Daily Papers

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

The 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 .

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.

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.

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

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Agentic systems built on large language models (LLMs) offer promising capabilities for automating complex workflows in healthcare AI. We introduce mAIstro, an open-source, autonomous multi-agentic framework for end-to-end development and deployment of medical AI models. The system orchestrates exploratory data analysis, radiomic feature extraction, image segmentation, classification, and regression through a natural language interface, requiring no coding from the user. Built on a modular architecture, mAIstro supports both open- and closed-source LLMs, and was evaluated using a large and diverse set of prompts across 16 open-source datasets, covering a wide range of imaging modalities, anatomical regions, and data types. The agents successfully executed all tasks, producing interpretable outputs and validated models. This work presents the first agentic framework capable of unifying data analysis, AI model development, and inference across varied healthcare applications, offering a reproducible and extensible foundation for clinical and research AI integration. The code is available at: https://github.com/eltzanis/mAIstro

While holding great promise for improving and facilitating healthcare, large language models (LLMs) struggle to produce up-to-date responses on evolving topics due to outdated knowledge or hallucination. Retrieval-augmented generation (RAG) is a pivotal innovation that improves the accuracy and relevance of LLM responses by integrating LLMs with a search engine and external sources of knowledge. However, the quality of RAG responses can be largely impacted by the rank and density of key information in the retrieval results, such as the "lost-in-the-middle" problem. In this work, we aim to improve the robustness and reliability of the RAG workflow in the medical domain. Specifically, we propose a map-reduce strategy, BriefContext, to combat the "lost-in-the-middle" issue without modifying the model weights. We demonstrated the advantage of the workflow with various LLM backbones and on multiple QA datasets. This method promises to improve the safety and reliability of LLMs deployed in healthcare domains.

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.

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.

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

The integration of Artificial Intelligence (AI) into clinical settings presents a software engineering challenge, demanding a shift from isolated models to robust, governable, and reliable systems. However, brittle, prototype-derived architectures often plague industrial applications and a lack of systemic oversight, creating a ``responsibility vacuum'' where safety and accountability are compromised. This paper presents an industry case study of the ``Maria'' platform, a production-grade AI system in primary healthcare that addresses this gap. Our central hypothesis is that trustworthy clinical AI is achieved through the holistic integration of four foundational engineering pillars. We present a synergistic architecture that combines Clean Architecture for maintainability with an Event-driven architecture for resilience and auditability. We introduce the Agent as the primary unit of modularity, each possessing its own autonomous MLOps lifecycle. Finally, we show how a Human-in-the-Loop governance model is technically integrated not merely as a safety check, but as a critical, event-driven data source for continuous improvement. We present the platform as a reference architecture, offering practical lessons for engineers building maintainable, scalable, and accountable AI-enabled systems in high-stakes domains.

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

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.

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

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

Large language models (LLMs) have enabled a new class of agentic AI systems that reason, plan, and act by invoking external tools. However, most existing agentic architectures remain centralized and monolithic, limiting scalability, specialization, and interoperability. This paper proposes a framework for scalable agentic intelligence, termed the Internet of Agentic AI, in which autonomous, heterogeneous agents distributed across cloud and edge infrastructure dynamically form coalitions to execute task-driven workflows. We formalize a network-native model of agentic collaboration and introduce an incentive-compatible workflow-coalition feasibility framework that integrates capability coverage, network locality, and economic implementability. To enable scalable coordination, we formulate a minimum-effort coalition selection problem and propose a decentralized coalition formation algorithm. The proposed framework can operate as a coordination layer above the Model Context Protocol (MCP). A healthcare case study demonstrates how domain specialization, cloud-edge heterogeneity, and dynamic coalition formation enable scalable, resilient, and economically viable agentic workflows. This work lays the foundation for principled coordination and scalability in the emerging era of Internet of Agentic AI.

Focused Ultrasound Ablation Surgery (FUAS) has emerged as a promising non-invasive therapeutic modality, valued for its safety and precision. Nevertheless, its clinical implementation entails intricate tasks such as multimodal image interpretation, personalized dose planning, and real-time intraoperative decision-making processes that demand intelligent assistance to improve efficiency and reliability. We introduce FUAS-Agents, an autonomous agent system that leverages the multimodal understanding and tool-using capabilities of large language models (LLMs). By integrating patient profiles and MRI data, FUAS-Agents orchestrates a suite of specialized medical AI tools, including segmentation, treatment dose prediction, and clinical guideline retrieval, to generate personalized treatment plans comprising MRI image, dose parameters, and therapeutic strategies. We evaluate the system in a uterine fibroid treatment scenario. Human assessment by four senior FUAS experts indicates that 82.5%, 82.5%, 87.5%, and 97.5% of the generated plans were rated 4 or above (on a 5-point scale) in terms of completeness, accuracy, fluency, and clinical compliance, respectively. These results demonstrate the potential of LLM-driven agents in enhancing decision-making across complex clinical workflows, and exemplify a translational paradigm that combines general-purpose models with specialized expert systems to solve practical challenges in vertical healthcare domains.

The increasing administrative burden of medical documentation, particularly through Electronic Health Records (EHR), significantly reduces the time available for direct patient care and contributes to physician burnout. To address this issue, we propose MediNotes, an advanced generative AI framework designed to automate the creation of SOAP (Subjective, Objective, Assessment, Plan) notes from medical conversations. MediNotes integrates Large Language Models (LLMs), Retrieval-Augmented Generation (RAG), and Automatic Speech Recognition (ASR) to capture and process both text and voice inputs in real time or from recorded audio, generating structured and contextually accurate medical notes. The framework also incorporates advanced techniques like Quantized Low-Rank Adaptation (QLoRA) and Parameter-Efficient Fine-Tuning (PEFT) for efficient model fine-tuning in resource-constrained environments. Additionally, MediNotes offers a query-based retrieval system, allowing healthcare providers and patients to access relevant medical information quickly and accurately. Evaluations using the ACI-BENCH dataset demonstrate that MediNotes significantly improves the accuracy, efficiency, and usability of automated medical documentation, offering a robust solution to reduce the administrative burden on healthcare professionals while improving the quality of clinical workflows.

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.

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.

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.

EHR audit logs are a highly granular stream of events that capture clinician activities, and is a significant area of interest for research in characterizing clinician workflow on the electronic health record (EHR). Existing techniques to measure the complexity of workflow through EHR audit logs (audit logs) involve time- or frequency-based cross-sectional aggregations that are unable to capture the full complexity of a EHR session. We briefly evaluate the usage of transformer-based tabular language model (tabular LM) in measuring the entropy or disorderedness of action sequences within workflow and release the evaluated models publicly.

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

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.

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.

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

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.

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

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/.

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

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

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

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.

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.

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

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.

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.

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

Large Action Models (LAMs) have revolutionized intelligent automation, but their application in healthcare faces challenges due to privacy concerns, latency, and dependency on internet access. This report introduces an ondevice, multi-agent healthcare assistant that overcomes these limitations. The system utilizes smaller, task-specific agents to optimize resources, ensure scalability and high performance. Our proposed system acts as a one-stop solution for health care needs with features like appointment booking, health monitoring, medication reminders, and daily health reporting. Powered by the Qwen Code Instruct 2.5 7B model, the Planner and Caller Agents achieve an average RougeL score of 85.5 for planning and 96.5 for calling for our tasks while being lightweight for on-device deployment. This innovative approach combines the benefits of ondevice systems with multi-agent architectures, paving the way for user-centric healthcare solutions.

Continuity of care is crucial to ensuring positive health outcomes for patients discharged from an inpatient hospital setting, and improved information sharing can help. To share information, caregivers write discharge notes containing action items to share with patients and their future caregivers, but these action items are easily lost due to the lengthiness of the documents. In this work, we describe our creation of a dataset of clinical action items annotated over MIMIC-III, the largest publicly available dataset of real clinical notes. This dataset, which we call CLIP, is annotated by physicians and covers 718 documents representing 100K sentences. We describe the task of extracting the action items from these documents as multi-aspect extractive summarization, with each aspect representing a type of action to be taken. We evaluate several machine learning models on this task, and show that the best models exploit in-domain language model pre-training on 59K unannotated documents, and incorporate context from neighboring sentences. We also propose an approach to pre-training data selection that allows us to explore the trade-off between size and domain-specificity of pre-training datasets for this task.

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.

Hospitals and healthcare systems rely on operational decisions that determine patient flow, cost, and quality of care. Despite strong performance on medical knowledge and conversational benchmarks, foundation models trained on general text may lack the specialized knowledge required for these operational decisions. We introduce Lang1, a family of models (100M-7B parameters) pretrained on a specialized corpus blending 80B clinical tokens from NYU Langone Health's EHRs and 627B tokens from the internet. To rigorously evaluate Lang1 in real-world settings, we developed the REalistic Medical Evaluation (ReMedE), a benchmark derived from 668,331 EHR notes that evaluates five critical tasks: 30-day readmission prediction, 30-day mortality prediction, length of stay, comorbidity coding, and predicting insurance claims denial. In zero-shot settings, both general-purpose and specialized models underperform on four of five tasks (36.6%-71.7% AUROC), with mortality prediction being an exception. After finetuning, Lang1-1B outperforms finetuned generalist models up to 70x larger and zero-shot models up to 671x larger, improving AUROC by 3.64%-6.75% and 1.66%-23.66% respectively. We also observed cross-task scaling with joint finetuning on multiple tasks leading to improvement on other tasks. Lang1-1B effectively transfers to out-of-distribution settings, including other clinical tasks and an external health system. Our findings suggest that predictive capabilities for hospital operations require explicit supervised finetuning, and that this finetuning process is made more efficient by in-domain pretraining on EHR. Our findings support the emerging view that specialized LLMs can compete with generalist models in specialized tasks, and show that effective healthcare systems AI requires the combination of in-domain pretraining, supervised finetuning, and real-world evaluation beyond proxy benchmarks.

Reproducibility remains a significant challenge in machine learning (ML) for healthcare. In this field, datasets, model pipelines, and even task/cohort definitions are often private, leading to a significant barrier in sharing, iterating, and understanding ML results on electronic health record (EHR) datasets. In this paper, we address a significant part of this problem by introducing the Automatic Cohort Extraction System for Event-Stream Datasets (ACES). This tool is designed to simultaneously simplify the development of task/cohorts for ML in healthcare and enable the reproduction of these cohorts, both at an exact level for single datasets and at a conceptual level across datasets. To accomplish this, ACES provides (1) a highly intuitive and expressive configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion/exclusion criteria, and (2) a pipeline to automatically extract patient records that meet these defined criteria from real-world data. ACES can be automatically applied to any dataset in either the Medical Event Data Standard (MEDS) or EventStreamGPT (ESGPT) formats, or to *any* dataset for which the necessary task-specific predicates can be extracted in an event-stream form. ACES has the potential to significantly lower the barrier to entry for defining ML tasks, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies in this modality. ACES is available at https://github.com/justin13601/aces.

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.

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.

Surgical workflow recognition has numerous potential medical applications, such as the automatic indexing of surgical video databases and the optimization of real-time operating room scheduling, among others. As a result, phase recognition has been studied in the context of several kinds of surgeries, such as cataract, neurological, and laparoscopic surgeries. In the literature, two types of features are typically used to perform this task: visual features and tool usage signals. However, the visual features used are mostly handcrafted. Furthermore, the tool usage signals are usually collected via a manual annotation process or by using additional equipment. In this paper, we propose a novel method for phase recognition that uses a convolutional neural network (CNN) to automatically learn features from cholecystectomy videos and that relies uniquely on visual information. In previous studies, it has been shown that the tool signals can provide valuable information in performing the phase recognition task. Thus, we present a novel CNN architecture, called EndoNet, that is designed to carry out the phase recognition and tool presence detection tasks in a multi-task manner. To the best of our knowledge, this is the first work proposing to use a CNN for multiple recognition tasks on laparoscopic videos. Extensive experimental comparisons to other methods show that EndoNet yields state-of-the-art results for both tasks.

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

Addressing the imminent shortfall of 10 million health workers by 2030, predominantly in Low- and Middle-Income Countries (LMICs), this paper introduces an innovative approach that harnesses the power of Large Language Models (LLMs) integrated with machine translation models. This solution is engineered to meet the unique needs of Community Health Workers (CHWs), overcoming language barriers, cultural sensitivities, and the limited availability of medical dialog datasets. I have crafted a model that not only boasts superior translation capabilities but also undergoes rigorous fine-tuning on open-source datasets to ensure medical accuracy and is equipped with comprehensive safety features to counteract the risks of misinformation. Featuring a modular design, this approach is specifically structured for swift adaptation across various linguistic and cultural contexts, utilizing open-source components to significantly reduce healthcare operational costs. This strategic innovation markedly improves the accessibility and quality of healthcare services by providing CHWs with contextually appropriate medical knowledge and diagnostic tools. This paper highlights the transformative impact of this context-aware LLM, underscoring its crucial role in addressing the global healthcare workforce deficit and propelling forward healthcare outcomes in LMICs.

Healthcare systems continuously generate vast amounts of electronic health records (EHRs), commonly stored in the Fast Healthcare Interoperability Resources (FHIR) standard. Despite the wealth of information in these records, their complexity and volume make it difficult for users to retrieve and interpret crucial health insights. Recent advances in Large Language Models (LLMs) offer a solution, enabling semantic question answering (QA) over medical data, allowing users to interact with their health records more effectively. However, ensuring privacy and compliance requires edge and private deployments of LLMs. This paper proposes a novel approach to semantic QA over EHRs by first identifying the most relevant FHIR resources for a user query (Task1) and subsequently answering the query based on these resources (Task2). We explore the performance of privately hosted, fine-tuned LLMs, evaluating them against benchmark models such as GPT-4 and GPT-4o. Our results demonstrate that fine-tuned LLMs, while 250x smaller in size, outperform GPT-4 family models by 0.55% in F1 score on Task1 and 42% on Meteor Task in Task2. Additionally, we examine advanced aspects of LLM usage, including sequential fine-tuning, model self-evaluation (narcissistic evaluation), and the impact of training data size on performance. The models and datasets are available here: https://huggingface.co/genloop

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.

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.

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.

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.

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.

In this study, we provide solutions to two practical yet overlooked scenarios in federated learning for electronic health records (EHRs): firstly, we introduce EHRFL, a framework that facilitates federated learning across healthcare institutions with distinct medical coding systems and database schemas using text-based linearization of EHRs. Secondly, we focus on a scenario where a single healthcare institution initiates federated learning to build a model tailored for itself, in which the number of clients must be optimized in order to reduce expenses incurred by the host. For selecting participating clients, we present a novel precision-based method, leveraging data latents to identify suitable participants for the institution. Our empirical results show that EHRFL effectively enables federated learning across hospitals with different EHR systems. Furthermore, our results demonstrate the efficacy of our precision-based method in selecting reduced number of participating clients without compromising model performance, resulting in lower operational costs when constructing institution-specific models. We believe this work lays a foundation for the broader adoption of federated learning on EHRs.

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.

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.

With the advent of Large Language Models (LLMs), medical artificial intelligence (AI) has experienced substantial technological progress and paradigm shifts, highlighting the potential of LLMs to streamline healthcare delivery and improve patient outcomes. Considering this rapid technical progress, in this survey, we trace the recent advances of Medical Large Language Models (Med-LLMs), including the background, key findings, and mainstream techniques, especially for the evolution from general-purpose models to medical-specialized applications. Firstly, we delve into the foundational technology of Med-LLMs, indicating how general models can be progressively adapted and refined for the complicated medical tasks. Secondly, the wide-ranging applications of Med-LLMs are investigated across various healthcare domains, as well as an up-to-date review of existing Med-LLMs. The transformative impact of these models on daily medical practice is evident through their ability to assist clinicians, educators, and patients. Recognizing the importance of responsible innovation, we discuss the challenges associated with ensuring fairness, accountability, privacy, and robustness. Ethical considerations, rigorous evaluation methodologies, and the establishment of regulatory frameworks are crucial for building trustworthiness in the real-world system. We emphasize the need for ongoing scrutiny and development to maintain high standards of safety and reliability. Finally, we anticipate possible future trajectories for Med-LLMs, identifying key avenues for prudent expansion. By consolidating these insights, our review aims to provide professionals and researchers with a thorough understanding of the strengths and limitations of Med-LLMs, fostering a balanced and ethical approach to their integration into the healthcare ecosystem.

Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.

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.

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.

Understanding the workflow of surgical procedures in complex operating rooms requires a deep understanding of the interactions between clinicians and their environment. Surgical activity recognition (SAR) is a key computer vision task that detects activities or phases from multi-view camera recordings. Existing SAR models often fail to account for fine-grained clinician movements and multi-view knowledge, or they require calibrated multi-view camera setups and advanced point-cloud processing to obtain better results. In this work, we propose a novel calibration-free multi-view multi-modal pretraining framework called Multiview Pretraining for Video-Pose Surgical Activity Recognition PreViPS, which aligns 2D pose and vision embeddings across camera views. Our model follows CLIP-style dual-encoder architecture: one encoder processes visual features, while the other encodes human pose embeddings. To handle the continuous 2D human pose coordinates, we introduce a tokenized discrete representation to convert the continuous 2D pose coordinates into discrete pose embeddings, thereby enabling efficient integration within the dual-encoder framework. To bridge the gap between these two modalities, we propose several pretraining objectives using cross- and in-modality geometric constraints within the embedding space and incorporating masked pose token prediction strategy to enhance representation learning. Extensive experiments and ablation studies demonstrate improvements over the strong baselines, while data-efficiency experiments on two distinct operating room datasets further highlight the effectiveness of our approach. We highlight the benefits of our approach for surgical activity recognition in both multi-view and single-view settings, showcasing its practical applicability in complex surgical environments. Code will be made available at: https://github.com/CAMMA-public/PreViPS.

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

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.

De-identification of electronic health records (EHR) is a vital step towards advancing health informatics research and maximising the use of available data. It is a two-step process where step one is the identification of protected health information (PHI), and step two is replacing such PHI with surrogates. Despite the recent advances in automatic de-identification of EHR, significant obstacles remain if the abundant health data available are to be used to the full potential. Accuracy in de-identification could be considered a necessary, but not sufficient condition for the use of EHR without individual patient consent. We present here a comprehensive review of the progress to date, both the impressive successes in achieving high accuracy and the significant risks and challenges that remain. To best of our knowledge, this is the first paper to present a complete picture of end-to-end automatic de-identification. We review 18 recently published automatic de-identification systems -designed to de-identify EHR in the form of free text- to show the advancements made in improving the overall accuracy of the system, and in identifying individual PHI. We argue that despite the improvements in accuracy there remain challenges in surrogate generation and replacements of identified PHIs, and the risks posed to patient protection and privacy.

The advancement in healthcare has shifted focus toward patient-centric approaches, particularly in self-care and patient education, facilitated by access to Electronic Health Records (EHR). However, medical jargon in EHRs poses significant challenges in patient comprehension. To address this, we introduce a new task of automatically generating lay definitions, aiming to simplify complex medical terms into patient-friendly lay language. We first created the README dataset, an extensive collection of over 50,000 unique (medical term, lay definition) pairs and 300,000 mentions, each offering context-aware lay definitions manually annotated by domain experts. We have also engineered a data-centric Human-AI pipeline that synergizes data filtering, augmentation, and selection to improve data quality. We then used README as the training data for models and leveraged a Retrieval-Augmented Generation method to reduce hallucinations and improve the quality of model outputs. Our extensive automatic and human evaluations demonstrate that open-source mobile-friendly models, when fine-tuned with high-quality data, are capable of matching or even surpassing the performance of state-of-the-art closed-source large language models like ChatGPT. This research represents a significant stride in closing the knowledge gap in patient education and advancing patient-centric healthcare solutions.

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.

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

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

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

The deployment of large language models (LLMs) within the healthcare sector has sparked both enthusiasm and apprehension. These models exhibit the remarkable capability to provide proficient responses to free-text queries, demonstrating a nuanced understanding of professional medical knowledge. This comprehensive survey delves into the functionalities of existing LLMs designed for healthcare applications, elucidating the trajectory of their development, starting from traditional Pretrained Language Models (PLMs) to the present state of LLMs in healthcare sector. First, we explore the potential of LLMs to amplify the efficiency and effectiveness of diverse healthcare applications, particularly focusing on clinical language understanding tasks. These tasks encompass a wide spectrum, ranging from named entity recognition and relation extraction to natural language inference, multi-modal medical applications, document classification, and question-answering. Additionally, we conduct an extensive comparison of the most recent state-of-the-art LLMs in the healthcare domain, while also assessing the utilization of various open-source LLMs and highlighting their significance in healthcare applications. Furthermore, we present the essential performance metrics employed to evaluate LLMs in the biomedical domain, shedding light on their effectiveness and limitations. Finally, we summarize the prominent challenges and constraints faced by large language models in the healthcare sector, offering a holistic perspective on their potential benefits and shortcomings. This review provides a comprehensive exploration of the current landscape of LLMs in healthcare, addressing their role in transforming medical applications and the areas that warrant further research and development.

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.

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.

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

We aim to present a comprehensive overview of the latest advancements in utilizing Large Language Models (LLMs) within the healthcare sector, emphasizing their transformative impact across various medical domains. LLMs have become pivotal in supporting healthcare, including physicians, healthcare providers, and patients. Our review provides insight into the applications of Large Language Models (LLMs) in healthcare, specifically focusing on diagnostic and treatment-related functionalities. We shed light on how LLMs are applied in cancer care, dermatology, dental care, neurodegenerative disorders, and mental health, highlighting their innovative contributions to medical diagnostics and patient care. Throughout our analysis, we explore the challenges and opportunities associated with integrating LLMs in healthcare, recognizing their potential across various medical specialties despite existing limitations. Additionally, we offer an overview of handling diverse data types within the medical field.

The evaluation of Large Language Models (LLMs) in healthcare has been dominated by physician-centric, English-language benchmarks, creating a dangerous illusion of competence that ignores the interprofessional nature of patient care. To provide a more holistic and realistic assessment, we introduce HealthQA-BR, the first large-scale, system-wide benchmark for Portuguese-speaking healthcare. Comprising 5,632 questions from Brazil's national licensing and residency exams, it uniquely assesses knowledge not only in medicine and its specialties but also in nursing, dentistry, psychology, social work, and other allied health professions. We conducted a rigorous zero-shot evaluation of over 20 leading LLMs. Our results reveal that while state-of-the-art models like GPT 4.1 achieve high overall accuracy (86.6%), this top-line score masks alarming, previously unmeasured deficiencies. A granular analysis shows performance plummets from near-perfect in specialties like Ophthalmology (98.7%) to barely passing in Neurosurgery (60.0%) and, most notably, Social Work (68.4%). This "spiky" knowledge profile is a systemic issue observed across all models, demonstrating that high-level scores are insufficient for safety validation. By publicly releasing HealthQA-BR and our evaluation suite, we provide a crucial tool to move beyond single-score evaluations and toward a more honest, granular audit of AI readiness for the entire healthcare team.

Machine learning (ML) approaches have demonstrated promising results in a wide range of healthcare applications. Data plays a crucial role in developing ML-based healthcare systems that directly affect people's lives. Many of the ethical issues surrounding the use of ML in healthcare stem from structural inequalities underlying the way we collect, use, and handle data. Developing guidelines to improve documentation practices regarding the creation, use, and maintenance of ML healthcare datasets is therefore of critical importance. In this work, we introduce Healthsheet, a contextualized adaptation of the original datasheet questionnaire ~gebru2018datasheets for health-specific applications. Through a series of semi-structured interviews, we adapt the datasheets for healthcare data documentation. As part of the Healthsheet development process and to understand the obstacles researchers face in creating datasheets, we worked with three publicly-available healthcare datasets as our case studies, each with different types of structured data: Electronic health Records (EHR), clinical trial study data, and smartphone-based performance outcome measures. Our findings from the interviewee study and case studies show 1) that datasheets should be contextualized for healthcare, 2) that despite incentives to adopt accountability practices such as datasheets, there is a lack of consistency in the broader use of these practices 3) how the ML for health community views datasheets and particularly Healthsheets as diagnostic tool to surface the limitations and strength of datasets and 4) the relative importance of different fields in the datasheet to healthcare concerns.

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

Building agents, systems that perceive and act upon their environment with a degree of autonomy, has long been a focus of AI research. This pursuit has recently become vastly more practical with the emergence of large language models (LLMs) capable of using natural language to integrate information, follow instructions, and perform forms of "reasoning" and planning across a wide range of tasks. With its multimodal data streams and orchestrated workflows spanning multiple systems, radiology is uniquely suited to benefit from agents that can adapt to context and automate repetitive yet complex tasks. In radiology, LLMs and their multimodal variants have already demonstrated promising performance for individual tasks such as information extraction and report summarization. However, using LLMs in isolation underutilizes their potential to support complex, multi-step workflows where decisions depend on evolving context from multiple information sources. Equipping LLMs with external tools and feedback mechanisms enables them to drive systems that exhibit a spectrum of autonomy, ranging from semi-automated workflows to more adaptive agents capable of managing complex processes. This review examines the design of such LLM-driven agentic systems, highlights key applications, discusses evaluation methods for planning and tool use, and outlines challenges such as error cascades, tool-use efficiency, and health IT integration.

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.

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.

Multi-agent frameworks powered by large language models (LLMs) have demonstrated great success in automated planning and task execution. However, the effective adjustment of Agentic workflows during execution has not been well-studied. A effective workflow adjustment is crucial, as in many real-world scenarios, the initial plan must adjust to unforeseen challenges and changing conditions in real-time to ensure the efficient execution of complex tasks. In this paper, we define workflows as an activity-on-vertex (AOV) graphs. We continuously refine the workflow by dynamically adjusting task allocations based on historical performance and previous AOV with LLM agents. To further enhance system performance, we emphasize modularity in workflow design based on measuring parallelism and dependence complexity. Our proposed multi-agent framework achieved efficient sub-task concurrent execution, goal achievement, and error tolerance. Empirical results across different practical tasks demonstrate dramatic improvements in the efficiency of multi-agent frameworks through dynamic workflow updating and modularization.

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.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

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

Discharge summaries in Electronic Health Records (EHRs) are crucial for clinical decision-making, but their length and complexity make information extraction challenging, especially when dealing with accumulated summaries across multiple patient admissions. Large Language Models (LLMs) show promise in addressing this challenge by efficiently analyzing vast and complex data. Existing benchmarks, however, fall short in properly evaluating LLMs' capabilities in this context, as they typically focus on single-note information or limited topics, failing to reflect the real-world inquiries required by clinicians. To bridge this gap, we introduce EHRNoteQA, a novel benchmark built on the MIMIC-IV EHR, comprising 962 different QA pairs each linked to distinct patients' discharge summaries. Every QA pair is initially generated using GPT-4 and then manually reviewed and refined by three clinicians to ensure clinical relevance. EHRNoteQA includes questions that require information across multiple discharge summaries and covers eight diverse topics, mirroring the complexity and diversity of real clinical inquiries. We offer EHRNoteQA in two formats: open-ended and multi-choice question answering, and propose a reliable evaluation method for each. We evaluate 27 LLMs using EHRNoteQA and examine various factors affecting the model performance (e.g., the length and number of discharge summaries). Furthermore, to validate EHRNoteQA as a reliable proxy for expert evaluations in clinical practice, we measure the correlation between the LLM performance on EHRNoteQA, and the LLM performance manually evaluated by clinicians. Results show that LLM performance on EHRNoteQA have higher correlation with clinician-evaluated performance (Spearman: 0.78, Kendall: 0.62) compared to other benchmarks, demonstrating its practical relevance in evaluating LLMs in clinical settings.

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

With the advancement of telemedicine, both researchers and medical practitioners are working hand-in-hand to develop various techniques to automate various medical operations, such as diagnosis report generation. In this paper, we first present a multi-modal clinical conversation summary generation task that takes a clinician-patient interaction (both textual and visual information) and generates a succinct synopsis of the conversation. We propose a knowledge-infused, multi-modal, multi-tasking medical domain identification and clinical conversation summary generation (MM-CliConSummation) framework. It leverages an adapter to infuse knowledge and visual features and unify the fused feature vector using a gated mechanism. Furthermore, we developed a multi-modal, multi-intent clinical conversation summarization corpus annotated with intent, symptom, and summary. The extensive set of experiments, both quantitatively and qualitatively, led to the following findings: (a) critical significance of visuals, (b) more precise and medical entity preserving summary with additional knowledge infusion, and (c) a correlation between medical department identification and clinical synopsis generation. Furthermore, the dataset and source code are available at https://github.com/NLP-RL/MM-CliConSummation.

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff members, including physicians, nurses, and insurance review and health records teams. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and used the responses to create seed questions. We then manually linked these questions to two open-source EHR databases, MIMIC-III and eICU, and included various time expressions and held-out unanswerable questions in the dataset, which were also collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable. We believe our dataset, EHRSQL, can serve as a practical benchmark for developing and assessing QA models on structured EHR data and take a step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.

Healthcare monitoring is crucial for early detection, timely intervention, and the ongoing management of health conditions, ultimately improving individuals' quality of life. Recent research shows that Large Language Models (LLMs) have demonstrated impressive performance in supporting healthcare tasks. However, existing LLM-based healthcare solutions typically rely on cloud-based systems, which raise privacy concerns and increase the risk of personal information leakage. As a result, there is growing interest in running these models locally on devices like mobile phones and wearables to protect users' privacy. Small Language Models (SLMs) are potential candidates to solve privacy and computational issues, as they are more efficient and better suited for local deployment. However, the performance of SLMs in healthcare domains has not yet been investigated. This paper examines the capability of SLMs to accurately analyze health data, such as steps, calories, sleep minutes, and other vital statistics, to assess an individual's health status. Our results show that, TinyLlama, which has 1.1 billion parameters, utilizes 4.31 GB memory, and has 0.48s latency, showing the best performance compared other four state-of-the-art (SOTA) SLMs on various healthcare applications. Our results indicate that SLMs could potentially be deployed on wearable or mobile devices for real-time health monitoring, providing a practical solution for efficient and privacy-preserving healthcare.

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

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

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.

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.

A promising application of AI to healthcare is the retrieval of information from electronic health records (EHRs), e.g. to aid clinicians in finding relevant information for a consultation or to recruit suitable patients for a study. This requires search capabilities far beyond simple string matching, including the retrieval of concepts (diagnoses, symptoms, medications, etc.) related to the one in question. The suitability of AI methods for such applications is tested by predicting the relatedness of concepts with known relatedness scores. However, all existing biomedical concept relatedness datasets are notoriously small and consist of hand-picked concept pairs. We open-source a novel concept relatedness benchmark overcoming these issues: it is six times larger than existing datasets and concept pairs are chosen based on co-occurrence in EHRs, ensuring their relevance for the application of interest. We present an in-depth analysis of our new dataset and compare it to existing ones, highlighting that it is not only larger but also complements existing datasets in terms of the types of concepts included. Initial experiments with state-of-the-art embedding methods show that our dataset is a challenging new benchmark for testing concept relatedness models.

Purpose: With advancements in Large Language Models (LLMs) for healthcare, the need arises for competitive open-source models to protect the public interest. This work contributes to the field of open medical LLMs by optimizing key stages of data preprocessing and training, while showing how to improve model safety (through DPO) and efficacy (through RAG). The evaluation methodology used, which includes four different types of tests, defines a new standard for the field. The resultant models, shown to be competitive with the best private alternatives, are released with a permisive license. Methods: Building on top of strong base models like Llama 3.1 and Qwen 2.5, Aloe Beta uses a custom dataset to enhance public data with synthetic Chain of Thought examples. The models undergo alignment with Direct Preference Optimization, emphasizing ethical and policy-aligned performance in the presence of jailbreaking attacks. Evaluation includes close-ended, open-ended, safety and human assessments, to maximize the reliability of results. Results: Recommendations are made across the entire pipeline, backed by the solid performance of the Aloe Family. These models deliver competitive performance across healthcare benchmarks and medical fields, and are often preferred by healthcare professionals. On bias and toxicity, the Aloe Beta models significantly improve safety, showing resilience to unseen jailbreaking attacks. For a responsible release, a detailed risk assessment specific to healthcare is attached to the Aloe Family models. Conclusion: The Aloe Beta models, and the recipe that leads to them, are a significant contribution to the open-source medical LLM field, offering top-of-the-line performance while maintaining high ethical requirements. This work sets a new standard for developing and reporting aligned LLMs in healthcare.

The application of deep learning to nursing procedure activity understanding has the potential to greatly enhance the quality and safety of nurse-patient interactions. By utilizing the technique, we can facilitate training and education, improve quality control, and enable operational compliance monitoring. However, the development of automatic recognition systems in this field is currently hindered by the scarcity of appropriately labeled datasets. The existing video datasets pose several limitations: 1) these datasets are small-scale in size to support comprehensive investigations of nursing activity; 2) they primarily focus on single procedures, lacking expert-level annotations for various nursing procedures and action steps; and 3) they lack temporally localized annotations, which prevents the effective localization of targeted actions within longer video sequences. To mitigate these limitations, we propose NurViD, a large video dataset with expert-level annotation for nursing procedure activity understanding. NurViD consists of over 1.5k videos totaling 144 hours, making it approximately four times longer than the existing largest nursing activity datasets. Notably, it encompasses 51 distinct nursing procedures and 177 action steps, providing a much more comprehensive coverage compared to existing datasets that primarily focus on limited procedures. To evaluate the efficacy of current deep learning methods on nursing activity understanding, we establish three benchmarks on NurViD: procedure recognition on untrimmed videos, procedure and action recognition on trimmed videos, and action detection. Our benchmark and code will be available at https://github.com/minghu0830/NurViD-benchmark.

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.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

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

Surgical scene perception via videos are critical for advancing robotic surgery, telesurgery, and AI-assisted surgery, particularly in ophthalmology. However, the scarcity of diverse and richly annotated video datasets has hindered the development of intelligent systems for surgical workflow analysis. Existing datasets for surgical workflow analysis, which typically face challenges such as small scale, a lack of diversity in surgery and phase categories, and the absence of time-localized annotations, limit the requirements for action understanding and model generalization validation in complex and diverse real-world surgical scenarios. To address this gap, we introduce OphNet, a large-scale, expert-annotated video benchmark for ophthalmic surgical workflow understanding. OphNet features: 1) A diverse collection of 2,278 surgical videos spanning 66 types of cataract, glaucoma, and corneal surgeries, with detailed annotations for 102 unique surgical phases and 150 granular operations; 2) It offers sequential and hierarchical annotations for each surgery, phase, and operation, enabling comprehensive understanding and improved interpretability; 3) Moreover, OphNet provides time-localized annotations, facilitating temporal localization and prediction tasks within surgical workflows. With approximately 205 hours of surgical videos, OphNet is about 20 times larger than the largest existing surgical workflow analysis benchmark. Our dataset and code have been made available at: https://github.com/minghu0830/OphNet-benchmark.

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

The reliability of medical LLM evaluation is critically undermined by data contamination and knowledge obsolescence, leading to inflated scores on static benchmarks. To address these challenges, we introduce LiveClin, a live benchmark designed for approximating real-world clinical practice. Built from contemporary, peer-reviewed case reports and updated biannually, LiveClin ensures clinical currency and resists data contamination. Using a verified AI-human workflow involving 239 physicians, we transform authentic patient cases into complex, multimodal evaluation scenarios that span the entire clinical pathway. The benchmark currently comprises 1,407 case reports and 6,605 questions. Our evaluation of 26 models on LiveClin reveals the profound difficulty of these real-world scenarios, with the top-performing model achieving a Case Accuracy of just 35.7%. In benchmarking against human experts, Chief Physicians achieved the highest accuracy, followed closely by Attending Physicians, with both surpassing most models. LiveClin thus provides a continuously evolving, clinically grounded framework to guide the development of medical LLMs towards closing this gap and achieving greater reliability and real-world utility. Our data and code are publicly available at https://github.com/AQ-MedAI/LiveClin.

Analyzing Open Source Intelligence (OSINT) from large volumes of data is critical for drafting and publishing comprehensive CTI reports. This process usually follows a three-stage workflow -- triage, deep search and TI drafting. While Large Language Models (LLMs) offer a promising route toward automation, existing benchmarks still have limitations. These benchmarks often consist of tasks that do not reflect real-world analyst workflows. For example, human analysts rarely receive tasks in the form of multiple-choice questions. Also, existing benchmarks often rely on model-centric metrics that emphasize lexical overlap rather than actionable, detailed insights essential for security analysts. Moreover, they typically fail to cover the complete three-stage workflow. To address these issues, we introduce CyberThreat-Eval, which is collected from the daily CTI workflow of a world-leading company. This expert-annotated benchmark assesses LLMs on practical tasks across all three stages as mentioned above. It utilizes analyst-centric metrics that measure factual accuracy, content quality, and operational costs. Our evaluation using this benchmark reveals important insights into the limitations of current LLMs. For example, LLMs often lack the nuanced expertise required to handle complex details and struggle to distinguish between correct and incorrect information. To address these challenges, the CTI workflow incorporates both external ground-truth databases and human expert knowledge. TRA allows human experts to iteratively provide feedback for continuous improvement. The code is available at https://github.com/xschen-beb/CyberThreat-Eval{GitHub} and https://huggingface.co/datasets/xse/CyberThreat-Eval{HuggingFace}.

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

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

In this study, we investigated the ability of the large language model (LLM) to enhance healthcare data interoperability. We leveraged the LLM to convert clinical texts into their corresponding FHIR resources. Our experiments, conducted on 3,671 snippets of clinical text, demonstrated that the LLM not only streamlines the multi-step natural language processing and human calibration processes but also achieves an exceptional accuracy rate of over 90% in exact matches when compared to human annotations.

The introduction of computerized medical records in hospitals has reduced burdensome operations like manual writing and information fetching. However, the data contained in medical records are still far underutilized, primarily because extracting them from unstructured textual medical records takes time and effort. Information Extraction, a subfield of Natural Language Processing, can help clinical practitioners overcome this limitation, using automated text-mining pipelines. In this work, we created the first Italian neuropsychiatric Named Entity Recognition dataset, PsyNIT, and used it to develop a Large Language Model for this task. Moreover, we conducted several experiments with three external independent datasets to implement an effective multicenter model, with overall F1-score 84.77%, Precision 83.16%, Recall 86.44%. The lessons learned are: (i) the crucial role of a consistent annotation process and (ii) a fine-tuning strategy that combines classical methods with a "few-shot" approach. This allowed us to establish methodological guidelines that pave the way for future implementations in this field and allow Italian hospitals to tap into important research opportunities.

Medical dictation systems are essential tools in modern healthcare, enabling accurate and efficient conversion of speech into written medical documentation. The main objective of this paper is to create a domain-specific system for Greek medical speech transcriptions. The ultimate goal is to assist healthcare professionals by reducing the overload of manual documentation and improving workflow efficiency. Towards this goal, we develop a system that combines automatic speech recognition techniques with text correction model, allowing better handling of domain-specific terminology and linguistic variations in Greek. Our approach leverages both acoustic and textual modeling to create more realistic and reliable transcriptions. We focused on adapting existing language and speech technologies to the Greek medical context, addressing challenges such as complex medical terminology and linguistic inconsistencies. Through domain-specific fine-tuning, our system achieves more accurate and coherent transcriptions, contributing to the development of practical language technologies for the Greek healthcare sector.

Digital twin technology has is anticipated to transform healthcare, enabling personalized medicines and support, earlier diagnoses, simulated treatment outcomes, and optimized surgical plans. Digital twins are readily gaining traction in industries like manufacturing, supply chain logistics, and civil infrastructure. Not in patient care, however. The challenge of modeling complex diseases with multimodal patient data and the computational complexities of analyzing it have stifled digital twin adoption in the biomedical vertical. Yet, these major obstacles can potentially be handled by approaching these models in a different way. This paper proposes a novel framework for addressing the barriers to clinical twin modeling created by computational costs and modeling complexities. We propose structuring patient health data as a knowledge graph and using closed-form continuous-time liquid neural networks, for real-time analytics. By synthesizing multimodal patient data and leveraging the flexibility and efficiency of closed form continuous time networks and knowledge graph ontologies, our approach enables real time insights, personalized medicine, early diagnosis and intervention, and optimal surgical planning. This novel approach provides a comprehensive and adaptable view of patient health along with real-time analytics, paving the way for digital twin simulations and other anticipated benefits in healthcare.

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

Acupuncture is a form of medicine that involves inserting needles into targeted areas of the body and requires knowledge of both Traditional Chinese Medicine (TCM) and Evidence-Based Medicine (EBM). The process of acquiring such knowledge and using it for practical treatment is challenging due to the need for a deep understanding of human anatomy and the ability to apply both TCM and EBM approaches. Visual aids have been introduced to aid in understanding the alignment of acupuncture points with key elements of the human body, and are indispensable tools for both learners and expert acupuncturists. However, they are often not enough to enable effective practice and fail to fully support the learning process. Novel approaches based on immersive visualization and Virtual Reality (VR) have shown promise in many healthcare settings due to their unique advantages in terms of realism and interactions, but it is still unknown whether and how VR can possibly be beneficial to acupuncture training and treatment. Following participatory design protocols such as observations and semi-structured interviews with eight doctors and nine students, we explore the needs and pain points of current acupuncture workflows at the intersection of EBM and TCM in China and the United States. We highlight opportunities for introducing VR in today's acupuncture training and treatment workflows, and discuss two design approaches that build on 11 specific challenges spanning education, diagnosis, treatment, and communication.

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

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

In this review, we explore the potential applications of Artificial General Intelligence (AGI) models in healthcare, focusing on foundational Large Language Models (LLMs), Large Vision Models, and Large Multimodal Models. We emphasize the importance of integrating clinical expertise, domain knowledge, and multimodal capabilities into AGI models. In addition, we lay out key roadmaps that guide the development and deployment of healthcare AGI models. Throughout the review, we provide critical perspectives on the potential challenges and pitfalls associated with deploying large-scale AGI models in the medical field. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare and beyond.