Daily Papers

Despite the rapid progress of Multimodal Large Language Models (MLLMs), their ability to perform reliable visual grounding in high-stakes clinical software environments remains underexplored. Existing GUI benchmarks largely focus on isolated, single-step grounding queries, overlooking the sequential, workflow-driven reasoning required in real-world medical interfaces, where tasks evolve across independent steps and dynamic interface states. We introduce MedSPOT, a workflow-aware sequential grounding benchmark for clinical GUI environments. Unlike prior benchmarks that treat grounding as a standalone prediction task, MedSPOT models procedural interaction as a sequence of structured spatial decisions. The benchmark comprises 216 task-driven videos with 597 annotated keyframes, in which each task consists of 2 to 3 interdependent grounding steps within realistic medical workflows. This design captures interface hierarchies, contextual dependencies, and fine-grained spatial precision under evolving conditions. To evaluate procedural robustness, we propose a strict sequential evaluation protocol that terminates task assessment upon the first incorrect grounding prediction, explicitly measuring error propagation in multi-step workflows. We further introduce a comprehensive failure taxonomy, including edge bias, small-target errors, no prediction, near miss, far miss, and toolbar confusion, to enable systematic diagnosis of model behavior in clinical GUI settings. By shifting evaluation from isolated grounding to workflow-aware sequential reasoning, MedSPOT establishes a realistic and safety-critical benchmark for assessing multimodal models in medical software environments. Code and data are available at: https://github.com/Tajamul21/MedSPOT.

Medical care follows complex clinical pathways that extend beyond isolated physician-patient encounters, emphasizing decision-making and transitions between different stages. Current benchmarks focusing on static exams or isolated dialogues inadequately evaluate large language models (LLMs) in dynamic clinical scenarios. We introduce CP-Env, a controllable agentic hospital environment designed to evaluate LLMs across end-to-end clinical pathways. CP-Env simulates a hospital ecosystem with patient and physician agents, constructing scenarios ranging from triage and specialist consultation to diagnostic testing and multidisciplinary team meetings for agent interaction. Following real hospital adaptive flow of healthcare, it enables branching, long-horizon task execution. We propose a three-tiered evaluation framework encompassing Clinical Efficacy, Process Competency, and Professional Ethics. Results reveal that most models struggle with pathway complexity, exhibiting hallucinations and losing critical diagnostic details. Interestingly, excessive reasoning steps can sometimes prove counterproductive, while top models tend to exhibit reduced tool dependency through internalized knowledge. CP-Env advances medical AI agents development through comprehensive end-to-end clinical evaluation. We provide the benchmark and evaluation tools for further research and development at https://github.com/SPIRAL-MED/CP_ENV.

Recent large language models (LLMs) have demonstrated significant advancements, particularly in their ability to serve as agents thereby surpassing their traditional role as chatbots. These agents can leverage their planning and tool utilization capabilities to address tasks specified at a high level. However, a standardized dataset to benchmark the agent capabilities of LLMs in medical applications is currently lacking, making the evaluation of LLMs on complex tasks in interactive healthcare environments challenging. To address this gap, we introduce MedAgentBench, a broad evaluation suite designed to assess the agent capabilities of large language models within medical records contexts. MedAgentBench encompasses 300 patient-specific clinically-derived tasks from 10 categories written by human physicians, realistic profiles of 100 patients with over 700,000 data elements, a FHIR-compliant interactive environment, and an accompanying codebase. The environment uses the standard APIs and communication infrastructure used in modern EMR systems, so it can be easily migrated into live EMR systems. MedAgentBench presents an unsaturated agent-oriented benchmark that current state-of-the-art LLMs exhibit some ability to succeed at. The best model (Claude 3.5 Sonnet v2) achieves a success rate of 69.67%. However, there is still substantial space for improvement which gives the community a next direction to optimize. Furthermore, there is significant variation in performance across task categories. MedAgentBench establishes this and is publicly available at https://github.com/stanfordmlgroup/MedAgentBench , offering a valuable framework for model developers to track progress and drive continuous improvements in the agent capabilities of large language models within the medical domain.

Large language models (LLMs) integrated into agent-driven workflows hold immense promise for healthcare, yet a significant gap exists between their potential and practical implementation within clinical settings. To address this, we present a practitioner-oriented field manual for deploying generative agents that use electronic health record (EHR) data. This guide is informed by our experience deploying the "irAE-Agent", an automated system to detect immune-related adverse events from clinical notes at Mass General Brigham, and by structured interviews with 21 clinicians, engineers, and informatics leaders involved in the project. Our analysis reveals a critical misalignment in clinical AI development: less than 20% of our effort was dedicated to prompt engineering and model development, while over 80% was consumed by the sociotechnical work of implementation. We distill this effort into five "heavy lifts": data integration, model validation, ensuring economic value, managing system drift, and governance. By providing actionable solutions for each of these challenges, this field manual shifts the focus from algorithmic development to the essential infrastructure and implementation work required to bridge the "valley of death" and successfully translate generative AI from pilot projects into routine clinical care.

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the potential of advanced clinical trial tools that aggregate and predict based on the latest medical data, we propose an integrated solution to enhance their accessibility and utility. We introduce Clinical Agent System (ClinicalAgent), a clinical multi-agent system designed for clinical trial tasks, leveraging GPT-4, multi-agent architectures, LEAST-TO-MOST, and ReAct reasoning technology. This integration not only boosts LLM performance in clinical contexts but also introduces novel functionalities. The proposed method achieves competitive predictive performance in clinical trial outcome prediction (0.7908 PR-AUC), obtaining a 0.3326 improvement over the standard prompt Method. Publicly available code can be found at https://anonymous.4open.science/r/ClinicalAgent-6671.

Hospital information systems (HIS) have become an essential part of healthcare institutions and now incorporate prescribing support software. Prescription support software allows for structured information capture, which improves the safety, appropriateness and efficiency of prescriptions and reduces the number of adverse drug events (ADEs). However, such a system increases the amount of time physicians spend at a computer entering information instead of providing medical care. In addition, any new visiting clinician must learn to manage complex interfaces since each HIS has its own interfaces. In this paper, we present a natural language interface for e-prescribing software in the form of a spoken dialogue system accessible on a smartphone. This system allows prescribers to record their prescriptions verbally, a form of interaction closer to their usual practice. The system extracts the formal representation of the prescription ready to be checked by the prescribing software and uses the dialogue to request mandatory information, correct errors or warn of particular situations. Since, to the best of our knowledge, there is no existing voice-based prescription dialogue system, we present the system developed in a low-resource environment, focusing on dialogue modeling, semantic extraction and data augmentation. The system was evaluated in the wild with 55 participants. This evaluation showed that our system has an average prescription time of 66.15 seconds for physicians and 35.64 seconds for other experts, and a task success rate of 76\% for physicians and 72\% for other experts. All evaluation data were recorded and annotated to form PxCorpus, the first spoken drug prescription corpus that has been made fully available to the community (https://doi.org/10.5281/zenodo.6524162).

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

Real-world clinical text-to-SQL requires reasoning over heterogeneous EHR tables, temporal windows, and patient-similarity cohorts to produce executable queries. We introduce CLINSQL, a benchmark of 633 expert-annotated tasks on MIMIC-IV v3.1 that demands multi-table joins, clinically meaningful filters, and executable SQL. Solving CLINSQL entails navigating schema metadata and clinical coding systems, handling long contexts, and composing multi-step queries beyond traditional text-to-SQL. We evaluate 22 proprietary and open-source models under Chain-of-Thought self-refinement and use rubric-based SQL analysis with execution checks that prioritize critical clinical requirements. Despite recent advances, performance remains far from clinical reliability: on the test set, GPT-5-mini attains 74.7% execution score, DeepSeek-R1 leads open-source at 69.2% and Gemini-2.5-Pro drops from 85.5% on Easy to 67.2% on Hard. Progress on CLINSQL marks tangible advances toward clinically reliable text-to-SQL for real-world EHR analytics.

We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We address a critical problem of structuring clinical notes into clinical data, according to international interoperability standards. We collect and annotate data for three subtasks, namely, international patient summary, clinical impression and medical encounter. We then supervised fine-tuned a state-of-the-art LLM using public and credentialed clinical data. The training is orchestrated in a way that the target model can first support basic clinical tasks such as abbreviation expansion and temporal information extraction, and then learn to perform more complex downstream clinical tasks. Moreover, we address several modeling challenges in the healthcare context, e.g., extra long context window. Our blind pairwise evaluation shows that SoftTiger outperforms other popular open-source models and GPT-3.5, comparable to Gemini-pro, with a mild gap from GPT-4. We believe that LLMs may become a step-stone towards healthcare digitalization and democratization. Therefore, we publicly release SoftTiger models at scales of 13 billion and 70 billion parameters, as well as datasets and code for our innovative scalable evaluation, hopefully, making a significant contribution to the healthcare industry.

The increasing use of tools and solutions based on Large Language Models (LLMs) for various tasks in the medical domain has become a prominent trend. Their use in this highly critical and sensitive domain has thus raised important questions about their robustness, especially in response to variations in input, and the reliability of the generated outputs. This study addresses these questions by constructing a textual dataset based on the ICD-10-CM code descriptions, widely used in US hospitals and containing many clinical terms, and their easily reproducible rephrasing. We then benchmarked existing embedding models, either generalist or specialized in the clinical domain, in a semantic search task where the goal was to correctly match the rephrased text to the original description. Our results showed that generalist models performed better than clinical models, suggesting that existing clinical specialized models are more sensitive to small changes in input that confuse them. The highlighted problem of specialized models may be due to the fact that they have not been trained on sufficient data, and in particular on datasets that are not diverse enough to have a reliable global language understanding, which is still necessary for accurate handling of medical documents.

Current medical language models, adapted from large language models (LLMs), typically predict ICD code-based diagnosis from electronic health records (EHRs) because these labels are readily available. However, ICD codes do not capture the nuanced, context-rich reasoning clinicians use for diagnosis. Clinicians synthesize diverse patient data and reference clinical practice guidelines (CPGs) to make evidence-based decisions. This misalignment limits the clinical utility of existing models. We introduce GARMLE-G, a Generation-Augmented Retrieval framework that grounds medical language model outputs in authoritative CPGs. Unlike conventional Retrieval-Augmented Generation based approaches, GARMLE-G enables hallucination-free outputs by directly retrieving authoritative guideline content without relying on model-generated text. It (1) integrates LLM predictions with EHR data to create semantically rich queries, (2) retrieves relevant CPG knowledge snippets via embedding similarity, and (3) fuses guideline content with model output to generate clinically aligned recommendations. A prototype system for hypertension diagnosis was developed and evaluated on multiple metrics, demonstrating superior retrieval precision, semantic relevance, and clinical guideline adherence compared to RAG-based baselines, while maintaining a lightweight architecture suitable for localized healthcare deployment. This work provides a scalable, low-cost, and hallucination-free method for grounding medical language models in evidence-based clinical practice, with strong potential for broader clinical deployment.

The deployment of Large Language Models (LLMs) in high-stakes clinical settings demands rigorous and reliable evaluation. However, existing medical benchmarks remain static, suffering from two critical limitations: (1) data contamination, where test sets inadvertently leak into training corpora, leading to inflated performance estimates; and (2) temporal misalignment, failing to capture the rapid evolution of medical knowledge. Furthermore, current evaluation metrics for open-ended clinical reasoning often rely on either shallow lexical overlap (e.g., ROUGE) or subjective LLM-as-a-Judge scoring, both inadequate for verifying clinical correctness. To bridge these gaps, we introduce LiveMedBench, a continuously updated, contamination-free, and rubric-based benchmark that weekly harvests real-world clinical cases from online medical communities, ensuring strict temporal separation from model training data. We propose a Multi-Agent Clinical Curation Framework that filters raw data noise and validates clinical integrity against evidence-based medical principles. For evaluation, we develop an Automated Rubric-based Evaluation Framework that decomposes physician responses into granular, case-specific criteria, achieving substantially stronger alignment with expert physicians than LLM-as-a-Judge. To date, LiveMedBench comprises 2,756 real-world cases spanning 38 medical specialties and multiple languages, paired with 16,702 unique evaluation criteria. Extensive evaluation of 38 LLMs reveals that even the best-performing model achieves only 39.2%, and 84% of models exhibit performance degradation on post-cutoff cases, confirming pervasive data contamination risks. Error analysis further identifies contextual application-not factual knowledge-as the dominant bottleneck, with 35-48% of failures stemming from the inability to tailor medical knowledge to patient-specific constraints.

Recent advances in medical large language models (LLMs), multimodal models, and agents demand evaluation frameworks that reflect real clinical workflows and safety constraints. We present MedBench v4, a nationwide, cloud-based benchmarking infrastructure comprising over 700,000 expert-curated tasks spanning 24 primary and 91 secondary specialties, with dedicated tracks for LLMs, multimodal models, and agents. Items undergo multi-stage refinement and multi-round review by clinicians from more than 500 institutions, and open-ended responses are scored by an LLM-as-a-judge calibrated to human ratings. We evaluate 15 frontier models. Base LLMs reach a mean overall score of 54.1/100 (best: Claude Sonnet 4.5, 62.5/100), but safety and ethics remain low (18.4/100). Multimodal models perform worse overall (mean 47.5/100; best: GPT-5, 54.9/100), with solid perception yet weaker cross-modal reasoning. Agents built on the same backbones substantially improve end-to-end performance (mean 79.8/100), with Claude Sonnet 4.5-based agents achieving up to 85.3/100 overall and 88.9/100 on safety tasks. MedBench v4 thus reveals persisting gaps in multimodal reasoning and safety for base models, while showing that governance-aware agentic orchestration can markedly enhance benchmarked clinical readiness without sacrificing capability. By aligning tasks with Chinese clinical guidelines and regulatory priorities, the platform offers a practical reference for hospitals, developers, and policymakers auditing medical AI.

VR simulation in Health Professions (HP) education demonstrates huge potential, but fixed learning content with little customization limits its application beyond lab environments. To address these limitations in the context of VR for patient communication training, we conducted a user-centered study involving semi-structured interviews with advanced HP students to understand their challenges in clinical communication training and perceptions of VR-based solutions. From this, we derived design insights emphasizing the importance of realistic scenarios, simple interactions, and unpredictable dialogues. Building on these insights, we developed the Virtual AI Patient Simulator (VAPS), a novel VR system powered by Large Language Models (LLMs) and Embodied Conversational Agents (ECAs), supporting dynamic and customizable patient interactions for immersive learning. We also provided an example of how clinical professors could use user-friendly design forms to create personalized scenarios that align with course objectives in VAPS and discuss future implications of integrating AI-driven technologies into VR education.

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.

The utilization of large language models (LLMs) in the Healthcare domain has generated both excitement and concern due to their ability to effectively respond to freetext queries with certain professional knowledge. This survey outlines the capabilities of the currently developed LLMs for Healthcare and explicates their development process, with the aim of providing an overview of the development roadmap from traditional Pretrained Language Models (PLMs) to LLMs. Specifically, we first explore the potential of LLMs to enhance the efficiency and effectiveness of various Healthcare applications highlighting both the strengths and limitations. Secondly, we conduct a comparison between the previous PLMs and the latest LLMs, as well as comparing various LLMs with each other. Then we summarize related Healthcare training data, training methods, optimization strategies, and usage. Finally, the unique concerns associated with deploying LLMs in Healthcare settings are investigated, particularly regarding fairness, accountability, transparency and ethics. Our survey provide a comprehensive investigation from perspectives of both computer science and Healthcare specialty. Besides the discussion about Healthcare concerns, we supports the computer science community by compiling a collection of open source resources, such as accessible datasets, the latest methodologies, code implementations, and evaluation benchmarks in the Github. Summarily, we contend that a significant paradigm shift is underway, transitioning from PLMs to LLMs. This shift encompasses a move from discriminative AI approaches to generative AI approaches, as well as a shift from model-centered methodologies to datacentered methodologies.

Doctor-patient consultations require multi-turn, context-aware communication tailored to diverse patient personas. Training or evaluating doctor LLMs in such settings requires realistic patient interaction systems. However, existing simulators often fail to reflect the full range of personas seen in clinical practice. To address this, we introduce PatientSim, a patient simulator that generates realistic and diverse patient personas for clinical scenarios, grounded in medical expertise. PatientSim operates using: 1) clinical profiles, including symptoms and medical history, derived from real-world data in the MIMIC-ED and MIMIC-IV datasets, and 2) personas defined by four axes: personality, language proficiency, medical history recall level, and cognitive confusion level, resulting in 37 unique combinations. We evaluated eight LLMs for factual accuracy and persona consistency. The top-performing open-source model, Llama 3.3, was validated by four clinicians to confirm the robustness of our framework. As an open-source, customizable platform, PatientSim provides a reproducible and scalable solution that can be customized for specific training needs. Offering a privacy-compliant environment, it serves as a robust testbed for evaluating medical dialogue systems across diverse patient presentations and shows promise as an educational tool for healthcare.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

Specialized clinical AI assistants are rapidly entering medical practice, often framed as safer or more reliable than general-purpose large language models (LLMs). Yet, unlike frontier models, these clinical tools are rarely subjected to independent, quantitative evaluation, creating a critical evidence gap despite their growing influence on diagnosis, triage, and guideline interpretation. We assessed two widely deployed clinical AI systems (OpenEvidence and UpToDate Expert AI) against three state-of-the-art generalist LLMs (GPT-5, Gemini 3 Pro, and Claude Sonnet 4.5) using a 1,000-item mini-benchmark combining MedQA (medical knowledge) and HealthBench (clinician-alignment) tasks. Generalist models consistently outperformed clinical tools, with GPT-5 achieving the highest scores, while OpenEvidence and UpToDate demonstrated deficits in completeness, communication quality, context awareness, and systems-based safety reasoning. These findings reveal that tools marketed for clinical decision support may often lag behind frontier LLMs, underscoring the urgent need for transparent, independent evaluation before deployment in patient-facing workflows.

Clinicians spend large amounts of time on clinical documentation, and inefficiencies impact quality of care and increase clinician burnout. Despite the promise of electronic medical records (EMR), the transition from paper-based records has been negatively associated with clinician wellness, in part due to poor user experience, increased burden of documentation, and alert fatigue. In this study, we present Almanac Copilot, an autonomous agent capable of assisting clinicians with EMR-specific tasks such as information retrieval and order placement. On EHR-QA, a synthetic evaluation dataset of 300 common EHR queries based on real patient data, Almanac Copilot obtains a successful task completion rate of 74% (n = 221 tasks) with a mean score of 2.45 over 3 (95% CI:2.34-2.56). By automating routine tasks and streamlining the documentation process, our findings highlight the significant potential of autonomous agents to mitigate the cognitive load imposed on clinicians by current EMR systems.

Large Language Models (LLMs) present immense potential in the medical field, yet concerns over data privacy, regulatory compliance, and model stability restrict their widespread adoption. Although the distillation of high-performing closed-source LLMs has proven effective for general tasks, their application in healthcare is limited due to reduced domain knowledge and remnants of alignment behavior hindering clinical tasks. To address these challenges, we propose Dialogue-Based Knowledge Encoding (DBKE). DBKE enhances models' implicit knowledge base and primes them for conversational recall, augmenting their conversational capabilities and enabling a soft alignment for subsequent use cases. By transforming dense academic source text into synthetic dialogue, DBKE broadens the model's knowledge base and enables a soft alignment that guides downstream behaviours. We present Clinical Camel, an open-source, healthcare-focused conversational model, to showcase the effectiveness of DBKE. Clinical Camel outperforms GPT-3.5 on the United States Medical Licensing Examination (USMLE) Step 1 and Step 3 with scores of 53.2 % and 58.2 %, respectively, compared to GPT-3.5's scores of 36.1 % and 55.7 %. Clinical Camel adeptly handles multi-stage clinical case problems, provides adaptive counseling, and generates clinical notes. However, it is prone to hallucinations, which pose a significant obstacle in safety-critical settings. The performance of Clinical Camel underscores the importance of continued research and development of open-source models for the safe and effective integration of LLMs in healthcare settings.

With the growing use of language models (LMs) in clinical environments, there is an immediate need to evaluate the accuracy and safety of LM-generated medical text. Currently, such evaluation relies solely on manual physician review. However, detecting errors in LM-generated text is challenging because 1) manual review is costly and 2) expert-composed reference outputs are often unavailable in real-world settings. While the "LM-as-judge" paradigm (a LM evaluating another LM) offers scalable evaluation, even frontier LMs can miss subtle but clinically significant errors. To address these challenges, we propose MedVAL, a self-supervised framework that leverages synthetic data to train evaluator LMs to assess whether LM-generated medical outputs are factually consistent with inputs, without requiring physician labels or reference outputs. To evaluate LM performance, we introduce MedVAL-Bench, a dataset containing 840 outputs annotated by physicians, following a physician-defined taxonomy of risk levels and error categories. Across 6 diverse medical tasks and 10 state-of-the-art LMs spanning open-source, proprietary, and medically adapted models, MedVAL fine-tuning significantly improves (p < 0.001) alignment with physicians on both seen and unseen tasks, increasing average F1 scores from 66% to 83%, with per-sample safety classification scores up to 86%. MedVAL improves the performance of even the best-performing proprietary LM (GPT-4o) by 8%. To support a scalable, risk-aware pathway towards clinical integration, we open-source the 1) codebase ( https://github.com/StanfordMIMI/MedVAL ), 2) MedVAL-Bench ( https://huggingface.co/datasets/stanfordmimi/MedVAL-Bench ), and 3) MedVAL-4B ( https://huggingface.co/stanfordmimi/MedVAL-4B ), the best-performing open-source LM. Our research provides the first evidence of LMs approaching expert-level validation ability for medical text.

We present ICU-Sepsis, an environment that can be used in benchmarks for evaluating reinforcement learning (RL) algorithms. Sepsis management is a complex task that has been an important topic in applied RL research in recent years. Therefore, MDPs that model sepsis management can serve as part of a benchmark to evaluate RL algorithms on a challenging real-world problem. However, creating usable MDPs that simulate sepsis care in the ICU remains a challenge due to the complexities involved in acquiring and processing patient data. ICU-Sepsis is a lightweight environment that models personalized care of sepsis patients in the ICU. The environment is a tabular MDP that is widely compatible and is challenging even for state-of-the-art RL algorithms, making it a valuable tool for benchmarking their performance. However, we emphasize that while ICU-Sepsis provides a standardized environment for evaluating RL algorithms, it should not be used to draw conclusions that guide medical practice.

The proliferation of Large Language Models (LLMs) presents transformative potential for healthcare, yet practical deployment is hindered by the absence of frameworks that assess real-world clinical utility. Existing benchmarks test static knowledge, failing to capture the dynamic, application-oriented capabilities required in clinical practice. To bridge this gap, we introduce a Medical LLM Benchmark MLB, a comprehensive benchmark evaluating LLMs on both foundational knowledge and scenario-based reasoning. MLB is structured around five core dimensions: Medical Knowledge (MedKQA), Safety and Ethics (MedSE), Medical Record Understanding (MedRU), Smart Services (SmartServ), and Smart Healthcare (SmartCare). The benchmark integrates 22 datasets (17 newly curated) from diverse Chinese clinical sources, covering 64 clinical specialties. Its design features a rigorous curation pipeline involving 300 licensed physicians. Besides, we provide a scalable evaluation methodology, centered on a specialized judge model trained via Supervised Fine-Tuning (SFT) on expert annotations. Our comprehensive evaluation of 10 leading models reveals a critical translational gap: while the top-ranked model, Kimi-K2-Instruct (77.3% accuracy overall), excels in structured tasks like information extraction (87.8% accuracy in MedRU), performance plummets in patient-facing scenarios (61.3% in SmartServ). Moreover, the exceptional safety score (90.6% in MedSE) of the much smaller Baichuan-M2-32B highlights that targeted training is equally critical. Our specialized judge model, trained via SFT on a 19k expert-annotated medical dataset, achieves 92.1% accuracy, an F1-score of 94.37%, and a Cohen's Kappa of 81.3% for human-AI consistency, validating a reproducible and expert-aligned evaluation protocol. MLB thus provides a rigorous framework to guide the development of clinically viable LLMs.

Large language models (LLMs) have the potential to transform medicine, but real-world clinical scenarios contain extraneous information that can hinder performance. The rise of assistive technologies like ambient dictation, which automatically generates draft notes from live patient encounters, has the potential to introduce additional noise making it crucial to assess the ability of LLM's to filter relevant data. To investigate this, we developed MedDistractQA, a benchmark using USMLE-style questions embedded with simulated real-world distractions. Our findings show that distracting statements (polysemous words with clinical meanings used in a non-clinical context or references to unrelated health conditions) can reduce LLM accuracy by up to 17.9%. Commonly proposed solutions to improve model performance such as retrieval-augmented generation (RAG) and medical fine-tuning did not change this effect and in some cases introduced their own confounders and further degraded performance. Our findings suggest that LLMs natively lack the logical mechanisms necessary to distinguish relevant from irrelevant clinical information, posing challenges for real-world applications. MedDistractQA and our results highlights the need for robust mitigation strategies to enhance LLM resilience to extraneous information.

Clinical question answering over electronic health records (EHRs) can help clinicians and patients access relevant medical information more efficiently. However, many recent approaches rely on large cloud-based models, which are difficult to deploy in clinical environments due to privacy constraints and computational requirements. In this work, we investigate how far grounded EHR question answering can be pushed when restricted to a single notebook. We participate in all four subtasks of the ArchEHR-QA 2026 shared task and evaluate several approaches designed to run on commodity hardware. All experiments are conducted locally without external APIs or cloud infrastructure. Our results show that such systems can achieve competitive performance on the shared task leaderboards. In particular, our submissions perform above average in two subtasks, and we observe that smaller models can approach the performance of much larger systems when properly configured. These findings suggest that privacy-preserving EHR QA systems running fully locally are feasible with current models and commodity hardware. The source code is available at https://github.com/ibrahimey/ArchEHR-QA-2026.

Data science plays a critical role in clinical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing well in general coding tests. However, these tests do not assess LLMs' ability to handle data science tasks in medicine, nor do they explore their practical utility in clinical research. To address this, we developed a dataset consisting of 293 real-world data science coding tasks, based on 39 published clinical studies, covering 128 tasks in Python and 165 tasks in R. This dataset simulates realistic clinical research scenarios using patient data. Our findings reveal that cutting-edge LLMs struggle to generate perfect solutions, frequently failing to follow input instructions, understand target data, and adhere to standard analysis practices. Consequently, LLMs are not yet ready to fully automate data science tasks. We benchmarked advanced adaptation methods and found two to be particularly effective: chain-of-thought prompting, which provides a step-by-step plan for data analysis, which led to a 60% improvement in code accuracy; and self-reflection, enabling LLMs to iteratively refine their code, yielding a 38% accuracy improvement. Building on these insights, we developed a platform that integrates LLMs into the data science workflow for medical professionals. In a user study with five medical doctors, we found that while LLMs cannot fully automate coding tasks, they significantly streamline the programming process. We found that 80% of their submitted code solutions were incorporated from LLM-generated code, with up to 96% reuse in some cases. Our analysis highlights the potential of LLMs, when integrated into expert workflows, to enhance data science efficiency in clinical research.

Clinical dialogue represents a complex duality requiring both the empathetic fluency of natural conversation and the rigorous precision of evidence-based medicine. While Large Language Models possess unprecedented linguistic capabilities, their architectural reliance on reactive and stateless processing often favors probabilistic plausibility over factual veracity. This structural limitation has catalyzed a paradigm shift in medical AI from generative text prediction to agentic autonomy, where the model functions as a central reasoning engine capable of deliberate planning and persistent memory. Moving beyond existing reviews that primarily catalog downstream applications, this survey provides a first-principles analysis of the cognitive architecture underpinning this shift. We introduce a novel taxonomy structured along the orthogonal axes of knowledge source and agency objective to delineate the provenance of clinical knowledge against the system's operational scope. This framework facilitates a systematic analysis of the intrinsic trade-offs between creativity and reliability by categorizing methods into four archetypes: Latent Space Clinicians, Emergent Planners, Grounded Synthesizers, and Verifiable Workflow Automators. For each paradigm, we deconstruct the technical realization across the entire cognitive pipeline, encompassing strategic planning, memory management, action execution, collaboration, and evolution to reveal how distinct architectural choices balance the tension between autonomy and safety.

Synthetic Data Generation (SDG) based on Artificial Intelligence (AI) can transform the way clinical medicine is delivered by overcoming privacy barriers that currently render clinical data sharing difficult. This is the key to accelerating the development of digital tools contributing to enhanced patient safety. Such tools include robust data-driven clinical decision support systems, and example-based digital training tools that will enable healthcare professionals to improve their diagnostic performance for enhanced patient safety. This study focuses on the clinical evaluation of medical SDG, with a proof-of-concept investigation on diagnosing Inflammatory Bowel Disease (IBD) using Wireless Capsule Endoscopy (WCE) images. Its scientific contributions include a) a novel protocol for the systematic Clinical Evaluation of Medical Image Synthesis (CEMIS); b) a novel variational autoencoder-based model for the generation of high-resolution synthetic WCE images; and c) a comprehensive evaluation of the synthetic images using the CEMIS protocol by 10 international WCE specialists, in terms of image quality, diversity, and realism, as well as their utility for clinical decision-making. The results show that TIDE-II generates clinically plausible, very realistic WCE images, of improved quality compared to relevant state-of-the-art generative models. Concludingly, CEMIS can serve as a reference for future research on medical image-generation techniques, while the adaptation/extension of the architecture of TIDE-II to other imaging domains can be promising.

Operating rooms (ORs) are complex, high-stakes environments requiring precise understanding of interactions among medical staff, tools, and equipment for enhancing surgical assistance, situational awareness, and patient safety. Current datasets fall short in scale, realism and do not capture the multimodal nature of OR scenes, limiting progress in OR modeling. To this end, we introduce MM-OR, a realistic and large-scale multimodal spatiotemporal OR dataset, and the first dataset to enable multimodal scene graph generation. MM-OR captures comprehensive OR scenes containing RGB-D data, detail views, audio, speech transcripts, robotic logs, and tracking data and is annotated with panoptic segmentations, semantic scene graphs, and downstream task labels. Further, we propose MM2SG, the first multimodal large vision-language model for scene graph generation, and through extensive experiments, demonstrate its ability to effectively leverage multimodal inputs. Together, MM-OR and MM2SG establish a new benchmark for holistic OR understanding, and open the path towards multimodal scene analysis in complex, high-stakes environments. Our code, and data is available at https://github.com/egeozsoy/MM-OR.

Large Language Models (LLMs) hold great promise to revolutionize current clinical systems for their superior capacities on medical text processing tasks and medical licensing exams. Meanwhile, traditional ML models such as SVM and XGBoost have still been mainly adopted in clinical prediction tasks. An emerging question is Can LLMs beat traditional ML models in clinical prediction? Thus, we build a new benchmark ClinicalBench to comprehensively study the clinical predictive modeling capacities of both general-purpose and medical LLMs, and compare them with traditional ML models. ClinicalBench embraces three common clinical prediction tasks, two databases, 14 general-purpose LLMs, 8 medical LLMs, and 11 traditional ML models. Through extensive empirical investigation, we discover that both general-purpose and medical LLMs, even with different model scales, diverse prompting or fine-tuning strategies, still cannot beat traditional ML models in clinical prediction yet, shedding light on their potential deficiency in clinical reasoning and decision-making. We call for caution when practitioners adopt LLMs in clinical applications. ClinicalBench can be utilized to bridge the gap between LLMs' development for healthcare and real-world clinical practice.

Numerous medical systems powered by Large Language Models (LLMs) have achieved remarkable progress in diverse healthcare tasks. However, research on their medication safety remains limited due to the lack of real world datasets, constrained by privacy and accessibility issues. Moreover, evaluation of LLMs in realistic clinical consultation settings, particularly regarding medication safety, is still underexplored. To address these gaps, we propose a framework that simulates and evaluates clinical consultations to systematically assess the medication safety capabilities of LLMs. Within this framework, we generate inquiry diagnosis dialogues with embedded medication risks and construct a dedicated medication safety database, RxRisk DB, containing 6,725 contraindications, 28,781 drug interactions, and 14,906 indication-drug pairs. A two-stage filtering strategy ensures clinical realism and professional quality, resulting in the benchmark RxSafeBench with 2,443 high-quality consultation scenarios. We evaluate leading open-source and proprietary LLMs using structured multiple choice questions that test their ability to recommend safe medications under simulated patient contexts. Results show that current LLMs struggle to integrate contraindication and interaction knowledge, especially when risks are implied rather than explicit. Our findings highlight key challenges in ensuring medication safety in LLM-based systems and provide insights into improving reliability through better prompting and task-specific tuning. RxSafeBench offers the first comprehensive benchmark for evaluating medication safety in LLMs, advancing safer and more trustworthy AI-driven clinical decision support.

Large language models (LLMs) hold great promise for assisting clinical interviews due to their fluent interactive capabilities and extensive medical knowledge. However, the lack of high-quality interview dialogue data and widely accepted evaluation methods has significantly impeded this process. So we propose CliniChat, a framework that integrates multi-source knowledge to enable LLMs to simulate real-world clinical interviews. It consists of two modules: Clini-Recon and Clini-Eval, each responsible for reconstructing and evaluating interview dialogues, respectively. By incorporating three sources of knowledge, Clini-Recon transforms clinical notes into systematic, professional, and empathetic interview dialogues. Clini-Eval combines a comprehensive evaluation metric system with a two-phase automatic evaluation approach, enabling LLMs to assess interview performance like experts. We contribute MedQA-Dialog, a high-quality synthetic interview dialogue dataset, and CliniChatGLM, a model specialized for clinical interviews. Experimental results demonstrate that CliniChatGLM's interview capabilities undergo a comprehensive upgrade, particularly in history-taking, achieving state-of-the-art performance.

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.

Diagnosing and managing a patient is a complex, sequential decision making process that requires physicians to obtain information -- such as which tests to perform -- and to act upon it. Recent advances in artificial intelligence (AI) and large language models (LLMs) promise to profoundly impact clinical care. However, current evaluation schemes overrely on static medical question-answering benchmarks, falling short on interactive decision-making that is required in real-life clinical work. Here, we present AgentClinic: a multimodal benchmark to evaluate LLMs in their ability to operate as agents in simulated clinical environments. In our benchmark, the doctor agent must uncover the patient's diagnosis through dialogue and active data collection. We present two open medical agent benchmarks: a multimodal image and dialogue environment, AgentClinic-NEJM, and a dialogue-only environment, AgentClinic-MedQA. We embed cognitive and implicit biases both in patient and doctor agents to emulate realistic interactions between biased agents. We find that introducing bias leads to large reductions in diagnostic accuracy of the doctor agents, as well as reduced compliance, confidence, and follow-up consultation willingness in patient agents. Evaluating a suite of state-of-the-art LLMs, we find that several models that excel in benchmarks like MedQA are performing poorly in AgentClinic-MedQA. We find that the LLM used in the patient agent is an important factor for performance in the AgentClinic benchmark. We show that both having limited interactions as well as too many interaction reduces diagnostic accuracy in doctor agents. The code and data for this work is publicly available at https://AgentClinic.github.io.

In this work, we introduce MedAgentSim, an open-source simulated clinical environment with doctor, patient, and measurement agents designed to evaluate and enhance LLM performance in dynamic diagnostic settings. Unlike prior approaches, our framework requires doctor agents to actively engage with patients through multi-turn conversations, requesting relevant medical examinations (e.g., temperature, blood pressure, ECG) and imaging results (e.g., MRI, X-ray) from a measurement agent to mimic the real-world diagnostic process. Additionally, we incorporate self improvement mechanisms that allow models to iteratively refine their diagnostic strategies. We enhance LLM performance in our simulated setting by integrating multi-agent discussions, chain-of-thought reasoning, and experience-based knowledge retrieval, facilitating progressive learning as doctor agents interact with more patients. We also introduce an evaluation benchmark for assessing the LLM's ability to engage in dynamic, context-aware diagnostic interactions. While MedAgentSim is fully automated, it also supports a user-controlled mode, enabling human interaction with either the doctor or patient agent. Comprehensive evaluations in various simulated diagnostic scenarios demonstrate the effectiveness of our approach. Our code, simulation tool, and benchmark are available at https://medagentsim.netlify.app/.

The integration of Computer-Assisted Diagnosis (CAD) with Large Language Models (LLMs) holds great potential in clinical applications, specifically in the roles of virtual family doctors and clinic assistants. However, current works in this field are plagued by limitations, specifically a restricted scope of applicable image domains and the provision of unreliable medical advice. This restricts their overall processing capabilities. Furthermore, the mismatch in writing style between LLMs and radiologists undermines their practical usefulness. To tackle these challenges, we introduce ChatCAD+, which is designed to be universal and reliable. It is capable of handling medical images from diverse domains and leveraging up-to-date information from reputable medical websites to provide reliable medical advice. Additionally, it incorporates a template retrieval system that improves report generation performance via exemplar reports. This approach ensures greater consistency with the expertise of human professionals. The source code is available at https://github.com/zhaozh10/ChatCAD.

Objectives: While Large Language Models (LLMs) have been widely used to assist clinicians and support patients, no existing work has explored dialogue systems for standard diagnostic interviews and assessments. This study aims to bridge the gap in mental healthcare accessibility by developing an LLM-powered dialogue system that replicates clinician behavior. Materials and Methods: We introduce TRUST, a framework of cooperative LLM modules capable of conducting formal diagnostic interviews and assessments for Post-Traumatic Stress Disorder (PTSD). To guide the generation of appropriate clinical responses, we propose a Dialogue Acts schema specifically designed for clinical interviews. Additionally, we develop a patient simulation approach based on real-life interview transcripts to replace time-consuming and costly manual testing by clinicians. Results: A comprehensive set of evaluation metrics is designed to assess the dialogue system from both the agent and patient simulation perspectives. Expert evaluations by conversation and clinical specialists show that TRUST performs comparably to real-life clinical interviews. Discussion: Our system performs at the level of average clinicians, with room for future enhancements in communication styles and response appropriateness. Conclusions: Our TRUST framework shows its potential to facilitate mental healthcare availability.

Medical calculators are fundamental to quantitative, evidence-based clinical practice. However, their real-world use is an adaptive, multi-stage process, requiring proactive EHR data acquisition, scenario-dependent calculator selection, and multi-step computation, whereas current benchmarks focus only on static single-step calculations with explicit instructions. To address these limitations, we introduce MedMCP-Calc, the first benchmark for evaluating LLMs in realistic medical calculator scenarios through Model Context Protocol (MCP) integration. MedMCP-Calc comprises 118 scenario tasks across 4 clinical domains, featuring fuzzy task descriptions mimicking natural queries, structured EHR database interaction, external reference retrieval, and process-level evaluation. Our evaluation of 23 leading models reveals critical limitations: even top performers like Claude Opus 4.5 exhibit substantial gaps, including difficulty selecting appropriate calculators for end-to-end workflows given fuzzy queries, poor performance in iterative SQL-based database interactions, and marked reluctance to leverage external tools for numerical computation. Performance also varies considerably across clinical domains. Building on these findings, we develop CalcMate, a fine-tuned model incorporating scenario planning and tool augmentation, achieving state-of-the-art performance among open-source models. Benchmark and Codes are available in https://github.com/SPIRAL-MED/MedMCP-Calc.

Integrating language models (LMs) in healthcare systems holds great promise for improving medical workflows and decision-making. However, a critical barrier to their real-world adoption is the lack of reliable evaluation of their trustworthiness, especially in multilingual healthcare settings. Existing LMs are predominantly trained in high-resource languages, making them ill-equipped to handle the complexity and diversity of healthcare queries in mid- and low-resource languages, posing significant challenges for deploying them in global healthcare contexts where linguistic diversity is key. In this work, we present CLINIC, a Comprehensive Multilingual Benchmark to evaluate the trustworthiness of language models in healthcare. CLINIC systematically benchmarks LMs across five key dimensions of trustworthiness: truthfulness, fairness, safety, robustness, and privacy, operationalized through 18 diverse tasks, spanning 15 languages (covering all the major continents), and encompassing a wide array of critical healthcare topics like disease conditions, preventive actions, diagnostic tests, treatments, surgeries, and medications. Our extensive evaluation reveals that LMs struggle with factual correctness, demonstrate bias across demographic and linguistic groups, and are susceptible to privacy breaches and adversarial attacks. By highlighting these shortcomings, CLINIC lays the foundation for enhancing the global reach and safety of LMs in healthcare across diverse languages.

Currently, evaluating vision-language models (VLMs) in medical imaging tasks oversimplifies clinical reality by relying on pre-selected 2D images that demand significant manual labor to curate. This setup misses the core challenge of realworld diagnostics: a true clinical agent must actively navigate full 3D volumes across multiple sequences or modalities to gather evidence and ultimately support a final decision. To address this, we propose MEDOPENCLAW, an auditable runtime designed to let VLMs operate dynamically within standard medical tools or viewers (e.g., 3D Slicer). On top of this runtime, we introduce MEDFLOWBENCH, a full-study medical imaging benchmark covering multi-sequence brain MRI and lung CT/PET. It systematically evaluates medical agentic capabilities across viewer-only, tool-use, and open-method tracks. Initial results reveal a critical insight: while state-of-the-art LLMs/VLMs (e.g., Gemini 3.1 Pro and GPT-5.4) can successfully navigate the viewer to solve basic study-level tasks, their performance paradoxically degrades when given access to professional support tools due to a lack of precise spatial grounding. By bridging the gap between static-image perception and interactive clinical workflows, MEDOPENCLAW and MEDFLOWBENCH establish a reproducible foundation for developing auditable, full-study medical imaging agents.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

As the performance of large language models (LLMs) continues to advance, their adoption is expanding across a wide range of domains, including the medical field. The integration of LLMs into medical applications raises critical safety concerns, particularly due to their use by users with diverse roles, e.g. patients and clinicians, and the potential for model's outputs to directly affect human health. Despite the domain-specific capabilities of medical LLMs, prior safety evaluations have largely focused only on general safety benchmarks. In this paper, we introduce a safety evaluation protocol tailored to the medical domain in both patient user and clinician user perspectives, alongside general safety assessments and quantitatively analyze the safety of medical LLMs. We bridge a gap in the literature by building the PatientSafetyBench containing 466 samples over 5 critical categories to measure safety from the perspective of the patient. We apply our red-teaming protocols on the MediPhi model collection as a case study. To our knowledge, this is the first work to define safety evaluation criteria for medical LLMs through targeted red-teaming taking three different points of view - patient, clinician, and general user - establishing a foundation for safer deployment in medical domains.

In response to the pressing need for advanced clinical problem-solving tools in healthcare, we introduce BooksMed, a novel framework based on a Large Language Model (LLM). BooksMed uniquely emulates human cognitive processes to deliver evidence-based and reliable responses, utilizing the GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) framework to effectively quantify evidence strength. For clinical decision-making to be appropriately assessed, an evaluation metric that is clinically aligned and validated is required. As a solution, we present ExpertMedQA, a multispecialty clinical benchmark comprised of open-ended, expert-level clinical questions, and validated by a diverse group of medical professionals. By demanding an in-depth understanding and critical appraisal of up-to-date clinical literature, ExpertMedQA rigorously evaluates LLM performance. BooksMed outperforms existing state-of-the-art models Med-PaLM 2, Almanac, and ChatGPT in a variety of medical scenarios. Therefore, a framework that mimics human cognitive stages could be a useful tool for providing reliable and evidence-based responses to clinical inquiries.

The advent of foundation models (FMs) as an emerging suite of AI techniques has struck a wave of opportunities in computational healthcare. The interactive nature of these models, guided by pre-training data and human instructions, has ignited a data-centric AI paradigm that emphasizes better data characterization, quality, and scale. In healthcare AI, obtaining and processing high-quality clinical data records has been a longstanding challenge, ranging from data quantity, annotation, patient privacy, and ethics. In this survey, we investigate a wide range of data-centric approaches in the FM era (from model pre-training to inference) towards improving the healthcare workflow. We discuss key perspectives in AI security, assessment, and alignment with human values. Finally, we offer a promising outlook of FM-based analytics to enhance the performance of patient outcome and clinical workflow in the evolving landscape of healthcare and medicine. We provide an up-to-date list of healthcare-related foundation models and datasets at https://github.com/Yunkun-Zhang/Data-Centric-FM-Healthcare .

Clinical information extraction, which involves structuring clinical concepts from unstructured medical text, remains a challenging problem that could benefit from the inclusion of tabular background information available in electronic health records. Existing open-source datasets lack explicit links between structured features and clinical concepts in the text, motivating the need for a new research dataset. We introduce SimSUM, a benchmark dataset of 10,000 simulated patient records that link unstructured clinical notes with structured background variables. Each record simulates a patient encounter in the domain of respiratory diseases and includes tabular data (e.g., symptoms, diagnoses, underlying conditions) generated from a Bayesian network whose structure and parameters are defined by domain experts. A large language model (GPT-4o) is prompted to generate a clinical note describing the encounter, including symptoms and relevant context. These notes are annotated with span-level symptom mentions. We conduct an expert evaluation to assess note quality and run baseline predictive models on both the tabular and textual data. The SimSUM dataset is primarily designed to support research on clinical information extraction in the presence of tabular background variables, which can be linked through domain knowledge to concepts of interest to be extracted from the text -- namely, symptoms in the case of SimSUM. Secondary uses include research on the automation of clinical reasoning over both tabular data and text, causal effect estimation in the presence of tabular and/or textual confounders, and multi-modal synthetic data generation. SimSUM is not intended for training clinical decision support systems or production-grade models, but rather to facilitate reproducible research in a simplified and controlled setting.

With the advent of Vision-Language Models (VLMs), medical artificial intelligence (AI) has experienced significant technological progress and paradigm shifts. This survey provides an extensive review of recent advancements in Medical Vision-Language Models (Med-VLMs), which integrate visual and textual data to enhance healthcare outcomes. We discuss the foundational technology behind Med-VLMs, illustrating how general models are adapted for complex medical tasks, and examine their applications in healthcare. The transformative impact of Med-VLMs on clinical practice, education, and patient care is highlighted, alongside challenges such as data scarcity, narrow task generalization, interpretability issues, and ethical concerns like fairness, accountability, and privacy. These limitations are exacerbated by uneven dataset distribution, computational demands, and regulatory hurdles. Rigorous evaluation methods and robust regulatory frameworks are essential for safe integration into healthcare workflows. Future directions include leveraging large-scale, diverse datasets, improving cross-modal generalization, and enhancing interpretability. Innovations like federated learning, lightweight architectures, and Electronic Health Record (EHR) integration are explored as pathways to democratize access and improve clinical relevance. This review aims to provide a comprehensive understanding of Med-VLMs' strengths and limitations, fostering their ethical and balanced adoption in healthcare.

Large-scale clinical databases offer opportunities for medical research, but their complexity creates barriers to effective use. The Medical Information Mart for Intensive Care (MIMIC-IV), one of the world's largest open-source electronic health record databases, traditionally requires both SQL proficiency and clinical domain expertise. We introduce M3, a system that enables natural language querying of MIMIC-IV data through the Model Context Protocol. With a single command, M3 retrieves MIMIC-IV from PhysioNet, launches a local SQLite instance or connects to hosted BigQuery, and allows researchers to pose clinical questions in plain English. We evaluated M3 using one hundred questions from the EHRSQL 2024 benchmark with two language models: the proprietary Claude Sonnet 4 achieved 94% accuracy, while the open-source gpt-oss-20B (deployable locally on consumer hardware) achieved 93% accuracy. Both models translate natural language into SQL, execute queries against MIMIC-IV, and return structured results alongside the underlying query for verification. Error analysis revealed that most failures stemmed from complex temporal reasoning or ambiguous question phrasing rather than fundamental architectural limitations. The comparable performance of a smaller open-source model demonstrates that privacy-preserving local deployment is viable for sensitive clinical data analysis. M3 lowers technical barriers to critical care data analysis while maintaining security through OAuth2 authentication, query validation, and comprehensive audit logging.

Large Language Models (LLMs) have shown the potential to significantly contribute to patient care, diagnostics, and administrative processes. Emerging biomedical LLMs address healthcare-specific challenges, including privacy demands and computational constraints. However, evaluation of these models has primarily been limited to non-clinical tasks, which do not reflect the complexity of practical clinical applications. Additionally, there has been no thorough comparison between biomedical and general-domain LLMs for clinical tasks. To fill this gap, we present the Clinical Language Understanding Evaluation (CLUE), a benchmark tailored to evaluate LLMs on real-world clinical tasks. CLUE includes two novel datasets derived from MIMIC IV discharge letters and four existing tasks designed to test the practical applicability of LLMs in healthcare settings. Our evaluation covers several biomedical and general domain LLMs, providing insights into their clinical performance and applicability. CLUE represents a step towards a standardized approach to evaluating and developing LLMs in healthcare to align future model development with the real-world needs of clinical application. We publish our evaluation and data generation scripts: https://github.com/dadaamin/CLUE

The development of clinical natural language processing (NLP) systems is severely hampered by the sensitive nature of medical records, which restricts data sharing under stringent privacy regulations, particularly in France and the broader European Union. To address this gap, we introduce PARHAF, a large open-source corpus of clinical documents in French. PARHAF comprises expert-authored clinical reports describing realistic yet entirely fictitious patient cases, making it anonymous and freely shareable by design. The corpus was developed using a structured protocol that combined clinician expertise with epidemiological guidance from the French National Health Data System (SNDS), ensuring broad clinical coverage. A total of 104 medical residents across 18 specialties authored and peer-reviewed the reports following predefined clinical scenarios and document templates. The corpus contains 7394 clinical reports covering 5009 patient cases across a wide range of medical and surgical specialties. It includes a general-purpose component designed to approximate real-world hospitalization distributions, and four specialized subsets that support information-extraction use cases in oncology, infectious diseases, and diagnostic coding. Documents are released under a CC-BY open license, with a portion temporarily embargoed to enable future benchmarking under controlled conditions. PARHAF provides a valuable resource for training and evaluating French clinical language models in a fully privacy-preserving setting, and establishes a replicable methodology for building shareable synthetic clinical corpora in other languages and health systems.

Clinical calculators play a vital role in healthcare by offering accurate evidence-based predictions for various purposes such as prognosis. Nevertheless, their widespread utilization is frequently hindered by usability challenges, poor dissemination, and restricted functionality. Augmenting large language models with extensive collections of clinical calculators presents an opportunity to overcome these obstacles and improve workflow efficiency, but the scalability of the manual curation process poses a significant challenge. In response, we introduce AgentMD, a novel language agent capable of curating and applying clinical calculators across various clinical contexts. Using the published literature, AgentMD has automatically curated a collection of 2,164 diverse clinical calculators with executable functions and structured documentation, collectively named RiskCalcs. Manual evaluations show that RiskCalcs tools achieve an accuracy of over 80% on three quality metrics. At inference time, AgentMD can automatically select and apply the relevant RiskCalcs tools given any patient description. On the newly established RiskQA benchmark, AgentMD significantly outperforms chain-of-thought prompting with GPT-4 (87.7% vs. 40.9% in accuracy). Additionally, we also applied AgentMD to real-world clinical notes for analyzing both population-level and risk-level patient characteristics. In summary, our study illustrates the utility of language agents augmented with clinical calculators for healthcare analytics and patient care.

Large language models have exhibited exceptional performance on various Natural Language Processing (NLP) tasks, leveraging techniques such as the pre-training, and instruction fine-tuning. Despite these advances, their effectiveness in medical applications is limited, due to challenges such as factual inaccuracies, reasoning abilities, and lack grounding in real-world experience. In this study, we present ClinicalGPT, a language model explicitly designed and optimized for clinical scenarios. By incorporating extensive and diverse real-world data, such as medical records, domain-specific knowledge, and multi-round dialogue consultations in the training process, ClinicalGPT is better prepared to handle multiple clinical task. Furthermore, we introduce a comprehensive evaluation framework that includes medical knowledge question-answering, medical exams, patient consultations, and diagnostic analysis of medical records. Our results demonstrate that ClinicalGPT significantly outperforms other models in these tasks, highlighting the effectiveness of our approach in adapting large language models to the critical domain of healthcare.

For clinical data integration and healthcare services, the HL7 FHIR standard has established itself as a desirable format for interoperability between complex health data. Previous attempts at automating the translation from free-form clinical notes into structured FHIR resources rely on modular, rule-based systems or LLMs with instruction tuning and constrained decoding. Since they frequently suffer from limited generalizability and structural inconformity, we propose an end-to-end framework powered by LLM agents, code execution, and healthcare terminology database tools to address these issues. Our solution, called Infherno, is designed to adhere to the FHIR document schema and competes well with a human baseline in predicting FHIR resources from unstructured text. The implementation features a front end for custom and synthetic data and both local and proprietary models, supporting clinical data integration processes and interoperability across institutions.

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical narratives to support applications like automated coding, clinical trial cohort identification, and clinical decision support. The leaderboard provides a standardized platform for assessing diverse language models, including encoder and decoder architectures, on their ability to identify and classify clinical entities across multiple medical domains. A curated collection of openly available clinical datasets is utilized, encompassing entities such as diseases, symptoms, medications, procedures, and laboratory measurements. Importantly, these entities are standardized according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, ensuring consistency and interoperability across different healthcare systems and datasets, and a comprehensive evaluation of model performance. Performance of models is primarily assessed using the F1-score, and it is complemented by various assessment modes to provide comprehensive insights into model performance. The report also includes a brief analysis of models evaluated to date, highlighting observed trends and limitations. By establishing this benchmarking framework, the leaderboard aims to promote transparency, facilitate comparative analyses, and drive innovation in clinical entity recognition tasks, addressing the need for robust evaluation methods in healthcare NLP.

Clinical evidence, derived from rigorous research and data analysis, provides healthcare professionals with reliable scientific foundations for informed decision-making. Integrating clinical evidence into real-time practice is challenging due to the enormous workload, complex professional processes, and time constraints. This highlights the need for tools that automate evidence synthesis to support more efficient and accurate decision making in clinical settings. This study introduces Quicker, an evidence-based clinical decision support system powered by large language models (LLMs), designed to automate evidence synthesis and generate clinical recommendations modeled after standard clinical guideline development processes. Quicker implements a fully automated chain that covers all phases, from questions to clinical recommendations, and further enables customized decision-making through integrated tools and interactive user interfaces. To evaluate Quicker's capabilities, we developed the Q2CRBench-3 benchmark dataset, based on clinical guideline development records for three different diseases. Experimental results highlighted Quicker's strong performance, with fine-grained question decomposition tailored to user preferences, retrieval sensitivities comparable to human experts, and literature screening performance approaching comprehensive inclusion of relevant studies. In addition, Quicker-assisted evidence assessment effectively supported human reviewers, while Quicker's recommendations were more comprehensive and logically coherent than those of clinicians. In system-level testing, collaboration between a single reviewer and Quicker reduced the time required for recommendation development to 20-40 minutes. In general, our findings affirm the potential of Quicker to help physicians make quicker and more reliable evidence-based clinical decisions.

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 3,943 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at https://github.com/dustn1259/EHRCon.

Large language models (LLMs) such as GPT-4o and o1 have demonstrated strong performance on clinical natural language processing (NLP) tasks across multiple medical benchmarks. Nonetheless, two high-impact NLP tasks - structured tabular reporting from nurse dictations and medical order extraction from doctor-patient consultations - remain underexplored due to data scarcity and sensitivity, despite active industry efforts. Practical solutions to these real-world clinical tasks can significantly reduce the documentation burden on healthcare providers, allowing greater focus on patient care. In this paper, we investigate these two challenging tasks using private and open-source clinical datasets, evaluating the performance of both open- and closed-weight LLMs, and analyzing their respective strengths and limitations. Furthermore, we propose an agentic pipeline for generating realistic, non-sensitive nurse dictations, enabling structured extraction of clinical observations. To support further research in both areas, we release SYNUR and SIMORD, the first open-source datasets for nurse observation extraction and medical order extraction.

Large Language Models (LLMs) are increasingly utilized for mental health support; however, current safety benchmarks often fail to detect the complex, longitudinal risks inherent in therapeutic dialogue. We introduce an evaluation framework that pairs AI psychotherapists with simulated patient agents equipped with dynamic cognitive-affective models and assesses therapy session simulations against a comprehensive quality of care and risk ontology. We apply this framework to a high-impact test case, Alcohol Use Disorder, evaluating six AI agents (including ChatGPT, Gemini, and Character.AI) against a clinically-validated cohort of 15 patient personas representing diverse clinical phenotypes. Our large-scale simulation (N=369 sessions) reveals critical safety gaps in the use of AI for mental health support. We identify specific iatrogenic risks, including the validation of patient delusions ("AI Psychosis") and failure to de-escalate suicide risk. Finally, we validate an interactive data visualization dashboard with diverse stakeholders, including AI engineers and red teamers, mental health professionals, and policy experts (N=9), demonstrating that this framework effectively enables stakeholders to audit the "black box" of AI psychotherapy. These findings underscore the critical safety risks of AI-provided mental health support and the necessity of simulation-based clinical red teaming before deployment.

Large language models (LLMs) are increasingly envisioned as decision-support tools in clinical practice, yet safe clinical reasoning demands integrating heterogeneous knowledge bases -- trials, primary studies, regulatory documents, and cost data -- under strict accuracy constraints. Existing evaluations often rely on synthetic prompts, reduce the task to single-hop factoid queries, or conflate reasoning with open-ended generation, leaving their real-world utility unclear. To close this gap, we present MedBrowseComp, the first benchmark that systematically tests an agent's ability to reliably retrieve and synthesize multi-hop medical facts from live, domain-specific knowledge bases. MedBrowseComp contains more than 1,000 human-curated questions that mirror clinical scenarios where practitioners must reconcile fragmented or conflicting information to reach an up-to-date conclusion. Applying MedBrowseComp to frontier agentic systems reveals performance shortfalls as low as ten percent, exposing a critical gap between current LLM capabilities and the rigor demanded in clinical settings. MedBrowseComp therefore offers a clear testbed for reliable medical information seeking and sets concrete goals for future model and toolchain upgrades. You can visit our project page at: https://moreirap12.github.io/mbc-browse-app/

The integration of Large Language Models (LLMs) into healthcare promises to transform medical diagnostics, research, and patient care. Yet, the progression of medical LLMs faces obstacles such as complex training requirements, rigorous evaluation demands, and the dominance of proprietary models that restrict academic exploration. Transparent, comprehensive access to LLM resources is essential for advancing the field, fostering reproducibility, and encouraging innovation in healthcare AI. We present Hippocrates, an open-source LLM framework specifically developed for the medical domain. In stark contrast to previous efforts, it offers unrestricted access to its training datasets, codebase, checkpoints, and evaluation protocols. This open approach is designed to stimulate collaborative research, allowing the community to build upon, refine, and rigorously evaluate medical LLMs within a transparent ecosystem. Also, we introduce Hippo, a family of 7B models tailored for the medical domain, fine-tuned from Mistral and LLaMA2 through continual pre-training, instruction tuning, and reinforcement learning from human and AI feedback. Our models outperform existing open medical LLMs models by a large-margin, even surpassing models with 70B parameters. Through Hippocrates, we aspire to unlock the full potential of LLMs not just to advance medical knowledge and patient care but also to democratize the benefits of AI research in healthcare, making them available across the globe.

The emergence of large language models (LLMs) has significantly influenced numerous fields, including healthcare, by enhancing the capabilities of automated systems to process and generate human-like text. However, despite their advancements, the reliability and accuracy of LLMs in medical contexts remain critical concerns. Current evaluation methods often lack robustness and fail to provide a comprehensive assessment of LLM performance, leading to potential risks in clinical settings. In this work, we propose Med-CoDE, a specifically designed evaluation framework for medical LLMs to address these challenges. The framework leverages a critique-based approach to quantitatively measure the degree of disagreement between model-generated responses and established medical ground truths. This framework captures both accuracy and reliability in medical settings. The proposed evaluation framework aims to fill the existing gap in LLM assessment by offering a systematic method to evaluate the quality and trustworthiness of medical LLMs. Through extensive experiments and case studies, we illustrate the practicality of our framework in providing a comprehensive and reliable evaluation of medical LLMs.

Global healthcare providers are exploring use of large language models (LLMs) to provide medical advice to the public. LLMs now achieve nearly perfect scores on medical licensing exams, but this does not necessarily translate to accurate performance in real-world settings. We tested if LLMs can assist members of the public in identifying underlying conditions and choosing a course of action (disposition) in ten medical scenarios in a controlled study with 1,298 participants. Participants were randomly assigned to receive assistance from an LLM (GPT-4o, Llama 3, Command R+) or a source of their choice (control). Tested alone, LLMs complete the scenarios accurately, correctly identifying conditions in 94.9% of cases and disposition in 56.3% on average. However, participants using the same LLMs identified relevant conditions in less than 34.5% of cases and disposition in less than 44.2%, both no better than the control group. We identify user interactions as a challenge to the deployment of LLMs for medical advice. Standard benchmarks for medical knowledge and simulated patient interactions do not predict the failures we find with human participants. Moving forward, we recommend systematic human user testing to evaluate interactive capabilities prior to public deployments in healthcare.

We introduce MedAgentGYM, the first publicly available training environment designed to enhance coding-based medical reasoning capabilities in large language model (LLM) agents. MedAgentGYM comprises 72,413 task instances across 129 categories derived from authentic real-world biomedical scenarios. Tasks are encapsulated within executable coding environments, each featuring detailed task descriptions, interactive feedback mechanisms, verifiable ground-truth annotations, and scalable training trajectory generation. Extensive benchmarking of over 30 LLMs reveals a notable performance disparity between commercial API-based models and open-source counterparts. Leveraging MedAgentGYM, Med-Copilot-7B achieves substantial performance gains through supervised fine-tuning (+36.44%) and continued reinforcement learning (+42.47%), emerging as an affordable and privacy-preserving alternative competitive with gpt-4o. By offering both a comprehensive benchmark and accessible, expandable training resources within unified execution environments, MedAgentGYM delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical research and practice.

Unstructured clinical notes contain essential patient information but are challenging for physicians to search and interpret efficiently. Although large language models (LLMs) have shown promise in question answering (QA), most existing systems lack transparency, usability, and alignment with clinical workflows. This work introduces an interactive QA system that enables physicians to query clinical notes via text or voice and receive extractive answers highlighted directly in the note for traceability. The system was built using OpenAI models with zero-shot prompting and evaluated across multiple metrics, including exact string match, word overlap, SentenceTransformer similarity, and BERTScore. Results show that while exact match scores ranged from 47 to 62 percent, semantic similarity scores exceeded 87 percent, indicating strong contextual alignment even when wording varied. To assess usability, the system was also evaluated using simulated clinical personas. Seven diverse physician and nurse personas interacted with the system across scenario-based tasks and provided structured feedback. The evaluations highlighted strengths in intuitive design and answer accessibility, alongside opportunities for enhancing explanation clarity.

Physicians spend significant time documenting clinical encounters, a burden that contributes to professional burnout. To address this, robust automation tools for medical documentation are crucial. We introduce MedSynth -- a novel dataset of synthetic medical dialogues and notes designed to advance the Dialogue-to-Note (Dial-2-Note) and Note-to-Dialogue (Note-2-Dial) tasks. Informed by an extensive analysis of disease distributions, this dataset includes over 10,000 dialogue-note pairs covering over 2000 ICD-10 codes. We demonstrate that our dataset markedly enhances the performance of models in generating medical notes from dialogues, and dialogues from medical notes. The dataset provides a valuable resource in a field where open-access, privacy-compliant, and diverse training data are scarce. Code is available at https://github.com/ahmadrezarm/MedSynth/tree/main and the dataset is available at https://huggingface.co/datasets/Ahmad0067/MedSynth.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Artificial intelligence has significantly advanced healthcare, particularly through large language models (LLMs) that excel in medical question answering benchmarks. However, their real-world clinical application remains limited due to the complexities of doctor-patient interactions. To address this, we introduce AI Hospital, a multi-agent framework simulating dynamic medical interactions between Doctor as player and NPCs including Patient, Examiner, Chief Physician. This setup allows for realistic assessments of LLMs in clinical scenarios. We develop the Multi-View Medical Evaluation (MVME) benchmark, utilizing high-quality Chinese medical records and NPCs to evaluate LLMs' performance in symptom collection, examination recommendations, and diagnoses. Additionally, a dispute resolution collaborative mechanism is proposed to enhance diagnostic accuracy through iterative discussions. Despite improvements, current LLMs exhibit significant performance gaps in multi-turn interactions compared to one-step approaches. Our findings highlight the need for further research to bridge these gaps and improve LLMs' clinical diagnostic capabilities. Our data, code, and experimental results are all open-sourced at https://github.com/LibertFan/AI_Hospital.

Multimodal agentic pipelines are transforming human-computer interaction by enabling efficient and accessible automation of complex, real-world tasks. However, recent efforts have focused on short-horizon or general-purpose applications (e.g., mobile or desktop interfaces), leaving long-horizon automation for domain-specific systems, particularly in healthcare, largely unexplored. To address this, we introduce CareFlow, a high-quality human-annotated benchmark comprising complex, long-horizon software workflows across medical annotation tools, DICOM viewers, EHR systems, and laboratory information systems. On this benchmark, existing vision-language models (VLMs) perform poorly, struggling with long-horizon reasoning and multi-step interactions in medical contexts. To overcome this, we propose CarePilot, a multi-agent framework based on the actor-critic paradigm. The Actor integrates tool grounding with dual-memory mechanisms (long-term and short-term experience) to predict the next semantic action from the visual interface and system state. The Critic evaluates each action, updates memory based on observed effects, and either executes or provides corrective feedback to refine the workflow. Through iterative agentic simulation, the Actor learns to perform more robust and reasoning-aware predictions during inference. Our experiments show that CarePilot achieves state-of-the-art performance, outperforming strong closed-source and open-source multimodal baselines by approximately 15.26% and 3.38%, respectively, on our benchmark and out-of-distribution dataset.

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

In natural language processing applied to the clinical domain, utilizing large language models has emerged as a promising avenue for error detection and correction on clinical notes, a knowledge-intensive task for which annotated data is scarce. This paper presents MedReAct'N'MedReFlex, which leverages a suite of four LLM-based medical agents. The MedReAct agent initiates the process by observing, analyzing, and taking action, generating trajectories to guide the search to target a potential error in the clinical notes. Subsequently, the MedEval agent employs five evaluators to assess the targeted error and the proposed correction. In cases where MedReAct's actions prove insufficient, the MedReFlex agent intervenes, engaging in reflective analysis and proposing alternative strategies. Finally, the MedFinalParser agent formats the final output, preserving the original style while ensuring the integrity of the error correction process. One core component of our method is our RAG pipeline based on our ClinicalCorp corpora. Among other well-known sources containing clinical guidelines and information, we preprocess and release the open-source MedWiki dataset for clinical RAG application. Our results demonstrate the central role of our RAG approach with ClinicalCorp leveraged through the MedReAct'N'MedReFlex framework. It achieved the ninth rank on the MEDIQA-CORR 2024 final leaderboard.

The rapid advancement of Large Language Models (LLMs) has stimulated interest in multi-agent collaboration for addressing complex medical tasks. However, the practical advantages of multi-agent collaboration approaches remain insufficiently understood. Existing evaluations often lack generalizability, failing to cover diverse tasks reflective of real-world clinical practice, and frequently omit rigorous comparisons against both single-LLM-based and established conventional methods. To address this critical gap, we introduce MedAgentBoard, a comprehensive benchmark for the systematic evaluation of multi-agent collaboration, single-LLM, and conventional approaches. MedAgentBoard encompasses four diverse medical task categories: (1) medical (visual) question answering, (2) lay summary generation, (3) structured Electronic Health Record (EHR) predictive modeling, and (4) clinical workflow automation, across text, medical images, and structured EHR data. Our extensive experiments reveal a nuanced landscape: while multi-agent collaboration demonstrates benefits in specific scenarios, such as enhancing task completeness in clinical workflow automation, it does not consistently outperform advanced single LLMs (e.g., in textual medical QA) or, critically, specialized conventional methods that generally maintain better performance in tasks like medical VQA and EHR-based prediction. MedAgentBoard offers a vital resource and actionable insights, emphasizing the necessity of a task-specific, evidence-based approach to selecting and developing AI solutions in medicine. It underscores that the inherent complexity and overhead of multi-agent collaboration must be carefully weighed against tangible performance gains. All code, datasets, detailed prompts, and experimental results are open-sourced at https://medagentboard.netlify.app/.

Large language models (LLMs) have been applied to tasks in healthcare, ranging from medical exam questions to responding to patient questions. With increasing institutional partnerships between companies producing LLMs and healthcare systems, real world clinical application is coming closer to reality. As these models gain traction, it is essential for healthcare practitioners to understand what LLMs are, their development, their current and potential applications, and the associated pitfalls when utilized in medicine. This review and accompanying tutorial aim to give an overview of these topics to aid healthcare practitioners in understanding the rapidly changing landscape of LLMs as applied to medicine.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n = 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

Long-form clinical videos are central to visual evidence-based decision-making, with growing importance for applications such as surgical robotics and related settings. However, current multimodal large language models typically process videos with passive sampling or weakly grounded inspection, which limits their ability to iteratively locate, verify, and justify predictions with temporally targeted evidence. To close this gap, we propose MedScope, a tool-using clinical video reasoning model that performs coarse-to-fine evidence seeking over long-form procedures. By interleaving intermediate reasoning with targeted tool calls and verification on retrieved observations, MedScope produces more accurate and trustworthy predictions that are explicitly grounded in temporally localized visual evidence. To address the lack of high-fidelity supervision, we build ClinVideoSuite, an evidence-centric, fine-grained clinical video suite. We then optimize MedScope with Grounding-Aware Group Relative Policy Optimization (GA-GRPO), which directly reinforces tool use with grounding-aligned rewards and evidence-weighted advantages. On full and fine-grained video understanding benchmarks, MedScope achieves state-of-the-art performance in both in-domain and out-of-domain evaluations. Our approach illuminates a path toward medical AI agents that can genuinely "think with videos" through tool-integrated reasoning. We will release our code, models, and data.

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

Since the COVID-19 pandemic, clinicians have seen a large and sustained influx in patient portal messages, significantly contributing to clinician burnout. To the best of our knowledge, there are no large-scale public patient portal messages corpora researchers can use to build tools to optimize clinician portal workflows. Informed by our ongoing work with a regional hospital, this study introduces an LLM-powered framework for configurable and realistic patient portal message generation. Our approach leverages few-shot grounded text generation, requiring only a small number of de-identified patient portal messages to help LLMs better match the true style and tone of real data. Clinical experts in our team deem this framework as HIPAA-friendly, unlike existing privacy-preserving approaches to synthetic text generation which cannot guarantee all sensitive attributes will be protected. Through extensive quantitative and human evaluation, we show that our framework produces data of higher quality than comparable generation methods as well as all related datasets. We believe this work provides a path forward for (i) the release of large-scale synthetic patient message datasets that are stylistically similar to ground-truth samples and (ii) HIPAA-friendly data generation which requires minimal human de-identification efforts.

Med42-v2 introduces a suite of clinical large language models (LLMs) designed to address the limitations of generic models in healthcare settings. These models are built on Llama3 architecture and fine-tuned using specialized clinical data. They underwent multi-stage preference alignment to effectively respond to natural prompts. While generic models are often preference-aligned to avoid answering clinical queries as a precaution, Med42-v2 is specifically trained to overcome this limitation, enabling its use in clinical settings. Med42-v2 models demonstrate superior performance compared to the original Llama3 models in both 8B and 70B parameter configurations and GPT-4 across various medical benchmarks. These LLMs are developed to understand clinical queries, perform reasoning tasks, and provide valuable assistance in clinical environments. The models are now publicly available at https://huggingface.co/m42-health{https://huggingface.co/m42-health}.

Problem: Effective patient-centered communication is a core competency for physicians. However, both seasoned providers and medical trainees report decreased confidence in leading conversations on sensitive topics such as goals of care or end-of-life discussions. The significant administrative burden and the resources required to provide dedicated training in leading difficult conversations has been a long-standing problem in medical education. Approach: In this work, we present a novel educational tool designed to facilitate interactive, real-time simulations of difficult conversations in a video-based format through the use of multimodal generative artificial intelligence (AI). Leveraging recent advances in language modeling, computer vision, and generative audio, this tool creates realistic, interactive scenarios with avatars, or "synthetic patients." These synthetic patients interact with users throughout various stages of medical care using a custom-built video chat application, offering learners the chance to practice conversations with patients from diverse belief systems, personalities, and ethnic backgrounds. Outcomes: While the development of this platform demanded substantial upfront investment in labor, it offers a highly-realistic simulation experience with minimal financial investment. For medical trainees, this educational tool can be implemented within programs to simulate patient-provider conversations and can be incorporated into existing palliative care curriculum to provide a scalable, high-fidelity simulation environment for mastering difficult conversations. Next Steps: Future developments will explore enhancing the authenticity of these encounters by working with patients to incorporate their histories and personalities, as well as employing the use of AI-generated evaluations to offer immediate, constructive feedback to learners post-simulation.

With the proliferation of Large Language Models (LLMs) in diverse domains, there is a particular need for unified evaluation standards in clinical medical scenarios, where models need to be examined very thoroughly. We present CliMedBench, a comprehensive benchmark with 14 expert-guided core clinical scenarios specifically designed to assess the medical ability of LLMs across 7 pivot dimensions. It comprises 33,735 questions derived from real-world medical reports of top-tier tertiary hospitals and authentic examination exercises. The reliability of this benchmark has been confirmed in several ways. Subsequent experiments with existing LLMs have led to the following findings: (i) Chinese medical LLMs underperform on this benchmark, especially where medical reasoning and factual consistency are vital, underscoring the need for advances in clinical knowledge and diagnostic accuracy. (ii) Several general-domain LLMs demonstrate substantial potential in medical clinics, while the limited input capacity of many medical LLMs hinders their practical use. These findings reveal both the strengths and limitations of LLMs in clinical scenarios and offer critical insights for medical research.

Extracting patient information from unstructured text is a critical task in health decision-support and clinical research. Large language models (LLMs) have shown the potential to accelerate clinical curation via few-shot in-context learning, in contrast to supervised learning which requires much more costly human annotations. However, despite drastic advances in modern LLMs such as GPT-4, they still struggle with issues regarding accuracy and interpretability, especially in mission-critical domains such as health. Here, we explore a general mitigation framework using self-verification, which leverages the LLM to provide provenance for its own extraction and check its own outputs. This is made possible by the asymmetry between verification and generation, where the latter is often much easier than the former. Experimental results show that our method consistently improves accuracy for various LLMs in standard clinical information extraction tasks. Additionally, self-verification yields interpretations in the form of a short text span corresponding to each output, which makes it very efficient for human experts to audit the results, paving the way towards trustworthy extraction of clinical information in resource-constrained scenarios. To facilitate future research in this direction, we release our code and prompts.

Artificial intelligence (AI) and large language models (LLMs) in healthcare require advanced clinical skills (CS), yet current benchmarks fail to evaluate these comprehensively. We introduce MedQA-CS, an AI-SCE framework inspired by medical education's Objective Structured Clinical Examinations (OSCEs), to address this gap. MedQA-CS evaluates LLMs through two instruction-following tasks, LLM-as-medical-student and LLM-as-CS-examiner, designed to reflect real clinical scenarios. Our contributions include developing MedQA-CS, a comprehensive evaluation framework with publicly available data and expert annotations, and providing the quantitative and qualitative assessment of LLMs as reliable judges in CS evaluation. Our experiments show that MedQA-CS is a more challenging benchmark for evaluating clinical skills than traditional multiple-choice QA benchmarks (e.g., MedQA). Combined with existing benchmarks, MedQA-CS enables a more comprehensive evaluation of LLMs' clinical capabilities for both open- and closed-source LLMs.

Large language models (LLMs) show promise in drafting responses to patient portal messages, yet their integration into clinical workflows raises various concerns, including whether they would actually save clinicians time and effort in their portal workload. We investigate LLM alignment with individual clinicians through a comprehensive evaluation of the patient message response drafting task. We develop a novel taxonomy of thematic elements in clinician responses and propose a novel evaluation framework for assessing clinician editing load of LLM-drafted responses at both content and theme levels. We release an expert-annotated dataset and conduct large-scale evaluations of local and commercial LLMs using various adaptation techniques including thematic prompting, retrieval-augmented generation, supervised fine-tuning, and direct preference optimization. Our results reveal substantial epistemic uncertainty in aligning LLM drafts with clinician responses. While LLMs demonstrate capability in drafting certain thematic elements, they struggle with clinician-aligned generation in other themes, particularly question asking to elicit further information from patients. Theme-driven adaptation strategies yield improvements across most themes. Our findings underscore the necessity of adapting LLMs to individual clinician preferences to enable reliable and responsible use in patient-clinician communication workflows.

Clinical notes contain information about patients that goes beyond structured data like lab values and medications. However, clinical notes have been underused relative to structured data, because notes are high-dimensional and sparse. This work develops and evaluates representations of clinical notes using bidirectional transformers (ClinicalBERT). ClinicalBERT uncovers high-quality relationships between medical concepts as judged by humans. ClinicalBert outperforms baselines on 30-day hospital readmission prediction using both discharge summaries and the first few days of notes in the intensive care unit. Code and model parameters are available.

Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models pose significant obstacles for hospitals in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking the flexibility to perform well across both. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to four times longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MTF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field.

Documentation burden is a major contributor to clinician burnout, which is rising nationally and is an urgent threat to our ability to care for patients. Artificial intelligence (AI) chatbots, such as ChatGPT, could reduce clinician burden by assisting with documentation. Although many hospitals are actively integrating such systems into electronic medical record systems, AI chatbots utility and impact on clinical decision-making have not been studied for this intended use. We are the first to examine the utility of large language models in assisting clinicians draft responses to patient questions. In our two-stage cross-sectional study, 6 oncologists responded to 100 realistic synthetic cancer patient scenarios and portal messages developed to reflect common medical situations, first manually, then with AI assistance. We find AI-assisted responses were longer, less readable, but provided acceptable drafts without edits 58% of time. AI assistance improved efficiency 77% of time, with low harm risk (82% safe). However, 7.7% unedited AI responses could severely harm. In 31% cases, physicians thought AI drafts were human-written. AI assistance led to more patient education recommendations, fewer clinical actions than manual responses. Results show promise for AI to improve clinician efficiency and patient care through assisting documentation, if used judiciously. Monitoring model outputs and human-AI interaction remains crucial for safe implementation.

As large language models (LLMs) advance in conversational and reasoning capabilities, their practical application in healthcare has become a critical research focus. However, there is a notable gap between the performance of medical LLMs on static benchmarks such as USMLE and their utility in real-world clinical decision-making. This discrepancy arises because traditional exams fail to capture the dynamic, interactive nature of medical consultations. To address this challenge, we introduce a novel dynamic verification framework that moves beyond static answer verifier, establishing a large-scale, high-fidelity interactive reinforcement learning system. Our framework comprises two key components: a Patient Simulator that creates realistic clinical environments using de-identified medical records, and a Clinical Rubrics Generator that dynamically produces multi-dimensional evaluation metrics. Building on this foundation, we develop Baichuan-M2, a 32B-parameter medical augmented reasoning model trained through a multi-stage reinforcement learning strategy with an improved Group Relative Policy Optimization (GRPO) algorithm. Evaluated on HealthBench, Baichuan-M2 outperforms all other open-source models and most advanced closed-source counterparts, achieving a score above 32 on the challenging HealthBench Hard benchmark-previously exceeded only by GPT-5. Our work demonstrates that robust dynamic verifier system is essential for aligning LLM capabilities with practical clinical applications, establishing a new Pareto front in the performance-parameter trade-off for medical AI deployment.

Real-world clinical decision-making grapples with integrating information from diverse data modalities, including medical text, 2D/3D images, and video, leading to inefficiencies and potential diagnostic oversights. While generalist vision-language models (VLMs) offer promise, their medical development faces challenges of opaque pipelines, data scarcity, and architectural inflexibility. Here we present Hulu-Med, a transparent medical VLM that unifies understanding across all these modalities. Built upon a unified patch-based vision encoder and an LLM decoder, Hulu-Med was progressively trained on 16.7 million (M) samples to scale from 2D to 3D and video comprehension. The medical-aware token reduction enables efficient training, requiring only 4,000 to 40,000 GPU hours for 7B to 32B parameter variants. Extensive evaluation across 30 benchmarks exhibits state-of-the-art performance, surpassing leading open-source models and competing with proprietary systems in tasks spanning visual question-answering, medical report generation, and complex reasoning in multilingual and rare disease scenarios. By open-sourcing our complete pipeline, we establish that high-performance medical VLM can be achieved transparently, providing a foundational tool for accessible and impactful clinical AI. Code is released on https://github.com/ZJUI-AI4H/Hulu-Med{https://github.com/ZJUI-AI4H/Hulu-Med}.

Continuum robots are advancing bronchoscopy procedures by accessing complex lung airways and enabling targeted interventions. However, their development is limited by the lack of realistic training and test environments: Real data is difficult to collect due to ethical constraints and patient safety concerns, and developing autonomy algorithms requires realistic imaging and physical feedback. We present ROOM (Realistic Optical Observation in Medicine), a comprehensive simulation framework designed for generating photorealistic bronchoscopy training data. By leveraging patient CT scans, our pipeline renders multi-modal sensor data including RGB images with realistic noise and light specularities, metric depth maps, surface normals, optical flow and point clouds at medically relevant scales. We validate the data generated by ROOM in two canonical tasks for medical robotics -- multi-view pose estimation and monocular depth estimation, demonstrating diverse challenges that state-of-the-art methods must overcome to transfer to these medical settings. Furthermore, we show that the data produced by ROOM can be used to fine-tune existing depth estimation models to overcome these challenges, also enabling other downstream applications such as navigation. We expect that ROOM will enable large-scale data generation across diverse patient anatomies and procedural scenarios that are challenging to capture in clinical settings. Code and data: https://github.com/iamsalvatore/room.

Electronic health records (EHRs) are multimodal by nature, consisting of structured tabular features like lab tests and unstructured clinical notes. In real-life clinical practice, doctors use complementary multimodal EHR data sources to get a clearer picture of patients' health and support clinical decision-making. However, most EHR predictive models do not reflect these procedures, as they either focus on a single modality or overlook the inter-modality interactions/redundancy. In this work, we propose MEDFuse, a Multimodal EHR Data Fusion framework that incorporates masked lab-test modeling and large language models (LLMs) to effectively integrate structured and unstructured medical data. MEDFuse leverages multimodal embeddings extracted from two sources: LLMs fine-tuned on free clinical text and masked tabular transformers trained on structured lab test results. We design a disentangled transformer module, optimized by a mutual information loss to 1) decouple modality-specific and modality-shared information and 2) extract useful joint representation from the noise and redundancy present in clinical notes. Through comprehensive validation on the public MIMIC-III dataset and the in-house FEMH dataset, MEDFuse demonstrates great potential in advancing clinical predictions, achieving over 90% F1 score in the 10-disease multi-label classification task.

While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains deidentified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of CLMBR-T-base, a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaptation. Our model and dataset are available via a research data use agreement from the Stanford AIMI Center. Code to reproduce our results are available at our Github repo: https://github.com/som-shahlab/ehrshot-benchmark

Recent advances in Large Language Models (LLMs) have enabled researchers to focus on practical repository-level tasks in software engineering domain. In this work, we consider a cornerstone task for automating work with software repositories-environment setup, i.e., a task of configuring a repository-specific development environment on a system. Existing studies on environment setup introduce innovative agentic strategies, but their evaluation is often based on small datasets that may not capture the full range of configuration challenges encountered in practice. To address this gap, we introduce a comprehensive environment setup benchmark EnvBench. It encompasses 329 Python and 665 JVM-based (Java, Kotlin) repositories, with a focus on repositories that present genuine configuration challenges, excluding projects that can be fully configured by simple deterministic scripts. To enable further benchmark extension and usage for model tuning, we implement two automatic metrics: a static analysis check for missing imports in Python and a compilation check for JVM languages. We demonstrate the applicability of our benchmark by evaluating three environment setup approaches, including a simple zero-shot baseline and two agentic workflows, that we test with two powerful LLM backbones, GPT-4o and GPT-4o-mini. The best approach manages to successfully configure 6.69% repositories for Python and 29.47% repositories for JVM, suggesting that EnvBench remains challenging for current approaches. Our benchmark suite is publicly available at https://github.com/JetBrains-Research/EnvBench. The dataset and experiment trajectories are available at https://jb.gg/envbench.

Foundation Models (FMs) trained on Electronic Health Records (EHRs) have achieved state-of-the-art results on numerous clinical prediction tasks. However, most existing EHR FMs have context windows of <1k tokens. This prevents them from modeling full patient EHRs which can exceed 10k's of events. Recent advancements in subquadratic long-context architectures (e.g., Mamba) offer a promising solution. However, their application to EHR data has not been well-studied. We address this gap by presenting the first systematic evaluation of the effect of context length on modeling EHR data. We find that longer context models improve predictive performance -- our Mamba-based model surpasses the prior state-of-the-art on 9/14 tasks on the EHRSHOT prediction benchmark. For clinical applications, however, model performance alone is insufficient -- robustness to the unique properties of EHR is crucial. Thus, we also evaluate models across three previously underexplored properties of EHR data: (1) the prevalence of "copy-forwarded" diagnoses which creates artificial repetition of tokens within EHR sequences; (2) the irregular time intervals between EHR events which can lead to a wide range of timespans within a context window; and (3) the natural increase in disease complexity over time which makes later tokens in the EHR harder to predict than earlier ones. Stratifying our EHRSHOT results, we find that higher levels of each property correlate negatively with model performance, but that longer context models are more robust to more extreme levels of these properties. Our work highlights the potential for using long-context architectures to model EHR data, and offers a case study for identifying new challenges in modeling sequential data motivated by domains outside of natural language. We release our models and code at: https://github.com/som-shahlab/long_context_clues

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page https://github.com/Glenj01/Medical-Coding.

Background: Clinical documentation represents a significant burden for healthcare providers, with physicians spending up to 2 hours daily on administrative tasks. Recent advances in large language models (LLMs) offer promising solutions, but privacy concerns and computational requirements limit their adoption in healthcare settings. Objective: To develop and evaluate a privacy-preserving, on-device medical transcription system using a fine-tuned Llama 3.2 1B model capable of generating structured medical notes from medical transcriptions while maintaining complete data sovereignty entirely in the browser. Methods: We fine-tuned a Llama 3.2 1B model using Parameter-Efficient Fine-Tuning (PEFT) with LoRA on 1,500 synthetic medical transcription-to-structured note pairs. The model was evaluated against the base Llama 3.2 1B on two datasets: 100 endocrinology transcripts and 140 modified ACI benchmark cases. Evaluation employed both statistical metrics (ROUGE, BERTScore, BLEURT) and LLM-as-judge assessments across multiple clinical quality dimensions. Results: The fine-tuned OnDevice model demonstrated substantial improvements over the base model. On the ACI benchmark, ROUGE-1 scores increased from 0.346 to 0.496, while BERTScore F1 improved from 0.832 to 0.866. Clinical quality assessments showed marked reduction in major hallucinations (from 85 to 35 cases) and enhanced factual correctness (2.81 to 3.54 on 5-point scale). Similar improvements were observed on the internal evaluation dataset, with composite scores increasing from 3.13 to 4.43 (+41.5%). Conclusions: Fine-tuning compact LLMs for medical transcription yields clinically meaningful improvements while enabling complete on-device browser deployment. This approach addresses key barriers to AI adoption in healthcare: privacy preservation, cost reduction, and accessibility for resource-constrained environments.

Although large language models (LLMs) demonstrate expert-level medical knowledge, aligning their open-ended outputs with fine-grained clinician preferences remains challenging. Existing methods often rely on coarse objectives or unreliable automated judges that are weakly grounded in professional guidelines. We propose a two-stage framework to address this gap. First, we introduce HealthRubrics, a dataset of 7,034 physician-verified preference examples in which clinicians refine LLM-drafted rubrics to meet rigorous medical standards. Second, we distill these rubrics into HealthPrinciples: 119 broadly reusable, clinically grounded principles organized by clinical dimensions, enabling scalable supervision beyond manual annotation. We use HealthPrinciples for (1) offline alignment by synthesizing rubrics for unlabeled queries and (2) an inference-time tool for guided self-revision. A 30B parameter model that activates only 3B parameters at inference trained with our framework achieves 33.4% on HealthBench-Hard, outperforming much larger models including Deepseek-R1 and o3, establishing a resource-efficient baseline for clinical alignment.

Despite growing interest in using large language models (LLMs) in healthcare, current explorations do not assess the real-world utility and safety of LLMs in clinical settings. Our objective was to determine whether two LLMs can serve information needs submitted by physicians as questions to an informatics consultation service in a safe and concordant manner. Sixty six questions from an informatics consult service were submitted to GPT-3.5 and GPT-4 via simple prompts. 12 physicians assessed the LLM responses' possibility of patient harm and concordance with existing reports from an informatics consultation service. Physician assessments were summarized based on majority vote. For no questions did a majority of physicians deem either LLM response as harmful. For GPT-3.5, responses to 8 questions were concordant with the informatics consult report, 20 discordant, and 9 were unable to be assessed. There were 29 responses with no majority on "Agree", "Disagree", and "Unable to assess". For GPT-4, responses to 13 questions were concordant, 15 discordant, and 3 were unable to be assessed. There were 35 responses with no majority. Responses from both LLMs were largely devoid of overt harm, but less than 20% of the responses agreed with an answer from an informatics consultation service, responses contained hallucinated references, and physicians were divided on what constitutes harm. These results suggest that while general purpose LLMs are able to provide safe and credible responses, they often do not meet the specific information need of a given question. A definitive evaluation of the usefulness of LLMs in healthcare settings will likely require additional research on prompt engineering, calibration, and custom-tailoring of general purpose models.

At the heart of medicine lies the physician-patient dialogue, where skillful history-taking paves the way for accurate diagnosis, effective management, and enduring trust. Artificial Intelligence (AI) systems capable of diagnostic dialogue could increase accessibility, consistency, and quality of care. However, approximating clinicians' expertise is an outstanding grand challenge. Here, we introduce AMIE (Articulate Medical Intelligence Explorer), a Large Language Model (LLM) based AI system optimized for diagnostic dialogue. AMIE uses a novel self-play based simulated environment with automated feedback mechanisms for scaling learning across diverse disease conditions, specialties, and contexts. We designed a framework for evaluating clinically-meaningful axes of performance including history-taking, diagnostic accuracy, management reasoning, communication skills, and empathy. We compared AMIE's performance to that of primary care physicians (PCPs) in a randomized, double-blind crossover study of text-based consultations with validated patient actors in the style of an Objective Structured Clinical Examination (OSCE). The study included 149 case scenarios from clinical providers in Canada, the UK, and India, 20 PCPs for comparison with AMIE, and evaluations by specialist physicians and patient actors. AMIE demonstrated greater diagnostic accuracy and superior performance on 28 of 32 axes according to specialist physicians and 24 of 26 axes according to patient actors. Our research has several limitations and should be interpreted with appropriate caution. Clinicians were limited to unfamiliar synchronous text-chat which permits large-scale LLM-patient interactions but is not representative of usual clinical practice. While further research is required before AMIE could be translated to real-world settings, the results represent a milestone towards conversational diagnostic AI.

The advancement of natural language processing (NLP) systems in healthcare hinges on language model ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient's medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba, with 130 million and 2.8 billion parameters, demonstrates a superior performance in modeling clinical language across extended text lengths compared to Mamba and clinical Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and accuracy, outperforming existing clinical language models and general domain large models like GPT-4 in longitudinal clinical notes information extraction tasks.

Clinical question answering systems have the potential to provide clinicians with relevant and timely answers to their questions. Nonetheless, despite the advances that have been made, adoption of these systems in clinical settings has been slow. One issue is a lack of question-answering datasets which reflect the real-world needs of health professionals. In this work, we present RealMedQA, a dataset of realistic clinical questions generated by humans and an LLM. We describe the process for generating and verifying the QA pairs and assess several QA models on BioASQ and RealMedQA to assess the relative difficulty of matching answers to questions. We show that the LLM is more cost-efficient for generating "ideal" QA pairs. Additionally, we achieve a lower lexical similarity between questions and answers than BioASQ which provides an additional challenge to the top two QA models, as per the results. We release our code and our dataset publicly to encourage further research.

The rapid development of Large Language Models (LLMs) for healthcare applications has spurred calls for holistic evaluation beyond frequently-cited benchmarks like USMLE, to better reflect real-world performance. While real-world assessments are valuable indicators of utility, they often lag behind the pace of LLM evolution, likely rendering findings obsolete upon deployment. This temporal disconnect necessitates a comprehensive upfront evaluation that can guide model selection for specific clinical applications. We introduce MEDIC, a framework assessing LLMs across five critical dimensions of clinical competence: medical reasoning, ethics and bias, data and language understanding, in-context learning, and clinical safety. MEDIC features a novel cross-examination framework quantifying LLM performance across areas like coverage and hallucination detection, without requiring reference outputs. We apply MEDIC to evaluate LLMs on medical question-answering, safety, summarization, note generation, and other tasks. Our results show performance disparities across model sizes, baseline vs medically finetuned models, and have implications on model selection for applications requiring specific model strengths, such as low hallucination or lower cost of inference. MEDIC's multifaceted evaluation reveals these performance trade-offs, bridging the gap between theoretical capabilities and practical implementation in healthcare settings, ensuring that the most promising models are identified and adapted for diverse healthcare applications.

The absence of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. Although various methods of explainable artificial intelligence (XAI) have been suggested, there is a lack of literature that delves into their practicality and assesses them based on criteria that could foster trust in clinical environments. To address this gap this study evaluates two popular XAI methods used for explaining predictive models in the healthcare context in terms of whether they (i) generate domain-appropriate representation, i.e. coherent with respect to the application task, (ii) impact clinical workflow and (iii) are consistent. To that end, explanations generated at the cohort and patient levels were analysed. The paper reports the first benchmarking of the XAI methods applied to risk prediction models obtained by evaluating the concordance between generated explanations and the trigger of a future clinical deterioration episode recorded by the data collection system. We carried out an analysis using two Electronic Medical Records (EMR) datasets sourced from Australian major hospitals. The findings underscore the limitations of state-of-the-art XAI methods in the clinical context and their potential benefits. We discuss these limitations and contribute to the theoretical development of trustworthy XAI solutions where clinical decision support guides the choice of intervention by suggesting the pattern or drivers for clinical deterioration in the future.

Clinical notes contain rich data, which is unexploited in predictive modeling compared to structured data. In this work, we developed a new text representation Clinical XLNet for clinical notes which also leverages the temporal information of the sequence of the notes. We evaluated our models on prolonged mechanical ventilation prediction problem and our experiments demonstrated that Clinical XLNet outperforms the best baselines consistently.

Large Language Models (LLMs) are increasingly used for clinical decision support, where hallucinations and unsafe suggestions may pose direct risks to patient safety. These risks are particularly challenging as they often manifest as subtle clinical errors that evade detection by generic metrics, while expert-authored fine-grained rubrics remain costly to construct and difficult to scale. In this paper, we propose a retrieval-augmented multi-agent framework designed to automate the generation of instance-specific evaluation rubrics. Our approach grounds evaluation in authoritative medical evidence by decomposing retrieved content into atomic facts and synthesizing them with user interaction constraints to form verifiable, fine-grained evaluation criteria. Evaluated on HealthBench, our framework achieves a Clinical Intent Alignment (CIA) score of 60.12%, a statistically significant improvement over the GPT-4o baseline (55.16%). In discriminative tests, our rubrics yield a mean score delta (μ_Δ = 8.658) and an AUROC of 0.977, nearly doubling the quality separation achieved by GPT-4o baseline (4.972). Beyond evaluation, our rubrics effectively guide response refinement, improving quality by 9.2% (from 59.0% to 68.2%). This provides a scalable and transparent foundation for both evaluating and improving medical LLMs. The code is available at https://anonymous.4open.science/r/Automated-Rubric-Generation-AF3C/.

While Multi-Agent Systems (MAS) show potential for complex clinical decision support, the field remains hindered by architectural fragmentation and the lack of standardized multimodal integration. Current medical MAS research suffers from non-uniform data ingestion pipelines, inconsistent visual-reasoning evaluation, and a lack of cross-specialty benchmarking. To address these challenges, we present MedMASLab, a unified framework and benchmarking platform for multimodal medical multi-agent systems. MedMASLab introduces: (1) A standardized multimodal agent communication protocol that enables seamless integration of 11 heterogeneous MAS architectures across 24 medical modalities. (2) An automated clinical reasoning evaluator, a zero-shot semantic evaluation paradigm that overcomes the limitations of lexical string-matching by leveraging large vision-language models to verify diagnostic logic and visual grounding. (3) The most extensive benchmark to date, spanning 11 organ systems and 473 diseases, standardizing data from 11 clinical benchmarks. Our systematic evaluation reveals a critical domain-specific performance gap: while MAS improves reasoning depth, current architectures exhibit significant fragility when transitioning between specialized medical sub-domains. We provide a rigorous ablation of interaction mechanisms and cost-performance trade-offs, establishing a new technical baseline for future autonomous clinical systems. The source code and data is publicly available at: https://github.com/NUS-Project/MedMASLab/

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

In this work, we introduce Multiple Embedding Model for EHR (MEME), an approach that views Electronic Health Records (EHR) as multimodal data. This approach incorporates "pseudo-notes", textual representations of tabular EHR concepts such as diagnoses and medications, and allows us to effectively employ Large Language Models (LLMs) for EHR representation. This framework also adopts a multimodal approach, embedding each EHR modality separately. We demonstrate the effectiveness of MEME by applying it to several tasks within the Emergency Department across multiple hospital systems. Our findings show that MEME surpasses the performance of both single modality embedding methods and traditional machine learning approaches. However, we also observe notable limitations in generalizability across hospital institutions for all tested models.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

The development of large language models tailored for handling patients' clinical notes is often hindered by the limited accessibility and usability of these notes due to strict privacy regulations. To address these challenges, we first create synthetic large-scale clinical notes using publicly available case reports extracted from biomedical literature. We then use these synthetic notes to train our specialized clinical large language model, Asclepius. While Asclepius is trained on synthetic data, we assess its potential performance in real-world applications by evaluating it using real clinical notes. We benchmark Asclepius against several other large language models, including GPT-3.5-turbo and other open-source alternatives. To further validate our approach using synthetic notes, we also compare Asclepius with its variants trained on real clinical notes. Our findings convincingly demonstrate that synthetic clinical notes can serve as viable substitutes for real ones when constructing high-performing clinical language models. This conclusion is supported by detailed evaluations conducted by both GPT-4 and medical professionals. All resources including weights, codes, and data used in the development of Asclepius are made publicly accessible for future research.

Current mental-health conversational systems are usually based on fixed, generic dialogue patterns. This paper proposes an adaptive framework based on large language models that aims to personalize therapeutic interaction according to a user's psychological state, quantified with the Acceptance of Illness Scale (AIS). The framework defines three specialized agents, L, M, and H, each linked to a different level of illness acceptance, and adjusts conversational behavior over time using continuous feedback signals. The AIS-stratified architecture is treated as a diegetic prototype placed in a plausible near-future setting and examined through the method of design fiction. By embedding the architecture in narrative scenarios, the study explores how such agents might influence access to care and therapeutic relationship. The goal is to show how clinically informed personalization, technical feasibility, and speculative scenario analysis can together inform the responsible design of LLM-based companions for mental-health support.

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%.

Recruiting patients to participate in clinical trials can be challenging and time-consuming. Usually, participation in a clinical trial is initiated by a healthcare professional and proposed to the patient. Promoting clinical trials directly to patients via online recruitment might help to reach them more efficiently. In this study, we address the case where a patient is initiating their own recruitment process and wants to determine whether they are eligible for a given clinical trial, using their own language to describe their medical profile. To study whether this creates difficulties in the patient trial matching process, we design a new dataset and task, Natural Language Inference for Patient Recruitment (NLI4PR), in which patient language profiles must be matched to clinical trials. We create it by adapting the TREC 2022 Clinical Trial Track dataset, which provides patients' medical profiles, and rephrasing them manually using patient language. We also use the associated clinical trial reports where the patients are either eligible or excluded. We prompt several open-source Large Language Models on our task and achieve from 56.5 to 71.8 of F1 score using patient language, against 64.7 to 73.1 for the same task using medical language. When using patient language, we observe only a small loss in performance for the best model, suggesting that having the patient as a starting point could be adopted to help recruit patients for clinical trials. The corpus and code bases are all freely available on our Github and HuggingFace repositories.

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

Prompt learning is a new paradigm in the Natural Language Processing (NLP) field which has shown impressive performance on a number of natural language tasks with common benchmarking text datasets in full, few-shot, and zero-shot train-evaluation setups. Recently, it has even been observed that large but frozen pre-trained language models (PLMs) with prompt learning outperform smaller but fine-tuned models. However, as with many recent NLP trends, the performance of even the largest PLMs such as GPT-3 do not perform well on specialized domains (e.g. medical text), and the common practice to achieve State of the Art (SoTA) results still consists of pre-training and fine-tuning the PLMs on downstream tasks. The reliance on fine-tuning large PLMs is problematic in clinical settings where data is often held in non-GPU environments, and more resource efficient methods of training specialized domain models is crucial. We investigated the viability of prompt learning on clinically meaningful decision tasks and directly compared with more traditional fine-tuning methods. Results are partially in line with the prompt learning literature, with prompt learning able to match or improve on traditional fine-tuning with substantially fewer trainable parameters and requiring less training data. We argue that prompt learning therefore provides lower computational resource costs applicable to clinical settings, that can serve as an alternative to fine-tuning ever increasing in size PLMs. Complementary code to reproduce experiments presented in this work can be found at: https://github.com/NtaylorOX/Public_Clinical_Prompt.

Large language models (LLMs) have shown remarkable progress in encoding clinical knowledge and responding to complex medical queries with appropriate clinical reasoning. However, their applicability in subspecialist or complex medical settings remains underexplored. In this work, we probe the performance of AMIE, a research conversational diagnostic AI system, in the subspecialist domain of breast oncology care without specific fine-tuning to this challenging domain. To perform this evaluation, we curated a set of 50 synthetic breast cancer vignettes representing a range of treatment-naive and treatment-refractory cases and mirroring the key information available to a multidisciplinary tumor board for decision-making (openly released with this work). We developed a detailed clinical rubric for evaluating management plans, including axes such as the quality of case summarization, safety of the proposed care plan, and recommendations for chemotherapy, radiotherapy, surgery and hormonal therapy. To improve performance, we enhanced AMIE with the inference-time ability to perform web search retrieval to gather relevant and up-to-date clinical knowledge and refine its responses with a multi-stage self-critique pipeline. We compare response quality of AMIE with internal medicine trainees, oncology fellows, and general oncology attendings under both automated and specialist clinician evaluations. In our evaluations, AMIE outperformed trainees and fellows demonstrating the potential of the system in this challenging and important domain. We further demonstrate through qualitative examples, how systems such as AMIE might facilitate conversational interactions to assist clinicians in their decision making. However, AMIE's performance was overall inferior to attending oncologists suggesting that further research is needed prior to consideration of prospective uses.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Multimodal language models (MLMs) show promise for clinical decision support and diagnostic reasoning, raising the prospect of end-to-end automated medical image interpretation. However, clinicians are highly selective in adopting AI tools; a model that makes errors on seemingly simple perception tasks such as determining image orientation or identifying whether a CT scan is contrast-enhance are unlikely to be adopted for clinical tasks. We introduce Medblink, a benchmark designed to probe these models for such perceptual abilities. Medblink spans eight clinically meaningful tasks across multiple imaging modalities and anatomical regions, totaling 1,429 multiple-choice questions over 1,605 images. We evaluate 19 state-of-the-art MLMs, including general purpose (GPT4o, Claude 3.5 Sonnet) and domain specific (Med Flamingo, LLaVA Med, RadFM) models. While human annotators achieve 96.4% accuracy, the best-performing model reaches only 65%. These results show that current MLMs frequently fail at routine perceptual checks, suggesting the need to strengthen their visual grounding to support clinical adoption. Data is available on our project page.

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.