervention is dependent upon the ability to reliably extract the model's typical state when correctly solving a task. Our results suggest that reasoning performance can be modulated in the same manner as other information-processing tasks performed by LLMs and demonstrate that we are capable of improving performance on specific tasks via a simple intervention on the residual stream with no additional training.

Reasoning is a core capability in artificial intelligence systems, for which large language models (LLMs) have recently shown remarkable progress. However, most work focuses exclusively on deductive reasoning, which is problematic since other types of reasoning are also essential in solving real-world problems, and they are less explored. This work focuses on evaluating LLMs' inductive and abductive reasoning capabilities. We introduce a programmable and synthetic dataset, InAbHyD (pronounced in-a-bid), where each reasoning example consists of an incomplete world model and a set of observations. The task for the intelligent agent is to produce hypotheses to explain observations under the incomplete world model to solve each reasoning example. We propose a new metric to evaluate the quality of hypotheses based on Occam's Razor. We evaluate and analyze some state-of-the-art LLMs. Our analysis shows that LLMs can perform inductive and abductive reasoning in simple scenarios, but struggle with complex world models and producing high-quality hypotheses, even with popular reasoning-enhancing techniques such as in-context learning and RLVR.

Large Reasoning Models (LRMs) increasingly rely on reasoning traces with complex internal structures. However, existing work lacks a unified answer to three fundamental questions: (1) what defines high-quality reasoning, (2) how to reliably evaluate long, implicitly structured reasoning traces, and (3) how to use such evaluation signals for reasoning optimization. To address these challenges, we provide a unified perspective. (1) We introduce the ME^2 principle to characterize reasoning quality along macro- and micro-level concerning efficiency and effectiveness. (2) Built on this principle, we model reasoning traces as directed acyclic graphs (DAGs) and develop a DAG-based pairwise evaluation method, capturing complex reasoning structures. (3) Based on this method, we construct the TRM-Preference dataset and train a Thinking Reward Model (TRM) to evaluate reasoning quality at scale. Experiments show that thinking rewards serve as an effective optimization signal. At test time, selecting better reasoning leads to better outcomes (up to 19.3\% gain), and during RL training, thinking rewards enhance reasoning and performance (up to 3.9\% gain) across diverse tasks. Code and data are available at https://github.com/Simplified-Reasoning/TRM.

Thinking aloud is an effective meta-cognitive strategy human reasoners apply to solve difficult problems. We suggest to improve the reasoning ability of pre-trained neural language models in a similar way, namely by expanding a task's context with problem elaborations that are dynamically generated by the language model itself. Our main result is that dynamic problem elaboration significantly improves the zero-shot performance of GPT-2 in a deductive reasoning and natural language inference task: While the model uses a syntactic heuristic for predicting an answer, it is capable (to some degree) of generating reasoned additional context which facilitates the successful application of its heuristic. We explore different ways of generating elaborations, including fewshot learning, and find that their relative performance varies with the specific problem characteristics (such as problem difficulty). Moreover, the effectiveness of an elaboration can be explained in terms of the degree to which the elaboration semantically coheres with the corresponding problem. In particular, elaborations that are most faithful to the original problem description may boost accuracy by up to 24%.

Logical reasoning is a fundamental aspect of human intelligence and a key component of tasks like problem-solving and decision-making. Recent advancements have enabled Large Language Models (LLMs) to potentially exhibit reasoning capabilities, but complex logical reasoning remains a challenge. The state-of-the-art, solver-augmented language models, use LLMs to parse natural language logical questions into symbolic representations first and then adopt external logical solvers to take in the symbolic representations and output the answers. Despite their impressive performance, any parsing errors will inevitably result in the failure of the execution of the external logical solver and no answer to the logical questions. In this paper, we introduce LoGiPT, a novel language model that directly emulates the reasoning processes of logical solvers and bypasses the parsing errors by learning to strict adherence to solver syntax and grammar. LoGiPT is fine-tuned on a newly constructed instruction-tuning dataset derived from revealing and refining the invisible reasoning process of deductive solvers. Experimental results on two public deductive reasoning datasets demonstrate that LoGiPT outperforms state-of-the-art solver-augmented LMs and few-shot prompting methods on competitive LLMs like ChatGPT or GPT-4.

Achieving human-level intelligence requires refining the transition from the fast, intuitive System 1 to the slower, more deliberate System 2 reasoning. While System 1 excels in quick, heuristic decisions, System 2 relies on logical reasoning for more accurate judgments and reduced biases. Foundational Large Language Models (LLMs) excel at fast decision-making but lack the depth for complex reasoning, as they have not yet fully embraced the step-by-step analysis characteristic of true System 2 thinking. Recently, reasoning LLMs like OpenAI's o1/o3 and DeepSeek's R1 have demonstrated expert-level performance in fields such as mathematics and coding, closely mimicking the deliberate reasoning of System 2 and showcasing human-like cognitive abilities. This survey begins with a brief overview of the progress in foundational LLMs and the early development of System 2 technologies, exploring how their combination has paved the way for reasoning LLMs. Next, we discuss how to construct reasoning LLMs, analyzing their features, the core methods enabling advanced reasoning, and the evolution of various reasoning LLMs. Additionally, we provide an overview of reasoning benchmarks, offering an in-depth comparison of the performance of representative reasoning LLMs. Finally, we explore promising directions for advancing reasoning LLMs and maintain a real-time https://github.com/zzli2022/Awesome-Slow-Reason-System{GitHub Repository} to track the latest developments. We hope this survey will serve as a valuable resource to inspire innovation and drive progress in this rapidly evolving field.

Chain-of-thought emerges as a promising technique for eliciting reasoning capabilities from Large Language Models (LLMs). However, it does not always improve task performance or accurately represent reasoning processes, leaving unresolved questions about its usage. In this paper, we diagnose the underlying mechanism by comparing the reasoning process of LLMs with humans, using causal analysis to understand the relationships between the problem instruction, reasoning, and the answer in LLMs. Our empirical study reveals that LLMs often deviate from the ideal causal chain, resulting in spurious correlations and potential consistency errors (inconsistent reasoning and answers). We also examine various factors influencing the causal structure, finding that in-context learning with examples strengthens it, while post-training techniques like supervised fine-tuning and reinforcement learning on human feedback weaken it. To our surprise, the causal structure cannot be strengthened by enlarging the model size only, urging research on new techniques. We hope that this preliminary study will shed light on understanding and improving the reasoning process in LLM.

Despite achieving high accuracy on medical benchmarks, LLMs exhibit the Einstellung Effect in clinical diagnosis--relying on statistical shortcuts rather than patient-specific evidence, causing misdiagnosis in atypical cases. Existing benchmarks fail to detect this critical failure mode. We introduce MedEinst, a counterfactual benchmark with 5,383 paired clinical cases across 49 diseases. Each pair contains a control case and a "trap" case with altered discriminative evidence that flips the diagnosis. We measure susceptibility via Bias Trap Rate--probability of misdiagnosing traps despite correctly diagnosing controls. Extensive Evaluation of 17 LLMs shows frontier models achieve high baseline accuracy but severe bias trap rates. Thus, we propose ECR-Agent, aligning LLM reasoning with Evidence-Based Medicine standard via two components: (1) Dynamic Causal Inference (DCI) performs structured reasoning through dual-pathway perception, dynamic causal graph reasoning across three levels (association, intervention, counterfactual), and evidence audit for final diagnosis; (2) Critic-Driven Graph and Memory Evolution (CGME) iteratively refines the system by storing validated reasoning paths in an exemplar base and consolidating disease-specific knowledge into evolving illness graphs. Source code is to be released.

Large language models (LLMs) exhibit strong reasoning abilities, often attributed to few-shot or zero-shot chain-of-thought (CoT) prompting. While effective, these methods require labor-intensive prompt engineering, raising the question of whether reasoning can be induced without reliance on explicit prompts. In this work, we unlock the reasoning capabilities of LLMs without explicit prompting. Inspired by zero-shot CoT and CoT-decoding, we propose a novel decoding strategy that systematically nudges LLMs to continue reasoning, thereby preventing immature reasoning processes. Specifically, we monitor the model's generation and inject a designated phrase whenever it is likely to conclude its response prematurely, before completing the reasoning process. Our experimental evaluations on diverse reasoning benchmarks demonstrate that our proposed strategy substantially improves LLM reasoning capabilities, highlighting the potential of decoding-based interventions as an alternative to traditional prompting techniques.

Medical reasoning in large language models (LLMs) aims to emulate clinicians' diagnostic thinking, but current benchmarks such as MedQA-USMLE, MedMCQA, and PubMedQA often mix reasoning with factual recall. We address this by separating 11 biomedical QA benchmarks into reasoning- and knowledge-focused subsets using a PubMedBERT classifier that reaches 81 percent accuracy, comparable to human performance. Our analysis shows that only 32.8 percent of questions require complex reasoning. We evaluate biomedical models (HuatuoGPT-o1, MedReason, m1) and general-domain models (DeepSeek-R1, o4-mini, Qwen3), finding consistent gaps between knowledge and reasoning performance. For example, m1 scores 60.5 on knowledge but only 47.1 on reasoning. In adversarial tests where models are misled with incorrect initial reasoning, biomedical models degrade sharply, while larger or RL-trained general models show more robustness. To address this, we train BioMed-R1 using fine-tuning and reinforcement learning on reasoning-heavy examples. It achieves the strongest performance among similarly sized models. Further gains may come from incorporating clinical case reports and training with adversarial and backtracking scenarios.

One of the most widely used methods to evaluate LLMs are Multiple Choice Question (MCQ) tests. MCQ benchmarks enable the testing of LLM knowledge on almost any topic at scale as the results can be processed automatically. To help the LLM answer, a few examples called few shots can be included in the prompt. Moreover, the LLM can be asked to answer the question directly with the selected option or to first provide the reasoning and then the selected answer, which is known as chain of thought. In addition to checking whether the selected answer is correct, the evaluation can look at the LLM-estimated probability of its response as an indication of the confidence of the LLM in the response. In this paper, we study how the LLM confidence in its answer depends on whether the model has been asked to answer directly or to provide the reasoning before answering. The results of the evaluation of questions on a wide range of topics in seven different models show that LLMs are more confident in their answers when they provide reasoning before the answer. This occurs regardless of whether the selected answer is correct. Our hypothesis is that this behavior is due to the reasoning that modifies the probability of the selected answer, as the LLM predicts the answer based on the input question and the reasoning that supports the selection made. Therefore, LLM estimated probabilities seem to have intrinsic limitations that should be understood in order to use them in evaluation procedures. Interestingly, the same behavior has been observed in humans, for whom explaining an answer increases confidence in its correctness.

In medical scenarios, effectively retrieving external knowledge and leveraging it for rigorous logical reasoning is of significant importance. Despite their potential, existing work has predominantly focused on enhancing either retrieval or reasoning capabilities of the models in isolation, with little attention given to their joint optimization, which leads to limited coordination between the two processes. Additionally, current methods rely heavily on supervised fine-tuning (SFT), which can cause models to memorize existing problem-solving pathways, thereby restricting their generalization ability when confronted with novel problem contexts. Furthermore, while some studies have explored to improve retrieval-augmented reasoning in general domains via reinforcement learning, their reward function designs do not adequately capture the specific demands of the medical domain. To address these challenges, we introduce **Med-R^3**, a **Med**ical **R**etrieval-augmented **R**easoning framework driven by progressive **R**einforcement learning. In this framework, we first develop the model's ability to perform logical reasoning over medical problems. Subsequently, on the basis of this foundation, we adaptively optimize the retrieval capability to better align with the characteristics of knowledge corpus and external information utilization throughout the reasoning process. Finally, we conduct joint optimization of the model's retrieval and reasoning coordination. Extensive experiments indicate that **Med-R^3** could achieve state-of-the-art performances, with LLaMA3.1-8B-Instruct + Med-R^3 surpassing closed-sourced GPT-4o-mini by 3.93\% at a comparable parameter scale, while Qwen2.5-14B augmented with Med-R^3 shows a more substantial gain of 13.53\%.

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.