Real-World Clinical Workflows

We describe deploying imaging AI at six hospitals through PACS-AI, an open self-hosted platform. The binding constraint is not model accuracy but infrastructure to route studies, display results, capture feedback, and audit what runs. At one center, angiography models completed 515 of 607 jobs (84.8%); failures reflected absent diagnostic views, and 78.1% of 638 clinician ratings were positive. Publishing honest readiness levels for every model is itself a governance practice.

Many publications on robotic systems in healthcare describe early-stage work on low technology readiness levels. This paper describes how a mobile service robot approved as a medical device reaches higher technology readiness levels by adding peripheral functions and smaller improvements, which are pivotal for user acceptance in clinical environments and which often cannot be elicited by questioning users ex-ante as certain aspects only come in mind from testing the systems in clinical settings or operational environments. Especially developers of service robots in healthcare are advised to plan with such downstream developments, which can take significant implementation time, to obtain user acceptance and achieve widespread adoption of their robotic systems.

Large Language Models (LLMs) show great potential as clinical agents, yet existing benchmarks reduce clinical workflows to static predictions or unconstrained Markov Decision Processes (MDPs) with coarse action sets. To address this, we introduce GPAgentBench-2K, the first Constrained MDP (CMDP) LLM-agent benchmark for primary-care clinical decision-making, constructed from expert-validated records of real-world GP encounters. Our environment models a full spectrum of six foundational clinical actions, imposes a topological workflow prior over the action space, and operationalizes safety-informed abstention as a first-class outcome. Evaluating 16 state-of-the-art LLMs reveals a significant performance degradation as the action space scales. Crucially, we uncover a clinical quality-safety gap: even frontier models with the highest diagnosis accuracy violate safety constraints in over half of high-risk cases. Finally, we establish a reference point using Constrained Group Relative Policy Optimization (C-GRPO), and show that while explicitly modeling constraints improves performance over unconstrained RL methods, it remains far from clinically acceptable safety.

Breast Cancer Multidisciplinary Team (MDT) meetings manage increasingly complex cases under considerable time pressure, and documentation requirements can reduce clinical efficiency and decision quality. Existing AI based MDT workflows rely on cloud-based processing, limiting their use because patient discussions contain identifiable information. We developed a fully on-device AI pipeline using open-source Automatic Speech Recognition (ASR) and Large Language Models (LLMs) that transcribes breast cancer MDT discussions, structures clinical information, and generates treatment recommendations using retrieval-augmented generation (RAG) grounded in National Institute for Health and Care Excellence (NICE) guidance. The pipeline runs on a single NVIDIA Jetson AGX Orin, ensuring that patient audio, transcripts, and outputs remain within institutional infrastructure. Evaluation included two recorded simulated MDT discussions, ten clinically validated synthetic discussions, and 1,270 acoustically augmented recordings. Optimisation of Whisper large-v3 reduced word error rate by 20.7% and 24.4% on the recorded discussions and achieved performance within 0.58% WER and 1.58% word information lost of a commercial clinical ASR benchmark on augmented audio. MedGemma-RAG identified 2.3 times more MDT-concordant interventions than a proprietary cloud comparator (p = 0.020), with no significant difference in overall accuracy. Stakeholders identified automated documentation, treatment recommendation support, and case triage as the most credible near-term applications while highlighting workflow integration, governance, and clinician trust as key implementation challenges. These findings demonstrate the feasibility of privacy-preserving, fully on-device AI for MDT documentation and guideline-informed decision support, providing a foundation for prospective clinical evaluation.

Medical devices are becoming more software-intensive, connected, and AI-enabled. Their development requires risk-management evidence aligned with ISO 14971 and, for software, IEC 62304. This evidence must be kept consistent across requirements, design decisions, software changes, verification results, complaints, and post-market data. These tasks are costly and depend on scarce safety and domain experts. Large language models (LLMs) may reduce parts of this effort because medical-device safety work is highly document-based. However, current LLM-based safety-engineering studies often address isolated methods, rely on generic prompting or public examples, and provide limited support for source links, traceability, uncertainty handling, lifecycle updates, and recorded expert review. This limits their use in regulated medical-device development. This paper argues that the central research problem is not safety-text generation, but source-linked safety-knowledge support. We propose an evidence-grounded framework that connects device artifacts, controlled knowledge storage and retrieval, method-specific generation of candidate safety items, critique and uncertainty checks, and recorded expert review. The framework prepares, links, checks, and updates candidate safety artifacts for expert decision-making. It does not decide whether a device is safe and does not provide regulatory approval. We also outline an evaluation strategy using non-public or newly built medical-device case studies and expert reference analyses to assess coverage, correctness, relevance, traceability, duplicate rate, unsupported claims, and review effort.

Hallucinations are a major concern for the integration of artificial intelligence into medicine, although less explored in the realm of medical image processing. Unlike problems in natural text understanding and reasoning therewith, determining whether or not predictions derived from biomedical images and signals is less intuitively clear. This article suggests that topological errors could constitute hallucinations in a way that can be more readily measured and thus regulated. Certain of these properties for certain types of problems, such as biomedical signal segmentation, can be rephrased as linear temporal logic predicates, a number of which can be explicitly enforced using probabilistic graphical models. Our simulations show the potential of these explicitly constrained predicates for the case of automatic surgical phase recognition in robot-assisted hysterectomy, improving accuracy by approximately 10% while removing the vast majority of topological errors, suggesting that mathematical guarantees of correctness can supplement other empirical forms of regulating machine learning in medical image computing and computer-assisted interventions.

Heterogeneous computed tomography (CT) acquisitions and diverse downstream task requirements limit the transferability of fixed data preparation workflows across data sources and tasks. Existing approaches typically rely on manually designed or dataset-specific rules, making it difficult to accommodate changes in acquisition conditions and analytical objectives without manual intervention. Large language model (LLM)-based agents have shown promise for automating medical workflows, yet their potential for adaptive CT data preparation remains largely unexplored. To bridge this gap, we propose CT-PrepAgent, which enables adaptive CT data preparation through a bounded policy and controlled deterministic execution. Deterministic inspection constructs structured data--task profiles, from which a policy decides an eligible DICOM series or predefined preprocessing profile, while the controlled execution flow guards, resolves, executes, and verifies the decision with bounded recovery when enabled and safe quarantine otherwise. Across three public CT segmentation tasks, CT-PrepAgent derived data-task adaptive preprocessing decisions and achieved the highest macro-average Dice. On two private raw-DICOM cohorts, CT-PrepAgent increased verified output yield from 61.7% to 70.0% and yielded similar registration metrics on common verified outputs. Controlled fault and replay tests validate bounded recovery, safe quarantine, and policy-free replay under tested fault and drift settings.

We propose the SECUMAN ontology and shapes for representing and analysing cybersecurity risk-management documentation for medical devices. Cybersecurity risks are increasingly relevant for connected medical devices and may have direct consequences for patient safety. Current risk-management files are often maintained as semi-structured natural language text, which makes consistency checking, certification review, and reuse difficult. SECUMAN provides a formal OWL-based vocabulary for modelling security-risk context, assessment, control measures, and residual-risk evaluation, and uses SHACL constraints to check structural completeness and conformity with the intended documentation model. The ontology is aligned with VDE Spec 90025 and the related RISKMAN ontology and shapes, while extending their safety-oriented approach to concepts relevant to cybersecurity risk documentation such as threat scenarios, protection goals, attacker profiles, exposure levels, assets, and secure design arguments. SECUMAN is intended to support automated first-pass validation, traceability, and integration of cybersecurity and safety risk-management documentation.

Large language models and multimodal foundation models are enabling medical artificial intelligence (AI) systems to move beyond isolated prediction and undertake multistep clinical tasks that require planning, tool use, memory, iterative correction, and coordination among specialized agents. However, the scope of agentic AI in medicine remains unsettled, and current evaluation practices are not yet aligned with the requirements of clinical use. We conducted a scoping review with systematic evidence mapping across five electronic sources, screened 1,649 exportable records, and provisionally included 557 unique studies that met predefined criteria for goal-directed task execution, tool use, interaction with external resources, feedback-based refinement, or multi-agent collaboration. The included studies describe single agents that use external tools, workflows supported by retrieval and external knowledge, multimodal agents, and multi-agent systems applied to medical question answering, image interpretation, electronic health record analysis, drug safety, and clinical trial prediction. The evidence base remains dominated by public benchmarks, simulated settings, retrospective datasets, and small-scale expert evaluation. Process reliability, evidence traceability, uncertainty, safety, workflow impact, and external validity are evaluated less consistently. Clinical translation will depend on clearer definitions, reproducible evaluation, auditable oversight, interoperable system design, and prospective validation in real-world clinical workflows.

The introduction of new technologies, such as surgical robots, is driving the vision of a connected, smart operating room (OR). However, realizing this vision requires a deep understanding of surgical workflows, which relies on realistic datasets capturing the actions of all OR personnel from both full room and surgical field perspectives. Acquiring such data in real ORs is prohibitively challenging due to factors such as ethics committee approvals, limited space for camera installation, and sterility regulations preventing the use of tracking markers. We present a step-by-step methodology for re-enacting complete surgical procedures in a reconstructed OR. This approach enables the creation of repeatable and annotatable workflow datasets for training activity recognition models, generating scene graphs, and formalizing surgical process models. Developed for robot-assisted ophthalmic surgery, our methodology combines expert consultation, structured workflow formalization, OR reconstruction, role-based training, real OR observation, and iterative recording with post-take debriefing. We provide concrete recommendations to allow other research groups to seamlessly adopt this methodology for their own surgical domains.

Clinical biomarker workflows in translational research settings often rely on spreadsheet-driven tracking, manual quality control (QC) reconciliation, and loosely integrated systems, resulting in limited state visibility, delayed reporting, and increased operational risk. These challenges are particularly pronounced in multi-day assays such as Luminex-based quantification of Fragile X Messenger Ribonucleoprotein (FMRP), where HIPAA-compliant data governance, deterministic workflow progression, and coordinated communication across laboratory and clinical teams are required. This paper presents FMRP-LEAN, a HIPAA-compliant, AI-augmented Laboratory Information Management System (LIMS) architecture that formalizes biospecimen lifecycle management through a finite-state workflow model with explicit transition guards and dwell-time observability. The system integrates a self-hosted Supabase/PostgreSQL stack deployed within hospital-controlled infrastructure, hybrid edge-internal isolation with encrypted tunneling and loopback-only services, and bi-directional REDCap synchronization. A unified MRN-UUIDv7 identifier framework with QR-based tracking ensures traceable clinical-research linkage under PHI residency constraints. FMRP-LEAN incorporates automated statistical QC pre-screening and a governance-constrained AI operations module that operates exclusively on aggregate projections, with deterministic fallback guarantees. Deployment demonstrates improved workflow observability, reduced QC latency, and enhanced cross-role transparency between laboratory technicians, research coordinators, and patient-facing teams. The architecture provides a reproducible model for secure, state-explicit, and AI-augmented clinical research workflows in regulated healthcare environments.

Rehabilitation scoring systems are most useful when their outputs can be reviewed and interpreted within clinical workflows. This study presents PhaseAware, a compact framework for continuous rehabilitation quality assessment that combines a temporal backbone with phase- and body-group descriptors through a backbone-conditioned gated residual pathway. The model was evaluated on the UI-PRMD deep-squat protocol and further tested on the KIMORE squatting subset. On UI-PRMD, PhaseAware achieved an RMSE of 0.0230, corresponding to an 88.9% reduction relative to the accepted baseline. It also maintained favorable performance on KIMORE, suggesting that the phase-aware design transfers across related squatting protocols. In addition to score prediction, PhaseAware generates structured review cues based on phase- and body-level sensitivity, highlighting the movement stages and body regions most relevant to each prediction. The architecture employs a backbone-conditioned gated residual mechanism to stabilize feature representation, supporting use in resource-constrained settings. These cues are intended to support clinician review, boundary-case monitoring, and human-in-the-loop triage rather than autonomous decision-making. Overall, PhaseAware offers a practical and interpretable approach to rehabilitation scoring that may help integrate automated assessment into information systems while preserving clinician oversight.

Ensuring safety in Physical AI systems operating in real-world environments is a critical challenge, particularly in hospital wards where vulnerable patients, clinical staff, medical devices, and assistive robots coexist. In this paper, we reinterpret Clinical Pathways as explicit runtime safety specifications for embodied medical AI. We propose a conceptual robotic architecture that integrates wearable sensors, smart medical devices, and assistive robotic components into a unified framework for real-time safety monitoring. At its core, a Runtime Safety Monitor (RSM) evaluates multimodal physiological and system-level signals against clinically defined constraints derived from the prescribed care process. Rather than relying solely on statistical anomaly detection, the proposed approach combines temporal prediction, uncertainty-aware reasoning, and constraint-based verification to identify safety violations. The RSM targets three classes of events: physiological deviations from prescribed care, hardware and communication failures, and potential data tampering or misuse. This work contributes to Safe Physical AI by operationalizing domain-specific clinical knowledge as enforceable safety constraints, bridging learning-based perception and runtime safety monitoring to assist nursing staff in real-world hospital wards.

Computed Tomography (CT) diagnosis often relies on dynamic selection of imaging phases, such as non-contrast, arterial, or venous phases, based on preliminary findings, clinical suspicion, and diagnostic guidelines. This phase-wise decision process is critical for reducing unnecessary radiation exposure while supporting timely staging and treatment planning. However, phase-selection protocols can vary across hospitals, regions, and guidelines, while most existing CT-based AI methods assume that all phases are available and focus on static tasks under a fixed imaging phase, failing to model whether additional phases are required. This limitation stems from heterogeneous multi-phase representations, the need for knowledge-guided phase control beyond visual cues, and the lack of supervision for phase-sufficiency decisions in existing datasets. To address these challenges, we propose Policy-Driven CT-Agent (PD-CTAgent) for clinically consistent CT phase selection and diagnostic reasoning. PD-CTAgent introduces a Clinical Structure Abstraction Module (CSAM) to harmonize heterogeneous CT phases into a unified, phase-aware evidence representation. Based on this representation, a Knowledge-Guided Diagnostic Control Model (KDCM) evaluates phase sufficiency and iteratively requests additional phases when necessary. The policy-driven agent design further allows PD-CTAgent to flexibly follow different institutional, regional, or guideline-specific diagnostic protocols. Together, PD-CTAgent bridges static CT analysis and real-world clinical workflows. Experiments on two public datasets, LIDC and MCT-LTDiag, and one private dataset demonstrate its effectiveness and clinical consistency. Code will be made public upon acceptance.

Autonomous computational pathology (ACP) converts high-level pathology analysis goals into executable, traceable and clinically bounded workflows. Realizing this capability requires adapting general agentic harness systems to pathology-specific tasks, tools, evidence standards and clinical claim boundaries. We contribute ACP-Bench, a framework that adapts existing harness systems from computational pathology support toward ACP workflow capability. ACP-Bench evaluates 41 pathology workflow tasks, including 24 biomarker, 7 morphology and 10 prognosis tasks spanning 6 body-system groups and 9 endpoint families. The benchmark evaluates 9 models and 3 harness groups (Claude Code, Codex and Open Code), yielding 369 complete trajectories. ACP-Bench evaluates each trajectory across workflow execution, diagnostic performance and clinical-boundary alignment, combining expert-adjudicated process audits, diagnostic assessment and pathologist-validated safety review. Across evaluated systems, workflow initiation, task interpretation and diagnostic reporting were more mature than tool-bound execution, result binding and reflective workflow revision, and formal end-to-end completion remained rare. ACP-Bench provides a reusable standard for auditing whether agentic systems can operationalize pathology workflows before claims of reliable clinical autonomy.

Agent-based AI has enabled the automation of tasks by exposing application tools and resources to large language models (LLMs). However, to improve scope and accuracy, agents are often given access rights that exceed those of ordinary users, introducing significant security risks. AI is routinely integrated into applications with a disregard to security, risking data exposure and breaching regulations. This paper applies the AI Trust, Risk, and Security Management (TRiSM) framework to a medical report-generation application to demonstrate how an insecure agent workflow can be transformed into security-conscious agentic workflow. Both workflows were evaluated across five LLMs (Claude Haiku 4.5, GPT-4.1-nano, GPT-4.1-mini, GPT-5.4-mini, and Gemini 2.5 Flash) on two report types, totalling 800 generations and 500 attack scenarios including RAG poisoning, data-field injection, and client-side network injection. The TRiSM-guided agentic workflow reduced mean attack success rates from 31% to 10% for RAG poisoning and from 42% to 25% for data-field injection, while eliminating the network injection vector entirely through server-side prompt construction. Furthermore, report accuracy increased by 14 percentage points (72.5% to 86.5%) with the agentic workflow, demonstrating a secure design which provides more reliable outputs. This paper contributes to knowledge by demonstrating least-privilege, defence in depth agentic workflows improving security and accuracy, while also highlighting model choice is a necessary architectural consideration.

Standardized assessment of uterine MRI remains challenging due to anatomical variability, observer dependence, and the lack of workflow-integrated automated analysis tools. This work presents Female-RHINO: (R)eproductive (H)ealth (I)maging A(N)alysis T(O)ol, a real-time AI-assisted framework for automated quantitative uterine MRI analysis and structured reporting during image acquisition. We present an end-to-end system that integrates inline communication with the MRI scanner and deep learning-based analysis to derive quantitative uterine biomarkers from sagittal T2-weighted pelvic MRI. The framework combines segmentation and anatomical landmark detection models trained and evaluated on more than 500 multi-center datasets spanning diverse protocols, vendors, and patient populations. It performs volumetry, detects and quantifies common incidental findings such as fibroids and Nabothian cysts, and extracts six anatomical landmarks for biometric assessment. Results are compiled into a structured clinician-oriented report with integrated visualizations, without manual interaction. Evaluation on independent retrospective and prospective cohorts demonstrated robust performance across varying acquisition settings. Mean Dice similarity coefficients were 0.82 for the uterus and 0.80 for fibroids, with lower but consistent agreement for Nabothian cysts. Landmark detection achieved a mean radial error of 3.7 mm. End-to-end processing was completed in under 70 seconds, enabling availability of results during the ongoing scan. Prospective deployment yielded immediate, standardized, and reproducible analyses supported by inter-observer agreement. The proposed system enables real-time scanner-integrated AI for automated uterine MRI analysis and reporting, with potential to improve standardization, efficiency, and clinical workflow in pelvic imaging.

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

Computational pathology has advanced rapidly with the emergence of foundation models, yet widespread adoption remains limited by substantial technical complexity and programming requirements. Here we present PathLab, an autonomous agentic framework that translates natural-language research objectives into executable and validated computational pathology workflows through the structured composition of domain-specific skills and tools. By organizing workflow generation around reusable methodological modules, including data preprocessing, model development, evaluation and interpretation, PathLab enables studies to be specified at the level of scientific intent rather than implementation details. We evaluated PathLab across 12 public datasets spanning four representative task families: region-of-interest classification, whole-slide image classification, segmentation and survival prediction. Across all task categories, PathLab achieved non-inferior performance relative to expert implementations, while consistently enforcing semantic validity of user prompts and proactively rejecting incompatible workflow specifications prior to execution. In controlled user studies, PathLab substantially reduced the time required to generate executable analytical pipelines and enabled domain experts without programming experience to independently design, execute and evaluate computational pathology studies. Together, these results establish PathLab as a reliable interface between biomedical intent and computational execution, enabling computational pathology studies to be designed at the level of scientific questions rather than programming expertise. By lowering technical barriers to advanced AI methodologies, PathLab provides a foundation for the broader democratization of computational pathology.

Linking FDA-approved medical devices to their underlying United States Patent and Trademark Office (USPTO) patents enables critical applications such as recall root-cause analysis, M&A-driven IP discovery, and technology trajectory mapping. However, this cross-domain entity linking task remains unexplored due to severe semantic gaps: FDA documents focus on clinical outcomes, while patents describe technical mechanisms, yielding minimal lexical overlap. We formalize medical device-patent linking as a challenging cross-domain entity linking problem characterized by label scarcity and domain shifts. Using cardiovascular devices as a high-impact, representative domain featuring diverse technologies, high recall rates, and abundant disclosures, we construct a benchmark with 434 devices, 698K patents, and 585 high-fidelity expert-verified pairs. To address these challenges, we propose Bridge-MedDevKG, a coarse-to-fine framework that integrates (1) MedDevOnto, a domain-specific ontology that anchors device concepts via three-tier UMLS normalization; (2) Multi-signal candidate generation fusing company affiliation, semantic similarity, and ontology-weighted entity overlap; and (3) Heterogeneous reranking with multi-signal scoring and XGBoost classification on hard negatives. Our approach achieves a conservative lower-bound recall of 91.6% on the gold standard with 50.9% noise reduction, substantially outperforming LLM baselines under comparable evaluation. The resulting MedDevKG provides 6.8M high-confidence links, laying a scalable foundation for regulatory-IP integration across medical specialties.

Background: Dermatology AI has mainly focused on image-based diagnosis, while chronic disease workflows have received less attention. We surveyed Indian dermatologists to map routine clinical challenges, with a focus on atopic dermatitis (AD), and assess current AI use. Methods: A nationwide cross-sectional survey commissioned by the Society for Eczema Studies included 377 practicing Indian dermatologists. The survey assessed clinical challenges, AD workflow barriers, AI use, adoption barriers, and ethical concerns. Analyses used descriptive statistics, chi-square tests, false discovery rate correction, and multivariable logistic regression. Results: Patient adherence (61.3%) and treatment planning in difficult or refractory cases (57.0%) were reported more often than diagnostic uncertainty (48.0%). In AD care, severity scoring was reported as a challenge by 47.7% and had the lowest satisfaction among measured workflow areas. Current AI use was reported by 49.9%, most often involving general large language models for literature synthesis, documentation, and academic tasks rather than specialized image analysis. Barriers differed by experience: dermatologists with more than 20 years of practice more often cited lack of training, while those with 5 years or less more often cited lack of clinical utility after trying AI tools. AI users were more likely than non-users to report concern about patient self-misdiagnosis and anxiety, which remained significant after adjustment for experience and academic affiliation. Conclusion: Respondents reported using general-purpose AI mainly for cognitive and administrative tasks, while their clinical needs centered on chronic disease management and AD workflow support. Clinician-supervised workflow tools may be more useful than standalone diagnostic applications.

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.

Autonomous agents are increasingly expected to support end-to-end medical-AI research workflows, moving beyond isolated prediction tasks or short-form clinical question answering. However, existing medical agent benchmarks primarily evaluate final outputs, providing limited visibility into agent behavior within the research process. To address this gap, we present AutoMedBench, a workflow-aware benchmark for autonomous medical-AI research across diverse medical imaging and multimodal inference tasks, organizing agent execution into a unified five-stage workflow (S1-S5): Plan, Setup, Validate, Inference, and Submit. It comprises long-horizon tasks with each run averaging 33 agent turns, spanning five research tracks: segmentation, image enhancement, visual question answering (VQA), report generation, and lesion detection. Each task is evaluated under two difficulty tiers, Lite and Standard, which use the same data and metrics but differ in the amount of task-brief scaffolding, and each run is scored using both final task performance and S1-S5 stage scores, enabling stage-level analysis from the initial task brief to the final submitted artifact. Across thousands of recorded runs, stage-level scoring reveals that Validate is the weakest workflow stage on average, whereas Setup is the strongest, suggesting that current agents are better at making pipelines executable than at verifying their reliability. Post-run error analysis further shows that verification and submission failures dominate tagged errors, accounting for 37.7% and 38.1% of fired codes respectively, whereas task-understanding errors are rare at 0.9%, and runs with one fired error code have a 48% lower overall score than runs with no error code on average.

This work proposes a context-aware middleware for medical workflow organization and efficiency improvement. In hospitals, laboratories and teleradiology companies, each physician or technician is specialized in a specific kind of diagnosis or analysis. Therefore, certain types of medical images are often forwarded to a certain physician or a certain group. This forwarding is time consuming. That is, repeatedly deciding who would be the best physician, whether he is available at a certain moment given a certain context is exhaustive and may be very inefficient. Thus, the proposed middleware has the ability to process and collect data from images analyzed by each medical staff. Based on the collected data and current clinical context, the middleware is able to infer who would be the best fit staff to receive a certain incoming medical image.

Clinical decision-making (CDM) is central to real-world clinical workflows, where clinicians infer diagnoses, select treatments, or anticipate future health outcomes under incomplete evidence. LLMs are increasingly used to support these decisions due to strong language capabilities, broad biomedical knowledge, and efficiency, yet the reliability of LLMs on real-world clinical decision tasks remains insufficiently understood. To evaluate CDM models, especially LLM-based models, an ideal and practical medical decision benchmark should be constructed via an automated yet reliable pipeline to ensure both scale and quality. Moreover, the grounding of a CDM benchmark in real patient EHRs can better support evaluation on practical CDM tasks that require substantive biomedical knowledge and clinical inference. To fill the gaps, we introduce EHRBench, an automated and reliable EHR-grounded benchmark for evaluating LLM-based clinical decision-making at scale. To ensure scalability and reliability, EHRBench is constructed through an EHR-LLM-KB(knowledge-base) interaction pipeline. For efficiency, we use a specialized LLM to automatically convert encounter-level EHR trajectories into structured templates and deterministically instantiate the templates into QA items. In parallel, we apply systematic KB-based verification and enrichment to filter hallucinated or ambiguous relations and to improve reliability. Using this pipeline, we construct nearly 1M (960,067) QA items spanning three core inference-required clinical decision tasks: diagnosis, treatment, and prognosis. We benchmark more than 30 representative LLMs on EHRBench and provide detailed analyses of performance and robustness. The results show consistent capability trends across settings, further validating the reliability of EHRBench and highlighting actionable gaps toward clinically reliable LLM systems.

Medical AI agents increasingly use external tools for diagnosis, treatment recommendation, and evidence retrieval, yet most existing approaches assume that task-appropriate tools are reliable within their intended scope. This assumption is fragile in real clinical settings, where even relevant tools may fail on challenging instances and lead to unsafe downstream decisions. To address this issue, we study medical tool use under imperfect-tool settings to correct failure instances missed by individual tools. Instance-dependent failure patterns create a gap between the best fixed single tool and an ideal instance-wise selector, which we refer to as the Single-Oracle risk gap. The core challenge is that conventional task-level tool selection cannot realize this gap, as it is inherently bounded by the performance of the best single tool. Motivated by this observation, we therefore account for instance-level heterogeneity and formulate tool use as an instance-level selection problem. Particularly, we propose a GRPO-based reinforcement learning framework with rewards for probabilistic risk minimization and disagreement-aware synergy learning, which promotes instance-level correction of erroneous tool consensus. Furthermore, an entropy-guided sampling strategy is adopted to upweight high-disagreement instances, which provide stronger signals for learning instance-specific tool synergy. These two components complement each other in mitigating instance-level heterogeneity and improving tool synergy. Experiments on two tasks and seven medical benchmarks show that our method consistently achieves robust and stable improvements over a broad range of baselines, highlighting the importance of synergy-aware tool use for reliable medical agentic systems.

Clinical pathways are disseminated as visual flowcharts where spatial topology, arrow direction, colour coding, and font weight encode critical triage logic that remains inaccessible to computational systems. We present PathWISE, a five-phase pipeline combining four LLM-based agents with a deterministic depth-first search auditor and a Java compiler critic, transforming these non-computable artefacts into validated, executable HL7 Clinical Quality Language (CQL) libraries deployable as FHIR CDS Hooks services. Purpose-built agents extract flowchart structure into a typed directed graph, perform deterministic path enumeration, conduct a structured semantic audit of every node's computability, generate terminology-constrained CQL definitions verified by the official Java CQL-to-ELM compiler, and produce routing logic covering 100% of enumerated patient journeys. Demonstrated across five UK NHS cancer pathways (colorectal, lung, skin, upper GI, and breast), PathWISE audits up to 183 nodes (182 under the Hybrid configuration), identifies 544 structured governance findings across four issue categories, achieves 100% syntactic compilation success, with UNCOMPUTABLE nodes receiving false placeholders that preserve compilability while surfacing governance gaps for clinical review, and produces zero hallucinated terminology codes for dictionary-covered concepts. Critically, PathWISE confines non-deterministic LLM inference to knowledge extraction while deterministic graph mathematics and a standard compiler underpin every verification step.

Adverse Outcome Pathways (AOP) are logic models that causally link biological mechanisms that can be measured in a lab to adverse outcomes, relevant to chemical regulatory endpoints. AOPs contextualize new approach methodologies (NAMs), in vitro and in silico methods used as alternatives to animal testing and the sequential events in an AOP serve as multi-scale models spanning biological scales. The AOP-Wiki serves as the global repository for AOPs. While the AOP-Wiki has played a central role in AOP expansion over the past decade, constraints within the current data model and application infrastructure limit the AOP-Wiki from supporting continued AOP growth and evolution. Yet, the transformative power of agentic AI has re-invigorated AOP-Wiki data modernization efforts at a time when core AOP principles can be harnessed to inform use of AI for aggregating and structuring AOP-relevant information. Seizing upon this momentum, we present AOP-Wiki EMOD 3.0, the third in a series of evidence model prototypes, which concretely demonstrates data model expansions and our vision for how the AOP-Wiki might be transformed to better serve regulatory science and emergent use of AOPs in biomedical and One Health contexts. We aim to lay a foundation to support computationally-generated AOPs and quantitative AOPs (qAOPs) by focussing on solutions for AOP-Wiki internal quality improvement, evidence structuring to enhance AOP FAIRness and AI-readiness, and improved integration between the AOP framework and NAMs to better serve next generation risk assessment.

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.

Existing medical-agent benchmarks deliver imaging as pre-selected samples, never as an environment the agent must navigate. We introduce ABRA, a radiology-agent benchmark in which the agent operates an OHIF viewer and an Orthanc DICOM server through twenty-one function-calling tools that span slice navigation, windowing, series selection, pixel-coordinate annotation, and structured reporting. ABRA contains 655 programmatically generated tasks across three difficulty tiers and eight types (viewer control, metadata QA, vision probe, annotation, longitudinal comparison, BI-RADS reporting, and oracle variants of annotation and BI-RADS reporting), drawn from LIDC-IDRI, Duke Breast Cancer MRI, and NLST New-Lesion LongCT. Each episode is scored along Planning, Execution, and Outcome (Bluethgen et al., 2025) by task-type-specific automatic scorers. Ten current models, five closed-weight and five open-weight, reach at least 89% Execution on real annotation but only 0-25% Outcome; on the paired oracle variant where a simulated detector supplies the finding, Outcome on the same task reaches 69-100% across the models evaluated, localising the bottleneck to perception rather than tool orchestration. Code, task generators, and scorers are released at https://github.com/Luab/ABRA

Clinical decision-making in emergency medicine demands rapid, accurate diagnoses under uncertainty. Despite benchmark progress, evidence for LLMs as interactive aids in live physician workflows remains sparse. MedSyn lets physicians iteratively query an LLM provided with the full clinical record while initially viewing only the chief complaint. Seven physicians (three seniors, four residents) completed baseline and AI-assisted sessions across 52 MIMIC-IV cases stratified by difficulty. Blinded evaluation showed residents' Hard-case correctness rose from 0.589 to 0.734; difficulty-standardised completely-correct rates confirmed a medium effect (Δ = 0.092; p = 0.071; d = 0.47). Automated metrics corroborated these gains: standardised any-match accuracy improved by 0.156 (p < 0.0001), and residents showed the largest F1 gain (Δ = 0.138; p < 0.0001). Dialogue analysis revealed expertise-dependent strategies (seniors asked targeted, hypothesis-driven questions; residents relied on broader queries) and cross-expertise concordance increased (Δ = 0.145; p < 0.0001). Interactive LLM support meaningfully enhances diagnostic reasoning.

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.

Evaluating large language models (LLMs) for medical applications remains challenging due to benchmark saturation, limited data accessibility, and insufficient coverage of relevant tasks. Existing suites have either saturated, heavily depend on restricted datasets, or lack comprehensive model coverage. We introduce Medmarks, a fully open-source evaluation suite with 30 benchmarks spanning question answering, information extraction, medical calculations, and open-ended clinical reasoning. We perform a systematic evaluation of 61 models across 71 configurations using verifiable metrics and LLM-as-a-Judge. Our results show that frontier reasoning models (Gemini 3 Pro Preview, GPT-5.1, & GPT-5.2) achieve the highest performance across both benchmarks, most frontier proprietary models are significantly more token efficient than open-weight alternatives, medically fine-tuned models outperform their generalist counterparts, and that models are susceptible to answer-order bias (particularly smaller models and Grok 4). A subset of our evals (Medmarks-T) can be directly used as reinforcement learning environments to post-train LLMs for medical reasoning. Code is available at https://github.com/MedARC-AI/Medmarks

With the emergence of large language models (LLMs) and AI agent frameworks, the human-AI co-work paradigm known as Vibe Coding is changing how people code, making it more accessible and productive. In scientific research, where workflows are more complex and the burden of specialized labor limits independent researchers and those in low-resource areas, the potential impact is even greater, particularly in biomedicine, which involves heterogeneous data modalities and multi-step analytical pipelines. In this paper, we introduce Vibe Medicine, a co-work paradigm in which clinicians and researchers direct skill-augmented AI agents through natural language to execute complex, multi-step biomedical workflows, while retaining the role of research director who specifies objectives, reviews intermediate results, and makes domain-informed decisions. The enabling infrastructure consists of three layers: capable LLMs, agent frameworks such as OpenClaw and Hermes Agent, and the OpenClaw medical skills collection, which includes more than 1,000 curated skills from multiple open-source repositories. We analyze the architecture and skill categories of this collection across ten biomedical domains, and present case studies covering rare disease diagnosis, drug repurposing, and clinical trial design that demonstrate end-to-end workflows in practice. We also identify the principal risks, such as hallucination, data privacy, and over-reliance, and outline directions toward more reliable, trustworthy, and clinically integrated agent-assisted research that advances research and technological equity and reduces health care resource disparities.

The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by fragmented distribution, inconsistent documentation, complex dependencies, and difficult-to-reproduce execution environments. As a result, reusing published tools and workflow adaptation to own date remains technically demanding and time-intensive, even for experienced users. Here, we present PoSyMed, an open and modular platform for the controlled integration, composition, and execution of bioinformatics tools and workflows. PoSyMed combines a backend-centered platform architecture with formal tool descriptions, controlled container-based build and execution processes, persistent workflow state, and a dialogue-based user interface. Large language models (LLM) are integrated not as autonomous decision-makers, but as human-computer interface with bounded semantic assistants that help identify tools, propose workflow steps, and support parameterization within a typed, validated, and human-supervised execution environment. PoSyMed is designed to improve reproducibility, traceability, and transparency in practical biomedical analysis within one platform. We describe the system architecture and evaluate its behavior across representative biological software scenarios with respect to workflow support, interaction design, and platform extensibility. PoSyMed is publicly available at https://apps.cosy.bio/posymed.

Safe clinical deployment of Large Language Models (LLMs) requires not only high accuracy but also robust uncertainty calibration to ensure models defer to clinicians when appropriate. Our paper investigates how social descriptors of a patient (specifically sexual orientation and religious affiliation) distort these uncertainty signals and model accuracy. Evaluating nine general-purpose and biomedical LLMs on 2,364 medical questions and their counterfactual variants, we demonstrate that identity markers cause a "calibration crisis". "Homosexual" markers consistently trigger performance drops, and intersectional identities produce idiosyncratic, non-additive harms to calibration. Moreover, a clinician-validated case study in an open-ended generation setting confirms that these failures are not an artifact of the multiple-choice format. Our results demonstrate that the presence of social identity cues does not merely shift predictions; it affects the reliability of confidence signals, posing a significant risk to equitable care and safe deployment in confidence-based clinical workflows.

Clinical ultrasound analysis demands models that generalize across heterogeneous organs, views, and devices, while supporting interpretable workflow-level analysis. Existing methods often rely on task-wise adaptation, and joint learning may be unstable due to cross-task interference, making it hard to deliver workflow-level outputs in practice. To address these challenges, we present USTri, a tri-stage ultrasound intelligence pipeline for unified multi-organ, multi-task analysis. Stage I trains a universal generalist USGen on different domains to learn broad, transferable priors that are robust to device and protocol variability. To better handle domain shifts and reach task-aligned performance while preserving ultrasound shared knowledge, Stage II builds USpec by keeping USGen frozen and finetuning dataset-specific heads. Stage III introduces USAgent, which mimics clinician workflows by orchestrating USpec specialists for multi-step inference and deterministic structured reports. On the FMC_UIA validation set, our model achieves the best overall performance across 4 task types and 27 datasets, outperforming state-of-the-art methods. Moreover, qualitative results show that USAgent produces clinically structured reports with high accuracy and interpretability. Our study suggests a scalable path to ultrasound intelligence that generalizes across heterogeneous ultrasound tasks and supports consistent end-to-end clinical workflows. The code is publicly available at: https://github.com/MacDunno/USTri.

Accurate segmentation of anatomical structures in medical images is essential for diagnosis and treatment planning. While recent interactive segmentation foundation models enhance generalization through large-scale multimodal pretraining, they still depend on precise prompts and can fail in underrepresented clinical contexts (e.g., small organs-at-risk). We present AtlasSegFM, an atlas-guided framework that customizes off-the-shelf foundation models to new clinical contexts with a single annotated example. AtlasSegFM 1) performs atlas-query registration to generate context-aware prompts, 2) refines the segmentation with a frozen foundation model, and 3) applies a lightweight adaptive fusion module to combine atlas priors with foundation-model inputs and predictions. Extensive experiments on six public and in-house datasets across radiotherapy and vascular scenarios show consistent gains, with the largest improvements on small and delicate structures. AtlasSegFM provides a lightweight, deployable solution for one-shot customization of segmentation foundation models in real-world clinical workflows.