Daily Papers

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

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

Since the release of the original CheXpert paper five years ago, CheXpert has become one of the most widely used and cited clinical AI datasets. The emergence of vision language models has sparked an increase in demands for sharing reports linked to CheXpert images, along with a growing interest among AI fairness researchers in obtaining demographic data. To address this, CheXpert Plus serves as a new collection of radiology data sources, made publicly available to enhance the scaling, performance, robustness, and fairness of models for all subsequent machine learning tasks in the field of radiology. CheXpert Plus is the largest text dataset publicly released in radiology, with a total of 36 million text tokens, including 13 million impression tokens. To the best of our knowledge, it represents the largest text de-identification effort in radiology, with almost 1 million PHI spans anonymized. It is only the second time that a large-scale English paired dataset has been released in radiology, thereby enabling, for the first time, cross-institution training at scale. All reports are paired with high-quality images in DICOM format, along with numerous image and patient metadata covering various clinical and socio-economic groups, as well as many pathology labels and RadGraph annotations. We hope this dataset will boost research for AI models that can further assist radiologists and help improve medical care. Data is available at the following URL: https://stanfordaimi.azurewebsites.net/datasets/5158c524-d3ab-4e02-96e9-6ee9efc110a1 Models are available at the following URL: https://github.com/Stanford-AIMI/chexpert-plus

Predicting clinical outcomes from preclinical data is essential for identifying safe and effective drug combinations. Current models rely on structural or target-based features to identify high-efficacy, low-toxicity drug combinations. However, these approaches fail to incorporate the multimodal data necessary for accurate, clinically-relevant predictions. Here, we introduce MADRIGAL, a multimodal AI model that learns from structural, pathway, cell viability, and transcriptomic data to predict drug combination effects across 953 clinical outcomes and 21842 compounds, including combinations of approved drugs and novel compounds in development. MADRIGAL uses a transformer bottleneck module to unify preclinical drug data modalities while handling missing data during training and inference--a major challenge in multimodal learning. It outperforms single-modality methods and state-of-the-art models in predicting adverse drug interactions. MADRIGAL performs virtual screening of anticancer drug combinations and supports polypharmacy management for type II diabetes and metabolic dysfunction-associated steatohepatitis (MASH). It identifies transporter-mediated drug interactions. MADRIGAL predicts resmetirom, the first and only FDA-approved drug for MASH, among therapies with the most favorable safety profile. It supports personalized cancer therapy by integrating genomic profiles from cancer patients. Using primary acute myeloid leukemia samples and patient-derived xenograft models, it predicts the efficacy of personalized drug combinations. Integrating MADRIGAL with a large language model allows users to describe clinical outcomes in natural language, improving safety assessment by identifying potential adverse interactions and toxicity risks. MADRIGAL provides a multimodal approach for designing combination therapies with improved predictive accuracy and clinical relevance.

Rapid and affordable methods of testing for COVID-19 infections are essential to reduce infection rates and prevent medical facilities from becoming overwhelmed. Current approaches of detecting COVID-19 require in-person testing with expensive kits that are not always easily accessible. This study demonstrates that crowdsourced cough audio samples recorded and acquired on smartphones from around the world can be used to develop an AI-based method that accurately predicts COVID-19 infection with an ROC-AUC of 77.1% (75.2%-78.3%). Furthermore, we show that our method is able to generalize to crowdsourced audio samples from Latin America and clinical samples from South Asia, without further training using the specific samples from those regions. As more crowdsourced data is collected, further development can be implemented using various respiratory audio samples to create a cough analysis-based machine learning (ML) solution for COVID-19 detection that can likely generalize globally to all demographic groups in both clinical and non-clinical settings.

In the pharmaceutical industry, the use of artificial intelligence (AI) has seen consistent growth over the past decade. This rise is attributed to major advancements in statistical machine learning methodologies, computational capabilities and the increased availability of large datasets. AI techniques are applied throughout different stages of drug development, ranging from drug discovery to post-marketing benefit-risk assessment. Kolluri et al. provided a review of several case studies that span these stages, featuring key applications such as protein structure prediction, success probability estimation, subgroup identification, and AI-assisted clinical trial monitoring. From a regulatory standpoint, there was a notable uptick in submissions incorporating AI components in 2021. The most prevalent therapeutic areas leveraging AI were oncology (27%), psychiatry (15%), gastroenterology (12%), and neurology (11%). The paradigm of personalized or precision medicine has gained significant traction in recent research, partly due to advancements in AI techniques hamburg2010path. This shift has had a transformative impact on the pharmaceutical industry. Departing from the traditional "one-size-fits-all" model, personalized medicine incorporates various individual factors, such as environmental conditions, lifestyle choices, and health histories, to formulate customized treatment plans. By utilizing sophisticated machine learning algorithms, clinicians and researchers are better equipped to make informed decisions in areas such as disease prevention, diagnosis, and treatment selection, thereby optimizing health outcomes for each individual.

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

Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa.nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa.nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10\% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa.nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

We introduce RJUA-QA, a novel medical dataset for question answering (QA) and reasoning with clinical evidence, contributing to bridge the gap between general large language models (LLMs) and medical-specific LLM applications. RJUA-QA is derived from realistic clinical scenarios and aims to facilitate LLMs in generating reliable diagnostic and advice. The dataset contains 2,132 curated Question-Context-Answer pairs, corresponding about 25,000 diagnostic records and clinical cases. The dataset covers 67 common urological disease categories, where the disease coverage exceeds 97.6\% of the population seeking medical services in urology. Each data instance in RJUA-QA comprises: (1) a question mirroring real patient to inquiry about clinical symptoms and medical conditions, (2) a context including comprehensive expert knowledge, serving as a reference for medical examination and diagnosis, (3) a doctor response offering the diagnostic conclusion and suggested examination guidance, (4) a diagnosed clinical disease as the recommended diagnostic outcome, and (5) clinical advice providing recommendations for medical examination. RJUA-QA is the first medical QA dataset for clinical reasoning over the patient inquiries, where expert-level knowledge and experience are required for yielding diagnostic conclusions and medical examination advice. A comprehensive evaluation is conducted to evaluate the performance of both medical-specific and general LLMs on the RJUA-QA dataset.

Current medical artificial intelligence systems are often limited to narrow applications, hindering their widespread adoption in clinical practice. To address this limitation, we propose MedVersa, a generalist learner that enables flexible learning and tasking for medical image interpretation. By leveraging a large language model as a learnable orchestrator, MedVersa can learn from both visual and linguistic supervision, support multimodal inputs, and perform real-time task specification. This versatility allows MedVersa to adapt to various clinical scenarios and perform multifaceted medical image analysis. We introduce MedInterp, the largest multimodal dataset to date for medical image interpretation, consisting of over 13 million annotated instances spanning 11 tasks across 3 modalities, to support the development of MedVersa. Our experiments demonstrate that MedVersa achieves state-of-the-art performance in 9 tasks, sometimes outperforming specialist counterparts by over 10%. MedVersa is the first to showcase the viability of multimodal generative medical AI in implementing multimodal outputs, inputs, and dynamic task specification, highlighting its potential as a multifunctional system for comprehensive medical image analysis. This generalist approach to medical image interpretation paves the way for more adaptable and efficient AI-assisted clinical decision-making.

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice.

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

Ensuring the accuracy of responses provided by large language models (LLMs) is crucial, particularly in clinical settings where incorrect information may directly impact patient health. To address this challenge, we construct K-QA, a dataset containing 1,212 patient questions originating from real-world conversations held on K Health (an AI-driven clinical platform). We employ a panel of in-house physicians to answer and manually decompose a subset of K-QA into self-contained statements. Additionally, we formulate two NLI-based evaluation metrics approximating recall and precision: (1) comprehensiveness, measuring the percentage of essential clinical information in the generated answer and (2) hallucination rate, measuring the number of statements from the physician-curated response contradicted by the LLM answer. Finally, we use K-QA along with these metrics to evaluate several state-of-the-art models, as well as the effect of in-context learning and medically-oriented augmented retrieval schemes developed by the authors. Our findings indicate that in-context learning improves the comprehensiveness of the models, and augmented retrieval is effective in reducing hallucinations. We make K-QA available to to the community to spur research into medically accurate NLP applications.

Skin disease is one of the most common types of human diseases, which may happen to everyone regardless of age, gender or race. Due to the high visual diversity, human diagnosis highly relies on personal experience; and there is a serious shortage of experienced dermatologists in many countries. To alleviate this problem, computer-aided diagnosis with state-of-the-art (SOTA) machine learning techniques would be a promising solution. In this paper, we aim at understanding the performance of convolutional neural network (CNN) based approaches. We first build two versions of skin disease datasets from Internet images: (a) Skin-10, which contains 10 common classes of skin disease with a total of 10,218 images; (b) Skin-100, which is a larger dataset that consists of 19,807 images of 100 skin disease classes. Based on these datasets, we benchmark several SOTA CNN models and show that the accuracy of skin-100 is much lower than the accuracy of skin-10. We then implement an ensemble method based on several CNN models and achieve the best accuracy of 79.01\% for Skin-10 and 53.54\% for Skin-100. We also present an object detection based approach by introducing bounding boxes into the Skin-10 dataset. Our results show that object detection can help improve the accuracy of some skin disease classes.

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

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.

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

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.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

The utilization of clinical reports for various secondary purposes, including health research and treatment monitoring, is crucial for enhancing patient care. Natural Language Processing (NLP) tools have emerged as valuable assets for extracting and processing relevant information from these reports. However, the availability of specialized language models for the clinical domain in Spanish has been limited. In this paper, we introduce EriBERTa, a bilingual domain-specific language model pre-trained on extensive medical and clinical corpora. We demonstrate that EriBERTa outperforms previous Spanish language models in the clinical domain, showcasing its superior capabilities in understanding medical texts and extracting meaningful information. Moreover, EriBERTa exhibits promising transfer learning abilities, allowing for knowledge transfer from one language to another. This aspect is particularly beneficial given the scarcity of Spanish clinical data.

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for better language representations. Interestingly, in the absence of enough clinical data to train a model from scratch, we applied mixed-domain pretraining and cross-domain transfer approaches to generate a performant bio-clinical model suitable for real-world clinical data. We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports. When compared against the competitive mBERT and BETO models, we outperform them in all NER tasks by a significant margin. Finally, we studied the impact of the model's vocabulary on the NER performances by offering an interesting vocabulary-centric analysis. The results confirm that domain-specific pretraining is fundamental to achieving higher performances in downstream NER tasks, even within a mid-resource scenario. To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine. Our best models are freely available in the HuggingFace hub: https://huggingface.co/BSC-TeMU.

Diagnosing and treating skin diseases require advanced visual skills across domains and the ability to synthesize information from multiple imaging modalities. While current deep learning models excel at specific tasks like skin cancer diagnosis from dermoscopic images, they struggle to meet the complex, multimodal requirements of clinical practice. Here, we introduce PanDerm, a multimodal dermatology foundation model pretrained through self-supervised learning on over 2 million real-world skin disease images from 11 clinical institutions across 4 imaging modalities. We evaluated PanDerm on 28 diverse benchmarks, including skin cancer screening, risk stratification, differential diagnosis of common and rare skin conditions, lesion segmentation, longitudinal monitoring, and metastasis prediction and prognosis. PanDerm achieved state-of-the-art performance across all evaluated tasks, often outperforming existing models when using only 10% of labeled data. We conducted three reader studies to assess PanDerm's potential clinical utility. PanDerm outperformed clinicians by 10.2% in early-stage melanoma detection through longitudinal analysis, improved clinicians' skin cancer diagnostic accuracy by 11% on dermoscopy images, and enhanced non-dermatologist healthcare providers' differential diagnosis by 16.5% across 128 skin conditions on clinical photographs. These results demonstrate PanDerm's potential to improve patient care across diverse clinical scenarios and serve as a model for developing multimodal foundation models in other medical specialties, potentially accelerating the integration of AI support in healthcare. The code can be found at https://github.com/SiyuanYan1/PanDerm.

Although large language models (LLMs) have been assessed for general medical knowledge using medical licensing exams, their ability to effectively support clinical decision-making tasks, such as selecting and using medical calculators, remains uncertain. Here, we evaluate the capability of both medical trainees and LLMs to recommend medical calculators in response to various multiple-choice clinical scenarios such as risk stratification, prognosis, and disease diagnosis. We assessed eight LLMs, including open-source, proprietary, and domain-specific models, with 1,009 question-answer pairs across 35 clinical calculators and measured human performance on a subset of 100 questions. While the highest-performing LLM, GPT-4o, provided an answer accuracy of 74.3% (CI: 71.5-76.9%), human annotators, on average, outperformed LLMs with an accuracy of 79.5% (CI: 73.5-85.0%). With error analysis showing that the highest-performing LLMs continue to make mistakes in comprehension (56.6%) and calculator knowledge (8.1%), our findings emphasize that humans continue to surpass LLMs on complex clinical tasks such as calculator recommendation.

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.

Like other fields of Traditional Medicines, Unani Medicines have been found as an effective medical practice for ages. It is still widely used in the subcontinent, particularly in Pakistan and India. However, Unani Medicines Practitioners are lacking modern IT applications in their everyday clinical practices. An Online Clinical Decision Support System may address this challenge to assist apprentice Unani Medicines practitioners in their diagnostic processes. The proposed system provides a web-based interface to enter the patient's symptoms, which are then automatically analyzed by our system to generate a list of probable diseases. The system allows practitioners to choose the most likely disease and inform patients about the associated treatment options remotely. The system consists of three modules: an Online Clinical Decision Support System, an Artificial Intelligence Inference Engine, and a comprehensive Unani Medicines Database. The system employs advanced AI techniques such as Decision Trees, Deep Learning, and Natural Language Processing. For system development, the project team used a technology stack that includes React, FastAPI, and MySQL. Data and functionality of the application is exposed using APIs for integration and extension with similar domain applications. The novelty of the project is that it addresses the challenge of diagnosing diseases accurately and efficiently in the context of Unani Medicines principles. By leveraging the power of technology, the proposed Clinical Decision Support System has the potential to ease access to healthcare services and information, reduce cost, boost practitioner and patient satisfaction, improve speed and accuracy of the diagnostic process, and provide effective treatments remotely. The application will be useful for Unani Medicines Practitioners, Patients, Government Drug Regulators, Software Developers, and Medical Researchers.

Coronavirus disease (COVID-19) is a pandemic disease, which has already caused thousands of causalities and infected several millions of people worldwide. Any technological tool enabling rapid screening of the COVID-19 infection with high accuracy can be crucially helpful to healthcare professionals. The main clinical tool currently in use for the diagnosis of COVID-19 is the Reverse transcription polymerase chain reaction (RT-PCR), which is expensive, less-sensitive and requires specialized medical personnel. X-ray imaging is an easily accessible tool that can be an excellent alternative in the COVID-19 diagnosis. This research was taken to investigate the utility of artificial intelligence (AI) in the rapid and accurate detection of COVID-19 from chest X-ray images. The aim of this paper is to propose a robust technique for automatic detection of COVID-19 pneumonia from digital chest X-ray images applying pre-trained deep-learning algorithms while maximizing the detection accuracy. A public database was created by the authors combining several public databases and also by collecting images from recently published articles. The database contains a mixture of 423 COVID-19, 1485 viral pneumonia, and 1579 normal chest X-ray images. Transfer learning technique was used with the help of image augmentation to train and validate several pre-trained deep Convolutional Neural Networks (CNNs). The networks were trained to classify two different schemes: i) normal and COVID-19 pneumonia; ii) normal, viral and COVID-19 pneumonia with and without image augmentation. The classification accuracy, precision, sensitivity, and specificity for both the schemes were 99.7%, 99.7%, 99.7% and 99.55% and 97.9%, 97.95%, 97.9%, and 98.8%, respectively.

As structured data are often insufficient, labels need to be extracted from free text in electronic health records when developing models for clinical information retrieval and decision support systems. One of the most important contextual properties in clinical text is negation, which indicates the absence of findings. We aimed to improve large scale extraction of labels by comparing three methods for negation detection in Dutch clinical notes. We used the Erasmus Medical Center Dutch Clinical Corpus to compare a rule-based method based on ContextD, a biLSTM model using MedCAT and (finetuned) RoBERTa-based models. We found that both the biLSTM and RoBERTa models consistently outperform the rule-based model in terms of F1 score, precision and recall. In addition, we systematically categorized the classification errors for each model, which can be used to further improve model performance in particular applications. Combining the three models naively was not beneficial in terms of performance. We conclude that the biLSTM and RoBERTa-based models in particular are highly accurate accurate in detecting clinical negations, but that ultimately all three approaches can be viable depending on the use case at hand.

Medication Extraction and Mining play an important role in healthcare NLP research due to its practical applications in hospital settings, such as their mapping into standard clinical knowledge bases (SNOMED-CT, BNF, etc.). In this work, we investigate state-of-the-art LLMs in text mining tasks on medications and their related attributes such as dosage, route, strength, and adverse effects. In addition, we explore different ensemble learning methods (Stack-Ensemble and Voting-Ensemble) to augment the model performances from individual LLMs. Our ensemble learning result demonstrated better performances than individually fine-tuned base models BERT, RoBERTa, RoBERTa-L, BioBERT, BioClinicalBERT, BioMedRoBERTa, ClinicalBERT, and PubMedBERT across general and specific domains. Finally, we build up an entity linking function to map extracted medical terminologies into the SNOMED-CT codes and the British National Formulary (BNF) codes, which are further mapped to the Dictionary of Medicines and Devices (dm+d), and ICD. Our model's toolkit and desktop applications are publicly available at https://github.com/HECTA-UoM/ensemble-NER.

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

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

Large language models (LLMs) are increasingly utilized in healthcare applications. However, their deployment in clinical practice raises significant safety concerns, including the potential spread of harmful information. This study systematically assesses the vulnerabilities of seven LLMs to three advanced black-box jailbreaking techniques within medical contexts. To quantify the effectiveness of these techniques, we propose an automated and domain-adapted agentic evaluation pipeline. Experiment results indicate that leading commercial and open-source LLMs are highly vulnerable to medical jailbreaking attacks. To bolster model safety and reliability, we further investigate the effectiveness of Continual Fine-Tuning (CFT) in defending against medical adversarial attacks. Our findings underscore the necessity for evolving attack methods evaluation, domain-specific safety alignment, and LLM safety-utility balancing. This research offers actionable insights for advancing the safety and reliability of AI clinicians, contributing to ethical and effective AI deployment in healthcare.

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

This work introduces the first benchmark for nursing value alignment, consisting of five core value dimensions distilled from international nursing codes: Altruism, Human Dignity, Integrity, Justice, and Professionalism. The benchmark comprises 1,100 real-world nursing behavior instances collected through a five-month longitudinal field study across three hospitals of varying tiers. These instances are annotated by five clinical nurses and then augmented with LLM-generated counterfactuals with reversed ethic polarity. Each original case is paired with a value-aligned and a value-violating version, resulting in 2,200 labeled instances that constitute the Easy-Level dataset. To increase adversarial complexity, each instance is further transformed into a dialogue-based format that embeds contextual cues and subtle misleading signals, yielding a Hard-Level dataset. We evaluate 23 state-of-the-art (SoTA) LLMs on their alignment with nursing values. Our findings reveal three key insights: (1) DeepSeek-V3 achieves the highest performance on the Easy-Level dataset (94.55), where Claude 3.5 Sonnet outperforms other models on the Hard-Level dataset (89.43), significantly surpassing the medical LLMs; (2) Justice is consistently the most difficult nursing value dimension to evaluate; and (3) in-context learning significantly improves alignment. This work aims to provide a foundation for value-sensitive LLMs development in clinical settings. The dataset and the code are available at https://huggingface.co/datasets/Ben012345/NurValues.

Large language models (LLMs) have exhibited remarkable capabilities across various domains and tasks, pushing the boundaries of our knowledge in learning and cognition. The latest model, OpenAI's o1, stands out as the first LLM with an internalized chain-of-thought technique using reinforcement learning strategies. While it has demonstrated surprisingly strong capabilities on various general language tasks, its performance in specialized fields such as medicine remains unknown. To this end, this report provides a comprehensive exploration of o1 on different medical scenarios, examining 3 key aspects: understanding, reasoning, and multilinguality. Specifically, our evaluation encompasses 6 tasks using data from 37 medical datasets, including two newly constructed and more challenging question-answering (QA) tasks based on professional medical quizzes from the New England Journal of Medicine (NEJM) and The Lancet. These datasets offer greater clinical relevance compared to standard medical QA benchmarks such as MedQA, translating more effectively into real-world clinical utility. Our analysis of o1 suggests that the enhanced reasoning ability of LLMs may (significantly) benefit their capability to understand various medical instructions and reason through complex clinical scenarios. Notably, o1 surpasses the previous GPT-4 in accuracy by an average of 6.2% and 6.6% across 19 datasets and two newly created complex QA scenarios. But meanwhile, we identify several weaknesses in both the model capability and the existing evaluation protocols, including hallucination, inconsistent multilingual ability, and discrepant metrics for evaluation. We release our raw data and model outputs at https://ucsc-vlaa.github.io/o1_medicine/ for future research.

The integration of Artificial Intelligence (AI), especially Large Language Models (LLMs), into the clinical diagnosis process offers significant potential to improve the efficiency and accessibility of medical care. While LLMs have shown some promise in the medical domain, their application in clinical diagnosis remains underexplored, especially in real-world clinical practice, where highly sophisticated, patient-specific decisions need to be made. Current evaluations of LLMs in this field are often narrow in scope, focusing on specific diseases or specialties and employing simplified diagnostic tasks. To bridge this gap, we introduce CliBench, a novel benchmark developed from the MIMIC IV dataset, offering a comprehensive and realistic assessment of LLMs' capabilities in clinical diagnosis. This benchmark not only covers diagnoses from a diverse range of medical cases across various specialties but also incorporates tasks of clinical significance: treatment procedure identification, lab test ordering and medication prescriptions. Supported by structured output ontologies, CliBench enables a precise and multi-granular evaluation, offering an in-depth understanding of LLM's capability on diverse clinical tasks of desired granularity. We conduct a zero-shot evaluation of leading LLMs to assess their proficiency in clinical decision-making. Our preliminary results shed light on the potential and limitations of current LLMs in clinical settings, providing valuable insights for future advancements in LLM-powered healthcare.

Cancer patients are increasingly turning to large language models (LLMs) as a new form of internet search for medical information, making it critical to assess how well these models handle complex, personalized questions. However, current medical benchmarks focus on medical exams or consumer-searched questions and do not evaluate LLMs on real patient questions with detailed clinical contexts. In this paper, we first evaluate LLMs on cancer-related questions drawn from real patients, reviewed by three hematology oncology physicians. While responses are generally accurate, with GPT-4-Turbo scoring 4.13 out of 5, the models frequently fail to recognize or address false presuppositions in the questions-posing risks to safe medical decision-making. To study this limitation systematically, we introduce Cancer-Myth, an expert-verified adversarial dataset of 585 cancer-related questions with false presuppositions. On this benchmark, no frontier LLM -- including GPT-4o, Gemini-1.Pro, and Claude-3.5-Sonnet -- corrects these false presuppositions more than 30% of the time. Even advanced medical agentic methods do not prevent LLMs from ignoring false presuppositions. These findings expose a critical gap in the clinical reliability of LLMs and underscore the need for more robust safeguards in medical AI systems.

Early detection of gastric cancer, a leading cause of cancer-related mortality worldwide, remains hampered by the limitations of current diagnostic technologies, leading to high rates of misdiagnosis and missed diagnoses. To address these challenges, we propose an integrated system that synergizes advanced hardware and software technologies to balance speed-accuracy. Our study introduces the One Class Twin Cross Learning (OCT-X) algorithm. Leveraging a novel fast double-threshold grid search strategy (FDT-GS) and a patch-based deep fully convolutional network, OCT-X maximizes diagnostic accuracy through real-time data processing and seamless lesion surveillance. The hardware component includes an all-in-one point-of-care testing (POCT) device with high-resolution imaging sensors, real-time data processing, and wireless connectivity, facilitated by the NI CompactDAQ and LabVIEW software. Our integrated system achieved an unprecedented diagnostic accuracy of 99.70%, significantly outperforming existing models by up to 4.47%, and demonstrated a 10% improvement in multirate adaptability. These findings underscore the potential of OCT-X as well as the integrated system in clinical diagnostics, offering a path toward more accurate, efficient, and less invasive early gastric cancer detection. Future research will explore broader applications, further advancing oncological diagnostics. Code is available at https://github.com/liu37972/Multirate-Location-on-OCT-X-Learning.git.

Machine learning techniques are effective for building predictive models because they identify patterns in large datasets. Development of a model for complex real-life problems often stop at the point of publication, proof of concept or when made accessible through some mode of deployment. However, a model in the medical domain risks becoming obsolete as patient demographics, systems and clinical practices change. The maintenance and monitoring of predictive model performance post-publication is crucial to enable their safe and effective long-term use. We will assess the infrastructure required to monitor the outputs of a machine learning algorithm, and present two scenarios with examples of monitoring and updates of models, firstly on a breast cancer prognosis model trained on public longitudinal data, and secondly on a neurodegenerative stratification algorithm that is currently being developed and tested in clinic.

There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model - GatorTron - using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on 5 clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve 5 clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og.

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.

We propose a simple approach for weighting self-connecting edges in a Graph Convolutional Network (GCN) and show its impact on depression detection from transcribed clinical interviews. To this end, we use a GCN for modeling non-consecutive and long-distance semantics to classify the transcriptions into depressed or control subjects. The proposed method aims to mitigate the limiting assumptions of locality and the equal importance of self-connections vs. edges to neighboring nodes in GCNs, while preserving attractive features such as low computational cost, data agnostic, and interpretability capabilities. We perform an exhaustive evaluation in two benchmark datasets. Results show that our approach consistently outperforms the vanilla GCN model as well as previously reported results, achieving an F1=0.84 on both datasets. Finally, a qualitative analysis illustrates the interpretability capabilities of the proposed approach and its alignment with previous findings in psychology.

Pre-trained transformers are often fine-tuned to aid clinical decision-making using limited clinical notes. Model interpretability is crucial, especially in high-stakes domains like medicine, to establish trust and ensure safety, which requires human engagement. We introduce SUFO, a systematic framework that enhances interpretability of fine-tuned transformer feature spaces. SUFO utilizes a range of analytic and visualization techniques, including Supervised probing, Unsupervised similarity analysis, Feature dynamics, and Outlier analysis to address key questions about model trust and interpretability. We conduct a case study investigating the impact of pre-training data where we focus on real-world pathology classification tasks, and validate our findings on MedNLI. We evaluate five 110M-sized pre-trained transformer models, categorized into general-domain (BERT, TNLR), mixed-domain (BioBERT, Clinical BioBERT), and domain-specific (PubMedBERT) groups. Our SUFO analyses reveal that: (1) while PubMedBERT, the domain-specific model, contains valuable information for fine-tuning, it can overfit to minority classes when class imbalances exist. In contrast, mixed-domain models exhibit greater resistance to overfitting, suggesting potential improvements in domain-specific model robustness; (2) in-domain pre-training accelerates feature disambiguation during fine-tuning; and (3) feature spaces undergo significant sparsification during this process, enabling clinicians to identify common outlier modes among fine-tuned models as demonstrated in this paper. These findings showcase the utility of SUFO in enhancing trust and safety when using transformers in medicine, and we believe SUFO can aid practitioners in evaluating fine-tuned language models for other applications in medicine and in more critical domains.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

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

The emergence of vision-language models has transformed medical AI, enabling unprecedented advances in diagnostic capability and clinical applications. However, progress in dermatology has lagged behind other medical domains due to the lack of standard image-text pairs. Existing dermatological datasets are limited in both scale and depth, offering only single-label annotations across a narrow range of diseases instead of rich textual descriptions, and lacking the crucial clinical context needed for real-world applications. To address these limitations, we present Derm1M, the first large-scale vision-language dataset for dermatology, comprising 1,029,761 image-text pairs. Built from diverse educational resources and structured around a standard ontology collaboratively developed by experts, Derm1M provides comprehensive coverage for over 390 skin conditions across four hierarchical levels and 130 clinical concepts with rich contextual information such as medical history, symptoms, and skin tone. To demonstrate Derm1M potential in advancing both AI research and clinical application, we pretrained a series of CLIP-like models, collectively called DermLIP, on this dataset. The DermLIP family significantly outperforms state-of-the-art foundation models on eight diverse datasets across multiple tasks, including zero-shot skin disease classification, clinical and artifacts concept identification, few-shot/full-shot learning, and cross-modal retrieval. Our dataset and code will be public.

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.

Recent immense breakthroughs in generative models such as in GPT4 have precipitated re-imagined ubiquitous usage of these models in all applications. One area that can benefit by improvements in artificial intelligence (AI) is healthcare. The note generation task from doctor-patient encounters, and its associated electronic medical record documentation, is one of the most arduous time-consuming tasks for physicians. It is also a natural prime potential beneficiary to advances in generative models. However with such advances, benchmarking is more critical than ever. Whether studying model weaknesses or developing new evaluation metrics, shared open datasets are an imperative part of understanding the current state-of-the-art. Unfortunately as clinic encounter conversations are not routinely recorded and are difficult to ethically share due to patient confidentiality, there are no sufficiently large clinic dialogue-note datasets to benchmark this task. Here we present the Ambient Clinical Intelligence Benchmark (ACI-BENCH) corpus, the largest dataset to date tackling the problem of AI-assisted note generation from visit dialogue. We also present the benchmark performances of several common state-of-the-art approaches.

The increased capabilities of generative AI have dramatically expanded its possible use cases in medicine. We provide a comprehensive overview of generative AI use cases for clinicians, patients, clinical trial organizers, researchers, and trainees. We then discuss the many challenges -- including maintaining privacy and security, improving transparency and interpretability, upholding equity, and rigorously evaluating models -- which must be overcome to realize this potential, and the open research directions they give rise to.

Advancements in high-throughput technologies have led to a shift from traditional hypothesis-driven methodologies to data-driven approaches. Multi-omics refers to the integrative analysis of data derived from multiple 'omes', such as genomics, proteomics, transcriptomics, metabolomics, and microbiomics. This approach enables a comprehensive understanding of biological systems by capturing different layers of biological information. Deep learning methods are increasingly utilized to integrate multi-omics data, offering insights into molecular interactions and enhancing research into complex diseases. However, these models, with their numerous interconnected layers and nonlinear relationships, often function as black boxes, lacking transparency in decision-making processes. To overcome this challenge, explainable artificial intelligence (xAI) methods are crucial for creating transparent models that allow clinicians to interpret and work with complex data more effectively. This review explores how xAI can improve the interpretability of deep learning models in multi-omics research, highlighting its potential to provide clinicians with clear insights, thereby facilitating the effective application of such models in clinical settings.

In Vitro Fertilization is among the most widespread treatments for infertility. One of its main challenges is the evaluation and selection of embryo for implantation, a process with large inter- and intra-clinician variability. Deep learning based methods are gaining attention, but their opaque nature compromises their acceptance in the clinical context, where transparency in the decision making is key. In this paper we analyze the current work in the explainability of AI-assisted embryo analysis models, identifying the limitations. We also discuss how these models could be integrated in the clinical context as decision support systems, considering the needs of clinicians and patients. Finally, we propose guidelines for the sake of increasing interpretability and trustworthiness, pushing this technology forward towards established clinical practice.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

Adverse drug events (ADEs) significantly impact clinical research, causing many clinical trial failures. ADE prediction is key for developing safer medications and enhancing patient outcomes. To support this effort, we introduce CT-ADE, a dataset for multilabel predictive modeling of ADEs in monopharmacy treatments. CT-ADE integrates data from 2,497 unique drugs, encompassing 168,984 drug-ADE pairs extracted from clinical trials, annotated with patient and contextual information, and comprehensive ADE concepts standardized across multiple levels of the MedDRA ontology. Preliminary analyses with large language models (LLMs) achieved F1-scores up to 55.90%. Models using patient and contextual information showed F1-score improvements of 21%-38% over models using only chemical structure data. Our results highlight the importance of target population and treatment regimens in the predictive modeling of ADEs, offering greater performance gains than LLM domain specialization and scaling. CT-ADE provides an essential tool for researchers aiming to leverage artificial intelligence and machine learning to enhance patient safety and minimize the impact of ADEs on pharmaceutical research and development. The dataset is publicly accessible at https://github.com/ds4dh/CT-ADE.

Stanford Medicine is building a new data platform for our academic research community to do better clinical data science. Hospitals have a large amount of patient data and researchers have demonstrated the ability to reuse that data and AI approaches to derive novel insights, support patient care, and improve care quality. However, the traditional data warehouse and Honest Broker approaches that are in current use, are not scalable. We are establishing a new secure Big Data platform that aims to reduce time to access and analyze data. In this platform, data is anonymized to preserve patient data privacy and made available preparatory to Institutional Review Board (IRB) submission. Furthermore, the data is standardized such that analysis done at Stanford can be replicated elsewhere using the same analytical code and clinical concepts. Finally, the analytics data warehouse integrates with a secure data science computational facility to support large scale data analytics. The ecosystem is designed to bring the modern data science community to highly sensitive clinical data in a secure and collaborative big data analytics environment with a goal to enable bigger, better and faster science.

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.

This paper introduces a new testbed CLIFT (Clinical Shift) for the clinical domain Question-answering task. The testbed includes 7.5k high-quality question answering samples to provide a diverse and reliable benchmark. We performed a comprehensive experimental study and evaluated several QA deep-learning models under the proposed testbed. Despite impressive results on the original test set, the performance degrades when applied to new test sets, which shows the distribution shift. Our findings emphasize the need for and the potential for increasing the robustness of clinical domain models under distributional shifts. The testbed offers one way to track progress in that direction. It also highlights the necessity of adopting evaluation metrics that consider robustness to natural distribution shifts. We plan to expand the corpus by adding more samples and model results. The full paper and the updated benchmark are available at github.com/openlifescience-ai/clift

We present a novel contribution to Spanish clinical natural language processing by introducing the largest publicly available clinical corpus, ClinText-SP, along with a state-of-the-art clinical encoder language model, RigoBERTa Clinical. Our corpus was meticulously curated from diverse open sources, including clinical cases from medical journals and annotated corpora from shared tasks, providing a rich and diverse dataset that was previously difficult to access. RigoBERTa Clinical, developed through domain-adaptive pretraining on this comprehensive dataset, significantly outperforms existing models on multiple clinical NLP benchmarks. By publicly releasing both the dataset and the model, we aim to empower the research community with robust resources that can drive further advancements in clinical NLP and ultimately contribute to improved healthcare applications.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

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.

Machine translation is indispensable in healthcare for enabling the global dissemination of medical knowledge across languages. However, complex medical terminology poses unique challenges to achieving adequate translation quality and accuracy. This study introduces a novel "LLMs-in-the-loop" approach to develop supervised neural machine translation models optimized specifically for medical texts. While large language models (LLMs) have demonstrated powerful capabilities, this research shows that small, specialized models trained on high-quality in-domain (mostly synthetic) data can outperform even vastly larger LLMs. Custom parallel corpora in six languages were compiled from scientific articles, synthetically generated clinical documents, and medical texts. Our LLMs-in-the-loop methodology employs synthetic data generation, rigorous evaluation, and agent orchestration to enhance performance. We developed small medical translation models using the MarianMT base model. We introduce a new medical translation test dataset to standardize evaluation in this domain. Assessed using BLEU, METEOR, ROUGE, and BERT scores on this test set, our MarianMT-based models outperform Google Translate, DeepL, and GPT-4-Turbo. Results demonstrate that our LLMs-in-the-loop approach, combined with fine-tuning high-quality, domain-specific data, enables specialized models to outperform general-purpose and some larger systems. This research, part of a broader series on expert small models, paves the way for future healthcare-related AI developments, including deidentification and bio-medical entity extraction models. Our study underscores the potential of tailored neural translation models and the LLMs-in-the-loop methodology to advance the field through improved data generation, evaluation, agent, and modeling techniques.

Rare diseases, including Inborn Errors of Metabolism (IEM), pose significant diagnostic challenges. Case reports serve as key but computationally underutilized resources to inform diagnosis. Clinical dense information extraction refers to organizing medical information into structured predefined categories. Large Language Models (LLMs) may enable scalable information extraction from case reports but are rarely evaluated for this task. We introduce CaseReportBench, an expert-annotated dataset for dense information extraction of case reports, focusing on IEMs. Using this dataset, we assess various models and prompting strategies, introducing novel approaches such as category-specific prompting and subheading-filtered data integration. Zero-shot chain-of-thought prompting offers little advantage over standard zero-shot prompting. Category-specific prompting improves alignment with the benchmark. The open-source model Qwen2.5-7B outperforms GPT-4o for this task. Our clinician evaluations show that LLMs can extract clinically relevant details from case reports, supporting rare disease diagnosis and management. We also highlight areas for improvement, such as LLMs' limitations in recognizing negative findings important for differential diagnosis. This work advances LLM-driven clinical natural language processing and paves the way for scalable medical AI applications.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Passively collected behavioral health data from ubiquitous sensors holds significant promise to provide mental health professionals insights from patient's daily lives; however, developing analysis tools to use this data in clinical practice requires addressing challenges of generalization across devices and weak or ambiguous correlations between the measured signals and an individual's mental health. To address these challenges, we take a novel approach that leverages large language models (LLMs) to synthesize clinically useful insights from multi-sensor data. We develop chain of thought prompting methods that use LLMs to generate reasoning about how trends in data such as step count and sleep relate to conditions like depression and anxiety. We first demonstrate binary depression classification with LLMs achieving accuracies of 61.1% which exceed the state of the art. While it is not robust for clinical use, this leads us to our key finding: even more impactful and valued than classification is a new human-AI collaboration approach in which clinician experts interactively query these tools and combine their domain expertise and context about the patient with AI generated reasoning to support clinical decision-making. We find models like GPT-4 correctly reference numerical data 75% of the time, and clinician participants express strong interest in using this approach to interpret self-tracking data.

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

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date. It is constructed from 285 datasets across 39 medical image modalities, 18 clinical-related tasks, 18 departments, and 4 perceptual granularities in a Visual Question Answering (VQA) format. Additionally, we implemented a lexical tree structure that allows users to customize evaluation tasks, accommodating various assessment needs and substantially supporting medical AI research and applications. We evaluated 50 LVLMs, and the results show that even the advanced GPT-4o only achieves an accuracy of 52%, indicating significant room for improvement. Moreover, we identified five key insufficiencies in current cutting-edge LVLMs that need to be addressed to advance the development of better medical applications. We believe that GMAI-MMBench will stimulate the community to build the next generation of LVLMs toward GMAI. Project Page: https://uni-medical.github.io/GMAI-MMBench.github.io/

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

The field of natural language processing (NLP) has recently seen a large change towards using pre-trained language models for solving almost any task. Despite showing great improvements in benchmark datasets for various tasks, these models often perform sub-optimal in non-standard domains like the clinical domain where a large gap between pre-training documents and target documents is observed. In this paper, we aim at closing this gap with domain-specific training of the language model and we investigate its effect on a diverse set of downstream tasks and settings. We introduce the pre-trained CLIN-X (Clinical XLM-R) language models and show how CLIN-X outperforms other pre-trained transformer models by a large margin for ten clinical concept extraction tasks from two languages. In addition, we demonstrate how the transformer model can be further improved with our proposed task- and language-agnostic model architecture based on ensembles over random splits and cross-sentence context. Our studies in low-resource and transfer settings reveal stable model performance despite a lack of annotated data with improvements of up to 47 F1 points when only 250 labeled sentences are available. Our results highlight the importance of specialized language models as CLIN-X for concept extraction in non-standard domains, but also show that our task-agnostic model architecture is robust across the tested tasks and languages so that domain- or task-specific adaptations are not required.

The detailed clinical records drafted by doctors after each patient's visit are crucial for medical practitioners and researchers. Automating the creation of these notes with language models can reduce the workload of doctors. However, training such models can be difficult due to the limited public availability of conversations between patients and doctors. In this paper, we introduce NoteChat, a cooperative multi-agent framework leveraging Large Language Models (LLMs) for generating synthetic doctor-patient conversations conditioned on clinical notes. NoteChat consists of Planning, Roleplay, and Polish modules. We provide a comprehensive automatic and human evaluation of NoteChat, comparing it with state-of-the-art models, including OpenAI's ChatGPT and GPT-4. Results demonstrate that NoteChat facilitates high-quality synthetic doctor-patient conversations, underscoring the untapped potential of LLMs in healthcare. This work represents the first instance of multiple LLMs cooperating to complete a doctor-patient conversation conditioned on clinical notes, offering promising avenues for the intersection of AI and healthcare

The increasing interest in developing Artificial Intelligence applications in the medical domain, suffers from the lack of high-quality dataset, mainly due to privacy-related issues. Moreover, the recent rising of Multimodal Large Language Models (MLLM) leads to a need for multimodal medical datasets, where clinical reports and findings are attached to the corresponding CT or MR scans. This paper illustrates the entire workflow for building the data set MedPix 2.0. Starting from the well-known multimodal dataset MedPix\textregistered, mainly used by physicians, nurses and healthcare students for Continuing Medical Education purposes, a semi-automatic pipeline was developed to extract visual and textual data followed by a manual curing procedure where noisy samples were removed, thus creating a MongoDB database. Along with the dataset, we developed a GUI aimed at navigating efficiently the MongoDB instance, and obtaining the raw data that can be easily used for training and/or fine-tuning MLLMs. To enforce this point, we also propose a CLIP-based model trained on MedPix 2.0 for scan classification tasks.

Large Language Models (LLMs) such as GPT & Llama have demonstrated significant achievements in summarization tasks but struggle with factual inaccuracies, a critical issue in clinical NLP applications where errors could lead to serious consequences. To counter the high costs and limited availability of expert-annotated data for factual alignment, this study introduces an innovative pipeline that utilizes >100B parameter GPT variants like GPT-3.5 & GPT-4 to act as synthetic experts to generate high-quality synthetics feedback aimed at enhancing factual consistency in clinical note summarization. Our research primarily focuses on edit feedback generated by these synthetic feedback experts without additional human annotations, mirroring and optimizing the practical scenario in which medical professionals refine AI system outputs. Although such 100B+ parameter GPT variants have proven to demonstrate expertise in various clinical NLP tasks, such as the Medical Licensing Examination, there is scant research on their capacity to act as synthetic feedback experts and deliver expert-level edit feedback for improving the generation quality of weaker (<10B parameter) LLMs like GPT-2 (1.5B) & Llama 2 (7B) in clinical domain. So in this work, we leverage 100B+ GPT variants to act as synthetic feedback experts offering expert-level edit feedback, that is used to reduce hallucinations and align weaker (<10B parameter) LLMs with medical facts using two distinct alignment algorithms (DPO & SALT), endeavoring to narrow the divide between AI-generated content and factual accuracy. This highlights the substantial potential of LLM-based synthetic edits in enhancing the alignment of clinical factuality.

Substance use disorders (SUDs) are a growing concern globally, necessitating enhanced understanding of the problem and its trends through data-driven research. Social media are unique and important sources of information about SUDs, particularly since the data in such sources are often generated by people with lived experiences. In this paper, we introduce Reddit-Impacts, a challenging Named Entity Recognition (NER) dataset curated from subreddits dedicated to discussions on prescription and illicit opioids, as well as medications for opioid use disorder. The dataset specifically concentrates on the lesser-studied, yet critically important, aspects of substance use--its clinical and social impacts. We collected data from chosen subreddits using the publicly available Application Programming Interface for Reddit. We manually annotated text spans representing clinical and social impacts reported by people who also reported personal nonmedical use of substances including but not limited to opioids, stimulants and benzodiazepines. Our objective is to create a resource that can enable the development of systems that can automatically detect clinical and social impacts of substance use from text-based social media data. The successful development of such systems may enable us to better understand how nonmedical use of substances affects individual health and societal dynamics, aiding the development of effective public health strategies. In addition to creating the annotated data set, we applied several machine learning models to establish baseline performances. Specifically, we experimented with transformer models like BERT, and RoBERTa, one few-shot learning model DANN by leveraging the full training dataset, and GPT-3.5 by using one-shot learning, for automatic NER of clinical and social impacts. The dataset has been made available through the 2024 SMM4H shared tasks.

In the healthcare domain, summarizing medical questions posed by patients is critical for improving doctor-patient interactions and medical decision-making. Although medical data has grown in complexity and quantity, the current body of research in this domain has primarily concentrated on text-based methods, overlooking the integration of visual cues. Also prior works in the area of medical question summarisation have been limited to the English language. This work introduces the task of multimodal medical question summarization for codemixed input in a low-resource setting. To address this gap, we introduce the Multimodal Medical Codemixed Question Summarization MMCQS dataset, which combines Hindi-English codemixed medical queries with visual aids. This integration enriches the representation of a patient's medical condition, providing a more comprehensive perspective. We also propose a framework named MedSumm that leverages the power of LLMs and VLMs for this task. By utilizing our MMCQS dataset, we demonstrate the value of integrating visual information from images to improve the creation of medically detailed summaries. This multimodal strategy not only improves healthcare decision-making but also promotes a deeper comprehension of patient queries, paving the way for future exploration in personalized and responsive medical care. Our dataset, code, and pre-trained models will be made publicly available.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

The recent introduction of synthetic correlated diffusion (CDI^s) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI^s is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI^s data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI^s imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI^s volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI^s imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

Despite significant advancements in general artificial intelligence, such as GPT-4, their effectiveness in the medical domain (general medical AI, GMAI) remains constrained due to the absence of specialized medical knowledge. To address this challenge, we present GMAI-VL-5.5M, a comprehensive multimodal medical dataset created by converting hundreds of specialized medical datasets into meticulously constructed image-text pairs. This dataset features comprehensive task coverage, diverse modalities, and high-quality image-text data. Building upon this multimodal dataset, we propose GMAI-VL, a general medical vision-language model with a progressively three-stage training strategy. This approach significantly enhances the model's ability by integrating visual and textual information, thereby improving its ability to process multimodal data and support accurate diagnosis and clinical decision-making. Experimental evaluations demonstrate that GMAI-VL achieves state-of-the-art results across a wide range of multimodal medical tasks, such as visual question answering and medical image diagnosis. Our contributions include the development of the GMAI-VL-5.5M dataset, the introduction of the GMAI-VL model, and the establishment of new benchmarks in multiple medical domains. Code and dataset will be released at https://github.com/uni-medical/GMAI-VL.

The lack of transparency and explainability hinders the clinical adoption of Machine learning (ML) algorithms. While explainable artificial intelligence (XAI) methods have been proposed, little research has focused on the agreement between these methods and expert clinical knowledge. This study applies current state-of-the-art explainability methods to clinical decision support algorithms developed for Electronic Medical Records (EMR) data to analyse the concordance between these factors and discusses causes for identified discrepancies from a clinical and technical perspective. Important factors for achieving trustworthy XAI solutions for clinical decision support are also discussed.

Off-policy reinforcement learning (RL) has proven to be a powerful framework for guiding agents' actions in environments with stochastic rewards and unknown or noisy state dynamics. In many real-world settings, these agents must operate in multiple environments, each with slightly different dynamics. For example, we may be interested in developing policies to guide medical treatment for patients with and without a given disease, or policies to navigate curriculum design for students with and without a learning disability. Here, we introduce nested policy fitted Q-iteration (NFQI), an RL framework that finds optimal policies in environments that exhibit such a structure. Our approach develops a nested Q-value function that takes advantage of the shared structure between two groups of observations from two separate environments while allowing their policies to be distinct from one another. We find that NFQI yields policies that rely on relevant features and perform at least as well as a policy that does not consider group structure. We demonstrate NFQI's performance using an OpenAI Gym environment and a clinical decision making RL task. Our results suggest that NFQI can develop policies that are better suited to many real-world clinical environments.

Collective insights from a group of experts have always proven to outperform an individual's best diagnostic for clinical tasks. For the task of medical image segmentation, existing research on AI-based alternatives focuses more on developing models that can imitate the best individual rather than harnessing the power of expert groups. In this paper, we introduce a single diffusion model-based approach that produces multiple plausible outputs by learning a distribution over group insights. Our proposed model generates a distribution of segmentation masks by leveraging the inherent stochastic sampling process of diffusion using only minimal additional learning. We demonstrate on three different medical image modalities- CT, ultrasound, and MRI that our model is capable of producing several possible variants while capturing the frequencies of their occurrences. Comprehensive results show that our proposed approach outperforms existing state-of-the-art ambiguous segmentation networks in terms of accuracy while preserving naturally occurring variation. We also propose a new metric to evaluate the diversity as well as the accuracy of segmentation predictions that aligns with the interest of clinical practice of collective insights.

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS. This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks.

Medical image segmentation has immense clinical applicability but remains a challenge despite advancements in deep learning. The Segment Anything Model (SAM) exhibits potential in this field, yet the requirement for expertise intervention and the domain gap between natural and medical images poses significant obstacles. This paper introduces a novel training-free evidential prompt generation method named EviPrompt to overcome these issues. The proposed method, built on the inherent similarities within medical images, requires only a single reference image-annotation pair, making it a training-free solution that significantly reduces the need for extensive labeling and computational resources. First, to automatically generate prompts for SAM in medical images, we introduce an evidential method based on uncertainty estimation without the interaction of clinical experts. Then, we incorporate the human prior into the prompts, which is vital for alleviating the domain gap between natural and medical images and enhancing the applicability and usefulness of SAM in medical scenarios. EviPrompt represents an efficient and robust approach to medical image segmentation, with evaluations across a broad range of tasks and modalities confirming its efficacy.

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

This study investigates the feasibility of automating clinical coding in Russian, a language with limited biomedical resources. We present a new dataset for ICD coding, which includes diagnosis fields from electronic health records (EHRs) annotated with over 10,000 entities and more than 1,500 unique ICD codes. This dataset serves as a benchmark for several state-of-the-art models, including BERT, LLaMA with LoRA, and RAG, with additional experiments examining transfer learning across domains (from PubMed abstracts to medical diagnosis) and terminologies (from UMLS concepts to ICD codes). We then apply the best-performing model to label an in-house EHR dataset containing patient histories from 2017 to 2021. Our experiments, conducted on a carefully curated test set, demonstrate that training with the automated predicted codes leads to a significant improvement in accuracy compared to manually annotated data from physicians. We believe our findings offer valuable insights into the potential for automating clinical coding in resource-limited languages like Russian, which could enhance clinical efficiency and data accuracy in these contexts.

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.

Skin conditions affect an estimated 1.9 billion people worldwide. A shortage of dermatologists causes long wait times and leads patients to seek dermatologic care from general practitioners. However, the diagnostic accuracy of general practitioners has been reported to be only 0.24-0.70 (compared to 0.77-0.96 for dermatologists), resulting in referral errors, delays in care, and errors in diagnosis and treatment. In this paper, we developed a deep learning system (DLS) to provide a differential diagnosis of skin conditions for clinical cases (skin photographs and associated medical histories). The DLS distinguishes between 26 skin conditions that represent roughly 80% of the volume of skin conditions seen in primary care. The DLS was developed and validated using de-identified cases from a teledermatology practice serving 17 clinical sites via a temporal split: the first 14,021 cases for development and the last 3,756 cases for validation. On the validation set, where a panel of three board-certified dermatologists defined the reference standard for every case, the DLS achieved 0.71 and 0.93 top-1 and top-3 accuracies respectively. For a random subset of the validation set (n=963 cases), 18 clinicians reviewed the cases for comparison. On this subset, the DLS achieved a 0.67 top-1 accuracy, non-inferior to board-certified dermatologists (0.63, p<0.001), and higher than primary care physicians (PCPs, 0.45) and nurse practitioners (NPs, 0.41). The top-3 accuracy showed a similar trend: 0.90 DLS, 0.75 dermatologists, 0.60 PCPs, and 0.55 NPs. These results highlight the potential of the DLS to augment general practitioners to accurately diagnose skin conditions by suggesting differential diagnoses that may not have been considered. Future work will be needed to prospectively assess the clinical impact of using this tool in actual clinical workflows.

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.

The emergent abilities of large language models (LLMs) have demonstrated great potential in solving medical questions. They can possess considerable medical knowledge, but may still hallucinate and are inflexible in the knowledge updates. While Retrieval-Augmented Generation (RAG) has been proposed to enhance the medical question-answering capabilities of LLMs with external knowledge bases, it may still fail in complex cases where multiple rounds of information-seeking are required. To address such an issue, we propose iterative RAG for medicine (i-MedRAG), where LLMs can iteratively ask follow-up queries based on previous information-seeking attempts. In each iteration of i-MedRAG, the follow-up queries will be answered by a vanilla RAG system and they will be further used to guide the query generation in the next iteration. Our experiments show the improved performance of various LLMs brought by i-MedRAG compared with vanilla RAG on complex questions from clinical vignettes in the United States Medical Licensing Examination (USMLE), as well as various knowledge tests in the Massive Multitask Language Understanding (MMLU) dataset. Notably, our zero-shot i-MedRAG outperforms all existing prompt engineering and fine-tuning methods on GPT-3.5, achieving an accuracy of 69.68\% on the MedQA dataset. In addition, we characterize the scaling properties of i-MedRAG with different iterations of follow-up queries and different numbers of queries per iteration. Our case studies show that i-MedRAG can flexibly ask follow-up queries to form reasoning chains, providing an in-depth analysis of medical questions. To the best of our knowledge, this is the first-of-its-kind study on incorporating follow-up queries into medical RAG.

As opposed to evaluating computation and logic-based reasoning, current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks.

Expert interpretation of anatomical images of the human brain is the central part of neuro-radiology. Several machine learning-based techniques have been proposed to assist in the analysis process. However, the ML models typically need to be trained to perform a specific task, e.g., brain tumour segmentation or classification. Not only do the corresponding training data require laborious manual annotations, but a wide variety of abnormalities can be present in a human brain MRI - even more than one simultaneously, which renders representation of all possible anomalies very challenging. Hence, a possible solution is an unsupervised anomaly detection (UAD) system that can learn a data distribution from an unlabelled dataset of healthy subjects and then be applied to detect out of distribution samples. Such a technique can then be used to detect anomalies - lesions or abnormalities, for example, brain tumours, without explicitly training the model for that specific pathology. Several Variational Autoencoder (VAE) based techniques have been proposed in the past for this task. Even though they perform very well on controlled artificially simulated anomalies, many of them perform poorly while detecting anomalies in clinical data. This research proposes a compact version of the "context-encoding" VAE (ceVAE) model, combined with pre and post-processing steps, creating a UAD pipeline (StRegA), which is more robust on clinical data, and shows its applicability in detecting anomalies such as tumours in brain MRIs. The proposed pipeline achieved a Dice score of 0.642pm0.101 while detecting tumours in T2w images of the BraTS dataset and 0.859pm0.112 while detecting artificially induced anomalies, while the best performing baseline achieved 0.522pm0.135 and 0.783pm0.111, respectively.

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

In this paper, a multi-scale visual transformer model, referred as GasHis-Transformer, is proposed for Gastric Histopathological Image Detection (GHID), which enables the automatic global detection of gastric cancer images. GasHis-Transformer model consists of two key modules designed to extract global and local information using a position-encoded transformer model and a convolutional neural network with local convolution, respectively. A publicly available hematoxylin and eosin (H&E) stained gastric histopathological image dataset is used in the experiment. Furthermore, a Dropconnect based lightweight network is proposed to reduce the model size and training time of GasHis-Transformer for clinical applications with improved confidence. Moreover, a series of contrast and extended experiments verify the robustness, extensibility and stability of GasHis-Transformer. In conclusion, GasHis-Transformer demonstrates high global detection performance and shows its significant potential in GHID task.

Radiotherapy (RT) planning is complex, subjective, and time-intensive. Advances in artificial intelligence (AI) promise to improve its precision, efficiency, and consistency, but progress is often limited by the scarcity of large, standardized datasets. To address this, we introduce the Automated Iterative RT Planning (AIRTP) system, a scalable solution for generating high-quality treatment plans. This scalable solution is designed to generate substantial volumes of consistently high-quality treatment plans, overcoming a key obstacle in the advancement of AI-driven RT planning. Our AIRTP pipeline adheres to clinical guidelines and automates essential steps, including organ-at-risk (OAR) contouring, helper structure creation, beam setup, optimization, and plan quality improvement, using AI integrated with RT planning software like Eclipse of Varian. Furthermore, a novel approach for determining optimization parameters to reproduce 3D dose distributions, i.e. a method to convert dose predictions to deliverable treatment plans constrained by machine limitations. A comparative analysis of plan quality reveals that our automated pipeline produces treatment plans of quality comparable to those generated manually, which traditionally require several hours of labor per plan. Committed to public research, the first data release of our AIRTP pipeline includes nine cohorts covering head-and-neck and lung cancer sites to support an AAPM 2025 challenge. This data set features more than 10 times the number of plans compared to the largest existing well-curated public data set to our best knowledge. Repo:{https://github.com/RiqiangGao/GDP-HMM_AAPMChallenge}

Medical visual question answering aims to support clinical decision-making by enabling models to answer natural language questions based on medical images. While recent advances in multi-modal learning have significantly improved performance, current methods still suffer from limited answer reliability and poor interpretability, impairing the ability of clinicians and patients to understand and trust model-generated answers. To address this, this work first proposes a Thinking with Visual Grounding (ThinkVG) dataset wherein the answer generation is decomposed into intermediate reasoning steps that explicitly ground relevant visual regions of the medical image, thereby providing fine-grained explainability. Furthermore, we introduce a novel verifiable reward mechanism for reinforcement learning to guide post-training, improving the alignment between the model's reasoning process and its final answer. Remarkably, our method achieves comparable performance using only one-eighth of the training data, demonstrating the efficiency and effectiveness of the proposal. The dataset is available at https://huggingface.co/datasets/BoKelvin/GEMeX-ThinkVG.

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

We present ReXVQA, the largest and most comprehensive benchmark for visual question answering (VQA) in chest radiology, comprising approximately 696,000 questions paired with 160,000 chest X-rays studies across training, validation, and test sets. Unlike prior efforts that rely heavily on template based queries, ReXVQA introduces a diverse and clinically authentic task suite reflecting five core radiological reasoning skills: presence assessment, location analysis, negation detection, differential diagnosis, and geometric reasoning. We evaluate eight state-of-the-art multimodal large language models, including MedGemma-4B-it, Qwen2.5-VL, Janus-Pro-7B, and Eagle2-9B. The best-performing model (MedGemma) achieves 83.24% overall accuracy. To bridge the gap between AI performance and clinical expertise, we conducted a comprehensive human reader study involving 3 radiology residents on 200 randomly sampled cases. Our evaluation demonstrates that MedGemma achieved superior performance (83.84% accuracy) compared to human readers (best radiology resident: 77.27%), representing a significant milestone where AI performance exceeds expert human evaluation on chest X-ray interpretation. The reader study reveals distinct performance patterns between AI models and human experts, with strong inter-reader agreement among radiologists while showing more variable agreement patterns between human readers and AI models. ReXVQA establishes a new standard for evaluating generalist radiological AI systems, offering public leaderboards, fine-grained evaluation splits, structured explanations, and category-level breakdowns. This benchmark lays the foundation for next-generation AI systems capable of mimicking expert-level clinical reasoning beyond narrow pathology classification. Our dataset will be open-sourced at https://huggingface.co/datasets/rajpurkarlab/ReXVQA

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

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 .

Multi-modal interpretation of biomedical images opens up novel opportunities in biomedical image analysis. Conventional AI approaches typically rely on disjointed training, i.e., Large Language Models (LLMs) for clinical text generation and segmentation models for target extraction, which results in inflexible real-world deployment and a failure to leverage holistic biomedical information. To this end, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation. UniBiomed is based on a novel integration of Multi-modal Large Language Model (MLLM) and Segment Anything Model (SAM), which effectively unifies the generation of clinical texts and the segmentation of corresponding biomedical objects for grounded interpretation. In this way, UniBiomed is capable of tackling a wide range of biomedical tasks across ten diverse biomedical imaging modalities. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, annotations, and text descriptions across ten imaging modalities. Extensive validation on 84 internal and external datasets demonstrated that UniBiomed achieves state-of-the-art performance in segmentation, disease recognition, region-aware diagnosis, visual question answering, and report generation. Moreover, unlike previous models that rely on clinical experts to pre-diagnose images and manually craft precise textual or visual prompts, UniBiomed can provide automated and end-to-end grounded interpretation for biomedical image analysis. This represents a novel paradigm shift in clinical workflows, which will significantly improve diagnostic efficiency. In summary, UniBiomed represents a novel breakthrough in biomedical AI, unlocking powerful grounded interpretation capabilities for more accurate and efficient biomedical image analysis.

Recent advances in AI foundation models have significant potential for lightening the clinical workload by mimicking the comprehensive and multi-faceted approaches used by medical professionals. In the field of radiation oncology, the integration of multiple modalities holds great importance, so the opportunity of foundational model is abundant. Inspired by this, here we present RO-LMM, a multi-purpose, comprehensive large multimodal model (LMM) tailored for the field of radiation oncology. This model effectively manages a series of tasks within the clinical workflow, including clinical context summarization, radiation treatment plan suggestion, and plan-guided target volume segmentation by leveraging the capabilities of LMM. In particular, to perform consecutive clinical tasks without error accumulation, we present a novel Consistency Embedding Fine-Tuning (CEFTune) technique, which boosts LMM's robustness to noisy inputs while preserving the consistency of handling clean inputs. We further extend this concept to LMM-driven segmentation framework, leading to a novel Consistency Embedding Segmentation~(CESEG) techniques. Experimental results including multi-centre validation confirm that our RO-LMM with CEFTune and CESEG results in promising performance for multiple clinical tasks with generalization capabilities.

Radiology report generation (RRG) aims to automatically generate free-text descriptions from clinical radiographs, e.g., chest X-Ray images. RRG plays an essential role in promoting clinical automation and presents significant help to provide practical assistance for inexperienced doctors and alleviate radiologists' workloads. Therefore, consider these meaningful potentials, research on RRG is experiencing explosive growth in the past half-decade, especially with the rapid development of deep learning approaches. Existing studies perform RRG from the perspective of enhancing different modalities, provide insights on optimizing the report generation process with elaborated features from both visual and textual information, and further facilitate RRG with the cross-modal interactions among them. In this paper, we present a comprehensive review of deep learning-based RRG from various perspectives. Specifically, we firstly cover pivotal RRG approaches based on the task-specific features of radiographs, reports, and the cross-modal relations between them, and then illustrate the benchmark datasets conventionally used for this task with evaluation metrics, subsequently analyze the performance of different approaches and finally offer our summary on the challenges and the trends in future directions. Overall, the goal of this paper is to serve as a tool for understanding existing literature and inspiring potential valuable research in the field of RRG.

Checklists are simple decision aids that are often used to promote safety and reliability in clinical applications. In this paper, we present a method to learn checklists for clinical decision support. We represent predictive checklists as discrete linear classifiers with binary features and unit weights. We then learn globally optimal predictive checklists from data by solving an integer programming problem. Our method allows users to customize checklists to obey complex constraints, including constraints to enforce group fairness and to binarize real-valued features at training time. In addition, it pairs models with an optimality gap that can inform model development and determine the feasibility of learning sufficiently accurate checklists on a given dataset. We pair our method with specialized techniques that speed up its ability to train a predictive checklist that performs well and has a small optimality gap. We benchmark the performance of our method on seven clinical classification problems, and demonstrate its practical benefits by training a short-form checklist for PTSD screening. Our results show that our method can fit simple predictive checklists that perform well and that can easily be customized to obey a rich class of custom constraints.

Early and accurate detection of brain abnormalities, such as tumors and strokes, is essential for timely intervention and improved patient outcomes. In this study, we present a deep learning-based system capable of identifying both brain tumors and strokes from MRI images, along with their respective stages. We have executed two groundbreaking strategies involving convolutional neural networks, MobileNet V2 and ResNet-50-optimized through transfer learning to classify MRI scans into five diagnostic categories. Our dataset, aggregated and augmented from various publicly available MRI sources, was carefully curated to ensure class balance and image diversity. To enhance model generalization and prevent overfitting, we applied dropout layers and extensive data augmentation. The models achieved strong performance, with training accuracy reaching 93\% and validation accuracy up to 88\%. While ResNet-50 demonstrated slightly better results, Mobile Net V2 remains a promising option for real-time diagnosis in low resource settings due to its lightweight architecture. This research offers a practical AI-driven solution for early brain abnormality detection, with potential for clinical deployment and future enhancement through larger datasets and multi modal inputs.

The rapid advancement of large language models (LLMs) has significantly impacted various domains, including healthcare and biomedicine. However, the phenomenon of hallucination, where LLMs generate outputs that deviate from factual accuracy or context, poses a critical challenge, especially in high-stakes domains. This paper conducts a scoping study of existing techniques for mitigating hallucinations in knowledge-based task in general and especially for medical domains. Key methods covered in the paper include Retrieval-Augmented Generation (RAG)-based techniques, iterative feedback loops, supervised fine-tuning, and prompt engineering. These techniques, while promising in general contexts, require further adaptation and optimization for the medical domain due to its unique demands for up-to-date, specialized knowledge and strict adherence to medical guidelines. Addressing these challenges is crucial for developing trustworthy AI systems that enhance clinical decision-making and patient safety as well as accuracy of biomedical scientific research.

Artificial intelligence has significantly advanced skin cancer diagnosis by enabling rapid and accurate detection of malignant lesions. In this domain, most publicly available image datasets consist of single, isolated skin lesions positioned at the center of the image. While these lesion-centric datasets have been fundamental for developing diagnostic algorithms, they lack the context of the surrounding skin, which is critical for improving lesion detection. The iToBoS dataset was created to address this challenge. It includes 16,954 images of skin regions from 100 participants, captured using 3D total body photography. Each image roughly corresponds to a 7 times 9 cm section of skin with all suspicious lesions annotated using bounding boxes. Additionally, the dataset provides metadata such as anatomical location, age group, and sun damage score for each image. This dataset aims to facilitate training and benchmarking of algorithms, with the goal of enabling early detection of skin cancer and deployment of this technology in non-clinical environments.

Scoliosis, a prevalent condition characterized by abnormal spinal curvature leading to deformity, requires precise assessment methods for effective diagnosis and management. The Cobb angle is a widely used scoliosis quantification method that measures the degree of curvature between the tilted vertebrae. Yet, manual measuring of Cobb angles is time-consuming and labor-intensive, fraught with significant interobserver and intraobserver variability. To address these challenges and the lack of interpretability found in certain existing automated methods, we have created fully automated software that not only precisely measures the Cobb angle but also provides clear visualizations of these measurements. This software integrates deep neural network-based spine region detection and segmentation, spine centerline identification, pinpointing the most significantly tilted vertebrae, and direct visualization of Cobb angles on the original images. Upon comparison with the assessments of 7 expert readers, our algorithm exhibited a mean deviation in Cobb angle measurements of 4.17 degrees, notably surpassing the manual approach's average intra-reader discrepancy of 5.16 degrees. The algorithm also achieved intra-class correlation coefficients (ICC) exceeding 0.96 and Pearson correlation coefficients above 0.944, reflecting robust agreement with expert assessments and superior measurement reliability. Through the comprehensive reader study and statistical analysis, we believe this algorithm not only ensures a higher consensus with expert readers but also enhances interpretability and reproducibility during assessments. It holds significant promise for clinical application, potentially aiding physicians in more accurate scoliosis assessment and diagnosis, thereby improving patient care.

We introduce CheXGenBench, a rigorous and multifaceted evaluation framework for synthetic chest radiograph generation that simultaneously assesses fidelity, privacy risks, and clinical utility across state-of-the-art text-to-image generative models. Despite rapid advancements in generative AI for real-world imagery, medical domain evaluations have been hindered by methodological inconsistencies, outdated architectural comparisons, and disconnected assessment criteria that rarely address the practical clinical value of synthetic samples. CheXGenBench overcomes these limitations through standardised data partitioning and a unified evaluation protocol comprising over 20 quantitative metrics that systematically analyse generation quality, potential privacy vulnerabilities, and downstream clinical applicability across 11 leading text-to-image architectures. Our results reveal critical inefficiencies in the existing evaluation protocols, particularly in assessing generative fidelity, leading to inconsistent and uninformative comparisons. Our framework establishes a standardised benchmark for the medical AI community, enabling objective and reproducible comparisons while facilitating seamless integration of both existing and future generative models. Additionally, we release a high-quality, synthetic dataset, SynthCheX-75K, comprising 75K radiographs generated by the top-performing model (Sana 0.6B) in our benchmark to support further research in this critical domain. Through CheXGenBench, we establish a new state-of-the-art and release our framework, models, and SynthCheX-75K dataset at https://raman1121.github.io/CheXGenBench/

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

Pathology Foundation Models (FMs) hold great promise for healthcare. Before they can be used in clinical practice, it is essential to ensure they are robust to variations between medical centers. We measure whether pathology FMs focus on biological features like tissue and cancer type, or on the well known confounding medical center signatures introduced by staining procedure and other differences. We introduce the Robustness Index. This novel robustness metric reflects to what degree biological features dominate confounding features. Ten current publicly available pathology FMs are evaluated. We find that all current pathology foundation models evaluated represent the medical center to a strong degree. Significant differences in the robustness index are observed. Only one model so far has a robustness index greater than one, meaning biological features dominate confounding features, but only slightly. A quantitative approach to measure the influence of medical center differences on FM-based prediction performance is described. We analyze the impact of unrobustness on classification performance of downstream models, and find that cancer-type classification errors are not random, but specifically attributable to same-center confounders: images of other classes from the same medical center. We visualize FM embedding spaces, and find these are more strongly organized by medical centers than by biological factors. As a consequence, the medical center of origin is predicted more accurately than the tissue source and cancer type. The robustness index introduced here is provided with the aim of advancing progress towards clinical adoption of robust and reliable pathology FMs.

Automated interpretation of CT images-particularly localizing and describing abnormal findings across multi-plane and whole-body scans-remains a significant challenge in clinical radiology. This work aims to address this challenge through four key contributions: (i) On taxonomy, we collaborate with senior radiologists to propose a comprehensive hierarchical classification system, with 404 representative abnormal findings across all body regions; (ii) On data, we contribute a dataset containing over 14.5K CT images from multiple planes and all human body regions, and meticulously provide grounding annotations for over 19K abnormalities, each linked to the detailed description and cast into the taxonomy; (iii) On model development, we propose OminiAbnorm-CT, which can automatically ground and describe abnormal findings on multi-plane and whole-body CT images based on text queries, while also allowing flexible interaction through visual prompts; (iv) On benchmarks, we establish three representative evaluation tasks based on real clinical scenarios. Through extensive experiments, we show that OminiAbnorm-CT can significantly outperform existing methods on all the tasks and metrics.

Medical Visual Question Answering (Med-VQA) answers clinical questions using medical images, aiding diagnosis. Designing the MedVQA system holds profound importance in assisting clinical diagnosis and enhancing diagnostic accuracy. Building upon this foundation, Hierarchical Medical VQA extends Medical VQA by organizing medical questions into a hierarchical structure and making level-specific predictions to handle fine-grained distinctions. Recently, many studies have proposed hierarchical MedVQA tasks and established datasets, However, several issues still remain: (1) imperfect hierarchical modeling leads to poor differentiation between question levels causing semantic fragmentation across hierarchies. (2) Excessive reliance on implicit learning in Transformer-based cross-modal self-attention fusion methods, which obscures crucial local semantic correlations in medical scenarios. To address these issues, this study proposes a HiCA-VQA method, including two modules: Hierarchical Prompting for fine-grained medical questions and Hierarchical Answer Decoders. The hierarchical prompting module pre-aligns hierarchical text prompts with image features to guide the model in focusing on specific image regions according to question types, while the hierarchical decoder performs separate predictions for questions at different levels to improve accuracy across granularities. The framework also incorporates a cross-attention fusion module where images serve as queries and text as key-value pairs. Experiments on the Rad-Restruct benchmark demonstrate that the HiCA-VQA framework better outperforms existing state-of-the-art methods in answering hierarchical fine-grained questions. This study provides an effective pathway for hierarchical visual question answering systems, advancing medical image understanding.

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

Following recent advancements in computer-aided detection and diagnosis systems for colonoscopy, the automated reporting of colonoscopy procedures is set to further revolutionize clinical practice. A crucial yet underexplored aspect in the development of these systems is the creation of computer vision models capable of autonomously segmenting full-procedure colonoscopy videos into anatomical sections and procedural phases. In this work, we aim to create the first open-access dataset for this task and propose a state-of-the-art approach, benchmarked against competitive models. We annotated the publicly available REAL-Colon dataset, consisting of 2.7 million frames from 60 complete colonoscopy videos, with frame-level labels for anatomical locations and colonoscopy phases across nine categories. We then present ColonTCN, a learning-based architecture that employs custom temporal convolutional blocks designed to efficiently capture long temporal dependencies for the temporal segmentation of colonoscopy videos. We also propose a dual k-fold cross-validation evaluation protocol for this benchmark, which includes model assessment on unseen, multi-center data.ColonTCN achieves state-of-the-art performance in classification accuracy while maintaining a low parameter count when evaluated using the two proposed k-fold cross-validation settings, outperforming competitive models. We report ablation studies to provide insights into the challenges of this task and highlight the benefits of the custom temporal convolutional blocks, which enhance learning and improve model efficiency. We believe that the proposed open-access benchmark and the ColonTCN approach represent a significant advancement in the temporal segmentation of colonoscopy procedures, fostering further open-access research to address this clinical need.

Large language models (LLMs) have received much attention and shown their potential in digital health, while their application in mental health is subject to ongoing debate. This systematic review aims to summarize and characterize the use of LLMs in mental health by investigating the strengths and limitations of the latest work in LLMs and discusses the challenges and opportunities for early screening, digital interventions, and other clinical applications in mental health. Following PRISMA guidelines, we examined English articles from PubMed, DBLP Computer Science Bibliography, and IEEE Xplore, published between 1 January 2017, and 1 September 2023, focusing on mental health and LLMs. The review analyzed 32 articles, including mental health analysis using social media datasets (n=13), mental health chatbots (n=10), and other mental health applications (n=9). Findings reveal LLMs' effectiveness in mental health issue detection and the enhancement of telepsychological services through personalised healthcare. Nonetheless, risks like text inconsistencies, hallucinatory content, and the lack of an ethical framework raise concerns about their clinical use. Despite these challenges, the advancement of LLMs underscores their potential as innovative clinical tools, necessitating further research and development. The review emphasizes that LLMs should complement, not replace, professional mental health services.

Nasal Cytology is a new and efficient clinical technique to diagnose rhinitis and allergies that is not much widespread due to the time-consuming nature of cell counting; that is why AI-aided counting could be a turning point for the diffusion of this technique. In this article we present the first dataset of rhino-cytological field images: the NCD (Nasal Cytology Dataset), aimed to train and deploy Object Detection models to support physicians and biologists during clinical practice. The real distribution of the cytotypes, populating the nasal mucosa has been replicated, sampling images from slides of clinical patients, and manually annotating each cell found on them. The correspondent object detection task presents non'trivial issues associated with the strong class imbalancement, involving the rarest cell types. This work contributes to some of open challenges by presenting a novel machine learning-based approach to aid the automated detection and classification of nasal mucosa cells: the DETR and YOLO models shown good performance in detecting cells and classifying them correctly, revealing great potential to accelerate the work of rhinology experts.

Osteoporotic vertebral compression fractures (VCFs) are prevalent in the elderly population, typically assessed on computed tomography (CT) scans by evaluating vertebral height loss. This assessment helps determine the fracture's impact on spinal stability and the need for surgical intervention. However, clinical data indicate that many VCFs exhibit irregular compression, complicating accurate diagnosis. While deep learning methods have shown promise in aiding VCFs screening, they often lack interpretability and sufficient sensitivity, limiting their clinical applicability. To address these challenges, we introduce a novel vertebra synthesis-height loss quantification-VCFs grading framework. Our proposed model, HealthiVert-GAN, utilizes a coarse-to-fine synthesis network designed to generate pseudo-healthy vertebral images that simulate the pre-fracture state of fractured vertebrae. This model integrates three auxiliary modules that leverage the morphology and height information of adjacent healthy vertebrae to ensure anatomical consistency. Additionally, we introduce the Relative Height Loss of Vertebrae (RHLV) as a quantification metric, which divides each vertebra into three sections to measure height loss between pre-fracture and post-fracture states, followed by fracture severity classification using a Support Vector Machine (SVM). Our approach achieves state-of-the-art classification performance on both the Verse2019 dataset and our private dataset, and it provides cross-sectional distribution maps of vertebral height loss. This practical tool enhances diagnostic sensitivity in clinical settings and assisting in surgical decision-making. Our code is available: https://github.com/zhibaishouheilab/HealthiVert-GAN.

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

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.

Recent advancements in Large Language Models (LLMs) have drawn increasing attention since the learned embeddings pretrained on large-scale datasets have shown powerful ability in various downstream applications. However, whether the learned knowledge by LLMs can be transferred to clinical cardiology remains unknown. In this work, we aim to bridge this gap by transferring the knowledge of LLMs to clinical Electrocardiography (ECG). We propose an approach for cardiovascular disease diagnosis and automatic ECG diagnosis report generation. We also introduce an additional loss function by Optimal Transport (OT) to align the distribution between ECG and language embedding. The learned embeddings are evaluated on two downstream tasks: (1) automatic ECG diagnosis report generation, and (2) zero-shot cardiovascular disease detection. Our approach is able to generate high-quality cardiac diagnosis reports and also achieves competitive zero-shot classification performance even compared with supervised baselines, which proves the feasibility of transferring knowledge from LLMs to the cardiac domain.

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.

Gathering histopathology slides from over 100 publicly available cohorts, we compile a diverse dataset of 460 million pathology tiles covering more than 30 cancer sites. Using this dataset, we train a large self-supervised vision transformer using DINOv2 and publicly release one iteration of this model for further experimentation, coined Phikon-v2. While trained on publicly available histology slides, Phikon-v2 surpasses our previously released model (Phikon) and performs on par with other histopathology foundation models (FM) trained on proprietary data. Our benchmarks include eight slide-level tasks with results reported on external validation cohorts avoiding any data contamination between pre-training and evaluation datasets. Our downstream training procedure follows a simple yet robust ensembling strategy yielding a +1.75 AUC increase across tasks and models compared to one-shot retraining (p<0.001). We compare Phikon (ViT-B) and Phikon-v2 (ViT-L) against 14 different histology feature extractors, making our evaluation the most comprehensive to date. Our result support evidences that DINOv2 handles joint model and data scaling better than iBOT. Also, we show that recent scaling efforts are overall beneficial to downstream performance in the context of biomarker prediction with GigaPath and H-Optimus-0 (two ViT-g with 1.1B parameters each) standing out. However, the statistical margins between the latest top-performing FMs remain mostly non-significant; some even underperform on specific indications or tasks such as MSI prediction - deposed by a 13x smaller model developed internally. While latest foundation models may exhibit limitations for clinical deployment, they nonetheless offer excellent grounds for the development of more specialized and cost-efficient histology encoders fueling AI-guided diagnostic tools.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

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.

The emergence of groundbreaking large language models capable of performing complex reasoning tasks holds significant promise for addressing various scientific challenges, including those arising in complex clinical scenarios. To enable their safe and effective deployment in real-world healthcare settings, it is urgently necessary to benchmark the diagnostic capabilities of current models systematically. Given the limitations of existing medical benchmarks in evaluating advanced diagnostic reasoning, we present DiagnosisArena, a comprehensive and challenging benchmark designed to rigorously assess professional-level diagnostic competence. DiagnosisArena consists of 1,113 pairs of segmented patient cases and corresponding diagnoses, spanning 28 medical specialties, deriving from clinical case reports published in 10 top-tier medical journals. The benchmark is developed through a meticulous construction pipeline, involving multiple rounds of screening and review by both AI systems and human experts, with thorough checks conducted to prevent data leakage. Our study reveals that even the most advanced reasoning models, o3-mini, o1, and DeepSeek-R1, achieve only 45.82%, 31.09%, and 17.79% accuracy, respectively. This finding highlights a significant generalization bottleneck in current large language models when faced with clinical diagnostic reasoning challenges. Through DiagnosisArena, we aim to drive further advancements in AIs diagnostic reasoning capabilities, enabling more effective solutions for real-world clinical diagnostic challenges. We provide the benchmark and evaluation tools for further research and development https://github.com/SPIRAL-MED/DiagnosisArena.

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

Industry standards require medical device manufacturers to perform implant-induced artefact testing in phantoms at a pre-clinical stage to define the extent of artefacts that can be expected during MRI. Once a device is commercially available, studies on volunteers, cadavers or patients are performed to investigate implant-induced artefacts and artefact reduction methods more in-depth. This study describes the design and evaluation of a realistic head phantom for pre-clinical implant-induced artefact testing in a relevant environment. A case study is performed where a state-of-the-art piezoelectric bone conduction implant is used in the 1.5 T and 3 T MRI environments. Images were acquired using clinical and novel metal artefact reducing (MARS) sequences at both field strengths. Artefact width and length were measured in a healthy volunteer and compared with artefact sizes obtained in the phantom. Artefact sizes are reported that are similar in shape between the phantom and a volunteer, yet with dimensions differing up to 20% between both. When the implant magnet is removed, the artefact size can be reduced below a diameter of 5 cm, whilst the presence of an implant magnet and splint creates higher artefacts up to 20 cm in diameter. Pulse sequences have been altered to reduce the scan time up to 7 minutes, while preserving the image quality. These results show that the anthropomorphic phantom can be used at a preclinical stage to provide clinically relevant images, illustrating the impact of the artefact on important brain structures.

Recent advances in large language models (LLMs) have demonstrated notable performance in medical licensing exams. However, comprehensive evaluation of LLMs across various healthcare roles, particularly in high-stakes clinical scenarios, remains a challenge. Existing benchmarks are typically text-based, English-centric, and focus primarily on medicines, which limits their ability to assess broader healthcare knowledge and multimodal reasoning. To address these gaps, we introduce KokushiMD-10, the first multimodal benchmark constructed from ten Japanese national healthcare licensing exams. This benchmark spans multiple fields, including Medicine, Dentistry, Nursing, Pharmacy, and allied health professions. It contains over 11588 real exam questions, incorporating clinical images and expert-annotated rationales to evaluate both textual and visual reasoning. We benchmark over 30 state-of-the-art LLMs, including GPT-4o, Claude 3.5, and Gemini, across both text and image-based settings. Despite promising results, no model consistently meets passing thresholds across domains, highlighting the ongoing challenges in medical AI. KokushiMD-10 provides a comprehensive and linguistically grounded resource for evaluating and advancing reasoning-centric medical AI across multilingual and multimodal clinical tasks.

This study investigates the development and assessment of an artificial human designed as a conversational AI chatbot, focusing on its role as a clinical psychologist. The project involved creating a specialized chatbot using the Character.ai platform. The chatbot was designed to engage users in psychological discussions, providing advice and support with a human-like touch. The study involved participants (N=27) from diverse backgrounds, including psychologists, AI researchers, and the general public, who interacted with the chatbot and provided feedback on its human-likeness, empathy, and engagement levels. Results indicate that while many users found the chatbot engaging and somewhat human-like, limitations were noted in areas such as empathy and nuanced understanding. The findings suggest that although conversational AI has made strides, it remains far from achieving the true human-like interaction necessary for Artificial General Intelligence (AGI). The study highlights the challenges and potential of AI in human-computer interactions, suggesting directions for future research and development to bridge the gap between current capabilities and AGI. The project was completed in November of 2022 before the release of chatGPT.

Wrist Fracture is the most common type of fracture with a high incidence rate. Conventional radiography (i.e. X-ray imaging) is used for wrist fracture detection routinely, but occasionally fracture delineation poses issues and an additional confirmation by computed tomography (CT) is needed for diagnosis. Recent advances in the field of Deep Learning (DL), a subfield of Artificial Intelligence (AI), have shown that wrist fracture detection can be automated using Convolutional Neural Networks. However, previous studies did not pay close attention to the difficult cases which can only be confirmed via CT imaging. In this study, we have developed and analyzed a state-of-the-art DL-based pipeline for wrist (distal radius) fracture detection -- DeepWrist, and evaluated it against one general population test set, and one challenging test set comprising only cases requiring confirmation by CT. Our results reveal that a typical state-of-the-art approach, such as DeepWrist, while having a near-perfect performance on the general independent test set, has a substantially lower performance on the challenging test set -- average precision of 0.99 (0.99-0.99) vs 0.64 (0.46-0.83), respectively. Similarly, the area under the ROC curve was of 0.99 (0.98-0.99) vs 0.84 (0.72-0.93), respectively. Our findings highlight the importance of a meticulous analysis of DL-based models before clinical use, and unearth the need for more challenging settings for testing medical AI systems.

Automatic medical report generation (MRG), which possesses significant research value as it can aid radiologists in clinical diagnosis and report composition, has garnered increasing attention. Despite recent progress, generating accurate reports remains arduous due to the requirement for precise clinical comprehension and disease diagnosis inference. Furthermore, owing to the limited accessibility of medical data and the imbalanced distribution of diseases, the underrepresentation of rare diseases in training data makes large-scale medical visual language models (LVLMs) prone to hallucinations, such as omissions or fabrications, severely undermining diagnostic performance and further intensifying the challenges for MRG in practice. In this study, to effectively mitigate hallucinations in medical report generation, we propose a chain-of-medical-thought approach (CoMT), which intends to imitate the cognitive process of human doctors by decomposing diagnostic procedures. The radiological features with different importance are structured into fine-grained medical thought chains to enhance the inferential ability during diagnosis, thereby alleviating hallucination problems and enhancing the diagnostic accuracy of MRG. The code and dataset have been released at https://github.com/FRENKIE-CHIANG/CoMT.

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application.

Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input for a second FCN. The second FCN solely segments lesions within the predicted liver ROIs of step 1. CFCN models were trained on an abdominal CT dataset comprising 100 hepatic tumor volumes. Validations on further datasets show that CFCN-based semantic liver and lesion segmentation achieves Dice scores over 94% for liver with computation times below 100s per volume. We further experimentally demonstrate the robustness of the proposed method on an 38 MRI liver tumor volumes and the public 3DIRCAD dataset.

Medical Visual Question Answering (MedVQA) is a promising field for developing clinical decision support systems, yet progress is often limited by the available datasets, which can lack clinical complexity and visual diversity. To address these gaps, we introduce Kvasir-VQA-x1, a new, large-scale dataset for gastrointestinal (GI) endoscopy. Our work significantly expands upon the original Kvasir-VQA by incorporating 159,549 new question-answer pairs that are designed to test deeper clinical reasoning. We developed a systematic method using large language models to generate these questions, which are stratified by complexity to better assess a model's inference capabilities. To ensure our dataset prepares models for real-world clinical scenarios, we have also introduced a variety of visual augmentations that mimic common imaging artifacts. The dataset is structured to support two main evaluation tracks: one for standard VQA performance and another to test model robustness against these visual perturbations. By providing a more challenging and clinically relevant benchmark, Kvasir-VQA-x1 aims to accelerate the development of more reliable and effective multimodal AI systems for use in clinical settings. The dataset is fully accessible and adheres to FAIR data principles, making it a valuable resource for the wider research community. Code and data: https://github.com/Simula/Kvasir-VQA-x1 and https://huggingface.co/datasets/SimulaMet/Kvasir-VQA-x1

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

Diabetic Retinopathy (DR), induced by diabetes, poses a significant risk of visual impairment. Accurate and effective grading of DR aids in the treatment of this condition. Yet existing models experience notable performance degradation on unseen domains due to domain shifts. Previous methods address this issue by simulating domain style through simple visual transformation and mitigating domain noise via learning robust representations. However, domain shifts encompass more than image styles. They overlook biases caused by implicit factors such as ethnicity, age, and diagnostic criteria. In our work, we propose a novel framework where representations of paired data from different domains are decoupled into semantic features and domain noise. The resulting augmented representation comprises original retinal semantics and domain noise from other domains, aiming to generate enhanced representations aligned with real-world clinical needs, incorporating rich information from diverse domains. Subsequently, to improve the robustness of the decoupled representations, class and domain prototypes are employed to interpolate the disentangled representations while data-aware weights are designed to focus on rare classes and domains. Finally, we devise a robust pixel-level semantic alignment loss to align retinal semantics decoupled from features, maintaining a balance between intra-class diversity and dense class features. Experimental results on multiple benchmarks demonstrate the effectiveness of our method on unseen domains. The code implementations are accessible on https://github.com/richard-peng-xia/DECO.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

In this paper, we release a largest ever medical Question Answering (QA) dataset with 26 million QA pairs. We benchmark many existing approaches in our dataset in terms of both retrieval and generation. Experimental results show that the existing models perform far lower than expected and the released dataset is still challenging in the pre-trained language model era. Moreover, we also experimentally show the benefit of the proposed dataset in many aspects: (i) trained models for other QA datasets in a zero-shot fashion; and (ii) as external knowledge for retrieval-augmented generation (RAG); and (iii) improving existing pre-trained language models by using the QA pairs as a pre-training corpus in continued training manner. We believe that this dataset will not only contribute to medical research but also facilitate both the patients and clinical doctors. See https://github.com/FreedomIntelligence/Huatuo-26M.

Urine sediment examination (USE) is one of the main tests used in the evaluation of diseases such as kidney, urinary, metabolic, and diabetes and to determine the density and number of various cells in the urine. USE's manual microscopy is a labor-intensive and time-consuming, imprecise, subjective process. Recently, automatic analysis of urine sediment has become inevitable in the medical field. In this study, we propose a dataset that can be used by artificial intelligence techniques to automatically identify particles in urine sediment images. The data set consists of 8509 particle images obtained by examining the particles in the urine sediment obtained from 409 patients from the Biochemistry Clinics of Elazig Fethi Sekin Central Hospital. Particle images are collected in 8 classes in total and these are Erythrocyte, Leukocyte, Epithelial, Bacteria, Yeast, Cylinders, Crystals, and others (sperm, etc.).

Recent advancements in Digital Pathology (DP), particularly through artificial intelligence and Foundation Models, have underscored the importance of large-scale, diverse, and richly annotated datasets. Despite their critical role, publicly available Whole Slide Image (WSI) datasets often lack sufficient scale, tissue diversity, and comprehensive clinical metadata, limiting the robustness and generalizability of AI models. In response, we introduce the HISTAI dataset, a large, multimodal, open-access WSI collection comprising over 60,000 slides from various tissue types. Each case in the HISTAI dataset is accompanied by extensive clinical metadata, including diagnosis, demographic information, detailed pathological annotations, and standardized diagnostic coding. The dataset aims to fill gaps identified in existing resources, promoting innovation, reproducibility, and the development of clinically relevant computational pathology solutions. The dataset can be accessed at https://github.com/HistAI/HISTAI.

Recent advances in reasoning-enhanced large language models (LLMs) and multimodal LLMs (MLLMs) have significantly improved performance in complex tasks, yet medical AI models often overlook the structured reasoning processes inherent in clinical practice. In this work, we present ChestX-Reasoner, a radiology diagnosis MLLM designed to leverage process supervision mined directly from clinical reports, reflecting the step-by-step reasoning followed by radiologists. We construct a large dataset by extracting and refining reasoning chains from routine radiology reports. Our two-stage training framework combines supervised fine-tuning and reinforcement learning guided by process rewards to better align model reasoning with clinical standards. We introduce RadRBench-CXR, a comprehensive benchmark featuring 59K visual question answering samples with 301K clinically validated reasoning steps, and propose RadRScore, a metric evaluating reasoning factuality, completeness, and effectiveness. ChestX-Reasoner outperforms existing medical and general-domain MLLMs in both diagnostic accuracy and reasoning ability, achieving 16%, 5.9%, and 18% improvements in reasoning ability compared to the best medical MLLM, the best general MLLM, and its base model, respectively, as well as 3.3%, 24%, and 27% improvements in outcome accuracy. All resources are open-sourced to facilitate further research in medical reasoning MLLMs.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

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

In this study, we aim to initiate the development of Radiology Foundation Model, termed as RadFM.We consider the construction of foundational models from the perspectives of data, model design, and evaluation thoroughly. Our contribution can be concluded as follows: (i), we construct a large-scale Medical Multi-modal Dataset, MedMD, consisting of 16M 2D and 3D medical scans. To the best of our knowledge, this is the first multi-modal dataset containing 3D medical scans. (ii), We propose an architecture that enables visually conditioned generative pre-training, allowing for the integration of text input interleaved with 2D or 3D medical scans to generate response for diverse radiologic tasks. The model was initially pre-trained on MedMD and subsequently domain-specific fine-tuned on RadMD, a radiologic cleaned version of MedMD, containing 3M radiologic visual-language pairs. (iii), we propose a new evaluation benchmark that comprises five tasks, aiming to comprehensively assess the capability of foundation models in handling practical clinical problems. Our experimental results confirm that RadFM significantly outperforms existing multi-modal foundation models. The codes, data, and model checkpoint will all be made publicly available to promote further research and development in the field.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.