Daily Papers

Large language models (LLMs) are increasingly used in healthcare, but their reliability is heavily influenced by user-driven factors such as question phrasing and the completeness of clinical information. In this study, we examined how misinformation framing, source authority, model persona, and omission of key clinical details affect the diagnostic accuracy and reliability of LLM outputs. We conducted two experiments: one introducing misleading external opinions with varying assertiveness (perturbation test), and another removing specific categories of patient information (ablation test). Using public datasets (MedQA and Medbullets), we evaluated proprietary models (GPT-4o, Claude 3.5 Sonnet, Claude 3.5 Haiku, Gemini 1.5 Pro, Gemini 1.5 Flash) and open-source models (LLaMA 3 8B, LLaMA 3 Med42 8B, DeepSeek R1 8B). All models were vulnerable to user-driven misinformation, with proprietary models especially affected by definitive and authoritative language. Assertive tone had the greatest negative impact on accuracy. In the ablation test, omitting physical exam findings and lab results caused the most significant performance drop. Although proprietary models had higher baseline accuracy, their performance declined sharply under misinformation. These results highlight the need for well-structured prompts and complete clinical context. Users should avoid authoritative framing of misinformation and provide full clinical details, especially for complex cases.

Chest X-rays (CXRs) play an integral role in driving critical decisions in disease management and patient care. While recent innovations have led to specialized models for various CXR interpretation tasks, these solutions often operate in isolation, limiting their practical utility in clinical practice. We present MedRAX, the first versatile AI agent that seamlessly integrates state-of-the-art CXR analysis tools and multimodal large language models into a unified framework. MedRAX dynamically leverages these models to address complex medical queries without requiring additional training. To rigorously evaluate its capabilities, we introduce ChestAgentBench, a comprehensive benchmark containing 2,500 complex medical queries across 7 diverse categories. Our experiments demonstrate that MedRAX achieves state-of-the-art performance compared to both open-source and proprietary models, representing a significant step toward the practical deployment of automated CXR interpretation systems. Data and code have been publicly available at https://github.com/bowang-lab/MedRAX

Accurate and efficient question-answering systems are essential for delivering high-quality patient care in the medical field. While Large Language Models (LLMs) have made remarkable strides across various domains, they continue to face significant challenges in medical question answering, particularly in understanding domain-specific terminologies and performing complex reasoning. These limitations undermine their effectiveness in critical medical applications. To address these issues, we propose a novel approach incorporating similar case generation within a multi-agent medical question-answering (MedQA) system. Specifically, we leverage the Llama3.1:70B model, a state-of-the-art LLM, in a multi-agent architecture to enhance performance on the MedQA dataset using zero-shot learning. Our method capitalizes on the model's inherent medical knowledge and reasoning capabilities, eliminating the need for additional training data. Experimental results show substantial performance gains over existing benchmark models, with improvements of 7% in both accuracy and F1-score across various medical QA tasks. Furthermore, we examine the model's interpretability and reliability in addressing complex medical queries. This research not only offers a robust solution for medical question answering but also establishes a foundation for broader applications of LLMs in the medical domain.

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.

Large Language Models (LLMs) have introduced a new era of proficiency in comprehending complex healthcare and biomedical topics. However, there is a noticeable lack of models in languages other than English and models that can interpret multi-modal input, which is crucial for global healthcare accessibility. In response, this study introduces Qilin-Med-VL, the first Chinese large vision-language model designed to integrate the analysis of textual and visual data. Qilin-Med-VL combines a pre-trained Vision Transformer (ViT) with a foundational LLM. It undergoes a thorough two-stage curriculum training process that includes feature alignment and instruction tuning. This method enhances the model's ability to generate medical captions and answer complex medical queries. We also release ChiMed-VL, a dataset consisting of more than 1M image-text pairs. This dataset has been carefully curated to enable detailed and comprehensive interpretation of medical data using various types of images.

Large language models (LLMs) hold immense promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. In this work, we present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and then conduct an empirical case study with Med-PaLM 2, resulting in the largest human evaluation study in this area to date. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases, and EquityMedQA, a collection of seven newly-released datasets comprising both manually-curated and LLM-generated questions enriched for adversarial queries. Both our human assessment framework and dataset design process are grounded in an iterative participatory approach and review of possible biases in Med-PaLM 2 answers to adversarial queries. Through our empirical study, we find that the use of a collection of datasets curated through a variety of methodologies, coupled with a thorough evaluation protocol that leverages multiple assessment rubric designs and diverse rater groups, surfaces biases that may be missed via narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. We emphasize that while our framework can identify specific forms of bias, it is not sufficient to holistically assess whether the deployment of an AI system promotes equitable health outcomes. We hope the broader community leverages and builds on these tools and methods towards realizing a shared goal of LLMs that promote accessible and equitable healthcare for all.

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

In the era of modern healthcare, swiftly generating medical question summaries is crucial for informed and timely patient care. Despite the increasing complexity and volume of medical data, existing studies have focused solely on text-based summarization, neglecting the integration of visual information. Recognizing the untapped potential of combining textual queries with visual representations of medical conditions, we introduce the Multimodal Medical Question Summarization (MMQS) Dataset. This dataset, a major contribution to our work, pairs medical queries with visual aids, facilitating a richer and more nuanced understanding of patient needs. We also propose a framework, utilizing the power of Contrastive Language Image Pretraining(CLIP) and Large Language Models(LLMs), consisting of four modules that identify medical disorders, generate relevant context, filter medical concepts, and craft visually aware summaries. Our comprehensive framework harnesses the power of CLIP, a multimodal foundation model, and various general-purpose LLMs, comprising four main modules: the medical disorder identification module, the relevant context generation module, the context filtration module for distilling relevant medical concepts and knowledge, and finally, a general-purpose LLM to generate visually aware medical question summaries. Leveraging our MMQS dataset, we showcase how visual cues from images enhance the generation of medically nuanced summaries. This multimodal approach not only enhances the decision-making process in healthcare but also fosters a more nuanced understanding of patient queries, laying the groundwork for future research in personalized and responsive medical care

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

With worldwide concerns surrounding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is a rapidly growing body of scientific literature on the virus. Clinicians, researchers, and policy-makers need to be able to search these articles effectively. In this work, we present a zero-shot ranking algorithm that adapts to COVID-related scientific literature. Our approach filters training data from another collection down to medical-related queries, uses a neural re-ranking model pre-trained on scientific text (SciBERT), and filters the target document collection. This approach ranks top among zero-shot methods on the TREC COVID Round 1 leaderboard, and exhibits a P@5 of 0.80 and an nDCG@10 of 0.68 when evaluated on both Round 1 and 2 judgments. Despite not relying on TREC-COVID data, our method outperforms models that do. As one of the first search methods to thoroughly evaluate COVID-19 search, we hope that this serves as a strong baseline and helps in the global crisis.

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

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

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.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Large Language Models (LLMs) have shown remarkable capabilities in general domains but often struggle with tasks requiring specialized knowledge. Conventional Retrieval-Augmented Generation (RAG) techniques typically retrieve external information from static knowledge bases, which can be outdated or incomplete, missing fine-grained clinical details essential for accurate medical question answering. In this work, we propose SearchRAG, a novel framework that overcomes these limitations by leveraging real-time search engines. Our method employs synthetic query generation to convert complex medical questions into search-engine-friendly queries and utilizes uncertainty-based knowledge selection to filter and incorporate the most relevant and informative medical knowledge into the LLM's input. Experimental results demonstrate that our method significantly improves response accuracy in medical question answering tasks, particularly for complex questions requiring detailed and up-to-date knowledge.

Current medical retrieval benchmarks primarily emphasize lexical or shallow semantic similarity, overlooking the reasoning-intensive demands that are central to clinical decision-making. In practice, physicians often retrieve authoritative medical evidence to support diagnostic hypotheses. Such evidence typically aligns with an inferred diagnosis rather than the surface form of a patient's symptoms, leading to low lexical or semantic overlap between queries and relevant documents. To address this gap, we introduce R2MED, the first benchmark explicitly designed for reasoning-driven medical retrieval. It comprises 876 queries spanning three tasks: Q&A reference retrieval, clinical evidence retrieval, and clinical case retrieval. These tasks are drawn from five representative medical scenarios and twelve body systems, capturing the complexity and diversity of real-world medical information needs. We evaluate 15 widely-used retrieval systems on R2MED and find that even the best model achieves only 31.4 nDCG@10, demonstrating the benchmark's difficulty. Classical re-ranking and generation-augmented retrieval methods offer only modest improvements. Although large reasoning models improve performance via intermediate inference generation, the best results still peak at 41.4 nDCG@10. These findings underscore a substantial gap between current retrieval techniques and the reasoning demands of real clinical tasks. We release R2MED as a challenging benchmark to foster the development of next-generation medical retrieval systems with enhanced reasoning capabilities. Data and code are available at https://github.com/R2MED/R2MED

The remarkable capabilities of large language models (LLMs) in language understanding and generation have not rendered them immune to hallucinations. LLMs can still generate plausible-sounding but factually incorrect or fabricated information. As LLM-empowered chatbots become popular, laypeople may frequently ask health-related queries and risk falling victim to these LLM hallucinations, resulting in various societal and healthcare implications. In this work, we conduct a pioneering study of hallucinations in LLM-generated responses to real-world healthcare queries from patients. We propose MedHalu, a carefully crafted first-of-its-kind medical hallucination dataset with a diverse range of health-related topics and the corresponding hallucinated responses from LLMs with labeled hallucination types and hallucinated text spans. We also introduce MedHaluDetect framework to evaluate capabilities of various LLMs in detecting hallucinations. We also employ three groups of evaluators -- medical experts, LLMs, and laypeople -- to study who are more vulnerable to these medical hallucinations. We find that LLMs are much worse than the experts. They also perform no better than laypeople and even worse in few cases in detecting hallucinations. To fill this gap, we propose expert-in-the-loop approach to improve hallucination detection through LLMs by infusing expert reasoning. We observe significant performance gains for all the LLMs with an average macro-F1 improvement of 6.3 percentage points for GPT-4.

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.

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 phrase grounding (MPG) aims to locate the most relevant region in a medical image, given a phrase query describing certain medical findings, which is an important task for medical image analysis and radiological diagnosis. However, existing visual grounding methods rely on general visual features for identifying objects in natural images and are not capable of capturing the subtle and specialized features of medical findings, leading to sub-optimal performance in MPG. In this paper, we propose MedRPG, an end-to-end approach for MPG. MedRPG is built on a lightweight vision-language transformer encoder and directly predicts the box coordinates of mentioned medical findings, which can be trained with limited medical data, making it a valuable tool in medical image analysis. To enable MedRPG to locate nuanced medical findings with better region-phrase correspondences, we further propose Tri-attention Context contrastive alignment (TaCo). TaCo seeks context alignment to pull both the features and attention outputs of relevant region-phrase pairs close together while pushing those of irrelevant regions far away. This ensures that the final box prediction depends more on its finding-specific regions and phrases. Experimental results on three MPG datasets demonstrate that our MedRPG outperforms state-of-the-art visual grounding approaches by a large margin. Additionally, the proposed TaCo strategy is effective in enhancing finding localization ability and reducing spurious region-phrase correlations.

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

Deep learning-based point cloud modeling has been widely investigated as an indispensable component of general shape analysis. Recently, transformer and state space model (SSM) have shown promising capacities in point cloud learning. However, limited research has been conducted on medical point clouds, which have great potential in disease diagnosis and treatment. This paper presents an SSM-based hierarchical feature learning framework for medical point cloud understanding. Specifically, we down-sample input into multiple levels through the farthest point sampling. At each level, we perform a series of k-nearest neighbor (KNN) queries to aggregate multi-scale structural information. To assist SSM in processing point clouds, we introduce coordinate-order and inside-out scanning strategies for efficient serialization of irregular points. Point features are calculated progressively from short neighbor sequences and long point sequences through vanilla and group Point SSM blocks, to capture both local patterns and long-range dependencies. To evaluate the proposed method, we build a large-scale medical point cloud dataset named MedPointS for anatomy classification, completion, and segmentation. Extensive experiments conducted on MedPointS demonstrate that our method achieves superior performance across all tasks. The dataset is available at https://flemme-docs.readthedocs.io/en/latest/medpoints.html. Code is merged to a public medical imaging platform: https://github.com/wlsdzyzl/flemme.

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

Large Language Models (LLMs) have demonstrated impressive capabilities across natural language processing tasks. However, their application to specialized domains such as medicine and biology requires further optimization to ensure factual accuracy, reliability, and contextual depth. We introduce MedBioLM, a domain-adapted biomedical question-answering model designed to enhance both short-form and long-form queries. By integrating fine-tuning and retrieval-augmented generation (RAG), MedBioLM dynamically incorporates domain-specific knowledge, improving reasoning abilities and factual accuracy. To evaluate its effectiveness, we fine-tuned the model on diverse biomedical QA datasets, covering structured multiple-choice assessments and complex clinical reasoning tasks. Fine-tuning significantly improves accuracy on benchmark datasets, while RAG enhances factual consistency. These results highlight the potential of domain-optimized LLMs in advancing biomedical research, medical education, and clinical decision support.

While recent advancements in commercial large language models (LM) have shown promising results in medical tasks, their closed-source nature poses significant privacy and security concerns, hindering their widespread use in the medical field. Despite efforts to create open-source models, their limited parameters often result in insufficient multi-step reasoning capabilities required for solving complex medical problems. To address this, we introduce Meerkat-7B, a novel medical AI system with 7 billion parameters. Meerkat-7B was trained using our new synthetic dataset consisting of high-quality chain-of-thought reasoning paths sourced from 18 medical textbooks, along with diverse instruction-following datasets. Our system achieved remarkable accuracy across seven medical benchmarks, surpassing GPT-3.5 by 13.1%, as well as outperforming the previous best 7B models such as MediTron-7B and BioMistral-7B by 13.4% and 9.8%, respectively. Notably, it surpassed the passing threshold of the United States Medical Licensing Examination (USMLE) for the first time for a 7B-parameter model. Additionally, our system offered more detailed free-form responses to clinical queries compared to existing 7B and 13B models, approaching the performance level of GPT-3.5. This significantly narrows the performance gap with large LMs, showcasing its effectiveness in addressing complex medical challenges.

Recent researches of large language models(LLM), which is pre-trained on massive general-purpose corpora, have achieved breakthroughs in responding human queries. However, these methods face challenges including limited data insufficiency to support extensive pre-training and can not align responses with users' instructions. To address these issues, we introduce a medical instruction dataset, CMedINS, containing six medical instructions derived from actual medical tasks, which effectively fine-tunes LLM in conjunction with other data. Subsequently, We launch our medical model, IIMedGPT, employing an efficient preference alignment method, Direct preference Optimization(DPO). The results show that our final model outperforms existing medical models in medical dialogue.Datsets, Code and model checkpoints will be released upon acceptance.

Large language models (LLMs) have become a disruptive force in the industry, introducing unprecedented capabilities in natural language processing, logical reasoning and so on. However, the challenges of knowledge updates and hallucination issues have limited the application of LLMs in medical scenarios, where retrieval-augmented generation (RAG) can offer significant assistance. Nevertheless, existing retrieve-then-read approaches generally digest the retrieved documents, without considering the timeliness, authoritativeness and commonality of retrieval. We argue that these approaches can be suboptimal, especially in real-world applications where information from different sources might conflict with each other and even information from the same source in different time scale might be different, and totally relying on this would deteriorate the performance of RAG approaches. We propose PolyRAG that carefully incorporate judges from different perspectives and finally integrate the polyviews for retrieval augmented generation in medical applications. Due to the scarcity of real-world benchmarks for evaluation, to bridge the gap we propose PolyEVAL, a benchmark consists of queries and documents collected from real-world medical scenarios (including medical policy, hospital & doctor inquiry and healthcare) with multiple tagging (e.g., timeliness, authoritativeness) on them. Extensive experiments and analysis on PolyEVAL have demonstrated the superiority of PolyRAG.

Limited labeled data makes it hard to train models from scratch in medical domain, and an important paradigm is pre-training and then fine-tuning. Large pre-trained models contain rich representations, which can be adapted to downstream medical tasks. However, existing methods either tune all the parameters or the task-specific layers of the pre-trained models, ignoring the input variations of medical images, and thus they are not efficient or effective. In this work, we aim to study parameter-efficient fine-tuning (PEFT) for medical image analysis, and propose a dynamic visual prompt tuning method, named DVPT. It can extract knowledge beneficial to downstream tasks from large models with a few trainable parameters. Firstly, the frozen features are transformed by an lightweight bottleneck layer to learn the domain-specific distribution of downstream medical tasks, and then a few learnable visual prompts are used as dynamic queries and then conduct cross-attention with the transformed features, attempting to acquire sample-specific knowledge that are suitable for each sample. Finally, the features are projected to original feature dimension and aggregated with the frozen features. This DVPT module can be shared between different Transformer layers, further reducing the trainable parameters. To validate DVPT, we conduct extensive experiments with different pre-trained models on medical classification and segmentation tasks. We find such PEFT method can not only efficiently adapt the pre-trained models to the medical domain, but also brings data efficiency with partial labeled data. For example, with 0.5\% extra trainable parameters, our method not only outperforms state-of-the-art PEFT methods, even surpasses the full fine-tuning by more than 2.20\% Kappa score on medical classification task. It can saves up to 60\% labeled data and 99\% storage cost of ViT-B/16.

Large language models (LLMs) are increasingly deployed in medical contexts, raising critical concerns about safety, alignment, and susceptibility to adversarial manipulation. While prior benchmarks assess model refusal capabilities for harmful prompts, they often lack clinical specificity, graded harmfulness levels, and coverage of jailbreak-style attacks. We introduce CARES (Clinical Adversarial Robustness and Evaluation of Safety), a benchmark for evaluating LLM safety in healthcare. CARES includes over 18,000 prompts spanning eight medical safety principles, four harm levels, and four prompting styles: direct, indirect, obfuscated, and role-play, to simulate both malicious and benign use cases. We propose a three-way response evaluation protocol (Accept, Caution, Refuse) and a fine-grained Safety Score metric to assess model behavior. Our analysis reveals that many state-of-the-art LLMs remain vulnerable to jailbreaks that subtly rephrase harmful prompts, while also over-refusing safe but atypically phrased queries. Finally, we propose a mitigation strategy using a lightweight classifier to detect jailbreak attempts and steer models toward safer behavior via reminder-based conditioning. CARES provides a rigorous framework for testing and improving medical LLM safety under adversarial and ambiguous conditions.

Retrieval Augmented Generation (RAG) complements the knowledge of Large Language Models (LLMs) by leveraging external information to enhance response accuracy for queries. This approach is widely applied in several fields by taking its advantage of injecting the most up-to-date information, and researchers are focusing on understanding and improving this aspect to unlock the full potential of RAG in such high-stakes applications. However, despite the potential of RAG to address these needs, the mechanisms behind the confidence levels of its outputs remain underexplored, although the confidence of information is very critical in some domains, such as finance, healthcare, and medicine. Our study focuses the impact of RAG on confidence within the medical domain under various configurations and models. We evaluate confidence by treating the model's predicted probability as its output and calculating Expected Calibration Error (ECE) and Adaptive Calibration Error (ACE) scores based on the probabilities and accuracy. In addition, we analyze whether the order of retrieved documents within prompts calibrates the confidence. Our findings reveal large variation in confidence and accuracy depending on the model, settings, and the format of input prompts. These results underscore the necessity of optimizing configurations based on the specific model and conditions.

People increasingly search online for answers to their medical questions but the rate at which medical questions are asked online significantly exceeds the capacity of qualified people to answer them. This leaves many questions unanswered or inadequately answered. Many of these questions are not unique, and reliable identification of similar questions would enable more efficient and effective question answering schema. COVID-19 has only exacerbated this problem. Almost every government agency and healthcare organization has tried to meet the informational need of users by building online FAQs, but there is no way for people to ask their question and know if it is answered on one of these pages. While many research efforts have focused on the problem of general question similarity, these approaches do not generalize well to domains that require expert knowledge to determine semantic similarity, such as the medical domain. In this paper, we show how a double fine-tuning approach of pretraining a neural network on medical question-answer pairs followed by fine-tuning on medical question-question pairs is a particularly useful intermediate task for the ultimate goal of determining medical question similarity. While other pretraining tasks yield an accuracy below 78.7% on this task, our model achieves an accuracy of 82.6% with the same number of training examples, an accuracy of 80.0% with a much smaller training set, and an accuracy of 84.5% when the full corpus of medical question-answer data is used. We also describe a currently live system that uses the trained model to match user questions to COVID-related FAQs.

Electronic medical records (EMR) contain sensitive personal information. For example, they may include details about infectious diseases, such as human immunodeficiency virus (HIV), or they may contain information about a mental illness. They may also contain other sensitive information such as medical details related to fertility treatments. Because EMRs are subject to confidentiality requirements, accessing and analyzing EMR databases is a privilege given to only a small number of individuals. Individuals who work at institutions that do not have access to EMR systems have no opportunity to gain hands-on experience with this valuable resource. Simulated medical databases are currently available; however, they are difficult to configure and are limited in their resemblance to real clinical databases. Generating highly accessible repositories of virtual patient EMRs while relying only minimally on real patient data is expected to serve as a valuable resource to a broader audience of medical personnel, including those who reside in underdeveloped countries.

The exponential surge in online health information, coupled with its increasing use by non-experts, highlights the pressing need for advanced Health Information Retrieval models that consider not only topical relevance but also the factual accuracy of the retrieved information, given the potential risks associated with health misinformation. To this aim, this paper introduces a solution driven by Retrieval-Augmented Generation (RAG), which leverages the capabilities of generative Large Language Models (LLMs) to enhance the retrieval of health-related documents grounded in scientific evidence. In particular, we propose a three-stage model: in the first stage, the user's query is employed to retrieve topically relevant passages with associated references from a knowledge base constituted by scientific literature. In the second stage, these passages, alongside the initial query, are processed by LLMs to generate a contextually relevant rich text (GenText). In the last stage, the documents to be retrieved are evaluated and ranked both from the point of view of topical relevance and factual accuracy by means of their comparison with GenText, either through stance detection or semantic similarity. In addition to calculating factual accuracy, GenText can offer a layer of explainability for it, aiding users in understanding the reasoning behind the retrieval. Experimental evaluation of our model on benchmark datasets and against baseline models demonstrates its effectiveness in enhancing the retrieval of both topically relevant and factually accurate health information, thus presenting a significant step forward in the health misinformation mitigation problem.

Current medical question answering systems have difficulty processing long, detailed and informally worded questions submitted by patients, called Consumer Health Questions (CHQs). To address this issue, we introduce a medical question understanding and answering system with knowledge grounding and semantic self-supervision. Our system is a pipeline that first summarizes a long, medical, user-written question, using a supervised summarization loss. Then, our system performs a two-step retrieval to return answers. The system first matches the summarized user question with an FAQ from a trusted medical knowledge base, and then retrieves a fixed number of relevant sentences from the corresponding answer document. In the absence of labels for question matching or answer relevance, we design 3 novel, self-supervised and semantically-guided losses. We evaluate our model against two strong retrieval-based question answering baselines. Evaluators ask their own questions and rate the answers retrieved by our baselines and own system according to their relevance. They find that our system retrieves more relevant answers, while achieving speeds 20 times faster. Our self-supervised losses also help the summarizer achieve higher scores in ROUGE, as well as in human evaluation metrics. We release our code to encourage further research.

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

Recently, deep learning-based language models have significantly enhanced text-to-SQL tasks, with promising applications in retrieving patient records within the medical domain. One notable challenge in such applications is discerning unanswerable queries. Through fine-tuning model, we demonstrate the feasibility of converting medical record inquiries into SQL queries. Additionally, we introduce an entropy-based method to identify and filter out unanswerable results. We further enhance result quality by filtering low-confidence SQL through log probability-based distribution, while grammatical and schema errors are mitigated by executing queries on the actual database. We experimentally verified that our method can filter unanswerable questions, which can be widely utilized even when the parameters of the model are not accessible, and that it can be effectively utilized in practice.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

This paper introduces MedMCQA, a new large-scale, Multiple-Choice Question Answering (MCQA) dataset designed to address real-world medical entrance exam questions. More than 194k high-quality AIIMS \& NEET PG entrance exam MCQs covering 2.4k healthcare topics and 21 medical subjects are collected with an average token length of 12.77 and high topical diversity. Each sample contains a question, correct answer(s), and other options which requires a deeper language understanding as it tests the 10+ reasoning abilities of a model across a wide range of medical subjects \& topics. A detailed explanation of the solution, along with the above information, is provided in this study.

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

In recent years, the application of Large Language Models (LLMs) in healthcare has shown significant promise in improving the accessibility and dissemination of medical knowledge. This paper presents a detailed study of various LLMs trained on the MedQuAD medical question-answering dataset, with a focus on identifying the most effective model for providing accurate medical information. Among the models tested, the Sentence-t5 combined with Mistral 7B demonstrated superior performance, achieving a precision score of 0.762. This model's enhanced capabilities are attributed to its advanced pretraining techniques, robust architecture, and effective prompt construction methodologies. By leveraging these strengths, the Sentence-t5 + Mistral 7B model excels in understanding and generating precise medical answers. Our findings highlight the potential of integrating sophisticated LLMs in medical contexts to facilitate efficient and accurate medical knowledge retrieval, thus significantly enhancing patient education and support.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

Medical question-answering (QA) is a critical task for evaluating how effectively large language models (LLMs) encode clinical knowledge and assessing their potential applications in medicine. Despite showing promise on multiple-choice tests, LLMs frequently struggle with open-ended medical questions, producing responses with dangerous hallucinations or lacking comprehensive coverage of critical aspects. Existing approaches attempt to address these challenges through domain-specific fine-tuning, but this proves resource-intensive and difficult to scale across models. To improve the comprehensiveness and factuality of medical responses, we propose a novel approach utilizing structured medical reasoning. Our method guides LLMs through an seven-step cognitive process inspired by clinical diagnosis, enabling more accurate and complete answers without additional training. Experiments on the MedLFQA benchmark demonstrate that our approach achieves the highest Factuality Score of 85.8, surpassing fine-tuned models. Notably, this improvement transfers to smaller models, highlighting the method's efficiency and scalability. Our code and datasets are available.

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

In this paper, we introduce MultiConIR, the first benchmark designed to evaluate retrieval models in multi-condition scenarios. Unlike existing datasets that primarily focus on single-condition queries from search engines, MultiConIR captures real-world complexity by incorporating five diverse domains: books, movies, people, medical cases, and legal documents. We propose three tasks to systematically assess retrieval and reranking models on multi-condition robustness, monotonic relevance ranking, and query format sensitivity. Our findings reveal that existing retrieval and reranking models struggle with multi-condition retrieval, with rerankers suffering severe performance degradation as query complexity increases. We further investigate the performance gap between retrieval and reranking models, exploring potential reasons for these discrepancies, and analysis the impact of different pooling strategies on condition placement sensitivity. Finally, we highlight the strengths of GritLM and Nv-Embed, which demonstrate enhanced adaptability to multi-condition queries, offering insights for future retrieval models. The code and datasets are available at https://github.com/EIT-NLP/MultiConIR.

BEIR is a benchmark dataset for zero-shot evaluation of information retrieval models across 18 different domain/task combinations. In recent years, we have witnessed the growing popularity of a representation learning approach to building retrieval models, typically using pretrained transformers in a supervised setting. This naturally begs the question: How effective are these models when presented with queries and documents that differ from the training data? Examples include searching in different domains (e.g., medical or legal text) and with different types of queries (e.g., keywords vs. well-formed questions). While BEIR was designed to answer these questions, our work addresses two shortcomings that prevent the benchmark from achieving its full potential: First, the sophistication of modern neural methods and the complexity of current software infrastructure create barriers to entry for newcomers. To this end, we provide reproducible reference implementations that cover the two main classes of approaches: learned dense and sparse models. Second, there does not exist a single authoritative nexus for reporting the effectiveness of different models on BEIR, which has led to difficulty in comparing different methods. To remedy this, we present an official self-service BEIR leaderboard that provides fair and consistent comparisons of retrieval models. By addressing both shortcomings, our work facilitates future explorations in a range of interesting research questions that BEIR enables.

Assessing the capabilities and limitations of large language models (LLMs) has garnered significant interest, yet the evaluation of multiple models in real-world scenarios remains rare. Multilingual evaluation often relies on translated benchmarks, which typically do not capture linguistic and cultural nuances present in the source language. This study provides an extensive assessment of 24 LLMs on real world data collected from Indian patients interacting with a medical chatbot in Indian English and 4 other Indic languages. We employ a uniform Retrieval Augmented Generation framework to generate responses, which are evaluated using both automated techniques and human evaluators on four specific metrics relevant to our application. We find that models vary significantly in their performance and that instruction tuned Indic models do not always perform well on Indic language queries. Further, we empirically show that factual correctness is generally lower for responses to Indic queries compared to English queries. Finally, our qualitative work shows that code-mixed and culturally relevant queries in our dataset pose challenges to evaluated models.

Large language models (LLMs) have shown impressive capabilities in natural language processing tasks, including dialogue generation. This research aims to conduct a novel comparative analysis of two prominent techniques, fine-tuning with LoRA (Low-Rank Adaptation) and the Retrieval-Augmented Generation (RAG) framework, in the context of doctor-patient chat conversations with multiple datasets of mixed medical domains. The analysis involves three state-of-the-art models: Llama-2, GPT, and the LSTM model. Employing real-world doctor-patient dialogues, we comprehensively evaluate the performance of models, assessing key metrics such as language quality (perplexity, BLEU score), factual accuracy (fact-checking against medical knowledge bases), adherence to medical guidelines, and overall human judgments (coherence, empathy, safety). The findings provide insights into the strengths and limitations of each approach, shedding light on their suitability for healthcare applications. Furthermore, the research investigates the robustness of the models in handling diverse patient queries, ranging from general health inquiries to specific medical conditions. The impact of domain-specific knowledge integration is also explored, highlighting the potential for enhancing LLM performance through targeted data augmentation and retrieval strategies.

Rare diseases present unique challenges in healthcare, often suffering from delayed diagnosis and fragmented information landscapes. The scarcity of reliable knowledge in these conditions poses a distinct challenge for Large Language Models (LLMs) in supporting clinical management and delivering precise patient information underscoring the need for focused training on these 'zebra' cases. We present Zebra-Llama, a specialized context-aware language model with high precision Retrieval Augmented Generation (RAG) capability, focusing on Ehlers-Danlos Syndrome (EDS) as our case study. EDS, affecting 1 in 5,000 individuals, exemplifies the complexities of rare diseases with its diverse symptoms, multiple subtypes, and evolving diagnostic criteria. By implementing a novel context-aware fine-tuning methodology trained on questions derived from medical literature, patient experiences, and clinical resources, along with expertly curated responses, Zebra-Llama demonstrates unprecedented capabilities in handling EDS-related queries. On a test set of real-world questions collected from EDS patients and clinicians, medical experts evaluated the responses generated by both models, revealing Zebra-Llama's substantial improvements over base model (Llama 3.1-8B-Instruct) in thoroughness (77.5% vs. 70.1%), accuracy (83.0% vs. 78.8%), clarity (74.7% vs. 72.0%) and citation reliability (70.6% vs. 52.3%). Released as an open-source resource, Zebra-Llama not only provides more accessible and reliable EDS information but also establishes a framework for developing specialized AI solutions for other rare conditions. This work represents a crucial step towards democratizing expert-level knowledge in rare disease management, potentially transforming how healthcare providers and patients navigate the complex landscape of rare diseases.

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

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate PaLM (a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM, on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. To resolve this we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

Large Language models have demonstrated excellent domain-specific question-answering capabilities when finetuned with a particular dataset of that specific domain. However, fine-tuning the models requires a significant amount of training time and a considerable amount of hardware. In this work, we propose CARE (Customer Assistance and Response Engine), a lightweight model made by fine-tuning Phi3.5-mini on very minimal hardware and data, designed to handle queries primarily across three domains: telecommunications support, medical support, and banking support. For telecommunications and banking, the chatbot addresses issues and problems faced by customers regularly in the above-mentioned domains. In the medical domain, CARE provides preliminary support by offering basic diagnoses and medical suggestions that a user might take before consulting a healthcare professional. Since CARE is built on Phi3.5-mini, it can be used even on mobile devices, increasing its usability. Our research also shows that CARE performs relatively well on various medical benchmarks, indicating that it can be used to make basic medical suggestions.

Large Language Models~(LLMs) have demonstrated capabilities across various applications but face challenges such as hallucination, limited reasoning abilities, and factual inconsistencies, especially when tackling complex, domain-specific tasks like question answering~(QA). While Knowledge Graphs~(KGs) have been shown to help mitigate these issues, research on the integration of LLMs with background KGs remains limited. In particular, user accessibility and the flexibility of the underlying KG have not been thoroughly explored. We introduce AGENTiGraph (Adaptive Generative ENgine for Task-based Interaction and Graphical Representation), a platform for knowledge management through natural language interaction. It integrates knowledge extraction, integration, and real-time visualization. AGENTiGraph employs a multi-agent architecture to dynamically interpret user intents, manage tasks, and integrate new knowledge, ensuring adaptability to evolving user requirements and data contexts. Our approach demonstrates superior performance in knowledge graph interactions, particularly for complex domain-specific tasks. Experimental results on a dataset of 3,500 test cases show AGENTiGraph significantly outperforms state-of-the-art zero-shot baselines, achieving 95.12\% accuracy in task classification and 90.45\% success rate in task execution. User studies corroborate its effectiveness in real-world scenarios. To showcase versatility, we extended AGENTiGraph to legislation and healthcare domains, constructing specialized KGs capable of answering complex queries in legal and medical contexts.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Medical consumer question answering (CQA) is crucial for empowering patients by providing personalized and reliable health information. Despite recent advances in large language models (LLMs) for medical QA, consumer-oriented and multilingual resources, particularly in low-resource languages like Persian, remain sparse. To bridge this gap, we present PerMedCQA, the first Persian-language benchmark for evaluating LLMs on real-world, consumer-generated medical questions. Curated from a large medical QA forum, PerMedCQA contains 68,138 question-answer pairs, refined through careful data cleaning from an initial set of 87,780 raw entries. We evaluate several state-of-the-art multilingual and instruction-tuned LLMs, utilizing MedJudge, a novel rubric-based evaluation framework driven by an LLM grader, validated against expert human annotators. Our results highlight key challenges in multilingual medical QA and provide valuable insights for developing more accurate and context-aware medical assistance systems. The data is publicly available on https://huggingface.co/datasets/NaghmehAI/PerMedCQA

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support, which has been demonstrated by their competitive performances in Medical QA. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations written by medical doctors which can be leveraged to establish various gold-based upper-bounds for comparison with LLMs performance. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs still has large room for improvement, especially for languages other than English. Furthermore, and despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. So far the benchmark is available in four languages, but we hope that this work may encourage further development to other languages.

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.

Retrieval-augmented generation (RAG) has emerged as a promising approach to enhance the performance of large language models (LLMs) in knowledge-intensive tasks such as those from medical domain. However, the sensitive nature of the medical domain necessitates a completely accurate and trustworthy system. While existing RAG benchmarks primarily focus on the standard retrieve-answer setting, they overlook many practical scenarios that measure crucial aspects of a reliable medical system. This paper addresses this gap by providing a comprehensive evaluation framework for medical question-answering (QA) systems in a RAG setting for these situations, including sufficiency, integration, and robustness. We introduce Medical Retrieval-Augmented Generation Benchmark (MedRGB) that provides various supplementary elements to four medical QA datasets for testing LLMs' ability to handle these specific scenarios. Utilizing MedRGB, we conduct extensive evaluations of both state-of-the-art commercial LLMs and open-source models across multiple retrieval conditions. Our experimental results reveals current models' limited ability to handle noise and misinformation in the retrieved documents. We further analyze the LLMs' reasoning processes to provides valuable insights and future directions for developing RAG systems in this critical medical domain.

We present MedConceptsQA, a dedicated open source benchmark for medical concepts question answering. The benchmark comprises of questions of various medical concepts across different vocabularies: diagnoses, procedures, and drugs. The questions are categorized into three levels of difficulty: easy, medium, and hard. We conducted evaluations of the benchmark using various Large Language Models. Our findings show that pre-trained clinical Large Language Models achieved accuracy levels close to random guessing on this benchmark, despite being pre-trained on medical data. However, GPT-4 achieves an absolute average improvement of nearly 27%-37% (27% for zero-shot learning and 37% for few-shot learning) when compared to clinical Large Language Models. Our benchmark serves as a valuable resource for evaluating the understanding and reasoning of medical concepts by Large Language Models. Our benchmark is available at https://huggingface.co/datasets/ofir408/MedConceptsQA

Medical visual question answering (Med-VQA) has tremendous potential in healthcare. However, the development of this technology is hindered by the lacking of publicly-available and high-quality labeled datasets for training and evaluation. In this paper, we present a large bilingual dataset, SLAKE, with comprehensive semantic labels annotated by experienced physicians and a new structural medical knowledge base for Med-VQA. Besides, SLAKE includes richer modalities and covers more human body parts than the currently available dataset. We show that SLAKE can be used to facilitate the development and evaluation of Med-VQA systems. The dataset can be downloaded from http://www.med-vqa.com/slake.

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.

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.

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.

LLMs are bound to transform healthcare with advanced decision support and flexible chat assistants. However, LLMs are prone to generate inaccurate medical content. To ground LLMs in high-quality medical knowledge, LLMs have been equipped with external knowledge via RAG, where unstructured medical knowledge is split into small text chunks that can be selectively retrieved and integrated into the LLMs context. Yet, existing RAG pipelines rely on raw, unstructured medical text, which can be noisy, uncurated and difficult for LLMs to effectively leverage. Systematic approaches to organize medical knowledge to best surface it to LLMs are generally lacking. To address these challenges, we introduce MIRIAD, a large-scale, curated corpus of 5,821,948 medical QA pairs, each rephrased from and grounded in a passage from peer-reviewed medical literature using a semi-automated pipeline combining LLM generation, filtering, grounding, and human annotation. Unlike prior medical corpora, which rely on unstructured text, MIRIAD encapsulates web-scale medical knowledge in an operationalized query-response format, which enables more targeted retrieval. Experiments on challenging medical QA benchmarks show that augmenting LLMs with MIRIAD improves accuracy up to 6.7% compared to unstructured RAG baselines with the same source corpus and with the same amount of retrieved text. Moreover, MIRIAD improved the ability of LLMs to detect medical hallucinations by 22.5 to 37% (increase in F1 score). We further introduce MIRIAD-Atlas, an interactive map of MIRIAD spanning 56 medical disciplines, enabling clinical users to visually explore, search, and refine medical knowledge. MIRIAD promises to unlock a wealth of down-stream applications, including medical information retrievers, enhanced RAG applications, and knowledge-grounded chat interfaces, which ultimately enables more reliable LLM applications in healthcare.

In this paper, we critically evaluate the capabilities of the state-of-the-art multimodal large language model, i.e., GPT-4 with Vision (GPT-4V), on Visual Question Answering (VQA) task. Our experiments thoroughly assess GPT-4V's proficiency in answering questions paired with images using both pathology and radiology datasets from 11 modalities (e.g. Microscopy, Dermoscopy, X-ray, CT, etc.) and fifteen objects of interests (brain, liver, lung, etc.). Our datasets encompass a comprehensive range of medical inquiries, including sixteen distinct question types. Throughout our evaluations, we devised textual prompts for GPT-4V, directing it to synergize visual and textual information. The experiments with accuracy score conclude that the current version of GPT-4V is not recommended for real-world diagnostics due to its unreliable and suboptimal accuracy in responding to diagnostic medical questions. In addition, we delineate seven unique facets of GPT-4V's behavior in medical VQA, highlighting its constraints within this complex arena. The complete details of our evaluation cases are accessible at https://github.com/ZhilingYan/GPT4V-Medical-Report.

Electronic Health Record (EHR) retrieval plays a pivotal role in various clinical tasks, but its development has been severely impeded by the lack of publicly available benchmarks. In this paper, we introduce a novel public EHR retrieval benchmark, CliniQ, to address this gap. We consider two retrieval settings: Single-Patient Retrieval and Multi-Patient Retrieval, reflecting various real-world scenarios. Single-Patient Retrieval focuses on finding relevant parts within a patient note, while Multi-Patient Retrieval involves retrieving EHRs from multiple patients. We build our benchmark upon 1,000 discharge summary notes along with the ICD codes and prescription labels from MIMIC-III, and collect 1,246 unique queries with 77,206 relevance judgments by further leveraging powerful LLMs as annotators. Additionally, we include a novel assessment of the semantic gap issue in EHR retrieval by categorizing matching types into string match and four types of semantic matches. On our proposed benchmark, we conduct a comprehensive evaluation of various retrieval methods, ranging from conventional exact match to popular dense retrievers. Our experiments find that BM25 sets a strong baseline and performs competitively to the dense retrievers, and general domain dense retrievers surprisingly outperform those designed for the medical domain. In-depth analyses on various matching types reveal the strengths and drawbacks of different methods, enlightening the potential for targeted improvement. We believe that our benchmark will stimulate the research communities to advance EHR retrieval systems.

Large language models (LLMs), such as ChatGPT, have received substantial attention due to their impressive human language understanding and generation capabilities. Therefore, the application of LLMs in medicine to assist physicians and patient care emerges as a promising research direction in both artificial intelligence and clinical medicine. To reflect this trend, this survey provides a comprehensive overview of the principles, applications, and challenges faced by LLMs in medicine. Specifically, we aim to address the following questions: 1) How can medical LLMs be built? 2) What are the downstream performances of medical LLMs? 3) How can medical LLMs be utilized in real-world clinical practice? 4) What challenges arise from the use of medical LLMs? and 5) How can we better construct and utilize medical LLMs? As a result, this survey aims to provide insights into the opportunities and challenges of LLMs in medicine and serve as a valuable resource for constructing practical and effective medical LLMs. A regularly updated list of practical guides on medical LLMs can be found at https://github.com/AI-in-Health/MedLLMsPracticalGuide.

Medical dialogue systems are promising in assisting in telemedicine to increase access to healthcare services, improve the quality of patient care, and reduce medical costs. To facilitate the research and development of medical dialogue systems, we build two large-scale medical dialogue datasets: MedDialog-EN and MedDialog-CN. MedDialog-EN is an English dataset containing 0.3 million conversations between patients and doctors and 0.5 million utterances. MedDialog-CN is an Chinese dataset containing 1.1 million conversations and 4 million utterances. To our best knowledge, MedDialog-(EN,CN) are the largest medical dialogue datasets to date. The dataset is available at https://github.com/UCSD-AI4H/Medical-Dialogue-System

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine.

Large Language Models (LLMs), although powerful in general domains, often perform poorly on domain-specific tasks like medical question answering (QA). Moreover, they tend to function as "black-boxes," making it challenging to modify their behavior. Addressing this, our study delves into model editing utilizing in-context learning, aiming to improve LLM responses without the need for fine-tuning or retraining. Specifically, we propose a comprehensive retrieval strategy to extract medical facts from an external knowledge base, and then we incorporate them into the query prompt for the LLM. Focusing on medical QA using the MedQA-SMILE dataset, we evaluate the impact of different retrieval models and the number of facts provided to the LLM. Notably, our edited Vicuna model exhibited an accuracy improvement from 44.46% to 48.54%. This work underscores the potential of model editing to enhance LLM performance, offering a practical approach to mitigate the challenges of black-box LLMs.

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language processing, and yet, their factual inaccuracies and hallucinations limits their application, particularly in critical domains like healthcare. Context retrieval methods, by introducing relevant information as input, have emerged as a crucial approach for enhancing LLM factuality and reliability. This study explores the boundaries of context retrieval methods within the healthcare domain, optimizing their components and benchmarking their performance against open and closed alternatives. Our findings reveal how open LLMs, when augmented with an optimized retrieval system, can achieve performance comparable to the biggest private solutions on established healthcare benchmarks (multiple-choice question answering). Recognizing the lack of realism of including the possible answers within the question (a setup only found in medical exams), and after assessing a strong LLM performance degradation in the absence of those options, we extend the context retrieval system in that direction. In particular, we propose OpenMedPrompt a pipeline that improves the generation of more reliable open-ended answers, moving this technology closer to practical application.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

This work introduces MediQAl, a French medical question answering dataset designed to evaluate the capabilities of language models in factual medical recall and reasoning over real-world clinical scenarios. MediQAl contains 32,603 questions sourced from French medical examinations across 41 medical subjects. The dataset includes three tasks: (i) Multiple-Choice Question with Unique answer, (ii) Multiple-Choice Question with Multiple answer, and (iii) Open-Ended Question with Short-Answer. Each question is labeled as Understanding or Reasoning, enabling a detailed analysis of models' cognitive capabilities. We validate the MediQAl dataset through extensive evaluation with 14 large language models, including recent reasoning-augmented models, and observe a significant performance gap between factual recall and reasoning tasks. Our evaluation provides a comprehensive benchmark for assessing language models' performance on French medical question answering, addressing a crucial gap in multilingual resources for the medical domain.

Recent research on large language models (LLMs) has primarily focused on their adaptation and application in specialized domains. The application of LLMs in the medical field is mainly concentrated on tasks such as the automation of medical report generation, summarization, diagnostic reasoning, and question-and-answer interactions between doctors and patients. The challenge of becoming a good teacher is more formidable than that of becoming a good student, and this study pioneers the application of LLMs in the field of medical education. In this work, we investigate the extent to which LLMs can generate medical qualification exam questions and corresponding answers based on few-shot prompts. Utilizing a real-world Chinese dataset of elderly chronic diseases, we tasked the LLMs with generating open-ended questions and answers based on a subset of sampled admission reports across eight widely used LLMs, including ERNIE 4, ChatGLM 4, Doubao, Hunyuan, Spark 4, Qwen, Llama 3, and Mistral. Furthermore, we engaged medical experts to manually evaluate these open-ended questions and answers across multiple dimensions. The study found that LLMs, after using few-shot prompts, can effectively mimic real-world medical qualification exam questions, whereas there is room for improvement in the correctness, evidence-based statements, and professionalism of the generated answers. Moreover, LLMs also demonstrate a decent level of ability to correct and rectify reference answers. Given the immense potential of artificial intelligence in the medical field, the task of generating questions and answers for medical qualification exams aimed at medical students, interns and residents can be a significant focus of future research.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

The recently unprecedented advancements in Large Language Models (LLMs) have propelled the medical community by establishing advanced medical-domain models. However, due to the limited collection of medical datasets, there are only a few comprehensive benchmarks available to gauge progress in this area. In this paper, we introduce a new medical question-answering (QA) dataset that contains massive manual instruction for solving Traditional Chinese Medicine examination tasks, called TCMD. Specifically, our TCMD collects massive questions across diverse domains with their annotated medical subjects and thus supports us in comprehensively assessing the capability of LLMs in the TCM domain. Extensive evaluation of various general LLMs and medical-domain-specific LLMs is conducted. Moreover, we also analyze the robustness of current LLMs in solving TCM QA tasks by introducing randomness. The inconsistency of the experimental results also reveals the shortcomings of current LLMs in solving QA tasks. We also expect that our dataset can further facilitate the development of LLMs in the TCM area.

Machine Reading Comprehension (MRC) holds a pivotal role in shaping Medical Question Answering Systems (QAS) and transforming the landscape of accessing and applying medical information. However, the inherent challenges in the medical field, such as complex terminology and question ambiguity, necessitate innovative solutions. One key solution involves integrating specialized medical datasets and creating dedicated datasets. This strategic approach enhances the accuracy of QAS, contributing to advancements in clinical decision-making and medical research. To address the intricacies of medical terminology, a specialized dataset was integrated, exemplified by a novel Span extraction dataset derived from emrQA but restructured into 163,695 questions and 4,136 manually obtained answers, this new dataset was called emrQA-msquad dataset. Additionally, for ambiguous questions, a dedicated medical dataset for the Span extraction task was introduced, reinforcing the system's robustness. The fine-tuning of models such as BERT, RoBERTa, and Tiny RoBERTa for medical contexts significantly improved response accuracy within the F1-score range of 0.75 to 1.00 from 10.1% to 37.4%, 18.7% to 44.7% and 16.0% to 46.8%, respectively. Finally, emrQA-msquad dataset is publicy available at https://huggingface.co/datasets/Eladio/emrqa-msquad.

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

This paper introduces MedExQA, a novel benchmark in medical question-answering, to evaluate large language models' (LLMs) understanding of medical knowledge through explanations. By constructing datasets across five distinct medical specialties that are underrepresented in current datasets and further incorporating multiple explanations for each question-answer pair, we address a major gap in current medical QA benchmarks which is the absence of comprehensive assessments of LLMs' ability to generate nuanced medical explanations. Our work highlights the importance of explainability in medical LLMs, proposes an effective methodology for evaluating models beyond classification accuracy, and sheds light on one specific domain, speech language pathology, where current LLMs including GPT4 lack good understanding. Our results show generation evaluation with multiple explanations aligns better with human assessment, highlighting an opportunity for a more robust automated comprehension assessment for LLMs. To diversify open-source medical LLMs (currently mostly based on Llama2), this work also proposes a new medical model, MedPhi-2, based on Phi-2 (2.7B). The model outperformed medical LLMs based on Llama2-70B in generating explanations, showing its effectiveness in the resource-constrained medical domain. We will share our benchmark datasets and the trained model.

Recent advancements in large language model(LLM) performance on medical multiple choice question (MCQ) benchmarks have stimulated interest from healthcare providers and patients globally. Particularly in low-and middle-income countries (LMICs) facing acute physician shortages and lack of specialists, LLMs offer a potentially scalable pathway to enhance healthcare access and reduce costs. However, their effectiveness in the Global South, especially across the African continent, remains to be established. In this work, we introduce AfriMed-QA, the first large scale Pan-African English multi-specialty medical Question-Answering (QA) dataset, 15,000 questions (open and closed-ended) sourced from over 60 medical schools across 16 countries, covering 32 medical specialties. We further evaluate 30 LLMs across multiple axes including correctness and demographic bias. Our findings show significant performance variation across specialties and geographies, MCQ performance clearly lags USMLE (MedQA). We find that biomedical LLMs underperform general models and smaller edge-friendly LLMs struggle to achieve a passing score. Interestingly, human evaluations show a consistent consumer preference for LLM answers and explanations when compared with clinician answers.

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

Medical text embedding models are foundational to a wide array of healthcare applications, ranging from clinical decision support and biomedical information retrieval to medical question answering, yet they remain hampered by two critical shortcomings. First, most models are trained on a narrow slice of medical and biological data, beside not being up to date in terms of methodology, making them ill suited to capture the diversity of terminology and semantics encountered in practice. Second, existing evaluations are often inadequate: even widely used benchmarks fail to generalize across the full spectrum of real world medical tasks. To address these gaps, we leverage MEDTE, a GTE model extensively fine-tuned on diverse medical corpora through self-supervised contrastive learning across multiple data sources, to deliver robust medical text embeddings. Alongside this model, we propose a comprehensive benchmark suite of 51 tasks spanning classification, clustering, pair classification, and retrieval modeled on the Massive Text Embedding Benchmark (MTEB) but tailored to the nuances of medical text. Our results demonstrate that this combined approach not only establishes a robust evaluation framework but also yields embeddings that consistently outperform state of the art alternatives in different tasks.

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

Hepato-pancreato-biliary (HPB) disorders represent a global public health challenge due to their high morbidity and mortality. Although large language models (LLMs) have shown promising performance in general medical question-answering tasks, the current evaluation benchmarks are mostly derived from standardized examinations or manually designed questions, lacking HPB coverage and clinical cases. To address these issues, we systematically eatablish an HPB disease evaluation benchmark comprising 3,535 closed-ended multiple-choice questions and 337 open-ended real diagnosis cases, which encompasses all the 33 main categories and 465 subcategories of HPB diseases defined in the International Statistical Classification of Diseases, 10th Revision (ICD-10). The multiple-choice questions are curated from public datasets and synthesized data, and the clinical cases are collected from prestigious medical journals, case-sharing platforms, and collaborating hospitals. By evalauting commercial and open-source general and medical LLMs on our established benchmark, namely ClinBench-HBP, we find that while commercial LLMs perform competently on medical exam questions, they exhibit substantial performance degradation on HPB diagnosis tasks, especially on complex, inpatient clinical cases. Those medical LLMs also show limited generalizability to HPB diseases. Our results reveal the critical limitations of current LLMs in the domain of HPB diseases, underscoring the imperative need for future medical LLMs to handle real, complex clinical diagnostics rather than simple medical exam questions. The benchmark will be released at https://clinbench-hpb.github.io.

Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code will be publicly available.

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

Recent large language models (LLMs) in the general domain, such as ChatGPT, have shown remarkable success in following instructions and producing human-like responses. However, such language models have not been learned individually and carefully for the medical domain, resulting in poor diagnostic accuracy and inability to give correct recommendations for medical diagnosis, medications, etc. To address this issue, we collected more than 700 diseases and their corresponding symptoms, recommended medications, and required medical tests, and then generated 5K doctor-patient conversations. By fine-tuning models of doctor-patient conversations, these models emerge with great potential to understand patients' needs, provide informed advice, and offer valuable assistance in a variety of medical-related fields. The integration of these advanced language models into healthcare can revolutionize the way healthcare professionals and patients communicate, ultimately improving the overall quality of care and patient outcomes. In addition, we will open all source code, datasets and model weights to advance the further development of dialogue models in the medical field. In addition, the training data, code, and weights of this project are available at: https://github.com/Kent0n-Li/ChatDoctor.

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and synthesis tasks. While general-purpose deep research agents have shown impressive capabilities, they struggle significantly with medical domain challenges, as evidenced by leading proprietary systems achieving limited accuracy on complex medical benchmarks. The key limitations are: (1) the model lacks sufficient dense medical knowledge for clinical reasoning, and (2) the framework is constrained by the absence of specialized retrieval tools tailored for medical contexts.We present a medical deep research agent that addresses these challenges through two core innovations. First, we develop a novel data synthesis framework using medical knowledge graphs, extracting the longest chains from subgraphs around rare medical entities to generate complex multi-hop question-answer pairs. Second, we integrate a custom-built private medical retrieval engine alongside general-purpose tools, enabling accurate medical information synthesis. Our approach generates 2100+ diverse trajectories across 12 medical specialties, each averaging 4.2 tool interactions.Through a two-stage training paradigm combining supervised fine-tuning and online reinforcement learning with composite rewards, our MedResearcher-R1-32B model demonstrates exceptional performance, establishing new state-of-the-art results on medical benchmarks while maintaining competitive performance on general deep research tasks. Our work demonstrates that strategic domain-specific innovations in architecture, tool design, and training data construction can enable smaller open-source models to outperform much larger proprietary systems in specialized domains.

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

Question Answering on Electronic Health Records (EHR-QA) has a significant impact on the healthcare domain, and it is being actively studied. Previous research on structured EHR-QA focuses on converting natural language queries into query language such as SQL or SPARQL (NLQ2Query), so the problem scope is limited to pre-defined data types by the specific query language. In order to expand the EHR-QA task beyond this limitation to handle multi-modal medical data and solve complex inference in the future, more primitive systemic language is needed. In this paper, we design the program-based model (NLQ2Program) for EHR-QA as the first step towards the future direction. We tackle MIMICSPARQL*, the graph-based EHR-QA dataset, via a program-based approach in a semi-supervised manner in order to overcome the absence of gold programs. Without the gold program, our proposed model shows comparable performance to the previous state-of-the-art model, which is an NLQ2Query model (0.9% gain). In addition, for a reliable EHR-QA model, we apply the uncertainty decomposition method to measure the ambiguity in the input question. We empirically confirmed data uncertainty is most indicative of the ambiguity in the input question.

Medical multiple-choice question answering (MCQA) is particularly difficult. Questions may describe patient symptoms and ask for the correct diagnosis, which requires domain knowledge and complex reasoning. Standard language modeling pretraining alone is not sufficient to achieve the best results. jin2020disease showed that focusing masked language modeling on disease name prediction when using medical encyclopedic paragraphs as input leads to considerable MCQA accuracy improvement. In this work, we show that (1) fine-tuning on generated MCQA dataset outperforms the masked language modeling based objective and (2) correctly masking the cues to the answers is critical for good performance. We release new pretraining datasets and achieve state-of-the-art results on 4 MCQA datasets, notably +5.7\% with base-size model on MedQA-USMLE.

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

In the expanding field of language model applications, medical knowledge representation remains a significant challenge due to the specialized nature of the domain. Large language models, such as GPT-4, obtain reasonable scores on medical question answering tasks, but smaller models are far behind. In this work, we introduce a method to improve the proficiency of a small language model in the medical domain by employing a two-fold approach. We first fine-tune the model on a corpus of medical textbooks. Then, we use GPT-4 to generate questions similar to the downstream task, prompted with textbook knowledge, and use them to fine-tune the model. Additionally, we introduce ECN-QA, a novel medical question answering dataset containing ``progressive questions'' composed of related sequential questions. We show the benefits of our training strategy on this dataset. The study's findings highlight the potential of small language models in the medical domain when appropriately fine-tuned. The code and weights are available at https://github.com/raidium-med/MQG.

Several studies showed that Large Language Models (LLMs) can answer medical questions correctly, even outperforming the average human score in some medical exams. However, to our knowledge, no study has been conducted to assess the ability of language models to validate existing or generated medical text for correctness and consistency. In this paper, we introduce MEDEC (https://github.com/abachaa/MEDEC), the first publicly available benchmark for medical error detection and correction in clinical notes, covering five types of errors (Diagnosis, Management, Treatment, Pharmacotherapy, and Causal Organism). MEDEC consists of 3,848 clinical texts, including 488 clinical notes from three US hospital systems that were not previously seen by any LLM. The dataset has been used for the MEDIQA-CORR shared task to evaluate seventeen participating systems [Ben Abacha et al., 2024]. In this paper, we describe the data creation methods and we evaluate recent LLMs (e.g., o1-preview, GPT-4, Claude 3.5 Sonnet, and Gemini 2.0 Flash) for the tasks of detecting and correcting medical errors requiring both medical knowledge and reasoning capabilities. We also conducted a comparative study where two medical doctors performed the same task on the MEDEC test set. The results showed that MEDEC is a sufficiently challenging benchmark to assess the ability of models to validate existing or generated notes and to correct medical errors. We also found that although recent LLMs have a good performance in error detection and correction, they are still outperformed by medical doctors in these tasks. We discuss the potential factors behind this gap, the insights from our experiments, the limitations of current evaluation metrics, and share potential pointers for future research.

Online medical consultation (OMC) restricts doctors to gathering patient information solely through inquiries, making the already complex sequential decision-making process of diagnosis even more challenging. Recently, the rapid advancement of large language models has demonstrated a significant potential to transform OMC. However, most studies have primarily focused on improving diagnostic accuracy under conditions of relatively sufficient information, while paying limited attention to the "inquiry" phase of the consultation process. This lack of focus has left the relationship between "inquiry" and "diagnosis" insufficiently explored. In this paper, we first extract real patient interaction strategies from authentic doctor-patient conversations and use these strategies to guide the training of a patient simulator that closely mirrors real-world behavior. By inputting medical records into our patient simulator to simulate patient responses, we conduct extensive experiments to explore the relationship between "inquiry" and "diagnosis" in the consultation process. Experimental results demonstrate that inquiry and diagnosis adhere to the Liebig's law: poor inquiry quality limits the effectiveness of diagnosis, regardless of diagnostic capability, and vice versa. Furthermore, the experiments reveal significant differences in the inquiry performance of various models. To investigate this phenomenon, we categorize the inquiry process into four types: (1) chief complaint inquiry; (2) specification of known symptoms; (3) inquiry about accompanying symptoms; and (4) gathering family or medical history. We analyze the distribution of inquiries across the four types for different models to explore the reasons behind their significant performance differences. We plan to open-source the weights and related code of our patient simulator at https://github.com/LIO-H-ZEN/PatientSimulator.

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Despite the vast repository of global medical knowledge predominantly being in English, local languages are crucial for delivering tailored healthcare services, particularly in areas with limited medical resources. To extend the reach of medical AI advancements to a broader population, we aim to develop medical LLMs across the six most widely spoken languages, encompassing a global population of 6.1 billion. This effort culminates in the creation of the ApolloCorpora multilingual medical dataset and the XMedBench benchmark. In the multilingual medical benchmark, the released Apollo models, at various relatively-small sizes (i.e., 0.5B, 1.8B, 2B, 6B, and 7B), achieve the best performance among models of equivalent size. Especially, Apollo-7B is the state-of-the-art multilingual medical LLMs up to 70B. Additionally, these lite models could be used to improve the multi-lingual medical capabilities of larger models without fine-tuning in a proxy-tuning fashion. We will open-source training corpora, code, model weights and evaluation benchmark.

Question answering (QA) systems have gained explosive attention in recent years. However, QA tasks in Vietnamese do not have many datasets. Significantly, there is mostly no dataset in the medical domain. Therefore, we built a Vietnamese Healthcare Question Answering dataset (ViHealthQA), including 10,015 question-answer passage pairs for this task, in which questions from health-interested users were asked on prestigious health websites and answers from highly qualified experts. This paper proposes a two-stage QA system based on Sentence-BERT (SBERT) using multiple negatives ranking (MNR) loss combined with BM25. Then, we conduct diverse experiments with many bag-of-words models to assess our system's performance. With the obtained results, this system achieves better performance than traditional methods.

Large Language Models (LLMs) constitute a breakthrough state-of-the-art Artificial Intelligence (AI) technology which is rapidly evolving and promises to aid in medical diagnosis either by assisting doctors or by simulating a doctor's workflow in more advanced and complex implementations. In this technical paper, we outline Cognitive Network Evaluation Toolkit for Medical Domains (COGNET-MD), which constitutes a novel benchmark for LLM evaluation in the medical domain. Specifically, we propose a scoring-framework with increased difficulty to assess the ability of LLMs in interpreting medical text. The proposed framework is accompanied with a database of Multiple Choice Quizzes (MCQs). To ensure alignment with current medical trends and enhance safety, usefulness, and applicability, these MCQs have been constructed in collaboration with several associated medical experts in various medical domains and are characterized by varying degrees of difficulty. The current (first) version of the database includes the medical domains of Psychiatry, Dentistry, Pulmonology, Dermatology and Endocrinology, but it will be continuously extended and expanded to include additional medical domains.

Recently, large language model (LLM) based artificial intelligence (AI) systems have demonstrated remarkable capabilities in natural language understanding and generation. However, these models face a significant challenge when it comes to sensitive applications, such as reasoning over medical knowledge and answering medical questions in a physician-like manner. Prior studies attempted to overcome this challenge by increasing the model size (>100B) to learn more general medical knowledge, while there is still room for improvement in LLMs with smaller-scale model sizes (<100B). In this work, we start from a pre-trained general LLM model (AntGLM-10B) and fine-tune it from a medical beginner towards a medical expert (called AntGLM-Med-10B), which leverages a 3-stage optimization procedure, i.e., general medical knowledge injection, medical domain instruction tuning, and specific medical task adaptation. Our contributions are threefold: (1) We specifically investigate how to adapt a pre-trained general LLM in medical domain, especially for a specific medical task. (2) We collect and construct large-scale medical datasets for each stage of the optimization process. These datasets encompass various data types and tasks, such as question-answering, medical reasoning, multi-choice questions, and medical conversations. (3) Specifically for multi-choice questions in the medical domain, we propose a novel Verification-of-Choice approach for prompting engineering, which significantly enhances the reasoning ability of LLMs. Remarkably, by combining the above approaches, our AntGLM-Med-10B model can outperform the most of LLMs on PubMedQA, including both general and medical LLMs, even when these LLMs have larger model size.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

There is a lack of benchmarks for evaluating large language models (LLMs) in long-form medical question answering (QA). Most existing medical QA evaluation benchmarks focus on automatic metrics and multiple-choice questions. While valuable, these benchmarks fail to fully capture or assess the complexities of real-world clinical applications where LLMs are being deployed. Furthermore, existing studies on evaluating long-form answer generation in medical QA are primarily closed-source, lacking access to human medical expert annotations, which makes it difficult to reproduce results and enhance existing baselines. In this work, we introduce a new publicly available benchmark featuring real-world consumer medical questions with long-form answer evaluations annotated by medical doctors. We performed pairwise comparisons of responses from various open and closed-source medical and general-purpose LLMs based on criteria such as correctness, helpfulness, harmfulness, and bias. Additionally, we performed a comprehensive LLM-as-a-judge analysis to study the alignment between human judgments and LLMs. Our preliminary results highlight the strong potential of open LLMs in medical QA compared to leading closed models. Code & Data: https://github.com/lavita-ai/medical-eval-sphere

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

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

The recent success of Large Language Models (LLMs) has had a significant impact on the healthcare field, providing patients with medical advice, diagnostic information, and more. However, due to a lack of professional medical knowledge, patients are easily misled by generated erroneous information from LLMs, which may result in serious medical problems. To address this issue, we focus on tuning the LLMs to be medical assistants who collaborate with more experienced doctors. We first conduct a two-stage survey by inspiration-feedback to gain a broad understanding of the real needs of doctors for medical assistants. Based on this, we construct a Chinese medical dataset called DoctorFLAN to support the entire workflow of doctors, which includes 92K Q\&A samples from 22 tasks and 27 specialists. Moreover, we evaluate LLMs in doctor-oriented scenarios by constructing the DoctorFLAN-test containing 550 single-turn Q\&A and DotaBench containing 74 multi-turn conversations. The evaluation results indicate that being a medical assistant still poses challenges for existing open-source models, but DoctorFLAN can help them significantly. It demonstrates that the doctor-oriented dataset and benchmarks we construct can complement existing patient-oriented work and better promote medical LLMs research.

We introduce MedXpertQA, a highly challenging and comprehensive benchmark to evaluate expert-level medical knowledge and advanced reasoning. MedXpertQA includes 4,460 questions spanning 17 specialties and 11 body systems. It includes two subsets, Text for text evaluation and MM for multimodal evaluation. Notably, MM introduces expert-level exam questions with diverse images and rich clinical information, including patient records and examination results, setting it apart from traditional medical multimodal benchmarks with simple QA pairs generated from image captions. MedXpertQA applies rigorous filtering and augmentation to address the insufficient difficulty of existing benchmarks like MedQA, and incorporates specialty board questions to improve clinical relevance and comprehensiveness. We perform data synthesis to mitigate data leakage risk and conduct multiple rounds of expert reviews to ensure accuracy and reliability. We evaluate 16 leading models on MedXpertQA. Moreover, medicine is deeply connected to real-world decision-making, providing a rich and representative setting for assessing reasoning abilities beyond mathematics and code. To this end, we develop a reasoning-oriented subset to facilitate the assessment of o1-like models.

Biomedical question-answering (QA) systems require effective retrieval and generation components to ensure accuracy, efficiency, and scalability. This study systematically examines a Retrieval-Augmented Generation (RAG) system for biomedical QA, evaluating retrieval strategies and response time trade-offs. We first assess state-of-the-art retrieval methods, including BM25, BioBERT, MedCPT, and a hybrid approach, alongside common data stores such as Elasticsearch, MongoDB, and FAISS, on a ~10% subset of PubMed (2.4M documents) to measure indexing efficiency, retrieval latency, and retriever performance in the end-to-end RAG system. Based on these insights, we deploy the final RAG system on the full 24M PubMed corpus, comparing different retrievers' impact on overall performance. Evaluations of the retrieval depth show that retrieving 50 documents with BM25 before reranking with MedCPT optimally balances accuracy (0.90), recall (0.90), and response time (1.91s). BM25 retrieval time remains stable (82ms), while MedCPT incurs the main computational cost. These results highlight previously not well-known trade-offs in retrieval depth, efficiency, and scalability for biomedical QA. With open-source code, the system is fully reproducible and extensible.

Recently, the increasing demand for superior medical services has highlighted the discrepancies in the medical infrastructure. With big data, especially texts, forming the foundation of medical services, there is an exigent need for effective natural language processing (NLP) solutions tailored to the healthcare domain. Conventional approaches leveraging pre-trained models present promising results in this domain and current large language models (LLMs) offer advanced foundation for medical text processing. However, most medical LLMs are trained only with supervised fine-tuning (SFT), even though it efficiently empowers LLMs to understand and respond to medical instructions but is ineffective in learning domain knowledge and aligning with human preference. Another engineering barrier that prevents current medical LLM from better text processing ability is their restricted context length (e.g., 2,048 tokens), making it hard for the LLMs to process long context, which is frequently required in the medical domain. In this work, we propose ChiMed-GPT, a new benchmark LLM designed explicitly for Chinese medical domain, with enlarged context length to 4,096 tokens and undergoes a comprehensive training regime with pre-training, SFT, and RLHF. Evaluations on real-world tasks including information extraction, question answering, and dialogue generation demonstrate ChiMed-GPT's superior performance over general domain LLMs. Furthermore, we analyze possible biases through prompting ChiMed-GPT to perform attitude scales regarding discrimination of patients, so as to contribute to further responsible development of LLMs in the medical domain. The code and model are released at https://github.com/synlp/ChiMed-GPT.

Medical Dialogue Generation serves a critical role in telemedicine by facilitating the dissemination of medical expertise to patients. Existing studies focus on incorporating textual representations, which have limited their ability to represent the semantics of text, such as ignoring important medical entities. To enhance the model's understanding of the textual semantics and the medical knowledge including entities and relations, we introduce the use of Abstract Meaning Representations (AMR) to construct graphical representations that delineate the roles of language constituents and medical entities within the dialogues. In this paper, We propose a novel framework that models dialogues between patients and healthcare professionals using AMR graphs, where the neural networks incorporate textual and graphical knowledge with a dual attention mechanism. Experimental results show that our framework outperforms strong baseline models in medical dialogue generation, demonstrating the effectiveness of AMR graphs in enhancing the representations of medical knowledge and logical relationships. Furthermore, to support future research in this domain, we provide the corresponding source code at https://github.com/Bernard-Yang/MedDiaAMR.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

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

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

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.

In this study, we present MedS-Bench, a comprehensive benchmark designed to evaluate the performance of large language models (LLMs) in clinical contexts. Unlike existing benchmarks that focus on multiple-choice question answering, MedS-Bench spans 11 high-level clinical tasks, including clinical report summarization, treatment recommendations, diagnosis, named entity recognition, and medical concept explanation, among others. We evaluated six leading LLMs, e.g., MEDITRON, Mistral, InternLM 2, Llama 3, GPT-4, and Claude-3.5 using few-shot prompting, and found that even the most sophisticated models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 13.5 million samples across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models across nearly all clinical tasks. To promote further advancements in the application of LLMs to clinical challenges, we have made the MedS-Ins dataset fully accessible and invite the research community to contribute to its expansion.Additionally, we have launched a dynamic leaderboard for MedS-Bench, which we plan to regularly update the test set to track progress and enhance the adaptation of general LLMs to the medical domain. Leaderboard: https://henrychur.github.io/MedS-Bench/. Github: https://github.com/MAGIC-AI4Med/MedS-Ins.

Follow-up question generation is an essential feature of dialogue systems as it can reduce conversational ambiguity and enhance modeling complex interactions. Conversational contexts often pose core NLP challenges such as (i) extracting relevant information buried in fragmented data sources, and (ii) modeling parallel thought processes. These two challenges occur frequently in medical dialogue as a doctor asks questions based not only on patient utterances but also their prior EHR data and current diagnostic hypotheses. Asking medical questions in asynchronous conversations compounds these issues as doctors can only rely on static EHR information to motivate follow-up questions. To address these challenges, we introduce FollowupQ, a novel framework for enhancing asynchronous medical conversation. FollowupQ is a multi-agent framework that processes patient messages and EHR data to generate personalized follow-up questions, clarifying patient-reported medical conditions. FollowupQ reduces requisite provider follow-up communications by 34%. It also improves performance by 17% and 5% on real and synthetic data, respectively. We also release the first public dataset of asynchronous medical messages with linked EHR data alongside 2,300 follow-up questions written by clinical experts for the wider NLP research community.

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

LLMs have demonstrated impressive performance in answering medical questions, such as passing scores on medical licensing examinations. However, medical board exam questions or general clinical questions do not capture the complexity of realistic clinical cases. Moreover, the lack of reference explanations means we cannot easily evaluate the reasoning of model decisions, a crucial component of supporting doctors in making complex medical decisions. To address these challenges, we construct two new datasets: JAMA Clinical Challenge and Medbullets. JAMA Clinical Challenge consists of questions based on challenging clinical cases, while Medbullets comprises USMLE Step 2&3 style clinical questions. Both datasets are structured as multiple-choice question-answering tasks, where each question is accompanied by an expert-written explanation. We evaluate four LLMs on the two datasets using various prompts. Experiments demonstrate that our datasets are harder than previous benchmarks. The inconsistency between automatic and human evaluations of model-generated explanations highlights the need to develop new metrics to support future research on explainable medical QA.

Medical Visual Question Answering (Med-VQA) combines computer vision and natural language processing to automatically answer clinical inquiries about medical images. However, current Med-VQA datasets exhibit two significant limitations: (1) they often lack visual and textual explanations for answers, hindering comprehension for patients and junior doctors; (2) they typically offer a narrow range of question formats, inadequately reflecting the diverse requirements in practical scenarios. These limitations pose significant challenges to the development of a reliable and user-friendly Med-VQA system. To address these challenges, we introduce a large-scale, Groundable, and Explainable Medical VQA benchmark for chest X-ray diagnosis (GEMeX), featuring several innovative components: (1) a multi-modal explainability mechanism that offers detailed visual and textual explanations for each question-answer pair, thereby enhancing answer comprehensibility; (2) four question types, open-ended, closed-ended, single-choice, and multiple-choice, to better reflect practical needs. With 151,025 images and 1,605,575 questions, GEMeX is the currently largest chest X-ray VQA dataset. Evaluation of 12 representative large vision language models (LVLMs) on GEMeX reveals suboptimal performance, underscoring the dataset's complexity. Meanwhile, we propose a strong model by fine-tuning an existing LVLM on the GEMeX training set. The substantial performance improvement showcases the dataset's effectiveness. The benchmark is available at https://www.med-vqa.com/GEMeX.

We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July, 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging topics at that state of the still-emerging pandemic. This paper provides a comprehensive overview of the structure and results of TREC-COVID. Specifically, the paper provides details on the background, task structure, topic structure, corpus, participation, pooling, assessment, judgments, results, top-performing systems, lessons learned, and benchmark datasets.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

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

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

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

Medicine, by its nature, is a multifaceted domain that requires the synthesis of information across various modalities. Medical generative vision-language models (VLMs) make a first step in this direction and promise many exciting clinical applications. However, existing models typically have to be fine-tuned on sizeable down-stream datasets, which poses a significant limitation as in many medical applications data is scarce, necessitating models that are capable of learning from few examples in real-time. Here we propose Med-Flamingo, a multimodal few-shot learner adapted to the medical domain. Based on OpenFlamingo-9B, we continue pre-training on paired and interleaved medical image-text data from publications and textbooks. Med-Flamingo unlocks few-shot generative medical visual question answering (VQA) abilities, which we evaluate on several datasets including a novel challenging open-ended VQA dataset of visual USMLE-style problems. Furthermore, we conduct the first human evaluation for generative medical VQA where physicians review the problems and blinded generations in an interactive app. Med-Flamingo improves performance in generative medical VQA by up to 20\% in clinician's rating and firstly enables multimodal medical few-shot adaptations, such as rationale generation. We release our model, code, and evaluation app under https://github.com/snap-stanford/med-flamingo.

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

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

The rapid advancement of language models has demonstrated the potential of artificial intelligence in the healthcare industry. However, small language models struggle with specialized domains in low-resource languages like Persian. While numerous medical-domain websites exist in Persian, no curated dataset or corpus has been available making ours the first of its kind. This study explores the enhancement of medical knowledge in a small language model by leveraging accessible online data, including a crawled corpus from medical magazines and a dataset of real doctor-patient QA pairs. We fine-tuned a baseline model using our curated data to improve its medical knowledge. Benchmark evaluations demonstrate that the fine-tuned model achieves improved accuracy in medical question answering and provides better responses compared to its baseline. This work highlights the potential of leveraging open-access online data to enrich small language models in medical fields, providing a novel solution for Persian medical AI applications suitable for resource-constrained environments.

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

The recent emergence of Medical Large Vision Language Models (Med-LVLMs) has enhanced medical diagnosis. However, current Med-LVLMs frequently encounter factual issues, often generating responses that do not align with established medical facts. Retrieval-Augmented Generation (RAG), which utilizes external knowledge, can improve the factual accuracy of these models but introduces two major challenges. First, limited retrieved contexts might not cover all necessary information, while excessive retrieval can introduce irrelevant and inaccurate references, interfering with the model's generation. Second, in cases where the model originally responds correctly, applying RAG can lead to an over-reliance on retrieved contexts, resulting in incorrect answers. To address these issues, we propose RULE, which consists of two components. First, we introduce a provably effective strategy for controlling factuality risk through the calibrated selection of the number of retrieved contexts. Second, based on samples where over-reliance on retrieved contexts led to errors, we curate a preference dataset to fine-tune the model, balancing its dependence on inherent knowledge and retrieved contexts for generation. We demonstrate the effectiveness of RULE on three medical VQA datasets, achieving an average improvement of 20.8% in factual accuracy. We publicly release our benchmark and code in https://github.com/richard-peng-xia/RULE.

Interactive medical questioning is essential in real-world clinical consultations, where physicians must actively gather information from patients. While medical Large Language Models (LLMs) have shown impressive capabilities in static medical question answering, they predominantly operate under a reactive paradigm: generating answers directly without seeking additional information, which risks incorrect diagnoses in such interactive settings. To address this limitation, we propose ProMed, a reinforcement learning (RL) framework that transitions medical LLMs toward a proactive paradigm, equipping them with the ability to ask clinically valuable questions before decision-making. At the core of ProMed is the Shapley Information Gain (SIG) reward, which quantifies the clinical utility of each question by combining the amount of newly acquired information with its contextual importance, estimated via Shapley values. We integrate SIG into a two-stage training pipeline: (1) SIG-Guided Model Initialization uses Monte Carlo Tree Search (MCTS) to construct high-reward interaction trajectories to supervise the model, and (2) SIG-Augmented Policy Optimization, which integrates SIG and enhances RL with a novel SIG-guided Reward Distribution Mechanism that assigns higher rewards to informative questions for targeted optimization. Extensive experiments on two newly curated partial-information medical benchmarks demonstrate that ProMed significantly outperforms state-of-the-art methods by an average of 6.29% and delivers a 54.45% gain over the reactive paradigm, while also generalizing robustly to out-of-domain cases.

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

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

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

Medical Visual Question Answering (MedVQA), which offers language responses to image-based medical inquiries, represents a challenging task and significant advancement in healthcare. It assists medical experts to swiftly interpret medical images, thereby enabling faster and more accurate diagnoses. However, the model interpretability and transparency of existing MedVQA solutions are often limited, posing challenges in understanding their decision-making processes. To address this issue, we devise a semi-automated annotation process to streamline data preparation and build new benchmark MedVQA datasets R-RAD, R-SLAKE and R-Path. These datasets provide intermediate medical decision-making rationales generated by multimodal large language models and human annotations for question-answering pairs in existing MedVQA datasets, i.e., VQA-RAD, SLAKE and PathVQA. Moreover, we design a novel framework, MedThink, which finetunes lightweight pretrained generative models by incorporating medical decision-making rationales. MedThink includes three distinct strategies to generate decision outcomes and corresponding rationales, thereby clearly showcasing the medical decision-making process during reasoning. Our comprehensive experiments show that our method achieves an accuracy of 83.5% on R-RAD, 86.3% on R-SLAKE and 87.2% on R-Path. These results significantly exceed those of existing state-of-the-art models with comparable parameters. Datasets and code will be released.

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

Large language models (LLMs) have recently become the leading source of answers for users' questions online. Despite their ability to offer eloquent answers, their accuracy and reliability can pose a significant challenge. This is especially true for sensitive domains such as biomedicine, where there is a higher need for factually correct answers. This paper introduces a biomedical retrieval-augmented generation (RAG) system designed to enhance the reliability of generated responses. The system is based on a fine-tuned LLM for the referenced question-answering, where retrieved relevant abstracts from PubMed are passed to LLM's context as input through a prompt. Its output is an answer based on PubMed abstracts, where each statement is referenced accordingly, allowing the users to verify the answer. Our retrieval system achieves an absolute improvement of 23% compared to the PubMed search engine. Based on the manual evaluation on a small sample, our fine-tuned LLM component achieves comparable results to GPT-4 Turbo in referencing relevant abstracts. We make the dataset used to fine-tune the models and the fine-tuned models based on Mistral-7B-instruct-v0.1 and v0.2 publicly available.

Large language models (LLMs) often fail to ask effective questions under uncertainty, making them unreliable in domains where proactive information-gathering is essential for decisionmaking. We present ALFA, a framework that improves LLM question-asking by (i) decomposing the notion of a "good" question into a set of theory-grounded attributes (e.g., clarity, relevance), (ii) controllably synthesizing attribute-specific question variations, and (iii) aligning models via preference-based optimization to explicitly learn to ask better questions along these fine-grained attributes. Focusing on clinical reasoning as a case study, we introduce the MediQ-AskDocs dataset, composed of 17k real-world clinical interactions augmented with 80k attribute-specific preference pairs of follow-up questions, as well as a novel expert-annotated interactive healthcare QA task to evaluate question-asking abilities. Models aligned with ALFA reduce diagnostic errors by 56.6% on MediQ-AskDocs compared to SOTA instruction-tuned LLMs, with a question-level win-rate of 64.4% and strong generalizability. Our findings suggest that explicitly guiding question-asking with structured, fine-grained attributes offers a scalable path to improve LLMs, especially in expert application domains.

Large Language Models (LLMs) have demonstrated remarkable success in diverse natural language processing (NLP) tasks in general domains. However, LLMs sometimes generate responses with the hallucination about medical facts due to limited domain knowledge. Such shortcomings pose potential risks in the utilization of LLMs within medical contexts. To address this challenge, we propose knowledge-tuning, which leverages structured medical knowledge bases for the LLMs to grasp domain knowledge efficiently and facilitate reliable response generation. We also release cMedKnowQA, a Chinese medical knowledge question-answering dataset constructed from medical knowledge bases to assess the medical knowledge proficiency of LLMs. Experimental results show that the LLMs which are knowledge-tuned with cMedKnowQA, can exhibit higher levels of accuracy in response generation compared with vanilla instruction-tuning and offer a new reliable way for the domain adaptation of LLMs.

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the BioASQ challenge, which involves biomedical semantic question-answering for Task 13b and biomedical question-answering for developing topics for the Synergy task. We deploy a selection of open-source large language models (LLMs) as retrieval-augmented generators to answer biomedical questions. Various models are used to process the questions. A majority voting system combines their output to determine the final answer for Yes/No questions, while for list and factoid type questions, the union of their answers in used. We evaluated 13 state-of-the-art open source LLMs, exploring all possible model combinations to contribute to the final answer, resulting in tailored LLM pipelines for each question type. Our findings provide valuable insight into which combinations of LLMs consistently produce superior results for specific question types. In the four rounds of the 2025 BioASQ challenge, our system achieved notable results: in the Synergy task, we secured 1st place for ideal answers and 2nd place for exact answers in round 2, as well as two shared 1st places for exact answers in round 3 and 4.

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

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.

Mental health remains a challenging problem all over the world, with issues like depression, anxiety becoming increasingly common. Large Language Models (LLMs) have seen a vast application in healthcare, specifically in answering medical questions. However, there is a lack of standard benchmarking datasets for question answering (QA) in mental health. Our work presents a novel multiple choice dataset, MHQA (Mental Health Question Answering), for benchmarking Language models (LMs). Previous mental health datasets have focused primarily on text classification into specific labels or disorders. MHQA, on the other hand, presents question-answering for mental health focused on four key domains: anxiety, depression, trauma, and obsessive/compulsive issues, with diverse question types, namely, factoid, diagnostic, prognostic, and preventive. We use PubMed abstracts as the primary source for QA. We develop a rigorous pipeline for LLM-based identification of information from abstracts based on various selection criteria and converting it into QA pairs. Further, valid QA pairs are extracted based on post-hoc validation criteria. Overall, our MHQA dataset consists of 2,475 expert-verified gold standard instances called MHQA-gold and ~56.1k pairs pseudo labeled using external medical references. We report F1 scores on different LLMs along with few-shot and supervised fine-tuning experiments, further discussing the insights for the scores.

Large language models (LLMs) have demonstrated impressive generative capabilities with the potential to innovate in medicine. However, the application of LLMs in real clinical settings remains challenging due to the lack of factual consistency in the generated content. In this work, we develop an augmented LLM framework, KG-Rank, which leverages a medical knowledge graph (KG) along with ranking and re-ranking techniques, to improve the factuality of long-form question answering (QA) in the medical domain. Specifically, when receiving a question, KG-Rank automatically identifies medical entities within the question and retrieves the related triples from the medical KG to gather factual information. Subsequently, KG-Rank innovatively applies multiple ranking techniques to refine the ordering of these triples, providing more relevant and precise information for LLM inference. To the best of our knowledge, KG-Rank is the first application of KG combined with ranking models in medical QA specifically for generating long answers. Evaluation on four selected medical QA datasets demonstrates that KG-Rank achieves an improvement of over 18% in ROUGE-L score. Additionally, we extend KG-Rank to open domains, including law, business, music, and history, where it realizes a 14% improvement in ROUGE-L score, indicating the effectiveness and great potential of KG-Rank.

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

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare seven public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting regime for medical question-answering (QA) tasks. For instance, across the tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 12.1% of cases, reach a (statistical) tie in 49.8% of cases, and are significantly worse than their base models in the remaining 38.2% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

With the rapid development of large language models (LLMs), assessing their performance on health-related inquiries has become increasingly essential. It is critical that these models provide accurate and trustworthy health information, as their application in real-world contexts--where misinformation can have serious consequences for individuals seeking medical advice and support--depends on their reliability. In this work, we present CHBench, the first comprehensive Chinese Health-related Benchmark designed to evaluate LLMs' capabilities in understanding physical and mental health across diverse scenarios. CHBench includes 6,493 entries related to mental health and 2,999 entries focused on physical health, covering a broad spectrum of topics. This dataset serves as a foundation for evaluating Chinese LLMs' capacity to comprehend and generate accurate health-related information. Our extensive evaluations of four popular Chinese LLMs demonstrate that there remains considerable room for improvement in their understanding of health-related information. The code is available at https://github.com/TracyGuo2001/CHBench.

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

Large reasoning models have recently made significant strides in mathematical and code reasoning, yet their success has not transferred smoothly to the medical domain. While multiple factors contribute to this disparity, a critical issue is the inadequate focus on the quality of intermediate reflection steps, which is particularly crucial in high-stakes medical scenarios. To address this challenge, we propose Med-REFL, a \textbf{Med}ical \textbf{R}easoning \textbf{E}nhancement via self-corrected \textbf{F}ine-grained ref\textbf{L}ection. Our method leverages a tree-of-thought approach to decompose medical questions into fine-grained reasoning paths, quantitatively evaluating each step and its subsequent reflections. These assessments enable automatic construction of direct preference optimization data, reducing reliance on expensive expert annotations while guiding models to identify and correct reasoning errors. Experimental results on the MedQA-USMLE benchmark demonstrate Med-REFL achieves consistent improvements, with average gains up to 4.11\%. Notably, it further boosts the state-of-the-art performance of 7B/8B models by an additional 4.13\%. Furthermore, Med-REFL exhibits strong generalization capabilities and robustness across several challenging medical question-answering datasets. Our work illustrates that prioritizing reflection quality leads to more accurate and trustworthy reasoning in medical AI applications. Checkpoints, code, and data can be found https://github.com/TianYin123/Med-REFL{here}.

Despite the impressive capabilities of Large Language Models (LLMs) in general medical domains, questions remain about their performance in diagnosing rare diseases. To answer this question, we aim to assess the diagnostic performance of LLMs in rare diseases, and explore methods to enhance their effectiveness in this area. In this work, we introduce a rare disease question-answering (ReDis-QA) dataset to evaluate the performance of LLMs in diagnosing rare diseases. Specifically, we collected 1360 high-quality question-answer pairs within the ReDis-QA dataset, covering 205 rare diseases. Additionally, we annotated meta-data for each question, facilitating the extraction of subsets specific to any given disease and its property. Based on the ReDis-QA dataset, we benchmarked several open-source LLMs, revealing that diagnosing rare diseases remains a significant challenge for these models. To facilitate retrieval augmentation generation for rare disease diagnosis, we collect the first rare diseases corpus (ReCOP), sourced from the National Organization for Rare Disorders (NORD) database. Specifically, we split the report of each rare disease into multiple chunks, each representing a different property of the disease, including their overview, symptoms, causes, effects, related disorders, diagnosis, and standard therapies. This structure ensures that the information within each chunk aligns consistently with a question. Experiment results demonstrate that ReCOP can effectively improve the accuracy of LLMs on the ReDis-QA dataset by an average of 8%. Moreover, it significantly guides LLMs to generate trustworthy answers and explanations that can be traced back to existing literature.

Large Multimodal Models (LMMs) have shown remarkable progress in the field of medical Visual Question Answering (Med-VQA), achieving high accuracy on existing benchmarks. However, their reliability under robust evaluation is questionable. This study reveals that state-of-the-art models, when subjected to simple probing evaluation, perform worse than random guessing on medical diagnosis questions. To address this critical evaluation problem, we introduce the Probing Evaluation for Medical Diagnosis (ProbMed) dataset to rigorously assess LMM performance in medical imaging through probing evaluation and procedural diagnosis. Particularly, probing evaluation features pairing original questions with negation questions with hallucinated attributes, while procedural diagnosis requires reasoning across various diagnostic dimensions for each image, including modality recognition, organ identification, clinical findings, abnormalities, and positional grounding. Our evaluation reveals that top-performing models like GPT-4V and Gemini Pro perform worse than random guessing on specialized diagnostic questions, indicating significant limitations in handling fine-grained medical inquiries. Besides, models like LLaVA-Med struggle even with more general questions, and results from CheXagent demonstrate the transferability of expertise across different modalities of the same organ, showing that specialized domain knowledge is still crucial for improving performance. This study underscores the urgent need for more robust evaluation to ensure the reliability of LMMs in critical fields like medical diagnosis, and current LMMs are still far from applicable to those fields.

Recently, Large Language Models (LLMs) have showcased remarkable capabilities in natural language understanding. While demonstrating proficiency in everyday conversations and question-answering situations, these models frequently struggle in domains that require precision, such as medical applications, due to their lack of domain-specific knowledge. In this paper, we describe the procedure for building a powerful, open-source language model specifically designed for medicine applications, termed as PMC-LLaMA. Our contributions are threefold: (i) we systematically investigate the process of adapting a general-purpose foundation language model towards medical domain, this involves data-centric knowledge injection through the integration of 4.8M biomedical academic papers and 30K medical textbooks, as well as comprehensive fine-tuning for alignment with domain-specific instructions; (ii) we contribute a large-scale, comprehensive dataset for instruction tuning. This dataset encompasses medical question-answering (QA), rationale for reasoning, and conversational dialogues, comprising a total of 202M tokens; (iii) we conduct thorough ablation studies to demonstrate the effectiveness of each proposed component. While evaluating on various public medical question-answering benchmarks, our lightweight PMCLLaMA, which consists of only 13 billion parameters, exhibits superior performance, even surpassing ChatGPT. All models, codes, datasets can be found in https://github.com/chaoyi-wu/PMC-LLaMA.

Large language models (LLMs) have performed well in providing general and extensive health suggestions in single-turn conversations, exemplified by systems such as ChatGPT, ChatGLM, ChatDoctor, DoctorGLM, and etc. However, the limited information provided by users during single turn results in inadequate personalization and targeting of the generated suggestions, which requires users to independently select the useful part. It is mainly caused by the missing ability to engage in multi-turn questioning. In real-world medical consultations, doctors usually employ a series of iterative inquiries to comprehend the patient's condition thoroughly, enabling them to provide effective and personalized suggestions subsequently, which can be defined as chain of questioning (CoQ) for LLMs. To improve the CoQ of LLMs, we propose BianQue, a ChatGLM-based LLM finetuned with the self-constructed health conversation dataset BianQueCorpus that is consist of multiple turns of questioning and health suggestions polished by ChatGPT. Experimental results demonstrate that the proposed BianQue can simultaneously balance the capabilities of both questioning and health suggestions, which will help promote the research and application of LLMs in the field of proactive health.

There is increasing interest in the application large language models (LLMs) to the medical field, in part because of their impressive performance on medical exam questions. While promising, exam questions do not reflect the complexity of real patient-doctor interactions. In reality, physicians' decisions are shaped by many complex factors, such as patient compliance, personal experience, ethical beliefs, and cognitive bias. Taking a step toward understanding this, our hypothesis posits that when LLMs are confronted with clinical questions containing cognitive biases, they will yield significantly less accurate responses compared to the same questions presented without such biases. In this study, we developed BiasMedQA, a benchmark for evaluating cognitive biases in LLMs applied to medical tasks. Using BiasMedQA we evaluated six LLMs, namely GPT-4, Mixtral-8x70B, GPT-3.5, PaLM-2, Llama 2 70B-chat, and the medically specialized PMC Llama 13B. We tested these models on 1,273 questions from the US Medical Licensing Exam (USMLE) Steps 1, 2, and 3, modified to replicate common clinically-relevant cognitive biases. Our analysis revealed varying effects for biases on these LLMs, with GPT-4 standing out for its resilience to bias, in contrast to Llama 2 70B-chat and PMC Llama 13B, which were disproportionately affected by cognitive bias. Our findings highlight the critical need for bias mitigation in the development of medical LLMs, pointing towards safer and more reliable applications in healthcare.

Medical benchmark datasets significantly contribute to developing Large Language Models (LLMs) for medical knowledge extraction, diagnosis, summarization, and other uses. Yet, current benchmarks are mainly derived from exam questions given to medical students or cases described in the medical literature, lacking the complexity of real-world patient cases that deviate from classic textbook abstractions. These include rare diseases, uncommon presentations of common diseases, and unexpected treatment responses. Here, we construct Clinically Uncommon Patient Cases and Diagnosis Dataset (CUPCase) based on 3,562 real-world case reports from BMC, including diagnoses in open-ended textual format and as multiple-choice options with distractors. Using this dataset, we evaluate the ability of state-of-the-art LLMs, including both general-purpose and Clinical LLMs, to identify and correctly diagnose a patient case, and test models' performance when only partial information about cases is available. Our findings show that general-purpose GPT-4o attains the best performance in both the multiple-choice task (average accuracy of 87.9%) and the open-ended task (BERTScore F1 of 0.764), outperforming several LLMs with a focus on the medical domain such as Meditron-70B and MedLM-Large. Moreover, GPT-4o was able to maintain 87% and 88% of its performance with only the first 20% of tokens of the case presentation in multiple-choice and free text, respectively, highlighting the potential of LLMs to aid in early diagnosis in real-world cases. CUPCase expands our ability to evaluate LLMs for clinical decision support in an open and reproducible manner.

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.

Large-scale language models (LLMs), such as ChatGPT, are capable of generating human-like responses for various downstream tasks, such as task-oriented dialogues and question answering. However, applying LLMs to medical domains remains challenging due to their inability to leverage domain-specific knowledge. In this study, we present the Large-scale Language Models Augmented with Medical Textbooks (LLM-AMT), which integrates authoritative medical textbooks as the cornerstone of its design, enhancing its proficiency in the specialized domain through plug-and-play modules, comprised of a Hybrid Textbook Retriever, supplemented by the Query Augmenter and the LLM Reader. Experimental evaluation on three open-domain medical question-answering tasks reveals a substantial enhancement in both the professionalism and accuracy of the LLM responses when utilizing LLM-AMT, exhibiting an improvement ranging from 11.4% to 13.2%. Despite being 100 times smaller, we found that medical textbooks as the retrieval corpus serves as a more valuable external knowledge source than Wikipedia in the medical domain. Our experiments show that textbook augmentation results in a performance improvement ranging from 9.7% to 12.2% over Wikipedia augmentation.

This study presents a comprehensive analysis and comparison of two predominant fine-tuning methodologies - full-parameter fine-tuning and parameter-efficient tuning - within the context of medical Large Language Models (LLMs). We developed and refined a series of LLMs, based on the Llama-2 architecture, specifically designed to enhance medical knowledge retrieval, reasoning, and question-answering capabilities. Our experiments systematically evaluate the effectiveness of these tuning strategies across various well-known medical benchmarks. Notably, our medical LLM Med42 showed an accuracy level of 72% on the US Medical Licensing Examination (USMLE) datasets, setting a new standard in performance for openly available medical LLMs. Through this comparative analysis, we aim to identify the most effective and efficient method for fine-tuning LLMs in the medical domain, thereby contributing significantly to the advancement of AI-driven healthcare applications.

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

Current ophthalmology clinical workflows are plagued by over-referrals, long waits, and complex and heterogeneous medical records. Large language models (LLMs) present a promising solution to automate various procedures such as triaging, preliminary tests like visual acuity assessment, and report summaries. However, LLMs have demonstrated significantly varied performance across different languages in natural language question-answering tasks, potentially exacerbating healthcare disparities in Low and Middle-Income Countries (LMICs). This study introduces the first multilingual ophthalmological question-answering benchmark with manually curated questions parallel across languages, allowing for direct cross-lingual comparisons. Our evaluation of 6 popular LLMs across 7 different languages reveals substantial bias across different languages, highlighting risks for clinical deployment of LLMs in LMICs. Existing debiasing methods such as Translation Chain-of-Thought or Retrieval-augmented generation (RAG) by themselves fall short of closing this performance gap, often failing to improve performance across all languages and lacking specificity for the medical domain. To address this issue, We propose CLARA (Cross-Lingual Reflective Agentic system), a novel inference time de-biasing method leveraging retrieval augmented generation and self-verification. Our approach not only improves performance across all languages but also significantly reduces the multilingual bias gap, facilitating equitable LLM application across the globe.