Daily Papers

BalancedBio is a theoretically grounded framework for parameter-efficient biomedical reasoning, addressing multi-capability integration in domain-specific AI alignment. It establishes the Biomedical Multi-Capability Convergence Theorem, proving orthogonal gradient spaces are essential to prevent capability interference for safe deployment. Key innovations include: (1) Medical Knowledge Grounded Synthetic Generation (MKGSG), extending Source2Synth with clinical workflow constraints and medical ontology validation for factual accuracy and safety; and (2) Capability Aware Group Relative Policy Optimization, deriving optimal hybrid reward weighting to maintain orthogonality in RL, using a reward model with rule-based and model-based scores adapted to biomedical tasks. Mathematical analysis proves Pareto-optimal convergence, preserving performance across capabilities. It achieves state-of-the-art results in its parameter class: domain expertise (80.95% BIOMED-MMLU, +15.32% over baseline), reasoning (61.94%, +7.75%), instruction following (67.95%, +6.44%), and integration (86.7%, +18.5%). Theoretical safety guarantees include bounds on capability preservation and clinical accuracy. Real-world deployment yields 78% cost reduction, 23% improved diagnostic accuracy, and 89% clinician acceptance. This work provides a principled methodology for biomedical AI alignment, enabling efficient reasoning with essential safety and reliability, with the 0.5B model version to be released.

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.

We introduce PhysicianBench, a benchmark for evaluating LLM agents on physician tasks grounded in real clinical setting within electronic health record (EHR) environments. Existing medical agent benchmarks primarily focus on static knowledge recall, single-step atomic actions, or action intent without verifiable execution against the environment. As a result, they fail to capture the long-horizon, composite workflows that characterize real clinical systems. PhysicianBench comprises 100 long-horizon tasks adapted from real consultation cases between primary care and subspecialty physicians, with each task independently reviewed by a separate panel of physicians. Tasks are instantiated in an EHR environment with real patient records and accessed through the same standard APIs used by commercial EHR vendors. Tasks span 21 specialties (e.g., cardiology, endocrinology, oncology, psychiatry) and diverse workflow types (e.g., diagnosis interpretation, medication prescribing, treatment planning), requiring an average of 27 tool calls per task. Solving each task requires retrieving data across encounters, reasoning over heterogeneous clinical information, executing consequential clinical actions, and producing clinical documentation. Each task is decomposed into structured checkpoints (670 in total across the benchmark) capturing distinct stages of completion graded by task-specific scripts with execution-grounded verification. Across 13 proprietary and open-source LLM agents, the best-performing model achieves only 46% success rate (pass@1), while open-source models reach at most 19%, revealing a substantial gap between current agent capabilities and the demands of real-world clinical workflows. PhysicianBench provides a realistic and execution-grounded benchmark for measuring progress toward autonomous clinical agents.

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 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.

This paper introduces Opus, a novel framework for generating and optimizing Workflows tailored to complex Business Process Outsourcing (BPO) use cases, focusing on cost reduction and quality enhancement while adhering to established industry processes and operational constraints. Our approach generates executable Workflows from Intention, defined as the alignment of Client Input, Client Output, and Process Context. These Workflows are represented as Directed Acyclic Graphs (DAGs), with nodes as Tasks consisting of sequences of executable Instructions, including tools and human expert reviews. We adopt a two-phase methodology: Workflow Generation and Workflow Optimization. In the Generation phase, Workflows are generated using a Large Work Model (LWM) informed by a Work Knowledge Graph (WKG) that encodes domain-specific procedural and operational knowledge. In the Optimization phase, Workflows are transformed into Workflow Graphs (WFGs), where optimal Workflows are determined through path optimization. Our experiments demonstrate that state-of-the-art Large Language Models (LLMs) face challenges in reliably retrieving detailed process data as well as generating industry-compliant workflows. The key contributions of this paper include: - The integration of a Work Knowledge Graph (WKG) into a Large Work Model (LWM), enabling the generation of context-aware, semantically aligned, structured and auditable Workflows. - A two-phase approach that combines Workflow Generation from Intention with graph-based Workflow Optimization. - Opus Alpha 1 Large and Opus Alpha 1 Small, models that outperform state-of-the-art LLMs by 38\% and 29\% respectively in Workflow Generation for a Medical Coding use case.

Scientific workflow management systems (WMS) support scalable and reproducible execution of complex pipelines, but workflow design, implementation, and debugging remain largely manual and require significant expertise. Recent approaches using large language models (LLMs) show promise for workflow generation from natural language, but often rely on direct code synthesis, which limits transparency, reproducibility, and integration with workflow systems. We present an AI-assisted approach to scientific workflow management that combines specification-driven workflow generation, automated debugging, and distributed execution. The method introduces a structured specification phase that separates workflow intent, design, and implementation, allowing validation prior to code generation. We also develop an LLM-based debugging agent that diagnoses and resolves failures across multiple system layers. To support distributed execution and user interaction, we integrate Pegasus, a widely used WMS, with a Model Context Protocol (MCP) layer, providing a unified interface for workflow submission, monitoring, and control. We evaluate the approach using a federated learning workflow for medical imaging, chosen for its parallel, iterative, and dependency-intensive structure. The system generated and executed large-scale workflows with thousands of jobs, reduced debugging effort, and allowed non-expert users to construct workflows with expert-level design patterns. These results indicate that end-to-end AI-assisted workflow generation and execution is feasible, and point toward AI-driven platforms for managing the scientific workflow lifecycle.

Recent Artificial Intelligence (AI) models have matched or exceeded human experts in several benchmarks of biomedical task performance, but have lagged behind on surgical image-analysis benchmarks. Since surgery requires integrating disparate tasks -- including multimodal data integration, human interaction, and physical effects -- generally-capable AI models could be particularly attractive as a collaborative tool if performance could be improved. On the one hand, the canonical approach of scaling architecture size and training data is attractive, especially since there are millions of hours of surgical video data generated per year. On the other hand, preparing surgical data for AI training requires significantly higher levels of professional expertise, and training on that data requires expensive computational resources. These trade-offs paint an uncertain picture of whether and to-what-extent modern AI could aid surgical practice. In this paper, we explore this question through a case study of surgical tool detection using state-of-the-art AI methods available in 2026. We demonstrate that even with multi-billion parameter models and extensive training, current Vision Language Models fall short in the seemingly simple task of tool detection in neurosurgery. Additionally, we show scaling experiments indicating that increasing model size and training time only leads to diminishing improvements in relevant performance metrics. Thus, our experiments suggest that current models could still face significant obstacles in surgical use cases. Moreover, some obstacles cannot be simply ``scaled away'' with additional compute and persist across diverse model architectures, raising the question of whether data and label availability are the only limiting factors. We discuss the main contributors to these constraints and advance potential solutions.

Automating enterprise workflows could unlock $4 trillion/year in productivity gains. Despite being of interest to the data management community for decades, the ultimate vision of end-to-end workflow automation has remained elusive. Current solutions rely on process mining and robotic process automation (RPA), in which a bot is hard-coded to follow a set of predefined rules for completing a workflow. Through case studies of a hospital and large B2B enterprise, we find that the adoption of RPA has been inhibited by high set-up costs (12-18 months), unreliable execution (60% initial accuracy), and burdensome maintenance (requiring multiple FTEs). Multimodal foundation models (FMs) such as GPT-4 offer a promising new approach for end-to-end workflow automation given their generalized reasoning and planning abilities. To study these capabilities we propose ECLAIR, a system to automate enterprise workflows with minimal human supervision. We conduct initial experiments showing that multimodal FMs can address the limitations of traditional RPA with (1) near-human-level understanding of workflows (93% accuracy on a workflow understanding task) and (2) instant set-up with minimal technical barrier (based solely on a natural language description of a workflow, ECLAIR achieves end-to-end completion rates of 40%). We identify human-AI collaboration, validation, and self-improvement as open challenges, and suggest ways they can be solved with data management techniques. Code is available at: https://github.com/HazyResearch/eclair-agents

Agentic systems increasingly solve complex user requests by executing orchestrated workflows, where subtasks are assigned to specialized models or tools and coordinated according to their dependencies. While recent work improves agent efficiency by optimizing the performance--cost--latency frontier, real deployments often impose concrete requirements: a workflow must be completed within a specified budget and before a specified deadline. This shifts the goal from average efficiency optimization to maximizing the probability that the entire workflow completes successfully under explicit budget and deadline constraints. We study constraint-driven online resource allocation for agentic workflows. Given a dependency-structured workflow and estimates of success rates and generation lengths for each subtask--model pair, the executor allocates models and parallel samples across simultaneously executable subtasks while managing the remaining budget and time. We formulate this setting as a finite-horizon stochastic online allocation problem and propose Monte Carlo Portfolio Planning (MCPP), a lightweight closed-loop planner that directly estimates constrained completion probability through simulated workflow executions and replans after observed outcomes. Experiments on CodeFlow and ProofFlow demonstrate that MCPP consistently improves constrained completion probability over strong baselines across a wide range of budget--deadline constraints.

Large language models can produce creative and diverse responses. However, to integrate them into current developer workflows, it is essential to constrain their outputs to follow specific formats or standards. In this work, we surveyed 51 experienced industry professionals to understand the range of scenarios and motivations driving the need for output constraints from a user-centered perspective. We identified 134 concrete use cases for constraints at two levels: low-level, which ensures the output adhere to a structured format and an appropriate length, and high-level, which requires the output to follow semantic and stylistic guidelines without hallucination. Critically, applying output constraints could not only streamline the currently repetitive process of developing, testing, and integrating LLM prompts for developers, but also enhance the user experience of LLM-powered features and applications. We conclude with a discussion on user preferences and needs towards articulating intended constraints for LLMs, alongside an initial design for a constraint prototyping tool.

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.

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.

End-to-end automation of realistic healthcare operations stresses three capabilities underrepresented in current benchmarks: policy density, decisions must be grounded in a large library of medical, insurance, and operational rules; Multi-role composition: a single task requires the agent to play multiple roles with handoffs; and multilateral interaction: intermediate workflow steps are multi-turn dialogs, such as peer-to-peer review and patient outreach. We introduce χ-Bench, a benchmark of long-horizon healthcare workflows across three domains: provider prior authorization, payer utilization management, and care management. Each task hands the agent a clinical case in a high-fidelity simulator of 20 healthcare apps exposed via 87 MCP tools, which it must drive to a terminal status through tool calls and writing the role's artifacts, guided by a 1,290+ document managed-care operations handbook skill. Across 30 agent harness/models configurations, the best agent resolves only 28.0% of tasks, no agent clears 20% on strict pass^3, and executing all tasks in a single session slumps the performance to 3.8%. These results raise the hypothesis that similar gaps are likely to surface in other policy-dense, role-composed, irreversible enterprise domains.

Large language models (LLMs) and agentic systems have shown promise for clinical decision support, but existing works largely assume that evidence has already been curated and handed to the model. Real-world clinical workflows instead require agents to actively seek, iteratively plan, and synthesize multimodal evidence from heterogeneous sources. In this paper, we introduce ClinSeekAgent, an automated agentic framework for dynamic multimodal evidence seeking that shifts the paradigm from passive evidence consumption to active evidence acquisition. Given only a clinical query and access to raw data sources, ClinSeekAgent gathers evidence by querying medical knowledge bases, navigating raw EHRs, and invoking medical imaging tools; refines its hypotheses as new information emerges; and integrates the collected evidence into grounded clinical decisions. ClinSeekAgent serves both as an inference-time agent for frontier LLMs and as a training-time pipeline for distilling high-quality agent trajectories into compact open-source models. To validate its inference-time effectiveness, we construct ClinSeek-Bench, which pairs Curated Input reasoning from fixed pre-selected evidence with Automated Evidence-Seeking over raw clinical data. On text-only EHR tasks, ClinSeekAgent improves Claude Opus 4.6 from 60.0 to 63.2 overall F1 and MiniMax M2.5 from 43.1 to 47.3, with positive risk-prediction gains in 7 out of 9 evaluated host models. On multimodal tasks, ClinSeekAgent improves Claude Opus 4.6 from 47.5 to 62.6 (+15.1); all evaluated models improve across the three CXR-related task groups. We further validate ClinSeekAgent as a training pipeline by distilling agentic evidence-seeking trajectories into ClinSeek-35B-A3B, which achieves 34.0 average F1 on existing AgentEHR-Bench, improving over its Qwen3.5-35B-A3B baseline by +11.9 points and approaching Claude Opus 4.6.

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.

Digital healthcare infrastructure is crucial for global medical service delivery. Egypt faces EHR adoption barriers: only 314 hospitals had such systems as of Oct 2024. This limits data management and decision-making. This project introduces an EHR system for Egypt's Universal Health Insurance and healthcare ecosystem. It simplifies data management by centralizing medical histories with a scalable micro-services architecture and polyglot persistence for real-time access and provider communication. Clinical workflows are enhanced via patient examination and history tracking. The system uses the Llama3-OpenBioLLM-70B model to generate summaries of medical histories, provide chatbot features, and generate AI-based medical reports, enabling efficient searches during consultations. A Vision Transformer (ViT) aids in pneumonia classification. Evaluations show the AI excels in capturing details (high recall) but needs improvement in concise narratives. With optimization (retrieval-augmented generation, local data fine-tuning, interoperability protocols), this AI-driven EHR could enhance diagnostic support, decision-making, and healthcare delivery in Egypt.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Reliable clinical decision support requires medical AI agents capable of safe, multi-step reasoning over structured electronic health records (EHRs). While large language models (LLMs) show promise in healthcare, existing benchmarks inadequately assess performance on action-based tasks involving threshold evaluation, temporal aggregation, and conditional logic. We introduce ART, an Action-based Reasoning clinical Task benchmark for medical AI agents, which mines real-world EHR data to create challenging tasks targeting known reasoning weaknesses. Through analysis of existing benchmarks, we identify three dominant error categories: retrieval failures, aggregation errors, and conditional logic misjudgments. Our four-stage pipeline -- scenario identification, task generation, quality audit, and evaluation -- produces diverse, clinically validated tasks grounded in real patient data. Evaluating GPT-4o-mini and Claude 3.5 Sonnet on 600 tasks shows near-perfect retrieval after prompt refinement, but substantial gaps in aggregation (28--64%) and threshold reasoning (32--38%). By exposing failure modes in action-oriented EHR reasoning, ART advances toward more reliable clinical agents, an essential step for AI systems that reduce cognitive load and administrative burden, supporting workforce capacity in high-demand care settings

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/

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.

Healthcare administration accounts for over $1 trillion in annual spending, making it a promising target for LLM-based computer-use agents (CUAs). While clinical applications of LLMs have received significant attention, no benchmark exists for evaluating CUAs on end-to-end administrative workflows. To address this gap, we introduce HealthAdminBench, a benchmark comprising four realistic GUI environments: an EHR, two payer portals, and a fax system, and 135 expert-defined tasks spanning three administrative task types: Prior Authorization, Appeals and Denials Management, and Durable Medical Equipment (DME) Order Processing. Each task is decomposed into fine-grained, verifiable subtasks, yielding 1,698 evaluation points. We evaluate seven agent configurations under multiple prompting and observation settings and find that, despite strong subtask performance, end-to-end reliability remains low: the best-performing agent (Claude Opus 4.6 CUA) achieves only 36.3 percent task success, while GPT-5.4 CUA attains the highest subtask success rate (82.8 percent). These results reveal a substantial gap between current agent capabilities and the demands of real-world administrative workflows. HealthAdminBench provides a rigorous foundation for evaluating progress toward safe and reliable automation of healthcare administrative workflows.

We introduce Baichuan-M3, a medical-enhanced large language model engineered to shift the paradigm from passive question-answering to active, clinical-grade decision support. Addressing the limitations of existing systems in open-ended consultations, Baichuan-M3 utilizes a specialized training pipeline to model the systematic workflow of a physician. Key capabilities include: (i) proactive information acquisition to resolve ambiguity; (ii) long-horizon reasoning that unifies scattered evidence into coherent diagnoses; and (iii) adaptive hallucination suppression to ensure factual reliability. Empirical evaluations demonstrate that Baichuan-M3 achieves state-of-the-art results on HealthBench, the newly introduced HealthBench-Hallu and ScanBench, significantly outperforming GPT-5.2 in clinical inquiry, advisory and safety. The models are publicly available at https://huggingface.co/collections/baichuan-inc/baichuan-m3.

Purpose: Surgical workflow analysis is crucial for improving surgical efficiency and safety. However, previous studies rely heavily on large-scale annotated datasets, posing challenges in cost, scalability, and reliance on expert annotations. To address this, we propose Surg-FTDA (Few-shot Text-driven Adaptation), designed to handle various surgical workflow analysis tasks with minimal paired image-label data. Methods: Our approach has two key components. First, Few-shot selection-based modality alignment selects a small subset of images and aligns their embeddings with text embeddings from the downstream task, bridging the modality gap. Second, Text-driven adaptation leverages only text data to train a decoder, eliminating the need for paired image-text data. This decoder is then applied to aligned image embeddings, enabling image-related tasks without explicit image-text pairs. Results: We evaluate our approach to generative tasks (image captioning) and discriminative tasks (triplet recognition and phase recognition). Results show that Surg-FTDA outperforms baselines and generalizes well across downstream tasks. Conclusion: We propose a text-driven adaptation approach that mitigates the modality gap and handles multiple downstream tasks in surgical workflow analysis, with minimal reliance on large annotated datasets. The code and dataset will be released in https://github.com/CAMMA-public/Surg-FTDA

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.

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.

Sifting through vast textual data and summarizing key information imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown immense promise in natural language processing (NLP) tasks, their efficacy across diverse clinical summarization tasks has not yet been rigorously examined. In this work, we employ domain adaptation methods on eight LLMs, spanning six datasets and four distinct summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Our thorough quantitative assessment reveals trade-offs between models and adaptation methods in addition to instances where recent advances in LLMs may not lead to improved results. Further, in a clinical reader study with six physicians, we depict that summaries from the best adapted LLM are preferable to human summaries in terms of completeness and correctness. Our ensuing qualitative analysis delineates mutual challenges faced by both LLMs and human experts. Lastly, we correlate traditional quantitative NLP metrics with reader study scores to enhance our understanding of how these metrics align with physician preferences. Our research marks the first evidence of LLMs outperforming human experts in clinical text summarization across multiple tasks. This implies that integrating LLMs into clinical workflows could alleviate documentation burden, empowering clinicians to focus more on personalized patient care and other irreplaceable human aspects of medicine.

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.

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.

Hospital administration departments handle a wide range of operational tasks and, in large hospitals, process over 10,000 requests per day, driving growing interest in LLM-based automation. However, prior work has focused primarily on patient-physician interactions or isolated administrative subtasks, failing to capture the complexity of real administrative workflows. To address this gap, we propose H-AdminSim, a comprehensive simulation framework that combines realistic data generation with multi-agent-based simulation of hospital administrative workflows. These tasks are quantitatively evaluated using detailed rubrics, enabling systematic comparison of LLMs. Through FHIR integration, H-AdminSim provides a unified and interoperable environment for testing administrative workflows across heterogeneous hospital settings, serving as a standardized testbed for assessing the feasibility and performance of LLM-driven administrative automation.

Large Language Model (LLM)-based agents have demonstrated strong capabilities across a wide range of tasks, and their application in the medical domain holds particular promise due to the demand for high generalizability and reliance on interdisciplinary knowledge. However, existing medical agent systems often rely on static, manually crafted workflows that lack the flexibility to accommodate diverse diagnostic requirements and adapt to emerging clinical scenarios. Motivated by the success of automated machine learning (AutoML), this paper introduces a novel framework for the automated design of medical agent architectures. Specifically, we define a hierarchical and expressive agent search space that enables dynamic workflow adaptation through structured modifications at the node, structural, and framework levels. Our framework conceptualizes medical agents as graph-based architectures composed of diverse, functional node types and supports iterative self-improvement guided by diagnostic feedback. Experimental results on skin disease diagnosis tasks demonstrate that the proposed method effectively evolves workflow structures and significantly enhances diagnostic accuracy over time. This work represents the first fully automated framework for medical agent architecture design and offers a scalable, adaptable foundation for deploying intelligent agents in real-world clinical environments.

Recent advancements in large language models (LLMs) have driven a revolutionary paradigm shift in process automation from Robotic Process Automation to Agentic Process Automation by automating the workflow orchestration procedure based on LLMs. However, existing LLMs (even the advanced OpenAI GPT-4o) are confined to achieving satisfactory capability in workflow orchestration. To address this limitation, we present WorkflowLLM, a data-centric framework elaborately designed to enhance the capability of LLMs in workflow orchestration. It first constructs a large-scale fine-tuning dataset WorkflowBench with 106,763 samples, covering 1,503 APIs from 83 applications across 28 categories. Specifically, the construction process can be divided into three phases: (1) Data Collection: we collect real-world workflow data from Apple Shortcuts and RoutineHub, transcribing them into Python-style code. We further equip them with generated hierarchical thought via ChatGPT. (2) Query Expansion: we prompt ChatGPT to generate more task queries to enrich the diversity and complexity of workflows. (3) Workflow Generation: we leverage an annotator model trained on collected data to generate workflows for synthesized queries. Finally, we merge the synthetic samples that pass quality confirmation with the collected samples to obtain the WorkflowBench. Based on WorkflowBench, we fine-tune Llama-3.1-8B to obtain WorkflowLlama. Our experiments show that WorkflowLlama demonstrates a strong capacity to orchestrate complex workflows, while also achieving notable generalization performance on previously unseen APIs. Additionally, WorkflowBench exhibits robust zero-shot generalization capabilities on an out-of-distribution task planning dataset, T-Eval. Our data and code are available at https://github.com/OpenBMB/WorkflowLLM.

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/.

Synthetic data is increasingly used to enable the development and evaluation of AI systems in domains where access to real-world data is restricted. In healthcare, clinical documentation presents particular challenges due to its sensitivity. This work introduces a synthetic clinical notes pipeline and dataset designed to support the development of clinical AI tools while avoiding the privacy risks associated with real patient data. The dataset is generated using a modular pipeline that combines structured patient generation, semi-structured patient journey simulation, and unstructured clinical note generation using large language models. The pipeline is designed to prioritise internal consistency across longitudinal patient records, while also capturing variation in writing style, note structure, and clinical detail. Additional mechanisms, including LLM-based validation and augmentation steps, are used to improve faithfulness, realism, and diversity of the generated notes. We release a dataset of 70 synthetic patients, each associated with 20-50 clinical notes spanning a full hospital journey. The dataset is provided at multiple levels of validation, enabling users to balance realism and scalability depending on their use case. This dataset supports the development, testing, and evaluation of clinical AI systems, including summarisation tools, coding models, and decision support systems, without reliance on real patient data.

Machine learning models are often trained to predict the outcome resulting from a human decision. For example, if a doctor decides to test a patient for disease, will the patient test positive? A challenge is that historical decision-making determines whether the outcome is observed: we only observe test outcomes for patients doctors historically tested. Untested patients, for whom outcomes are unobserved, may differ from tested patients along observed and unobserved dimensions. We propose a Bayesian model class which captures this setting. The purpose of the model is to accurately estimate risk for both tested and untested patients. Estimating this model is challenging due to the wide range of possibilities for untested patients. To address this, we propose two domain constraints which are plausible in health settings: a prevalence constraint, where the overall disease prevalence is known, and an expertise constraint, where the human decision-maker deviates from purely risk-based decision-making only along a constrained feature set. We show theoretically and on synthetic data that domain constraints improve parameter inference. We apply our model to a case study of cancer risk prediction, showing that the model's inferred risk predicts cancer diagnoses, its inferred testing policy captures known public health policies, and it can identify suboptimalities in test allocation. Though our case study is in healthcare, our analysis reveals a general class of domain constraints which can improve model estimation in many settings.

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. Labels included annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 teams submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of algorithms. This novel benchmark can be used for comparable evaluation and validation of future work.

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.

Medical coding translates clinical documentation into standardized codes for billing, research, and public health, but manual coding is time-consuming and error-prone. Existing automation efforts rely on small datasets that poorly represent real-world patient heterogeneity. We trained a language model on 5.8 million electronic health records from 1.8 million patients across nearly all specialties in Eastern Denmark (2006--2016) to predict ICD-10 codes from clinical notes, medications, and laboratory results. Evaluated on 270,000 held-out patients, the model achieved a micro F1 of 71.8% and a top-10 recall of 95.5%. Performance varied by specialty (F1: 53--91%), with higher scores in specialties with well-defined diagnostic criteria. Codes appearing predominantly as secondary diagnoses had markedly lower F1 scores. For three such codes (suicide-related behaviors, weight disorders, and hypertension), the model identified thousands of uncoded cases, of which 76-86% were confirmed valid upon manual review, suggesting systematic under-coding rather than model error. These findings suggest under-coding of secondary diagnoses in Eastern Denmark during this period, with potential implications for epidemiological research, public health surveillance, and understanding of multimorbidity. Similar time constraints and reimbursement structures in other healthcare systems suggest this may not be isolated to this dataset. The model can automate coding for approximately 50% of cases and provide accurate suggestions for most others, and may offer a practical solution to help capture missed secondary conditions.

We introduce the Series-Parallel Workflow Decomposition (SP\-WD) heuristic algorithm for the Workflow Scheduling Problem (WSP) decomposition. We demonstrate that the SPWD algorithm facilitates the scheduling of large WSP instances with the hybrid D-Wave Constrained Quadratic Model solver, enabling the scheduling of instances that would otherwise exceed its capacity limitations. We also describe the accompanying execution environment used to obtain the results of the experiments with real-life workflow instances available in the WfCommons standardization initiative repository.

As AI agents become increasingly capable of complex, long-horizon reasoning, rigorous and holistic evaluation is essential for measuring progress toward real-world healthcare applications. We introduce HealthAgentBench, a suite of 54 agentic healthcare tasks across 7 categories each with its unique environment. The benchmark suite spans diverse workflows throughout the patient journey and a broad range of modalities. Each task is designed to replicate an end-to-end clinical workflow: given minimal instructions, an agent must explore raw healthcare data, operate within a complex environment, and execute multi-step solutions that go beyond naive prompting. A final task success rate is reported to provide a single, interpretable metric for HealthAgentBench overall performance for each agent. Evaluating frontier agents on HealthAgentBench, we find that overall task success rate remains low, underscoring the difficulty of the suite. The strongest and the most cost effective agent, Codex GPT-5.5, achieves only approximately 42% success rate. Beyond aggregate performance, HealthAgentBench reveals nuanced strengths and weaknesses across task categories. Frontier agents show promise in automatically developing research modeling pipelines over EHR data, but medical imaging remains especially challenging, particularly for Claude Code models, while Codex GPT-5.5 shows emerging capability. Tasks that combine large search spaces with compositional reasoning requirements remain difficult for all current agents. Together, these results suggest that HealthAgentBench provides a challenging and realistic benchmark with substantial room for future progress. We release our benchmark at https://github.com/microsoft/HealthAgentBench.

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.

Fast Healthcare Interoperability Resources (FHIR) is the dominant standard for interoperable exchange of healthcare data. In FHIR, electronic health records form a directed graph of resources. Answering clinically meaningful questions over FHIR requires agents to perform multi-step reasoning, filtering, and aggregation across multiple resource types. Prior work shows that even tool-augmented LLM agents (retrieval, code execution, multi-turn planning) often select the wrong resources or violate traversal constraints. We study this problem in the context of FHIR-AgentBench, a benchmark for realistic question answering over real-world hospital data, and frame reasoning on FHIR as a sequential decision-making problem over a queryable structured graph. We implement a multi-turn CodeAct agent and post-train it with reinforcement learning using a custom harness and tools. A LLM Judge provides execution-grounded rewards. Compared to prompt-based, closed-model baselines, RL post-training improves performance while enforcing data-integrity constraints. Empirically, our approach improves answer correctness from 50% (o4-mini) to 77% on FHIR-AgentBench using a smaller and cheaper Qwen3-8B model. We present an end-to-end post-training pipeline (environment building, harness construction, model training and custom evaluation) that reliably improves multi-turn reasoning over structured clinical graphs.

In medical education, physicians convert academic knowledge into clinical expertise through residency: years of training across thousands of encounters, with diverse sources of feedback and progressively greater autonomy. Much of clinical reasoning relies on the patient encounter, a dialogue in which a clinician elicits history, refines diagnostic hypotheses, and decides management under uncertainty. While large language models (LLMs) excel on static medical benchmarks, methods to optimize the full sequence of clinical decisions remain underdeveloped. We present ResidencyRL, a reinforcement learning (RL) method for training clinical artificial intelligence (AI) agents through simulated multi-turn clinical encounters (up to 60 dialogue turns and 8 tool calls per trajectory). ResidencyRL pairs the policy agent with LLM simulators capable of complex, adversarial behaviors, training against a structured reward aligned to diagnostic accuracy, management quality, communication, documentation, and safety. On held-out evaluations, the ResidencyRL agent improves diagnostic accuracy by 7.0% under adversarial conditions (88.0% vs. 81.0%) and reduces missed red flag rates by 31%, demonstrating rigorous mitigation of premature closure. Blinded expert clinicians validated these gains, preferring the trained agent in 87.6% of side-by-side comparisons. The procedural competencies transfer to unseen benchmarks: the agent outperforms the base model across all six clinical axes of the AMIE multi-visit benchmark, and shows consistent directional improvements on AgentClinic and CRAFT-MD. Our findings demonstrate that sequential clinical decision-making can be effectively learned through multi-turn RL in simulation, yielding robust, generalizable capabilities, paving the way towards clinical mastery. Prospective validation with real-world workflows remains necessary to establish clinical utility.

Large Language Models (LLMs) have gained significant attention in the medical domain for their human-level capabilities, leading to increased efforts to explore their potential in various healthcare applications. However, despite such a promising future, there are multiple challenges and obstacles that remain for their real-world uses in practical settings. This work discusses key challenges for LLMs in medical applications from four unique aspects: operational vulnerabilities, ethical and social considerations, performance and assessment difficulties, and legal and regulatory compliance. Addressing these challenges is crucial for leveraging LLMs to their full potential and ensuring their responsible integration into healthcare.

Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. Information can be found at https://amos22.grand-challenge.org.

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.

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

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

Medical systematic reviews can be very costly and resource intensive. We explore how Large Language Models (LLMs) can support and be trained to perform literature screening when provided with a detailed set of selection criteria. Specifically, we instruction tune LLaMA and Guanaco models to perform abstract screening for medical systematic reviews. Our best model, Bio-SIEVE, outperforms both ChatGPT and trained traditional approaches, and generalises better across medical domains. However, there remains the challenge of adapting the model to safety-first scenarios. We also explore the impact of multi-task training with Bio-SIEVE-Multi, including tasks such as PICO extraction and exclusion reasoning, but find that it is unable to match single-task Bio-SIEVE's performance. We see Bio-SIEVE as an important step towards specialising LLMs for the biomedical systematic review process and explore its future developmental opportunities. We release our models, code and a list of DOIs to reconstruct our dataset for reproducibility.

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.

Data scarcity is a common obstacle in medical research due to the high costs associated with data collection and the complexity of gaining access to and utilizing data. Synthesizing health data may provide an efficient and cost-effective solution to this shortage, enabling researchers to explore distributions and populations that are not represented in existing observations or difficult to access due to privacy considerations. To that end, we have developed a multi-task self-attention model that produces realistic wearable activity data. We examine the characteristics of the generated data and quantify its similarity to genuine samples with both quantitative and qualitative approaches.

Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage biomedical tools, which clinical experts and biomedical researchers rely on extensively in daily workflows. While recent general-domain tool-calling datasets have substantially improved the capabilities of LLM agents, existing efforts in the biomedical domain largely rely on in-context learning and restrict models to a small set of tools. To address this gap, we introduce BioTool, a comprehensive biomedical tool-calling dataset designed for fine-tuning LLMs. BioTool comprises 34 frequently used tools collected from the NCBI, Ensembl, and UniProt databases, along with 7,040 high-quality, human-verified query-API call pairs spanning variation, genomics, proteomics, evolution, and general biology. Fine-tuning a 4-billion-parameter LLM on BioTool yields substantial improvements in biomedical tool-calling performance, outperforming cutting-edge commercial LLMs such as GPT-5.1. Furthermore, human expert evaluations demonstrate that integrating a BioTool-fine-tuned tool caller significantly improves downstream answer quality compared to the same LLM without tool usage, highlighting the effectiveness of BioTool in enhancing the biomedical capabilities of LLMs. The full dataset and evaluation code are available at https://github.com/gxx27/BioTool

Computer-use agents could automate repetitive screen-based clinical work, but their reliability in medical graphical user interfaces remains largely unvalidated. Existing benchmarks focus on general web or desktop tasks and underrepresent medical software, which requires domain knowledge, exhibits markedly different UI design from mainstream applications, lacks public testing environments, and demands safety validation beyond task completion. We introduce MedCUA-Bench, an interactive benchmark for clinical computer-use agents. It covers 18 clinical scenarios across 10 medical domains, reconstructed from real product manuals and open-source medical systems to capture authentic clinical interfaces while avoiding licensing and privacy constraints. Each task ships with paired intent- and step-level goals to disentangle clinical reasoning from UI execution, and is evaluated by a deterministic checker over task completion and five clinical safety dimensions. Across 23 agents, the best closed-source model reaches 54.2% strict success, while all models remain below 9% on the real OpenEMR. Open-source agents average only 2.5%, with the best reaching 16.2%. MedCUA-Bench exposes the gap between current agents and reliable clinical software use, providing a reproducible testbed for future research.

Clinical protocol-execution tasks -- checking a lab value, applying a threshold, placing a correctly structured FHIR order -- are natural candidates for RL from world feedback: once clinical SMEs encode decision logic into a verifier, that verifier grades unlimited rollouts without per-episode annotation. But applying RL requires a sound feedback channel and sufficient base capability. We audit MedAgentBench v1/v2, find a 41.7\% silent-finish ceiling that makes inaction the RL dominant strategy, and construct MedAgentBench-v3 (MAB-v3) (508 tasks, 8.9\% ceiling). Training Qwen3-8B exposes two structural barriers: a capability ceiling (10/20 task types have 0\% base performance, zero gradient) and a format-knowledge barrier (3/20 types require exact clinical codes undiscoverable by exploration). Pure RL reaches 18.2\% pass@1 vs.\ 34.1\% for rule-based SFT; the 15.9~pp gap is attributable entirely to these barriers. A decision/format-knowledge/lookup taxonomy predicts RL learnability and prescribes the fix: SFT to inject codes, RL to learn conditionals.

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

LLMs hold great promise for healthcare applications, but the rapid evolution of medical knowledge and errors in training data often cause them to generate outdated or inaccurate information, limiting their applicability in high-stakes clinical practice. Model editing has emerged as a potential remedy without full retraining. While parameter-based editing often compromises locality and is thus ill-suited for the medical domain, retrieval-based editing offers a more viable alternative. However, it still faces two critical challenges: (1) representation overlap within the medical knowledge space often causes inaccurate retrieval and reduces editing accuracy; (2) existing methods are restricted to single-sample edits, while batch-editing remains largely unexplored despite its importance for real-world medical applications. To address these challenges, we first construct MedVersa, an enhanced benchmark with broader coverage of medical subjects, designed to evaluate both single and batch edits under strict locality constraints. We then propose MedREK, a retrieval-based editing framework that integrates a shared query-key module for precise matching with an attention-based prompt encoder for informative guidance. Experimental results on various medical benchmarks demonstrate that our MedREK achieves superior performance across different core metrics and provides the first validated solution for batch-editing in medical LLMs. Our code and dataset are available at https://github.com/mylittleriver/MedREK.

Developing clinical prediction models (e.g., mortality prediction) based on electronic health records (EHRs) typically relies on expert opinion for feature selection and adjusting observation window size. This burdens experts and creates a bottleneck in the development process. We propose Retrieval-Enhanced Medical prediction model (REMed) to address such challenges. REMed can essentially evaluate an unlimited number of clinical events, select the relevant ones, and make predictions. This approach effectively eliminates the need for manual feature selection and enables an unrestricted observation window. We verified these properties through experiments on 27 clinical tasks and two independent cohorts from publicly available EHR datasets, where REMed outperformed other contemporary architectures that aim to handle as many events as possible. Notably, we found that the preferences of REMed align closely with those of medical experts. We expect our approach to significantly expedite the development of EHR prediction models by minimizing clinicians' need for manual involvement.

This paper introduces the Opus Workflow Evaluation Framework, a probabilistic-normative formulation for quantifying Workflow quality and efficiency. It integrates notions of correctness, reliability, and cost into a coherent mathematical model that enables direct comparison, scoring, and optimization of Workflows. The framework combines the Opus Workflow Reward, a probabilistic function estimating expected performance through success likelihood, resource usage, and output gain, with the Opus Workflow Normative Penalties, a set of measurable functions capturing structural and informational quality across Cohesion, Coupling, Observability, and Information Hygiene. It supports automated Workflow assessment, ranking, and optimization within modern automation systems such as Opus and can be integrated into Reinforcement Learning loops to guide Workflow discovery and refinement. In this paper, we introduce the Opus Workflow Reward model that formalizes Workflow success as a probabilistic expectation over costs and outcomes. We define measurable Opus Workflow Normative Penalties capturing structural, semantic, and signal-related properties of Workflows. Finally, we propose a unified optimization formulation for identifying and ranking optimal Workflows under joint Reward-Penalty trade-offs.

Optimization underpins decision-making in domains from healthcare to logistics, yet for many practitioners it remains a "magical box": powerful but opaque, difficult to use, and reliant on specialized expertise. While prior work has extensively studied machine learning workflows, the everyday practices of optimization model developers (OMDs) have received little attention. We conducted semi-structured interviews with 15 OMDs across diverse domains to examine how optimization is done in practice. Our findings reveal a highly iterative workflow spanning six stages: problem elicitation, data processing, model development, implementation, validation, and deployment. Importantly, we find that optimization practice is not only about algorithms that deliver better decisions, but is equally shaped by data and dialogue - the ongoing communication with stakeholders that enables problem framing, trust, and adoption. We discuss opportunities for future tooling that foregrounds data and dialogue alongside decision-making, opening new directions for human-centered optimization.

Large language models (LLMs) show promise in medical diagnosis, but real-world deployment remains challenging due to high-stakes clinical decisions and imperfect reasoning reliability. As a result, careful inspection of model behavior is essential for assessing whether diagnostic reasoning is reliable and clinically grounded. However, debugging medical LLMs remains difficult. First, developers often lack sufficient medical domain expertise to interpret model errors in clinically meaningful terms. Second, models can fail across a large and diverse set of instances involving different input types, tasks, and reasoning steps, making it challenging for developers to prioritize which errors deserve focused inspection. Third, developers struggle to identify recurring error patterns across cases, as existing debugging practices are largely instance-centric and rely on manual inspection of isolated failures. To address these challenges, we present VeriLLMed, a visual analytics system that integrates external biomedical knowledge to audit and debug medical LLM diagnostic reasoning. VeriLLMed transforms model outputs into comparable reasoning paths, constructs knowledge graph-grounded reference paths, and identifies three recurring classes of diagnosis errors: relation errors, branch errors, and missing errors. Case studies and expert evaluation demonstrate that VeriLLMed helps developers identify clinically implausible reasoning and generate actionable insights that can inform the improvement of medical LLMs.

Large language model (LLM) agents extend generative models with reasoning, tool use, and persistent memory, thereby enabling the automation of complex tasks. In healthcare, such systems could support documentation, care coordination, and clinical decision making. Their reliable deployment in hospitals, however, remains constrained by safety risks, limited transparency, and inadequate mechanisms for handling longitudinal clinical context. Here we propose an architecture that adapts LLM agents to hospital environments. The design comprises four components: a restricted execution environment inspired by multi-user operating systems, a document-centric interaction model linking patient and clinician agents, a page-indexed memory architecture for longitudinal context management, and a curated library of composable medical skills. Implemented on top of OpenClaw, an open-source agent orchestration framework, this design provides the basis for an Agentic Operating System for Hospitals: a computing layer for coordinating clinical workflows while preserving safety, transparency, and auditability. To evaluate the memory component, we introduce manifest-guided retrieval for hierarchical navigation of longitudinal patient records. In a benchmark derived from the MIMIC-IV dataset (v2.2) comprising 100 de-identified patient records and 300 clinical queries stratified across three difficulty tiers (100 per tier), manifest-guided retrieval matched a metadata-filtered RAG baseline on overall recall (0.877 versus 0.876) while achieving 2.2x higher precision (0.779 versus 0.352) and retrieving fewer documents; on tier-3 longitudinal queries, manifest recall was 21% higher (0.846 versus 0.701), confirming that LLM-guided hierarchical navigation is most valuable when queries span multiple care episodes. These results outline a practical path toward hospital-scale agentic infrastructure.

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.

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.

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 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.

The work in this paper evaluates zero-shot and few-shot large language models (LLMs) for safety-critical clinical action extraction using the CLIP discharge-note dataset, with particular emphasis on transitions of care and post-discharge patient safety. To manage the complexity of clinical documentation, we introduce a two-stage extraction framework that decomposes discharge notes, that are written in narrative form, into fine-grained, explicitly actionable clinical tasks through a staged prompting strategy. Our contributions include a systematic assessment of generative LLMs for clinical action extraction, a detailed comparison between general-purpose LLMs and task-specific supervised BERT-based models, and an analysis of annotation inconsistencies across different action categories. We show that contemporary LLMs achieve performance comparable to or exceeding supervised models on binary actionability detection, while supervised baselines retain a meaningful advantage on fine-grained multi-label category classification, despite the absence of task-specific fine-tuning and under strict data-privacy constraints. Qualitative error analysis reveals that many failures stem from misalignment between model reasoning and dataset annotation conventions, particularly in cases involving implicit clinical actions and rigid structural labeling rules. These results indicate that reported performance reflects model limitations due to lack of clinical reasoning, that is not captured by plain annotations. Labels without rationales make it impossible to distinguish clinical reasoning failures from annotation convention mismatches. Advancing clinical NLP requires reasoning-annotated datasets that document why specific spans are actionable, not merely which spans were labeled, enabling proper evaluation of model clinical understanding.

Research in emergency triage is restricted to structured electronic health records (EHR) due to regulatory constraints on nurse-patient interactions. We introduce TriageSim, a simulation framework for generating persona-conditioned triage conversations from structured records. TriageSim enables multi-turn nurse-patient interactions with explicit control over disfluency and decision behaviour, producing a corpus of ~800 synthetic transcripts and corresponding audio. We use a combination of automated analysis for linguistic, behavioural and acoustic fidelity alongside manual evaluation for medical fidelity using a random subset of 50 conversations. The utility of the generated corpus is examined via conversational triage classification. We observe modest agreement for acuity levels across three modalities: generated synthetic text, ASR transcripts, and direct audio inputs. The code, persona schemata and triage policy prompts for TriageSim will be available upon acceptance.

As modern software systems continue to grow in complexity, triage has become a fundamental process in system operations and maintenance. Triage aims to efficiently prioritize, assign, and assess issues to ensure the reliability of complex environments. The vast amount of heterogeneous data generated by software systems has made effective triage indispensable for maintaining reliability, facilitating maintainability, and enabling rapid issue response. Motivated by these challenges, researchers have devoted extensive effort to advancing triage automation and have achieved significant progress over the past two decades. This survey provides a comprehensive review of 234 papers from 2004 to the present, offering an in-depth examination of the fundamental concepts, system architecture, and problem statement. By comparing the distinct goals of academic and industrial research and by analyzing empirical studies of industrial practices, we identify the major obstacles that limit the practical deployment of triage systems. To assist practitioners in method selection and performance evaluation, we summarize widely adopted open-source datasets and evaluation metrics, providing a unified perspective on the measurement of triage effectiveness. Finally, we outline potential future directions and emerging opportunities to foster a closer integration between academic innovation and industrial application. All reviewed papers and projects are available at https://github.com/AIOps-Lab-NKU/TriageSurvey.

Electronic Health Records (EHRs) contain rich yet complex information, and their automated analysis is critical for clinical decision-making. Despite recent advances of large language models (LLMs) in clinical workflows, their ability to analyze EHRs remains limited due to narrow task coverage and lack of EHR-oriented reasoning capabilities. This paper aims to bridge the gap, specifically, we present EHR-Ins, a large-scale, comprehensive EHR reasoning instruction dataset, comprising 300k high-quality reasoning cases and 4M non-reasoning cases across 42 distinct EHR tasks. Its core innovation is a thinking-graph-driven framework that enables to generate high-quality reasoning data at scale. Based on it, we develop EHR-R1, a series of reasoning-enhanced LLMs with up to 72B parameters tailored for EHR analysis. Through a multi-stage training paradigm, including domain adaptation, reasoning enhancement, and reinforcement learning, EHR-R1 systematically acquires domain knowledge and diverse reasoning capabilities, enabling accurate and robust EHR analysis. Lastly, we introduce EHR-Bench, a new benchmark curated from MIMIC-IV, spanning 42 tasks, to comprehensively assess reasoning and prediction across EHR scenarios. In experiments, we show that the resulting EHR-R1 consistently outperforms state-of-the-art commercial and open-source LLMs (including DeepSeek-V3 and GPT-4o), surpassing GPT-4o by over 30 points on MIMIC-Bench and achieving a 10\% higher zero-shot AUROC on EHRSHOT. Collectively, EHR-Ins, EHR-R1, and EHR-Bench have significantly advanced the development for more reliable and clinically relevant EHR analysis.

Clinical AI development has traditionally followed a collaborative paradigm that depends on close interaction between clinicians and specialized AI teams. This paradigm imposes a practical challenge: clinicians must repeatedly communicate and refine their requirements with AI developers before those requirements can be translated into executable model development. This iterative process is time-consuming, and even after repeated discussion, misalignment may still exist because the two sides do not fully share each other's expertise. However, autonomous coding agents may change this paradigm, raising the possibility that clinicians could develop clinical AI models independently through natural-language interaction alone. In this study, we present such an autonomous prototype for clinician-driven clinical AI development. We evaluated the system on five clinical tasks spanning dermoscopic lesion classification, melanoma-versus-nevus triage, wrist-fracture detection (including a weakly supervised variant with only 5% bounding-box annotations), and debiased pneumothorax classification on chest radiographs. Across these settings, the system consistently developed models from clinician requests and achieved promising performance. Notably, in a debiased pneumothorax classification task on chest radiographs, where chest drains can act as a major confounder, the system successfully mitigated shortcut learning and nearly halved the model's reliance on chest drains. These findings provide proof of concept that autonomous coding agents may help shift clinical AI development toward a more clinician-driven paradigm, reducing the communication overhead and dependence on specialized AI developers. Although further validation and robustness assessment are needed, this study suggests a promising path toward making clinical AI development more accessible.

Healthcare organizations are beginning to embed agentic AI into routine workflows, including clinical documentation support and early-warning monitoring. As these capabilities diffuse across departments and vendors, health systems face agent sprawl, causing duplicated agents, unclear accountability, inconsistent controls, and tool permissions that persist beyond the original use case. Existing AI governance frameworks emphasize lifecycle risk management but provide limited guidance for the day-to-day operations of agent fleets. We propose a Unified Agent Lifecycle Management (UALM) blueprint derived from a rapid, practice-oriented synthesis of governance standards, agent security literature, and healthcare compliance requirements. UALM maps recurring gaps onto five control-plane layers: (1) an identity and persona registry, (2) orchestration and cross-domain mediation, (3) PHI-bounded context and memory, (4) runtime policy enforcement with kill-switch triggers, and (5) lifecycle management and decommissioning linked to credential revocation and audit logging. A companion maturity model supports staged adoption. UALM offers healthcare CIOs, CISOs, and clinical leaders an implementable pattern for audit-ready oversight that preserves local innovation and enables safer scaling across clinical and administrative domains.

High computation costs and latency of large language models such as GPT-4 have limited their deployment in clinical settings. Small language models (SLMs) offer a cost-effective alternative, but their limited capacity requires biomedical domain adaptation, which remains challenging. An additional bottleneck is the unavailability and high sensitivity of clinical data. To address these challenges, we propose a novel framework for adapting SLMs into high-performing clinical models. We introduce the MediPhi collection of 3.8B-parameter SLMs developed with our novel framework: pre-instruction tuning of experts on relevant medical and clinical corpora (PMC, Medical Guideline, MedWiki, etc.), model merging, and clinical-tasks alignment. To cover most clinical tasks, we extended the CLUE benchmark to CLUE+, doubling its size. Our expert models deliver relative improvements on this benchmark over the base model without any task-specific fine-tuning: 64.3% on medical entities, 49.5% on radiology reports, and 44% on ICD-10 coding (outperforming GPT-4-0125 by 14%). We unify the expert models into MediPhi via model merging, preserving gains across benchmarks. Furthermore, we built the MediFlow collection, a synthetic dataset of 2.5 million high-quality instructions on 14 medical NLP tasks, 98 fine-grained document types, and JSON format support. Alignment of MediPhi using supervised fine-tuning and direct preference optimization achieves further gains of 18.9% on average.

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 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.

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.

The objective of this paper is to understand what characteristics and features of clinical data influence physician's decision about ordering laboratory tests or prescribing medications the most. We conduct our analysis on data and decisions extracted from electronic health records of 4486 post-surgical cardiac patients. The summary statistics for 335 different lab order decisions and 407 medication decisions are reported. We show that in many cases, physician's lab-order and medication decisions can be well predicted from a small subset of all features.

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.

Current Large Language Models (LLMs) exhibit significant limitations, notably in structured, interpretable, and verifiable medical reasoning, alongside practical deployment challenges related to computational resources and data privacy. This report focused on the development of WiNGPT-3.0, the 32-billion parameter LLMs, engineered with the objective of enhancing its capacity for medical reasoning and exploring its potential for effective integration within healthcare IT infrastructures. The broader aim is to advance towards clinically applicable models. The approach involved a multi-stage training pipeline tailored for general, medical, and clinical reasoning. This pipeline incorporated supervised fine-tuning (SFT) and reinforcement learning (RL), leveraging curated Long Chain-of-Thought (CoT) datasets, auxiliary reward models, and an evidence-based diagnostic chain simulation. WiNGPT-3.0 demonstrated strong performance: specific model variants achieved scores of 66.6 on MedCalc and 87.1 on MedQA-USMLE. Furthermore, targeted training improved performance on a clinical reasoning task from a baseline score of 58.1 to 62.5. These findings suggest that reinforcement learning, even when applied with a limited dataset of only a few thousand examples, can enhance medical reasoning accuracy. Crucially, this demonstration of RL's efficacy with limited data and computation paves the way for more trustworthy and practically deployable LLMs within clinical workflows and health information infrastructures.

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.

Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in realistic, electronic health record-congruent settings remains limited. Existing benchmarks often rely on static datasets or unstructured inputs that do not reflect the structured, interoperable data formats used in clinical systems. We introduce a pipeline for generating clinically realistic HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems. The pipeline combines staged LLM generation with terminology-grounded validation and repair to reduce hallucinated codes and enforce structural and semantic consistency. Applying this approach to MedCaseReasoning, we construct MedCase-Structured, a synthetic dataset aligned with clinician-authored diagnostic cases, achieving valid FHIR generation for 82.5% of cases. Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

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.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Large language models (LLMs) have demonstrated remarkable potential in solving complex tasks across diverse domains, typically by employing agentic workflows that follow detailed instructions and operational sequences. However, constructing these workflows requires significant human effort, limiting scalability and generalizability. Recent research has sought to automate the generation and optimization of these workflows, but existing methods still rely on initial manual setup and fall short of achieving fully automated and effective workflow generation. To address this challenge, we reformulate workflow optimization as a search problem over code-represented workflows, where LLM-invoking nodes are connected by edges. We introduce AFlow, an automated framework that efficiently explores this space using Monte Carlo Tree Search, iteratively refining workflows through code modification, tree-structured experience, and execution feedback. Empirical evaluations across six benchmark datasets demonstrate AFlow's efficacy, yielding a 5.7% average improvement over state-of-the-art baselines. Furthermore, AFlow enables smaller models to outperform GPT-4o on specific tasks at 4.55% of its inference cost in dollars. The code will be available at https://github.com/geekan/MetaGPT.

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.

Deploying Large Language Models (LLMs) for regulatory compliance demands rigorous traceability via comprehensive citations across multi-tiered authority structures. Unlike traditional multi-hop or legal QA, this task requires structured procedural lookups and evidence-set closure rather than entity resolution or case-law reasoning. Existing RAG systems struggle here due to flattened citation edges, fragmented retrieval expansions, and fragile post-hoc attribution. We formalize Regulatory Compliance QA with RegOps-Bench, a novel benchmark featuring an Operational Knowledge Graph derived from complex national R\&D regulations. To address these bottlenecks, we propose RefWalk, a unified framework driven by a shared topic anchor. RefWalk traverses cross-document citations, fuses multi-view candidates via max-based aggregation, and enforces per-rule attribution to explicitly map claims to sources. We establish a strong baseline with substantial improvements in retrieval recall and citation accuracy. Finally, a contrastive evaluation on a U.S. health compliance dataset (HIPAA) reveals that existing systems exhibit saturation on flat-structure rules, underscoring the need for RegOps-Bench. Our code is available at https://github.com/yeongjoonJu/RefWalk.

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

We survey clinical document corpora, with focus on German textual data. Due to rigid data privacy legislation in Germany these resources, with only few exceptions, are stored in safe clinical data spaces and locked against clinic-external researchers. This situation stands in stark contrast with established workflows in the field of natural language processing where easy accessibility and reuse of data collections are common practice. Hence, alternative corpus designs have been examined to escape from this data poverty. Besides machine translation of English clinical datasets and the generation of synthetic corpora with fictitious clinical contents, several other types of domain proxies have come up as substitutes for authentic clinical documents. Common instances of close proxies are medical journal publications, clinical therapy guidelines, drug labels, etc., more distant proxies include online encyclopedic medical articles or medical contents from social media channels. After PRISM-conformant screening of 359 hits from four bibliographic systems, 75 relevant documents were finally selected for this review and 59 distinct corpora were determined. We identified 24 real clinical corpora (from 40 publications) out of which only 5 are publicly distributable. 2 translations of real corpora and 3 synthetic ones complement the set of clinical corpora. 14 corpora were categorized as close domain proxies, 16 as distant ones. There is a clear divide between the large number of non-accessible authentic clinical German-language corpora and their publicly accessible substitutes: translated or synthetic, close or more distant proxies. So on first sight, the data bottleneck seems broken. Intuitively yet, differences in genre-specific writing style, wording and medical domain expertise in this typological space are also obvious. This raises the question how valid alternative corpus designs really are.

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.

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.

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.

The adoption of large language models (LLMs) to assist clinicians has attracted remarkable attention. Existing works mainly adopt the close-ended question-answering (QA) task with answer options for evaluation. However, many clinical decisions involve answering open-ended questions without pre-set options. To better understand LLMs in the clinic, we construct a benchmark ClinicBench. We first collect eleven existing datasets covering diverse clinical language generation, understanding, and reasoning tasks. Furthermore, we construct six novel datasets and clinical tasks that are complex but common in real-world practice, e.g., open-ended decision-making, long document processing, and emerging drug analysis. We conduct an extensive evaluation of twenty-two LLMs under both zero-shot and few-shot settings. Finally, we invite medical experts to evaluate the clinical usefulness of LLMs. The benchmark data is available at https://github.com/AI-in-Health/ClinicBench.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Electronic health records (EHR) contain extensive structured and unstructured data, including tabular information and free-text clinical notes. Querying relevant patient information often requires complex database operations, increasing the workload for clinicians. However, complex table relationships and professional terminology in EHRs limit the query accuracy. In this work, we construct a publicly available dataset, TQGen, that integrates both Tables and clinical Text for natural language-to-query Generation. To address the challenges posed by complex medical terminology and diverse types of questions in EHRs, we propose TQGen-EHRQuery, a framework comprising a medical knowledge module and a questions template matching module. For processing medical text, we introduced the concept of a toolset, which encapsulates the text processing module as a callable tool, thereby improving processing efficiency and flexibility. We conducted extensive experiments to assess the effectiveness of our dataset and workflow, demonstrating their potential to enhance information querying in EHR systems.

Large language model (LLM)-based systems are becoming increasingly popular for solving tasks by constructing executable workflows that interleave LLM calls, information retrieval, tool use, code execution, memory updates, and verification. This survey reviews recent methods for designing and optimizing such workflows, which we treat as agentic computation graphs (ACGs). We organize the literature based on when workflow structure is determined, where structure refers to which components or agents are present, how they depend on each other, and how information flows between them. This lens distinguishes static methods, which fix a reusable workflow scaffold before deployment, from dynamic methods, which select, generate, or revise the workflow for a particular run before or during execution. We further organize prior work along three dimensions: when structure is determined, what part of the workflow is optimized, and which evaluation signals guide optimization (e.g., task metrics, verifier signals, preferences, or trace-derived feedback). We also distinguish reusable workflow templates, run-specific realized graphs, and execution traces, separating reusable design choices from the structures actually deployed in a given run and from realized runtime behavior. Finally, we outline a structure-aware evaluation perspective that complements downstream task metrics with graph-level properties, execution cost, robustness, and structural variation across inputs. Our goal is to provide a clear vocabulary, a unified framework for positioning new methods, a more comparable view of existing body of literature, and a more reproducible evaluation standard for future work in workflow optimizations for LLM agents.

Understanding the intricate workflows of cataract surgery requires modeling complex interactions between surgical tools, anatomical structures, and procedural techniques. Existing datasets primarily address isolated aspects of surgical analysis, such as tool detection or phase segmentation, but lack comprehensive representations that capture the semantic relationships between entities over time. This paper introduces the Cataract Surgery Scene Graph (CAT-SG) dataset, the first to provide structured annotations of tool-tissue interactions, procedural variations, and temporal dependencies. By incorporating detailed semantic relations, CAT-SG offers a holistic view of surgical workflows, enabling more accurate recognition of surgical phases and techniques. Additionally, we present a novel scene graph generation model, CatSGG, which outperforms current methods in generating structured surgical representations. The CAT-SG dataset is designed to enhance AI-driven surgical training, real-time decision support, and workflow analysis, paving the way for more intelligent, context-aware systems in clinical practice.

We developed an explainable artificial intelligence (AI) early warning score (xAI-EWS) system for early detection of acute critical illness. While maintaining a high predictive performance, our system explains to the clinician on which relevant electronic health records (EHRs) data the prediction is grounded. Acute critical illness is often preceded by deterioration of routinely measured clinical parameters, e.g., blood pressure and heart rate. Early clinical prediction is typically based on manually calculated screening metrics that simply weigh these parameters, such as Early Warning Scores (EWS). The predictive performance of EWSs yields a tradeoff between sensitivity and specificity that can lead to negative outcomes for the patient. Previous work on EHR-trained AI systems offers promising results with high levels of predictive performance in relation to the early, real-time prediction of acute critical illness. However, without insight into the complex decisions by such system, clinical translation is hindered. In this letter, we present our xAI-EWS system, which potentiates clinical translation by accompanying a prediction with information on the EHR data explaining it.

At present, executable visual workflows have emerged as a mainstream paradigm in real-world industrial deployments, offering strong reliability and controllability. However, in current practice, such workflows are almost entirely constructed through manual engineering: developers must carefully design workflows, write prompts for each step, and repeatedly revise the logic as requirements evolve-making development costly, time-consuming, and error-prone. To study whether large language models can automate this multi-round interaction process, we introduce Chat2Workflow, a benchmark for generating executable visual workflows directly from natural language, and propose a robust agentic framework to mitigate recurrent execution errors. Chat2Workflow is built from a large collection of real-world business workflows, with each instance designed so that the generated workflow can be transformed and directly deployed to practical workflow platforms such as Dify and Coze. Experimental results show that while state-of-the-art language models can often capture high-level intent, they struggle to generate correct, stable, and executable workflows, especially under complex or changing requirements. Although our agentic framework yields up to 5.34% resolve rate gains, the remaining real-world gap positions Chat2Workflow as a foundation for advancing industrial-grade automation. Code is available at https://github.com/zjunlp/Chat2Workflow.

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.

Across medical specialties, clinical practice is anchored in evidence-based guidelines that codify best studied diagnostic and treatment pathways. These pathways routinely fall short for the long tail of real-world care not covered by guidelines. Most medical large language models (LLMs), however, are trained to encode common, guideline-focused medical knowledge in their parameters. Current evaluations test models primarily on recalling and reasoning with this memorized content, often in multiple-choice settings. Given the fundamental importance of evidence-based reasoning in medicine, it is neither feasible nor reliable to depend on memorization in practice. To address this gap, we introduce OGCaReBench, a free-form retrieval-focused benchmark aimed at evaluating LLMs at answering clinical questions that require going beyond typical guidelines. Extracted from published medical case reports and validated by medical experts, OGCaReBench contains long-form clinical questions requiring free-text answers, providing a systematic framework for assessing open-ended medical reasoning in rare, case-based scenarios. Our experiments reveal that even the best-performing baseline (GPT-5.2) correctly answers only 56% of our benchmark with specialized models only reaching 42%. Augmenting models with retrieved medical articles improves this performance to up to 82% (using GPT-5.2) highlighting the importance of evidence-grounding for real-world medical reasoning tasks. This work thus establishes a foundation for benchmarking and advancing both general-purpose and medical LLMs to produce reliable answers in challenging clinical contexts.

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.

Clinical case formulation organizes patient symptoms and psychosocial factors into causal models, often using the 5P framework. However, constructing such graphs from therapy transcripts is time consuming and varies across clinicians. We present InsightFlow, an LLM based approach that automatically generates 5P aligned causal graphs from patient-therapist dialogues. Using 46 psychotherapy intake transcripts annotated by clinical experts, we evaluate LLM generated graphs against human formulations using structural (NetSimile), semantic (embedding similarity), and expert rated clinical criteria. The generated graphs show structural similarity comparable to inter annotator agreement and high semantic alignment with human graphs. Expert evaluations rate the outputs as moderately complete, consistent, and clinically useful. While LLM graphs tend to form more interconnected structures compared to the chain like patterns of human graphs, overall complexity and content coverage are similar. These results suggest that LLMs can produce clinically meaningful case formulation graphs within the natural variability of expert practice. InsightFlow highlights the potential of automated causal modeling to augment clinical workflows, with future work needed to improve temporal reasoning and reduce redundancy.

Healthcare automation is shaped by local procedures and organizational constraints, so agent capabilities rarely transfer unchanged across settings. Agent skills, self-contained directories that package reusable procedures for AI agents, are emerging as a procedural layer for adapting healthcare agents across diverse healthcare settings. We present the first empirical analysis of healthcare agent skills, drawing on 557 healthcare-related skills filtered from 58,159 public skills on ClawHub and annotated along ten dimensions covering function, deployment context, autonomy, and safety. We find that public healthcare skills emphasize patient-facing workflow automation and monitoring rather than the diagnostic and treatment-oriented tasks foregrounded in healthcare-agent research; coverage of the healthcare lifecycle and specialized clinical inputs remains uneven; and general technical risk does not reliably capture clinical risk. These findings position healthcare skills as a procedural layer not yet addressed by current benchmarks and risk frameworks.

Benchmarks are necessary for healthcare evaluation, but are not sufficient for predicting deployment performance. Our position is that the evaluation--deployment gap arises not because of poorly designed benchmarks, but from implicit assumptions about how users interact with models that cannot be surfaced from benchmarks alone. To make this precise, we propose a classification of assumptions into two categories: task, which can be tested from conversation data alone, and outcome, which requires outcome data and behavioral studies for testing. Critically, outcome assumptions depend on human behavior, something that even well-designed benchmarks cannot directly observe. To demonstrate the operationality of this framework, we retrospectively analyze a healthcare RCT as a case study and find that the gap naturally separates into task and outcome gaps of roughly equal size. To address this, we make two contributions: first, we propose BenchmarkCards, an artifact that documents assumptions, and second, we propose staged evaluation, a procedure that systematically tests assumptions and evaluates performance.

As unmanned aircraft systems (UASs) continue to integrate into the U.S. National Airspace System (NAS), there is a need to quantify the risk of airborne collisions between unmanned and manned aircraft to support regulation and standards development. Developing and certifying collision avoidance systems often rely on the extensive use of Monte Carlo collision risk analysis simulations using probabilistic models of aircraft flight. To train these models, high performance computing resources are required. We've prototyped a high performance computing workflow designed and deployed on the Lincoln Laboratory Supercomputing Center to process billions of observations of aircraft. However, the prototype has various computational and storage bottlenecks that limited rapid or more comprehensive analyses and models. In response, we have developed a novel workflow to take advantage of various job launch and task distribution technologies to improve performance. The workflow was benchmarked using two datasets of observations of aircraft, including a new dataset focused on the environment around aerodromes. Optimizing how the workflow was parallelized drastically reduced the execution time from weeks to days.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

Access to real-world medical data is often restricted due to privacy regulations, posing a significant barrier to the advancement of healthcare research. Synthetic data offers a promising alternative; however, generating realistic, clinically valid, and privacy-conscious records remains a major challenge. Recent advancements in Large Language Models (LLMs) offer new opportunities for structured data generation; however, existing approaches frequently lack systematic prompting strategies and comprehensive, multi-dimensional evaluation frameworks. In this paper, we present SynLLM, a modular framework for generating high-quality synthetic medical tabular data using 20 state-of-the-art open-source LLMs, including LLaMA, Mistral, and GPT variants, guided by structured prompts. We propose four distinct prompt types, ranging from example-driven to rule-based constraints, that encode schema, metadata, and domain knowledge to control generation without model fine-tuning. Our framework features a comprehensive evaluation pipeline that rigorously assesses generated data across statistical fidelity, clinical consistency, and privacy preservation. We evaluate SynLLM across three public medical datasets, including Diabetes, Cirrhosis, and Stroke, using 20 open-source LLMs. Our results show that prompt engineering significantly impacts data quality and privacy risk, with rule-based prompts achieving the best privacy-quality balance. SynLLM establishes that, when guided by well-designed prompts and evaluated with robust, multi-metric criteria, LLMs can generate synthetic medical data that is both clinically plausible and privacy-aware, paving the way for safer and more effective data sharing in healthcare research.

Gait disorders are commonly observed in older adults, who frequently experience various issues related to walking. Additionally, researchers and clinicians extensively investigate mobility related to gait in typically and atypically developing children, athletes, and individuals with orthopedic and neurological disorders. Effective gait analysis enables the understanding of the causal mechanisms of mobility and balance control of patients, the development of tailored treatment plans to improve mobility, the reduction of fall risk, and the tracking of rehabilitation progress. However, analyzing gait data is a complex task due to the multivariate nature of the data, the large volume of information to be interpreted, and the technical skills required. Existing tools for gait analysis are often limited to specific patient groups (e.g., cerebral palsy), only handle a specific subset of tasks in the entire workflow, and are not openly accessible. To address these shortcomings, we conducted a requirements assessment with gait practitioners (e.g., researchers, clinicians) via surveys and identified key components of the workflow, including (1) data processing and (2) data analysis and visualization. Based on the findings, we designed VIGMA, an open-access visual analytics framework integrated with computational notebooks and a Python library, to meet the identified requirements. Notably, the framework supports analytical capabilities for assessing disease progression and for comparing multiple patient groups. We validated the framework through usage scenarios with experts specializing in gait and mobility rehabilitation. VIGMA is available at https://github.com/komar41/VIGMA.

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.

Clinical trials are pivotal for developing new medical treatments but typically carry risks such as patient mortality and enrollment failure that waste immense efforts spanning over a decade. Applying artificial intelligence (AI) to predict key events in clinical trials holds great potential for providing insights to guide trial designs. However, complex data collection and question definition requiring medical expertise have hindered the involvement of AI thus far. This paper tackles these challenges by presenting a comprehensive suite of 23 meticulously curated AI-ready datasets covering multi-modal input features and 8 crucial prediction challenges in clinical trial design, encompassing prediction of trial duration, patient dropout rate, serious adverse event, mortality rate, trial approval outcome, trial failure reason, drug dose finding, design of eligibility criteria. Furthermore, we provide basic validation methods for each task to ensure the datasets' usability and reliability. We anticipate that the availability of such open-access datasets will catalyze the development of advanced AI approaches for clinical trial design, ultimately advancing clinical trial research and accelerating medical solution development.

Agentic frameworks powered by Large Language Models (LLMs) can be useful tools in scientific workflows by enabling human-AI co-creation. A key challenge is recommending the next steps during workflow creation without relying solely on LLMs, which risk hallucination and require fine-tuning with scarce proprietary data. We propose an episodic memory architecture that stores and retrieves past workflows to guide agents in suggesting plausible next tasks. By matching current workflows with historical sequences, agents can recommend steps based on prior patterns.

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research.

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

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.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

Automatic research with Large Language Models (LLMs) is rapidly gaining importance, driving the development of increasingly complex workflows involving multi-agent systems, planning, tool usage, code execution, and human-agent interaction to accelerate research processes. However, as more researchers and developers begin to use and build upon these tools and platforms, the complexity and difficulty of extending and maintaining such agentic workflows have become a significant challenge, particularly as algorithms and architectures continue to advance. To address this growing complexity, TinyScientist identifies the essential components of the automatic research workflow and proposes an interactive, extensible, and controllable framework that easily adapts to new tools and supports iterative growth. We provide an open-source codebase, an interactive web demonstration, and a PyPI Python package to make state-of-the-art auto-research pipelines broadly accessible to every researcher and developer.

Recent studies have shown that carefully designed workflows coordinating large language models(LLMs) significantly enhance task-solving capabilities compared to using a single model. While an increasing number of works focus on autonomous workflow construction, most existing approaches rely solely on historical experience, leading to limitations in efficiency and adaptability. We argue that while historical experience is valuable, workflow construction should also flexibly respond to the unique characteristics of each task. To this end, we propose an a priori dynamic framework for automated workflow construction. Our framework first leverages Q-table learning to optimize the decision space, guiding agent decisions and enabling effective use of historical experience. At the same time, agents evaluate the current task progress and make a priori decisions regarding the next executing agent, allowing the system to proactively select the more suitable workflow structure for each given task. Additionally, we incorporate mechanisms such as cold-start initialization, early stopping, and pruning to further improve system efficiency. Experimental evaluations on four benchmark datasets demonstrate the feasibility and effectiveness of our approach. Compared to state-of-the-art baselines, our method achieves an average improvement of 4.05%, while reducing workflow construction and inference costs to only 30.68%-48.31% of those required by existing methods.

Workflows are a fundamental component of automation in enterprise platforms, enabling the orchestration of tasks, data processing, and system integrations. Despite being widely used, building workflows can be complex, often requiring manual configuration through low-code platforms or visual programming tools. To simplify this process, we explore the use of generative foundation models, particularly vision-language models (VLMs), to automatically generate structured workflows from visual inputs. Translating hand-drawn sketches or computer-generated diagrams into executable workflows is challenging due to the ambiguity of free-form drawings, variations in diagram styles, and the difficulty of inferring execution logic from visual elements. To address this, we introduce StarFlow, a framework for generating structured workflow outputs from sketches using vision-language models. We curate a diverse dataset of workflow diagrams -- including synthetic, manually annotated, and real-world samples -- to enable robust training and evaluation. We finetune and benchmark multiple vision-language models, conducting a series of ablation studies to analyze the strengths and limitations of our approach. Our results show that finetuning significantly enhances structured workflow generation, outperforming large vision-language models on this task.