Daily Papers

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.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

LLMs have become increasingly capable at accomplishing a range of specialized-tasks and can be utilized to expand equitable access to medical knowledge. Most medical LLMs have involved extensive fine-tuning, leveraging specialized medical data and significant, thus costly, amounts of computational power. Many of the top performing LLMs are proprietary and their access is limited to very few research groups. However, open-source (OS) models represent a key area of growth for medical LLMs due to significant improvements in performance and an inherent ability to provide the transparency and compliance required in healthcare. We present OpenMedLM, a prompting platform which delivers state-of-the-art (SOTA) performance for OS LLMs on medical benchmarks. We evaluated a range of OS foundation LLMs (7B-70B) on four medical benchmarks (MedQA, MedMCQA, PubMedQA, MMLU medical-subset). We employed a series of prompting strategies, including zero-shot, few-shot, chain-of-thought (random selection and kNN selection), and ensemble/self-consistency voting. We found that OpenMedLM delivers OS SOTA results on three common medical LLM benchmarks, surpassing the previous best performing OS models that leveraged computationally costly extensive fine-tuning. The model delivers a 72.6% accuracy on the MedQA benchmark, outperforming the previous SOTA by 2.4%, and achieves 81.7% accuracy on the MMLU medical-subset, establishing itself as the first OS LLM to surpass 80% accuracy on this benchmark. Our results highlight medical-specific emergent properties in OS LLMs which have not yet been documented to date elsewhere, and showcase the benefits of further leveraging prompt engineering to improve the performance of accessible LLMs for medical applications.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

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.

In response to the pressing need for advanced clinical problem-solving tools in healthcare, we introduce BooksMed, a novel framework based on a Large Language Model (LLM). BooksMed uniquely emulates human cognitive processes to deliver evidence-based and reliable responses, utilizing the GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) framework to effectively quantify evidence strength. For clinical decision-making to be appropriately assessed, an evaluation metric that is clinically aligned and validated is required. As a solution, we present ExpertMedQA, a multispecialty clinical benchmark comprised of open-ended, expert-level clinical questions, and validated by a diverse group of medical professionals. By demanding an in-depth understanding and critical appraisal of up-to-date clinical literature, ExpertMedQA rigorously evaluates LLM performance. BooksMed outperforms existing state-of-the-art models Med-PaLM 2, Almanac, and ChatGPT in a variety of medical scenarios. Therefore, a framework that mimics human cognitive stages could be a useful tool for providing reliable and evidence-based responses to clinical inquiries.

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

Open domain question answering (OpenQA) tasks have been recently attracting more and more attention from the natural language processing (NLP) community. In this work, we present the first free-form multiple-choice OpenQA dataset for solving medical problems, MedQA, collected from the professional medical board exams. It covers three languages: English, simplified Chinese, and traditional Chinese, and contains 12,723, 34,251, and 14,123 questions for the three languages, respectively. We implement both rule-based and popular neural methods by sequentially combining a document retriever and a machine comprehension model. Through experiments, we find that even the current best method can only achieve 36.7\%, 42.0\%, and 70.1\% of test accuracy on the English, traditional Chinese, and simplified Chinese questions, respectively. We expect MedQA to present great challenges to existing OpenQA systems and hope that it can serve as a platform to promote much stronger OpenQA models from the NLP community in the future.

A pre-trained visual-language model, contrastive language-image pre-training (CLIP), successfully accomplishes various downstream tasks with text prompts, such as finding images or localizing regions within the image. Despite CLIP's strong multi-modal data capabilities, it remains limited in specialized environments, such as medical applications. For this purpose, many CLIP variants-i.e., BioMedCLIP, and MedCLIP-SAMv2-have emerged, but false positives related to normal regions persist. Thus, we aim to present a simple yet important goal of reducing false positives in medical anomaly detection. We introduce a Contrastive LAnguage Prompting (CLAP) method that leverages both positive and negative text prompts. This straightforward approach identifies potential lesion regions by visual attention to the positive prompts in the given image. To reduce false positives, we attenuate attention on normal regions using negative prompts. Extensive experiments with the BMAD dataset, including six biomedical benchmarks, demonstrate that CLAP method enhances anomaly detection performance. Our future plans include developing an automated fine prompting method for more practical usage.

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.

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.

In natural language processing applied to the clinical domain, utilizing large language models has emerged as a promising avenue for error detection and correction on clinical notes, a knowledge-intensive task for which annotated data is scarce. This paper presents MedReAct'N'MedReFlex, which leverages a suite of four LLM-based medical agents. The MedReAct agent initiates the process by observing, analyzing, and taking action, generating trajectories to guide the search to target a potential error in the clinical notes. Subsequently, the MedEval agent employs five evaluators to assess the targeted error and the proposed correction. In cases where MedReAct's actions prove insufficient, the MedReFlex agent intervenes, engaging in reflective analysis and proposing alternative strategies. Finally, the MedFinalParser agent formats the final output, preserving the original style while ensuring the integrity of the error correction process. One core component of our method is our RAG pipeline based on our ClinicalCorp corpora. Among other well-known sources containing clinical guidelines and information, we preprocess and release the open-source MedWiki dataset for clinical RAG application. Our results demonstrate the central role of our RAG approach with ClinicalCorp leveraged through the MedReAct'N'MedReFlex framework. It achieved the ninth rank on the MEDIQA-CORR 2024 final leaderboard.

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.

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.

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

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

The rapid development of multimodal large language models (MLLMs), such as GPT-4V, has led to significant advancements. However, these models still face challenges in medical multimodal capabilities due to limitations in the quantity and quality of medical vision-text data, stemming from data privacy concerns and high annotation costs. While pioneering approaches utilize PubMed's large-scale, de-identified medical image-text pairs to address these limitations, they still fall short due to inherent data noise. To tackle this, we refined medical image-text pairs from PubMed and employed MLLMs (GPT-4V) in an 'unblinded' capacity to denoise and reformat the data, resulting in the creation of the PubMedVision dataset with 1.3 million medical VQA samples. Our validation demonstrates that: (1) PubMedVision can significantly enhance the medical multimodal capabilities of current MLLMs, showing significant improvement in benchmarks including the MMMU Health & Medicine track; (2) manual checks by medical experts and empirical results validate the superior data quality of our dataset compared to other data construction methods. Using PubMedVision, we train a 34B medical MLLM HuatuoGPT-Vision, which shows superior performance in medical multimodal scenarios among open-source MLLMs.

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.

The past year has seen rapid acceleration in the development of large language models (LLMs). However, without proper steering and safeguards, LLMs will readily follow malicious instructions, provide unsafe advice, and generate toxic content. We introduce SimpleSafetyTests (SST) as a new test suite for rapidly and systematically identifying such critical safety risks. The test suite comprises 100 test prompts across five harm areas that LLMs, for the vast majority of applications, should refuse to comply with. We test 11 open-access and open-source LLMs and four closed-source LLMs, and find critical safety weaknesses. While some of the models do not give a single unsafe response, most give unsafe responses to more than 20% of the prompts, with over 50% unsafe responses in the extreme. Prepending a safety-emphasising system prompt substantially reduces the occurrence of unsafe responses, but does not completely stop them from happening. Trained annotators labelled every model response to SST (n = 3,000). We use these annotations to evaluate five AI safety filters (which assess whether a models' response is unsafe given a prompt) as a way of automatically evaluating models' performance on SST. The filters' performance varies considerably. There are also differences across the five harm areas, and on the unsafe versus safe responses. The widely-used Perspective API has 72% accuracy and a newly-created zero-shot prompt to OpenAI's GPT-4 performs best with 89% accuracy. Content Warning: This paper contains prompts and responses that relate to child abuse, suicide, self-harm and eating disorders, scams and fraud, illegal items, and physical harm.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety.

Although large language models (LLMs) often produce impressive outputs, it remains unclear how they perform in real-world scenarios requiring strong reasoning skills and expert domain knowledge. We set out to investigate whether close- and open-source models (GPT-3.5, LLama-2, etc.) can be applied to answer and reason about difficult real-world-based questions. We focus on three popular medical benchmarks (MedQA-USMLE, MedMCQA, and PubMedQA) and multiple prompting scenarios: Chain-of-Thought (CoT, think step-by-step), few-shot and retrieval augmentation. Based on an expert annotation of the generated CoTs, we found that InstructGPT can often read, reason and recall expert knowledge. Last, by leveraging advances in prompt engineering (few-shot and ensemble methods), we demonstrated that GPT-3.5 not only yields calibrated predictive distributions, but also reaches the passing score on three datasets: MedQA-USMLE 60.2%, MedMCQA 62.7% and PubMedQA 78.2%. Open-source models are closing the gap: Llama-2 70B also passed the MedQA-USMLE with 62.5% accuracy.

Foundation models trained on large-scale dataset gain a recent surge in CV and NLP. In contrast, development in biomedical domain lags far behind due to data scarcity. To address this issue, we build and release PMC-OA, a biomedical dataset with 1.6M image-caption pairs collected from PubMedCentral's OpenAccess subset, which is 8 times larger than before. PMC-OA covers diverse modalities or diseases, with majority of the image-caption samples aligned at finer-grained level, i.e., subfigure and subcaption. While pretraining a CLIP-style model on PMC-OA, our model named PMC-CLIP achieves state-of-the-art results on various downstream tasks, including image-text retrieval on ROCO, MedMNIST image classification, Medical VQA, i.e. +8.1% R@10 on image-text retrieval, +3.9% accuracy on image classification.

Large language models have the potential to be valuable in the healthcare industry, but it's crucial to verify their safety and effectiveness through rigorous evaluation. For this purpose, we comprehensively evaluated both open-source LLMs and Google's new multimodal LLM called Gemini across Medical reasoning, hallucination detection, and Medical Visual Question Answering tasks. While Gemini showed competence, it lagged behind state-of-the-art models like MedPaLM 2 and GPT-4 in diagnostic accuracy. Additionally, Gemini achieved an accuracy of 61.45\% on the medical VQA dataset, significantly lower than GPT-4V's score of 88\%. Our analysis revealed that Gemini is highly susceptible to hallucinations, overconfidence, and knowledge gaps, which indicate risks if deployed uncritically. We also performed a detailed analysis by medical subject and test type, providing actionable feedback for developers and clinicians. To mitigate risks, we applied prompting strategies that improved performance. Additionally, we facilitated future research and development by releasing a Python module for medical LLM evaluation and establishing a dedicated leaderboard on Hugging Face for medical domain LLMs. Python module can be found at https://github.com/promptslab/RosettaEval

The COVID-19 pandemic presents global challenges transcending boundaries of country, race, religion, and economy. The current gold standard method for COVID-19 detection is the reverse transcription polymerase chain reaction (RT-PCR) testing. However, this method is expensive, time-consuming, and violates social distancing. Also, as the pandemic is expected to stay for a while, there is a need for an alternate diagnosis tool which overcomes these limitations, and is deployable at a large scale. The prominent symptoms of COVID-19 include cough and breathing difficulties. We foresee that respiratory sounds, when analyzed using machine learning techniques, can provide useful insights, enabling the design of a diagnostic tool. Towards this, the paper presents an early effort in creating (and analyzing) a database, called Coswara, of respiratory sounds, namely, cough, breath, and voice. The sound samples are collected via worldwide crowdsourcing using a website application. The curated dataset is released as open access. As the pandemic is evolving, the data collection and analysis is a work in progress. We believe that insights from analysis of Coswara can be effective in enabling sound based technology solutions for point-of-care diagnosis of respiratory infection, and in the near future this can help to diagnose COVID-19.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Contrastive Language--Image Pre-training (CLIP) has shown remarkable success in learning with cross-modal supervision from extensive amounts of image--text pairs collected online. Thus far, the effectiveness of CLIP has been investigated primarily in general-domain multimodal problems. This work evaluates the effectiveness of CLIP for the task of Medical Visual Question Answering (MedVQA). To this end, we present PubMedCLIP, a fine-tuned version of CLIP for the medical domain based on PubMed articles. Our experiments are conducted on two MedVQA benchmark datasets and investigate two MedVQA methods, MEVF (Mixture of Enhanced Visual Features) and QCR (Question answering via Conditional Reasoning). For each of these, we assess the merits of visual representation learning using PubMedCLIP, the original CLIP, and state-of-the-art MAML (Model-Agnostic Meta-Learning) networks pre-trained only on visual data. We open source the code for our MedVQA pipeline and pre-training PubMedCLIP. CLIP and PubMedCLIP achieve improvements in comparison to MAML's visual encoder. PubMedCLIP achieves the best results with gains in the overall accuracy of up to 3%. Individual examples illustrate the strengths of PubMedCLIP in comparison to the previously widely used MAML networks. Visual representation learning with language supervision in PubMedCLIP leads to noticeable improvements for MedVQA. Our experiments reveal distributional differences in the two MedVQA benchmark datasets that have not been imparted in previous work and cause different back-end visual encoders in PubMedCLIP to exhibit different behavior on these datasets. Moreover, we witness fundamental performance differences of VQA in general versus medical domains.

Citations in scientific papers not only help us trace the intellectual lineage but also are a useful indicator of the scientific significance of the work. Citation intents prove beneficial as they specify the role of the citation in a given context. In this paper, we present CitePrompt, a framework which uses the hitherto unexplored approach of prompt-based learning for citation intent classification. We argue that with the proper choice of the pretrained language model, the prompt template, and the prompt verbalizer, we can not only get results that are better than or comparable to those obtained with the state-of-the-art methods but also do it with much less exterior information about the scientific document. We report state-of-the-art results on the ACL-ARC dataset, and also show significant improvement on the SciCite dataset over all baseline models except one. As suitably large labelled datasets for citation intent classification can be quite hard to find, in a first, we propose the conversion of this task to the few-shot and zero-shot settings. For the ACL-ARC dataset, we report a 53.86% F1 score for the zero-shot setting, which improves to 63.61% and 66.99% for the 5-shot and 10-shot settings, respectively.

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

This paper presents our team's participation in the MEDIQA-ClinicalNLP2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show its superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the potential of advanced clinical trial tools that aggregate and predict based on the latest medical data, we propose an integrated solution to enhance their accessibility and utility. We introduce Clinical Agent System (ClinicalAgent), a clinical multi-agent system designed for clinical trial tasks, leveraging GPT-4, multi-agent architectures, LEAST-TO-MOST, and ReAct reasoning technology. This integration not only boosts LLM performance in clinical contexts but also introduces novel functionalities. The proposed method achieves competitive predictive performance in clinical trial outcome prediction (0.7908 PR-AUC), obtaining a 0.3326 improvement over the standard prompt Method. Publicly available code can be found at https://anonymous.4open.science/r/ClinicalAgent-6671.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

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.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

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 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.

The emergence of text-to-image synthesis (TIS) models has significantly influenced digital image creation by producing high-quality visuals from written descriptions. Yet these models heavily rely on the quality and specificity of textual prompts, posing a challenge for novice users who may not be familiar with TIS-model-preferred prompt writing. Existing solutions relieve this via automatic model-preferred prompt generation from user queries. However, this single-turn manner suffers from limited user-centricity in terms of result interpretability and user interactivity. To address these issues, we propose DialPrompt, a multi-turn dialogue-based TIS prompt generation model that emphasises user-centricity. DialPrompt is designed to follow a multi-turn guidance workflow, where in each round of dialogue the model queries user with their preferences on possible optimization dimensions before generating the final TIS prompt. To achieve this, we mined 15 essential dimensions for high-quality prompts from advanced users and curated a multi-turn dataset. Through training on this dataset, DialPrompt can improve interpretability by allowing users to understand the correlation between specific phrases and image attributes. Additionally, it enables greater user control and engagement in the prompt generation process, leading to more personalized and visually satisfying outputs. Experiments indicate that DialPrompt achieves a competitive result in the quality of synthesized images, outperforming existing prompt engineering approaches by 5.7%. Furthermore, in our user evaluation, DialPrompt outperforms existing approaches by 46.5% in user-centricity score and is rated 7.9/10 by 19 human reviewers.

Large language models (LLMs) hold great promise in summarizing medical evidence. Most recent studies focus on the application of proprietary LLMs. Using proprietary LLMs introduces multiple risk factors, including a lack of transparency and vendor dependency. While open-source LLMs allow better transparency and customization, their performance falls short compared to proprietary ones. In this study, we investigated to what extent fine-tuning open-source LLMs can further improve their performance in summarizing medical evidence. Utilizing a benchmark dataset, MedReview, consisting of 8,161 pairs of systematic reviews and summaries, we fine-tuned three broadly-used, open-sourced LLMs, namely PRIMERA, LongT5, and Llama-2. Overall, the fine-tuned LLMs obtained an increase of 9.89 in ROUGE-L (95% confidence interval: 8.94-10.81), 13.21 in METEOR score (95% confidence interval: 12.05-14.37), and 15.82 in CHRF score (95% confidence interval: 13.89-16.44). The performance of fine-tuned LongT5 is close to GPT-3.5 with zero-shot settings. Furthermore, smaller fine-tuned models sometimes even demonstrated superior performance compared to larger zero-shot models. The above trends of improvement were also manifested in both human and GPT4-simulated evaluations. Our results can be applied to guide model selection for tasks demanding particular domain knowledge, such as medical evidence summarization.

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.

Large language models (LLMs) have displayed an impressive ability to harness natural language to perform complex tasks. In this work, we explore whether we can leverage this learned ability to find and explain patterns in data. Specifically, given a pre-trained LLM and data examples, we introduce interpretable autoprompting (iPrompt), an algorithm that generates a natural-language string explaining the data. iPrompt iteratively alternates between generating explanations with an LLM and reranking them based on their performance when used as a prompt. Experiments on a wide range of datasets, from synthetic mathematics to natural-language understanding, show that iPrompt can yield meaningful insights by accurately finding groundtruth dataset descriptions. Moreover, the prompts produced by iPrompt are simultaneously human-interpretable and highly effective for generalization: on real-world sentiment classification datasets, iPrompt produces prompts that match or even improve upon human-written prompts for GPT-3. Finally, experiments with an fMRI dataset show the potential for iPrompt to aid in scientific discovery. All code for using the methods and data here is made available on Github.

The primary goal of drug safety researchers and regulators is to promptly identify adverse drug reactions. Doing so may in turn prevent or reduce the harm to patients and ultimately improve public health. Evaluating and monitoring drug safety (i.e., pharmacovigilance) involves analyzing an ever growing collection of spontaneous reports from health professionals, physicians, and pharmacists, and information voluntarily submitted by patients. In this scenario, facilitating analysis of such reports via automation has the potential to rapidly identify safety signals. Unfortunately, public resources for developing natural language models for this task are scant. We present PHEE, a novel dataset for pharmacovigilance comprising over 5000 annotated events from medical case reports and biomedical literature, making it the largest such public dataset to date. We describe the hierarchical event schema designed to provide coarse and fine-grained information about patients' demographics, treatments and (side) effects. Along with the discussion of the dataset, we present a thorough experimental evaluation of current state-of-the-art approaches for biomedical event extraction, point out their limitations, and highlight open challenges to foster future research in this area.

As the capabilities of Large Language Models (LLMs) in healthcare and medicine continue to advance, there is a growing need for competitive open-source models that can safeguard public interest. With the increasing availability of highly competitive open base models, the impact of continued pre-training is increasingly uncertain. In this work, we explore the role of instruct tuning, model merging, alignment, red teaming and advanced inference schemes, as means to improve current open models. To that end, we introduce the Aloe family, a set of open medical LLMs highly competitive within its scale range. Aloe models are trained on the current best base models (Mistral, LLaMA 3), using a new custom dataset which combines public data sources improved with synthetic Chain of Thought (CoT). Aloe models undergo an alignment phase, becoming one of the first few policy-aligned open healthcare LLM using Direct Preference Optimization, setting a new standard for ethical performance in healthcare LLMs. Model evaluation expands to include various bias and toxicity datasets, a dedicated red teaming effort, and a much-needed risk assessment for healthcare LLMs. Finally, to explore the limits of current LLMs in inference, we study several advanced prompt engineering strategies to boost performance across benchmarks, yielding state-of-the-art results for open healthcare 7B LLMs, unprecedented at this scale.

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.

Coronavirus disease 2019 (Covid-19) is highly contagious with limited treatment options. Early and accurate diagnosis of Covid-19 is crucial in reducing the spread of the disease and its accompanied mortality. Currently, detection by reverse transcriptase polymerase chain reaction (RT-PCR) is the gold standard of outpatient and inpatient detection of Covid-19. RT-PCR is a rapid method, however, its accuracy in detection is only ~70-75%. Another approved strategy is computed tomography (CT) imaging. CT imaging has a much higher sensitivity of ~80-98%, but similar accuracy of 70%. To enhance the accuracy of CT imaging detection, we developed an open-source set of algorithms called CovidCTNet that successfully differentiates Covid-19 from community-acquired pneumonia (CAP) and other lung diseases. CovidCTNet increases the accuracy of CT imaging detection to 90% compared to radiologists (70%). The model is designed to work with heterogeneous and small sample sizes independent of the CT imaging hardware. In order to facilitate the detection of Covid-19 globally and assist radiologists and physicians in the screening process, we are releasing all algorithms and parametric details in an open-source format. Open-source sharing of our CovidCTNet enables developers to rapidly improve and optimize services, while preserving user privacy and data ownership.

Security concerns related to Large Language Models (LLMs) have been extensively explored, yet the safety implications for Multimodal Large Language Models (MLLMs), particularly in medical contexts (MedMLLMs), remain insufficiently studied. This paper delves into the underexplored security vulnerabilities of MedMLLMs, especially when deployed in clinical environments where the accuracy and relevance of question-and-answer interactions are critically tested against complex medical challenges. By combining existing clinical medical data with atypical natural phenomena, we redefine two types of attacks: mismatched malicious attack (2M-attack) and optimized mismatched malicious attack (O2M-attack). Using our own constructed voluminous 3MAD dataset, which covers a wide range of medical image modalities and harmful medical scenarios, we conduct a comprehensive analysis and propose the MCM optimization method, which significantly enhances the attack success rate on MedMLLMs. Evaluations with this dataset and novel attack methods, including white-box attacks on LLaVA-Med and transfer attacks on four other state-of-the-art models, indicate that even MedMLLMs designed with enhanced security features are vulnerable to security breaches. Our work underscores the urgent need for a concerted effort to implement robust security measures and enhance the safety and efficacy of open-source MedMLLMs, particularly given the potential severity of jailbreak attacks and other malicious or clinically significant exploits in medical settings. For further research and replication, anonymous access to our code is available at https://github.com/dirtycomputer/O2M_attack. Warning: Medical large model jailbreaking may generate content that includes unverified diagnoses and treatment recommendations. Always consult professional medical advice.

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.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Medical vision-and-language pre-training (Med-VLP) has shown promising improvements on many downstream medical tasks owing to its applicability to extracting generic representations from medical images and texts. Practically, there exist two typical types, i.e., the fusion-encoder type and the dual-encoder type, depending on whether a heavy fusion module is used. The former is superior at multi-modal tasks owing to the sufficient interaction between modalities; the latter is good at uni-modal and cross-modal tasks due to the single-modality encoding ability. To take advantage of these two types, we propose an effective yet straightforward scheme named PTUnifier to unify the two types. We first unify the input format by introducing visual and textual prompts, which serve as a feature bank that stores the most representative images/texts. By doing so, a single model could serve as a foundation model that processes various tasks adopting different input formats (i.e., image-only, text-only, and image-text-pair). Furthermore, we construct a prompt pool (instead of static ones) to improve diversity and scalability. Experimental results show that our approach achieves state-of-the-art results on a broad range of tasks, spanning uni-modal tasks (i.e., image/text classification and text summarization), cross-modal tasks (i.e., image-to-text generation and image-text/text-image retrieval), and multi-modal tasks (i.e., visual question answering), demonstrating the effectiveness of our approach. Note that the adoption of prompts is orthogonal to most existing Med-VLP approaches and could be a beneficial and complementary extension to these approaches.

COVID-19 (coronavirus disease 2019) pandemic caused by SARS-CoV-2 has led to a treacherous and devastating catastrophe for humanity. At the time of writing, no specific antivirus drugs or vaccines are recommended to control infection transmission and spread. The current diagnosis of COVID-19 is done by Reverse-Transcription Polymer Chain Reaction (RT-PCR) testing. However, this method is expensive, time-consuming, and not easily available in straitened regions. An interpretable and COVID-19 diagnosis AI framework is devised and developed based on the cough sounds features and symptoms metadata to overcome these limitations. The proposed framework's performance was evaluated using a medical dataset containing Symptoms and Demographic data of 30000 audio segments, 328 cough sounds from 150 patients with four cough classes ( COVID-19, Asthma, Bronchitis, and Healthy). Experiments' results show that the model captures the better and robust feature embedding to distinguish between COVID-19 patient coughs and several types of non-COVID-19 coughs with higher specificity and accuracy of 95.04 pm 0.18% and 96.83pm 0.18% respectively, all the while maintaining interpretability.

Multimodal Large Language Models (MLLMs) have tremendous potential to improve the accuracy, availability, and cost-effectiveness of healthcare by providing automated solutions or serving as aids to medical professionals. Despite promising first steps in developing medical MLLMs in the past few years, their capabilities and limitations are not well-understood. Recently, many benchmark datasets have been proposed that test the general medical knowledge of such models across a variety of medical areas. However, the systematic failure modes and vulnerabilities of such models are severely underexplored with most medical benchmarks failing to expose the shortcomings of existing models in this safety-critical domain. In this paper, we introduce MediConfusion, a challenging medical Visual Question Answering (VQA) benchmark dataset, that probes the failure modes of medical MLLMs from a vision perspective. We reveal that state-of-the-art models are easily confused by image pairs that are otherwise visually dissimilar and clearly distinct for medical experts. Strikingly, all available models (open-source or proprietary) achieve performance below random guessing on MediConfusion, raising serious concerns about the reliability of existing medical MLLMs for healthcare deployment. We also extract common patterns of model failure that may help the design of a new generation of more trustworthy and reliable MLLMs in healthcare.

Customer product reviews play a role in improving the quality of products and services for business organizations or their brands. Complaining is an attitude that expresses dissatisfaction with an event or a product not meeting customer expectations. In this paper, we build a Open-domain Complaint Detection dataset (UIT-ViOCD), including 5,485 human-annotated reviews on four categories about product reviews on e-commerce sites. After the data collection phase, we proceed to the annotation task and achieve the inter-annotator agreement Am of 87%. Then, we present an extensive methodology for the research purposes and achieve 92.16% by F1-score for identifying complaints. With the results, in the future, we aim to build a system for open-domain complaint detection in E-commerce websites.

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.

As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields. In medicine, these LLMs hold considerable promise for improving medical workflows, diagnostics, patient care, and education. Yet, there is an urgent need for open-source models that can be deployed on-premises to safeguard patient privacy. In our work, we present an innovative dataset consisting of over 160,000 entries, specifically crafted to fine-tune LLMs for effective medical applications. We investigate the impact of fine-tuning these datasets on publicly accessible pre-trained LLMs, and subsequently, we juxtapose the performance of pre-trained-only models against the fine-tuned models concerning the examinations that future medical doctors must pass to achieve certification.

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.

Medical knowledge is context-dependent and requires consistent reasoning across various natural language expressions of semantically equivalent phrases. This is particularly crucial for drug names, where patients often use brand names like Advil or Tylenol instead of their generic equivalents. To study this, we create a new robustness dataset, RABBITS, to evaluate performance differences on medical benchmarks after swapping brand and generic drug names using physician expert annotations. We assess both open-source and API-based LLMs on MedQA and MedMCQA, revealing a consistent performance drop ranging from 1-10\%. Furthermore, we identify a potential source of this fragility as the contamination of test data in widely used pre-training datasets. All code is accessible at https://github.com/BittermanLab/RABBITS, and a HuggingFace leaderboard is available at https://huggingface.co/spaces/AIM-Harvard/rabbits-leaderboard.

The recent explosion in the capabilities of large language models has led to a wave of interest in how best to prompt a model to perform a given task. While it may be tempting to simply choose a prompt based on average performance on a validation set, this can lead to a deployment where unexpectedly poor responses are generated, especially for the worst-off users. To mitigate this prospect, we propose Prompt Risk Control, a lightweight framework for selecting a prompt based on rigorous upper bounds on families of informative risk measures. We offer methods for producing bounds on a diverse set of metrics, including quantities that measure worst-case responses and disparities in generation quality across the population of users. In addition, we extend the underlying statistical bounding techniques to accommodate the possibility of distribution shifts in deployment. Experiments on applications such as open-ended chat, medical question summarization, and code generation highlight how such a framework can foster responsible deployment by reducing the risk of the worst outcomes.

This paper presents UMASS_BioNLP team participation in the MEDIQA-Chat 2023 shared task for Task-A and Task-C. We focus especially on Task-C and propose a novel LLMs cooperation system named a doctor-patient loop to generate high-quality conversation data sets. The experiment results demonstrate that our approaches yield reasonable performance as evaluated by automatic metrics such as ROUGE, medical concept recall, BLEU, and Self-BLEU. Furthermore, we conducted a comparative analysis between our proposed method and ChatGPT and GPT-4. This analysis also investigates the potential of utilizing cooperation LLMs to generate high-quality datasets.

The mining of adverse drug events (ADEs) is pivotal in pharmacovigilance, enhancing patient safety by identifying potential risks associated with medications, facilitating early detection of adverse events, and guiding regulatory decision-making. Traditional ADE detection methods are reliable but slow, not easily adaptable to large-scale operations, and offer limited information. With the exponential increase in data sources like social media content, biomedical literature, and Electronic Medical Records (EMR), extracting relevant ADE-related information from these unstructured texts is imperative. Previous ADE mining studies have focused on text-based methodologies, overlooking visual cues, limiting contextual comprehension, and hindering accurate interpretation. To address this gap, we present a MultiModal Adverse Drug Event (MMADE) detection dataset, merging ADE-related textual information with visual aids. Additionally, we introduce a framework that leverages the capabilities of LLMs and VLMs for ADE detection by generating detailed descriptions of medical images depicting ADEs, aiding healthcare professionals in visually identifying adverse events. Using our MMADE dataset, we showcase the significance of integrating visual cues from images to enhance overall performance. This approach holds promise for patient safety, ADE awareness, and healthcare accessibility, paving the way for further exploration in personalized healthcare.

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.

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

We present CovidQA, the beginnings of a question answering dataset specifically designed for COVID-19, built by hand from knowledge gathered from Kaggle's COVID-19 Open Research Dataset Challenge. To our knowledge, this is the first publicly available resource of its type, and intended as a stopgap measure for guiding research until more substantial evaluation resources become available. While this dataset, comprising 124 question-article pairs as of the present version 0.1 release, does not have sufficient examples for supervised machine learning, we believe that it can be helpful for evaluating the zero-shot or transfer capabilities of existing models on topics specifically related to COVID-19. This paper describes our methodology for constructing the dataset and presents the effectiveness of a number of baselines, including term-based techniques and various transformer-based models. The dataset is available at http://covidqa.ai/

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

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.

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

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

This paper explores the use of open generative Large Language Models (LLMs) for annotation tasks in the social sciences. The study highlights the challenges associated with proprietary models, such as limited reproducibility and privacy concerns, and advocates for the adoption of open (source) models that can be operated on independent devices. Two examples of annotation tasks, sentiment analysis in tweets and identification of leisure activities in childhood aspirational essays are provided. The study evaluates the performance of different prompting strategies and models (neural-chat-7b-v3-2, Starling-LM-7B-alpha, openchat_3.5, zephyr-7b-alpha and zephyr-7b-beta). The results indicate the need for careful validation and tailored prompt engineering. The study highlights the advantages of open models for data privacy and reproducibility.

We present Eir Thai Medical LLM, a large language model with 8 billion parameters, specifically designed to enhance the accuracy of handling medical tasks in the Thai language. This model focuses on providing clear and easy-to-understand answers for both healthcare professionals and patients, thereby improving the efficiency of diagnosis and treatment processes. Human evaluation was conducted to ensure that the model adheres to care standards and provides unbiased answers. To prioritize data security, the model is deployed within the hospital's internal network, ensuring both high security and faster processing speeds. The internal API connection is secured with encryption and strict authentication measures to prevent data leaks and unauthorized access. We evaluated several open-source large language models with 8 billion parameters on four medical benchmarks: MedQA, MedMCQA, PubMedQA, and the medical subset of MMLU. The best-performing baselines were used to develop Eir Thai Medical LLM. Our evaluation employed multiple questioning strategies, including zero-shot, few-shot, chain-of-thought reasoning, and ensemble/self-consistency voting methods. Our model outperformed commercially available Thai-language large language models by more than 10%. In addition, we developed enhanced model testing tailored for clinical use in Thai across 18 clinical tasks, where our model exceeded GPT-4o performance by more than 11%

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

Large Language Models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and the reasoning over specialized knowledge. To address these obstinate issues, we propose a novel Multi-disciplinary Collaboration (MC) framework for the medical domain that leverages role-playing LLM-based agents who participate in a collaborative multi-round discussion, thereby enhancing LLM proficiency and reasoning capabilities. This training-free and interpretable framework encompasses five critical steps: gathering domain experts, proposing individual analyses, summarising these analyses into a report, iterating over discussions until a consensus is reached, and ultimately making a decision. Our work particularly focuses on the zero-shot scenario, our results on nine data sets (MedQA, MedMCQA, PubMedQA, and six subtasks from MMLU) establish that our proposed MC framework excels at mining and harnessing the medical expertise in LLMs, as well as extending its reasoning abilities. Based on these outcomes, we further conduct a human evaluation to pinpoint and categorize common errors within our method, as well as ablation studies aimed at understanding the impact of various factors on overall performance. Our code can be found at https://github.com/gersteinlab/MedAgents.

In this paper we present a hybrid method for the automatic detection of dermatological pathologies in medical reports. We use a large language model combined with medical ontologies to predict, given a first appointment or follow-up medical report, the pathology a person may suffer from. The results show that teaching the model to learn the type, severity and location on the body of a dermatological pathology, as well as in which order it has to learn these three features, significantly increases its accuracy. The article presents the demonstration of state-of-the-art results for classification of medical texts with a precision of 0.84, micro and macro F1-score of 0.82 and 0.75, and makes both the method and the data set used available to the community.

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.

This study investigates GPT-4's assessment of its performance in healthcare applications. A simple prompting technique was used to prompt the LLM with questions taken from the United States Medical Licensing Examination (USMLE) questionnaire and it was tasked to evaluate its confidence score before posing the question and after asking the question. The questionnaire was categorized into two groups-questions with feedback (WF) and questions with no feedback(NF) post-question. The model was asked to provide absolute and relative confidence scores before and after each question. The experimental findings were analyzed using statistical tools to study the variability of confidence in WF and NF groups. Additionally, a sequential analysis was conducted to observe the performance variation for the WF and NF groups. Results indicate that feedback influences relative confidence but doesn't consistently increase or decrease it. Understanding the performance of LLM is paramount in exploring its utility in sensitive areas like healthcare. This study contributes to the ongoing discourse on the reliability of AI, particularly of LLMs like GPT-4, within healthcare, offering insights into how feedback mechanisms might be optimized to enhance AI-assisted medical education and decision support.

We introduce PubMedQA, a novel biomedical question answering (QA) dataset collected from PubMed abstracts. The task of PubMedQA is to answer research questions with yes/no/maybe (e.g.: Do preoperative statins reduce atrial fibrillation after coronary artery bypass grafting?) using the corresponding abstracts. PubMedQA has 1k expert-annotated, 61.2k unlabeled and 211.3k artificially generated QA instances. Each PubMedQA instance is composed of (1) a question which is either an existing research article title or derived from one, (2) a context which is the corresponding abstract without its conclusion, (3) a long answer, which is the conclusion of the abstract and, presumably, answers the research question, and (4) a yes/no/maybe answer which summarizes the conclusion. PubMedQA is the first QA dataset where reasoning over biomedical research texts, especially their quantitative contents, is required to answer the questions. Our best performing model, multi-phase fine-tuning of BioBERT with long answer bag-of-word statistics as additional supervision, achieves 68.1% accuracy, compared to single human performance of 78.0% accuracy and majority-baseline of 55.2% accuracy, leaving much room for improvement. PubMedQA is publicly available at https://pubmedqa.github.io.

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

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.

This research paper focuses on the challenges posed by hallucinations in large language models (LLMs), particularly in the context of the medical domain. Hallucination, wherein these models generate plausible yet unverified or incorrect information, can have serious consequences in healthcare applications. We propose a new benchmark and dataset, Med-HALT (Medical Domain Hallucination Test), designed specifically to evaluate and reduce hallucinations. Med-HALT provides a diverse multinational dataset derived from medical examinations across various countries and includes multiple innovative testing modalities. Med-HALT includes two categories of tests reasoning and memory-based hallucination tests, designed to assess LLMs's problem-solving and information retrieval abilities. Our study evaluated leading LLMs, including Text Davinci, GPT-3.5, LlaMa-2, MPT, and Falcon, revealing significant differences in their performance. The paper provides detailed insights into the dataset, promoting transparency and reproducibility. Through this work, we aim to contribute to the development of safer and more reliable language models in healthcare. Our benchmark can be found at medhalt.github.io

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

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

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

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

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

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.

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.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

Current Large Language Models (LLMs) benchmarks are often based on open-ended or close-ended QA evaluations, avoiding the requirement of human labor. Close-ended measurements evaluate the factuality of responses but lack expressiveness. Open-ended capture the model's capacity to produce discourse responses but are harder to assess for correctness. These two approaches are commonly used, either independently or together, though their relationship remains poorly understood. This work is focused on the healthcare domain, where both factuality and discourse matter greatly. It introduces a comprehensive, multi-axis suite for healthcare LLM evaluation, exploring correlations between open and close benchmarks and metrics. Findings include blind spots and overlaps in current methodologies. As an updated sanity check, we release a new medical benchmark--CareQA--, with both open and closed variants. Finally, we propose a novel metric for open-ended evaluations --Relaxed Perplexity-- to mitigate the identified limitations.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use tend to overlook the nuanced semantics of medical data, while only relying heavily on identities. Furthermore, these models face significant challenges in handling cases involving patients who are visiting the hospital for the first time, as they lack prior prescription histories to draw upon. To tackle these issues, we harness the powerful semantic comprehension and input-agnostic characteristics of Large Language Models (LLMs). Our research aims to transform existing medication recommendation methodologies using LLMs. In this paper, we introduce a novel approach called Large Language Model Distilling Medication Recommendation (LEADER). We begin by creating appropriate prompt templates that enable LLMs to suggest medications effectively. However, the straightforward integration of LLMs into recommender systems leads to an out-of-corpus issue specific to drugs. We handle it by adapting the LLMs with a novel output layer and a refined tuning loss function. Although LLM-based models exhibit remarkable capabilities, they are plagued by high computational costs during inference, which is impractical for the healthcare sector. To mitigate this, we have developed a feature-level knowledge distillation technique, which transfers the LLM's proficiency to a more compact model. Extensive experiments conducted on two real-world datasets, MIMIC-III and MIMIC-IV, demonstrate that our proposed model not only delivers effective results but also is efficient. To ease the reproducibility of our experiments, we release the implementation code online.

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

The goal of automated summarization techniques (Paice, 1990; Kupiec et al, 1995) is to condense text by focusing on the most critical information. Generative large language models (LLMs) have shown to be robust summarizers, yet traditional metrics struggle to capture resulting performance (Goyal et al, 2022) in more powerful LLMs. In safety-critical domains such as medicine, more rigorous evaluation is required, especially given the potential for LLMs to omit important information in the resulting summary. We propose MED-OMIT, a new omission benchmark for medical summarization. Given a doctor-patient conversation and a generated summary, MED-OMIT categorizes the chat into a set of facts and identifies which are omitted from the summary. We further propose to determine fact importance by simulating the impact of each fact on a downstream clinical task: differential diagnosis (DDx) generation. MED-OMIT leverages LLM prompt-based approaches which categorize the importance of facts and cluster them as supporting or negating evidence to the diagnosis. We evaluate MED-OMIT on a publicly-released dataset of patient-doctor conversations and find that MED-OMIT captures omissions better than alternative metrics.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

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

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.

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/.

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.

Prompt learning is a new paradigm in the Natural Language Processing (NLP) field which has shown impressive performance on a number of natural language tasks with common benchmarking text datasets in full, few-shot, and zero-shot train-evaluation setups. Recently, it has even been observed that large but frozen pre-trained language models (PLMs) with prompt learning outperform smaller but fine-tuned models. However, as with many recent NLP trends, the performance of even the largest PLMs such as GPT-3 do not perform well on specialized domains (e.g. medical text), and the common practice to achieve State of the Art (SoTA) results still consists of pre-training and fine-tuning the PLMs on downstream tasks. The reliance on fine-tuning large PLMs is problematic in clinical settings where data is often held in non-GPU environments, and more resource efficient methods of training specialized domain models is crucial. We investigated the viability of prompt learning on clinically meaningful decision tasks and directly compared with more traditional fine-tuning methods. Results are partially in line with the prompt learning literature, with prompt learning able to match or improve on traditional fine-tuning with substantially fewer trainable parameters and requiring less training data. We argue that prompt learning therefore provides lower computational resource costs applicable to clinical settings, that can serve as an alternative to fine-tuning ever increasing in size PLMs. Complementary code to reproduce experiments presented in this work can be found at: https://github.com/NtaylorOX/Public_Clinical_Prompt.

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

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics, diagnoses, and medications. This will enhance healthcare providers' ability to identify aspects of a patient's story communicated in the clinical notes and help make more informed decisions. In this work, we propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes; communicated implicitly or explicitly, identified either in a single sentence or across multiple sentences. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. Annotation based on our guidelines achieved a high inter-annotator agreement i.e. Fleiss' kappa (kappa) score of 0.72, and our model for identification of causal relations achieved a macro F1 score of 0.56 on the test data. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

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.

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.

Medical abstractive summarization faces the challenge of balancing faithfulness and informativeness. Current methods often sacrifice key information for faithfulness or introduce confabulations when prioritizing informativeness. While recent advancements in techniques like in-context learning (ICL) and fine-tuning have improved medical summarization, they often overlook crucial aspects such as faithfulness and informativeness without considering advanced methods like model reasoning and self-improvement. Moreover, the field lacks a unified benchmark, hindering systematic evaluation due to varied metrics and datasets. This paper addresses these gaps by presenting a comprehensive benchmark of six advanced abstractive summarization methods across three diverse datasets using five standardized metrics. Building on these findings, we propose uMedSum, a modular hybrid summarization framework that introduces novel approaches for sequential confabulation removal followed by key missing information addition, ensuring both faithfulness and informativeness. Our work improves upon previous GPT-4-based state-of-the-art (SOTA) medical summarization methods, significantly outperforming them in both quantitative metrics and qualitative domain expert evaluations. Notably, we achieve an average relative performance improvement of 11.8% in reference-free metrics over the previous SOTA. Doctors prefer uMedSum's summaries 6 times more than previous SOTA in difficult cases where there are chances of confabulations or missing information. These results highlight uMedSum's effectiveness and generalizability across various datasets and metrics, marking a significant advancement in medical summarization.

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

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

The 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.

During the COVID-19 pandemic, a significant effort has gone into developing ML-driven epidemic forecasting techniques. However, benchmarks do not exist to claim if a new AI/ML technique is better than the existing ones. The "covid-forecast-hub" is a collection of more than 30 teams, including us, that submit their forecasts weekly to the CDC. It is not possible to declare whether one method is better than the other using those forecasts because each team's submission may correspond to different techniques over the period and involve human interventions as the teams are continuously changing/tuning their approach. Such forecasts may be considered "human-expert" forecasts and do not qualify as AI/ML approaches, although they can be used as an indicator of human expert performance. We are interested in supporting AI/ML research in epidemic forecasting which can lead to scalable forecasting without human intervention. Which modeling technique, learning strategy, and data pre-processing technique work well for epidemic forecasting is still an open problem. To help advance the state-of-the-art AI/ML applied to epidemiology, a benchmark with a collection of performance points is needed and the current "state-of-the-art" techniques need to be identified. We propose EpiBench a platform consisting of community-driven benchmarks for AI/ML applied to epidemic forecasting to standardize the challenge with a uniform evaluation protocol. In this paper, we introduce a prototype of EpiBench which is currently running and accepting submissions for the task of forecasting COVID-19 cases and deaths in the US states and We demonstrate that we can utilize the prototype to develop an ensemble relying on fully automated epidemic forecasts (no human intervention) that reaches human-expert level ensemble currently being used by the CDC.

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.

Dengue fever presents a substantial challenge in developing countries where sanitation infrastructure is inadequate. The absence of comprehensive healthcare systems exacerbates the severity of dengue infections, potentially leading to life-threatening circumstances. Rapid response to dengue outbreaks is also challenging due to limited information exchange and integration. While timely dengue outbreak forecasts have the potential to prevent such outbreaks, the majority of dengue prediction studies have predominantly relied on data that impose significant burdens on individual countries for collection. In this study, our aim is to improve health equity in resource-constrained countries by exploring the effectiveness of high-resolution satellite imagery as a nontraditional and readily accessible data source. By leveraging the wealth of publicly available and easily obtainable satellite imagery, we present a scalable satellite extraction framework based on Sentinel Hub, a cloud-based computing platform. Furthermore, we introduce DengueNet, an innovative architecture that combines Vision Transformer, Radiomics, and Long Short-term Memory to extract and integrate spatiotemporal features from satellite images. This enables dengue predictions on an epi-week basis. To evaluate the effectiveness of our proposed method, we conducted experiments on five municipalities in Colombia. We utilized a dataset comprising 780 high-resolution Sentinel-2 satellite images for training and evaluation. The performance of DengueNet was assessed using the mean absolute error (MAE) metric. Across the five municipalities, DengueNet achieved an average MAE of 43.92. Our findings strongly support the efficacy of satellite imagery as a valuable resource for dengue prediction, particularly in informing public health policies within countries where manually collected data is scarce and dengue virus prevalence is severe.

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.

Over the course of the COVID-19 pandemic, large volumes of biomedical information concerning this new disease have been published on social media. Some of this information can pose a real danger to people's health, particularly when false information is shared, for instance recommendations on how to treat diseases without professional medical advice. Therefore, automatic fact-checking resources and systems developed specifically for the medical domain are crucial. While existing fact-checking resources cover COVID-19-related information in news or quantify the amount of misinformation in tweets, there is no dataset providing fact-checked COVID-19-related Twitter posts with detailed annotations for biomedical entities, relations and relevant evidence. We contribute CoVERT, a fact-checked corpus of tweets with a focus on the domain of biomedicine and COVID-19-related (mis)information. The corpus consists of 300 tweets, each annotated with medical named entities and relations. We employ a novel crowdsourcing methodology to annotate all tweets with fact-checking labels and supporting evidence, which crowdworkers search for online. This methodology results in moderate inter-annotator agreement. Furthermore, we use the retrieved evidence extracts as part of a fact-checking pipeline, finding that the real-world evidence is more useful than the knowledge indirectly available in pretrained language models.

Generating synthetic text addresses the challenge of data availability in privacy-sensitive domains such as healthcare. This study explores the applicability of synthetic data in real-world medical settings. We introduce MedSyn, a novel medical text generation framework that integrates large language models with a Medical Knowledge Graph (MKG). We use MKG to sample prior medical information for the prompt and generate synthetic clinical notes with GPT-4 and fine-tuned LLaMA models. We assess the benefit of synthetic data through application in the ICD code prediction task. Our research indicates that synthetic data can increase the classification accuracy of vital and challenging codes by up to 17.8% compared to settings without synthetic data. Furthermore, to provide new data for further research in the healthcare domain, we present the largest open-source synthetic dataset of clinical notes for the Russian language, comprising over 41k samples covering 219 ICD-10 codes.

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.

In this paper, we introduce InMD-X, a collection of multiple large language models specifically designed to cater to the unique characteristics and demands of Internal Medicine Doctors (IMD). InMD-X represents a groundbreaking development in natural language processing, offering a suite of language models fine-tuned for various aspects of the internal medicine field. These models encompass a wide range of medical sub-specialties, enabling IMDs to perform more efficient and accurate research, diagnosis, and documentation. InMD-X's versatility and adaptability make it a valuable tool for improving the healthcare industry, enhancing communication between healthcare professionals, and advancing medical research. Each model within InMD-X is meticulously tailored to address specific challenges faced by IMDs, ensuring the highest level of precision and comprehensiveness in clinical text analysis and decision support. This paper provides an overview of the design, development, and evaluation of InMD-X, showcasing its potential to revolutionize the way internal medicine practitioners interact with medical data and information. We present results from extensive testing, demonstrating the effectiveness and practical utility of InMD-X in real-world medical scenarios.

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

The breakthrough of OpenAI o1 highlights the potential of enhancing reasoning to improve LLM. Yet, most research in reasoning has focused on mathematical tasks, leaving domains like medicine underexplored. The medical domain, though distinct from mathematics, also demands robust reasoning to provide reliable answers, given the high standards of healthcare. However, verifying medical reasoning is challenging, unlike those in mathematics. To address this, we propose verifiable medical problems with a medical verifier to check the correctness of model outputs. This verifiable nature enables advancements in medical reasoning through a two-stage approach: (1) using the verifier to guide the search for a complex reasoning trajectory for fine-tuning LLMs, (2) applying reinforcement learning (RL) with verifier-based rewards to enhance complex reasoning further. Finally, we introduce HuatuoGPT-o1, a medical LLM capable of complex reasoning, which outperforms general and medical-specific baselines using only 40K verifiable problems. Experiments show complex reasoning improves medical problem-solving and benefits more from RL. We hope our approach inspires advancements in reasoning across medical and other specialized domains.

Doctors typically write in incomprehensible handwriting, making it difficult for both the general public and some pharmacists to understand the medications they have prescribed. It is not ideal for them to write the prescription quietly and methodically because they will be dealing with dozens of patients every day and will be swamped with work.As a result, their handwriting is illegible. This may result in reports or prescriptions consisting of short forms and cursive writing that a typical person or pharmacist won't be able to read properly, which will cause prescribed medications to be misspelled. However, some individuals are accustomed to writing prescriptions in regional languages because we all live in an area with a diversity of regional languages. It makes analyzing the content much more challenging. So, in this project, we'll use a recognition system to build a tool that can translate the handwriting of physicians in any language. This system will be made into an application which is fully autonomous in functioning. As the user uploads the prescription image the program will pre-process the image by performing image pre-processing, and word segmentations initially before processing the image for training. And it will be done for every language we require the model to detect. And as of the deduction model will be made using deep learning techniques including CNN, RNN, and LSTM, which are utilized to train the model. To match words from various languages that will be written in the system, Unicode will be used. Furthermore, fuzzy search and market basket analysis are employed to offer an end result that will be optimized from the pharmaceutical database and displayed to the user as a structured output.

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.

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 ten 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 and supervised fine-tuning regimes for medical question-answering (QA). For instance, across all tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 22.7% of cases, reach a (statistical) tie in 36.8% of cases, and are significantly worse than their base models in the remaining 40.5% 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 in zero-/few-shot prompting; 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. Meanwhile, we find that after fine-tuning on specific QA tasks, medical LLMs can show performance improvements, but the benefits do not carry over to tasks based on clinical notes. 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.

The global ramifications of the COVID-19 pandemic remain significant, exerting persistent pressure on nations even three years after its initial outbreak. Deep learning models have shown promise in improving COVID-19 diagnostics but require diverse and larger-scale datasets to improve performance. In this paper, we introduce COVIDx CXR-4, an expanded multi-institutional open-source benchmark dataset for chest X-ray image-based computer-aided COVID-19 diagnostics. COVIDx CXR-4 expands significantly on the previous COVIDx CXR-3 dataset by increasing the total patient cohort size by greater than 2.66 times, resulting in 84,818 images from 45,342 patients across multiple institutions. We provide extensive analysis on the diversity of the patient demographic, imaging metadata, and disease distributions to highlight potential dataset biases. To the best of the authors' knowledge, COVIDx CXR-4 is the largest and most diverse open-source COVID-19 CXR dataset and is made publicly available as part of an open initiative to advance research to aid clinicians against the COVID-19 disease.

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

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

We introduce KorMedMCQA, the first Korean multiple-choice question answering (MCQA) benchmark derived from Korean healthcare professional licensing examinations, covering from the year 2012 to year 2023. This dataset consists of a selection of questions from the license examinations for doctors, nurses, and pharmacists, featuring a diverse array of subjects. We conduct baseline experiments on various large language models, including proprietary/open-source, multilingual/Korean-additional pretrained, and clinical context pretrained models, highlighting the potential for further enhancements. We make our data publicly available on HuggingFace and provide a evaluation script via LM-Harness, inviting further exploration and advancement in Korean healthcare environments.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

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

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

Vision-language models (VLMs), which process image and text inputs, are increasingly integrated into chat assistants and other consumer AI applications. Without proper safeguards, however, VLMs may give harmful advice (e.g. how to self-harm) or encourage unsafe behaviours (e.g. to consume drugs). Despite these clear hazards, little work so far has evaluated VLM safety and the novel risks created by multimodal inputs. To address this gap, we introduce MSTS, a Multimodal Safety Test Suite for VLMs. MSTS comprises 400 test prompts across 40 fine-grained hazard categories. Each test prompt consists of a text and an image that only in combination reveal their full unsafe meaning. With MSTS, we find clear safety issues in several open VLMs. We also find some VLMs to be safe by accident, meaning that they are safe because they fail to understand even simple test prompts. We translate MSTS into ten languages, showing non-English prompts to increase the rate of unsafe model responses. We also show models to be safer when tested with text only rather than multimodal prompts. Finally, we explore the automation of VLM safety assessments, finding even the best safety classifiers to be lacking.

Retrieval-augmented models have proven to be effective in natural language processing tasks, yet there remains a lack of research on their optimization using variational inference. We introduce the Variational Open-Domain (VOD) framework for end-to-end training and evaluation of retrieval-augmented models, focusing on open-domain question answering and language modelling. The VOD objective, a self-normalized estimate of the R\'enyi variational bound, approximates the task marginal likelihood and is evaluated under samples drawn from an auxiliary sampling distribution (cached retriever and/or approximate posterior). It remains tractable, even for retriever distributions defined on large corpora. We demonstrate VOD's versatility by training reader-retriever BERT-sized models on multiple-choice medical exam questions. On the MedMCQA dataset, we outperform the domain-tuned Med-PaLM by +5.3% despite using 2.500times fewer parameters. Our retrieval-augmented BioLinkBERT model scored 62.9% on the MedMCQA and 55.0% on the MedQA-USMLE. Last, we show the effectiveness of our learned retriever component in the context of medical semantic search.

The integration of large language model (LLM) techniques in the field of medical analysis has brought about significant advancements, yet the scarcity of large, diverse, and well-annotated datasets remains a major challenge. Medical data and tasks, which vary in format, size, and other parameters, require extensive preprocessing and standardization for effective use in training LLMs. To address these challenges, we introduce MedINST, the Meta Dataset of Biomedical Instructions, a novel multi-domain, multi-task instructional meta-dataset. MedINST comprises 133 biomedical NLP tasks and over 7 million training samples, making it the most comprehensive biomedical instruction dataset to date. Using MedINST as the meta dataset, we curate MedINST32, a challenging benchmark with different task difficulties aiming to evaluate LLMs' generalization ability. We fine-tune several LLMs on MedINST and evaluate on MedINST32, showcasing enhanced cross-task generalization.

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.

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 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.

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

The development of large language models tailored for handling patients' clinical notes is often hindered by the limited accessibility and usability of these notes due to strict privacy regulations. To address these challenges, we first create synthetic large-scale clinical notes using publicly available case reports extracted from biomedical literature. We then use these synthetic notes to train our specialized clinical large language model, Asclepius. While Asclepius is trained on synthetic data, we assess its potential performance in real-world applications by evaluating it using real clinical notes. We benchmark Asclepius against several other large language models, including GPT-3.5-turbo and other open-source alternatives. To further validate our approach using synthetic notes, we also compare Asclepius with its variants trained on real clinical notes. Our findings convincingly demonstrate that synthetic clinical notes can serve as viable substitutes for real ones when constructing high-performing clinical language models. This conclusion is supported by detailed evaluations conducted by both GPT-4 and medical professionals. All resources including weights, codes, and data used in the development of Asclepius are made publicly accessible for future research.

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.

Background: Large language models (LLMs) are trained to follow directions, but this introduces a vulnerability to blindly comply with user requests even if they generate wrong information. In medicine, this could accelerate the generation of misinformation that impacts human well-being. Objectives/Methods: We analyzed compliance to requests to generate misleading content about medications in settings where models know the request is illogical. We investigated whether in-context directions and instruction-tuning of LLMs to prioritize logical reasoning over compliance reduced misinformation risk. Results: While all frontier LLMs complied with misinformation requests, both prompt-based and parameter-based approaches can improve the detection of logic flaws in requests and prevent the dissemination of medical misinformation. Conclusion: Shifting LLMs to prioritize logic over compliance could reduce risks of exploitation for medical misinformation.

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

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

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.

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.

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.

There is enormous enthusiasm and concerns in using large language models (LLMs) in healthcare, yet current assumptions are all based on general-purpose LLMs such as ChatGPT. This study develops a clinical generative LLM, GatorTronGPT, using 277 billion words of mixed clinical and English text with a GPT-3 architecture of 20 billion parameters. GatorTronGPT improves biomedical natural language processing for medical research. Synthetic NLP models trained using GatorTronGPT generated text outperform NLP models trained using real-world clinical text. Physicians Turing test using 1 (worst) to 9 (best) scale shows that there is no significant difference in linguistic readability (p = 0.22; 6.57 of GatorTronGPT compared with 6.93 of human) and clinical relevance (p = 0.91; 7.0 of GatorTronGPT compared with 6.97 of human) and that physicians cannot differentiate them (p < 0.001). This study provides insights on the opportunities and challenges of LLMs for medical research and healthcare.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of MedTem project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at https://github.com/HECTA-UoM/MedTem

Medical coding is the task of assigning medical codes to clinical free-text documentation. Healthcare professionals manually assign such codes to track patient diagnoses and treatments. Automated medical coding can considerably alleviate this administrative burden. In this paper, we reproduce, compare, and analyze state-of-the-art automated medical coding machine learning models. We show that several models underperform due to weak configurations, poorly sampled train-test splits, and insufficient evaluation. In previous work, the macro F1 score has been calculated sub-optimally, and our correction doubles it. We contribute a revised model comparison using stratified sampling and identical experimental setups, including hyperparameters and decision boundary tuning. We analyze prediction errors to validate and falsify assumptions of previous works. The analysis confirms that all models struggle with rare codes, while long documents only have a negligible impact. Finally, we present the first comprehensive results on the newly released MIMIC-IV dataset using the reproduced models. We release our code, model parameters, and new MIMIC-III and MIMIC-IV training and evaluation pipelines to accommodate fair future comparisons.

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 report generation from X-ray images is a challenging task, particularly in an unpaired setting where paired image-report data is unavailable for training. To address this challenge, we propose a novel model that leverages the available information in two distinct datasets, one comprising reports and the other consisting of images. The core idea of our model revolves around the notion that combining auto-encoding report generation with multi-modal (report-image) alignment can offer a solution. However, the challenge persists regarding how to achieve this alignment when pair correspondence is absent. Our proposed solution involves the use of auxiliary tasks, particularly contrastive learning and classification, to position related images and reports in close proximity to each other. This approach differs from previous methods that rely on pre-processing steps, such as using external information stored in a knowledge graph. Our model, named MedRAT, surpasses previous state-of-the-art methods, demonstrating the feasibility of generating comprehensive medical reports without the need for paired data or external tools.

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

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.

With the advent of Vision-Language Models (VLMs), medical artificial intelligence (AI) has experienced significant technological progress and paradigm shifts. This survey provides an extensive review of recent advancements in Medical Vision-Language Models (Med-VLMs), which integrate visual and textual data to enhance healthcare outcomes. We discuss the foundational technology behind Med-VLMs, illustrating how general models are adapted for complex medical tasks, and examine their applications in healthcare. The transformative impact of Med-VLMs on clinical practice, education, and patient care is highlighted, alongside challenges such as data scarcity, narrow task generalization, interpretability issues, and ethical concerns like fairness, accountability, and privacy. These limitations are exacerbated by uneven dataset distribution, computational demands, and regulatory hurdles. Rigorous evaluation methods and robust regulatory frameworks are essential for safe integration into healthcare workflows. Future directions include leveraging large-scale, diverse datasets, improving cross-modal generalization, and enhancing interpretability. Innovations like federated learning, lightweight architectures, and Electronic Health Record (EHR) integration are explored as pathways to democratize access and improve clinical relevance. This review aims to provide a comprehensive understanding of Med-VLMs' strengths and limitations, fostering their ethical and balanced adoption in healthcare.

A significant and growing number of published scientific articles is found to involve fraudulent practices, posing a serious threat to the credibility and safety of research in fields such as medicine. We propose Pub-Guard-LLM, the first large language model-based system tailored to fraud detection of biomedical scientific articles. We provide three application modes for deploying Pub-Guard-LLM: vanilla reasoning, retrieval-augmented generation, and multi-agent debate. Each mode allows for textual explanations of predictions. To assess the performance of our system, we introduce an open-source benchmark, PubMed Retraction, comprising over 11K real-world biomedical articles, including metadata and retraction labels. We show that, across all modes, Pub-Guard-LLM consistently surpasses the performance of various baselines and provides more reliable explanations, namely explanations which are deemed more relevant and coherent than those generated by the baselines when evaluated by multiple assessment methods. By enhancing both detection performance and explainability in scientific fraud detection, Pub-Guard-LLM contributes to safeguarding research integrity with a novel, effective, open-source tool.

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.

In recent years, there have been significant breakthroughs in the field of natural language processing, particularly with the development of large language models (LLMs). These LLMs have showcased remarkable capabilities on various benchmarks. In the healthcare field, the exact role LLMs and other future AI models will play remains unclear. There is a potential for these models in the future to be used as part of adaptive physician training, medical co-pilot applications, and digital patient interaction scenarios. The ability of AI models to participate in medical training and patient care will depend in part on their mastery of the knowledge content of specific medical fields. This study investigated the medical knowledge capability of LLMs, specifically in the context of internal medicine subspecialty multiple-choice test-taking ability. We compared the performance of several open-source LLMs (Koala 7B, Falcon 7B, Stable-Vicuna 13B, and Orca Mini 13B), to GPT-4 and Claude 2 on multiple-choice questions in the field of Nephrology. Nephrology was chosen as an example of a particularly conceptually complex subspecialty field within internal medicine. The study was conducted to evaluate the ability of LLM models to provide correct answers to nephSAP (Nephrology Self-Assessment Program) multiple-choice questions. The overall success of open-sourced LLMs in answering the 858 nephSAP multiple-choice questions correctly was 17.1% - 25.5%. In contrast, Claude 2 answered 54.4% of the questions correctly, whereas GPT-4 achieved a score of 73.3%. We show that current widely used open-sourced LLMs do poorly in their ability for zero-shot reasoning when compared to GPT-4 and Claude 2. The findings of this study potentially have significant implications for the future of subspecialty medical training and patient care.

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

Despite the success of Large Language Models (LLMs) in general image tasks, a gap persists in the medical field for a multimodal large model adept at handling the nuanced diversity of medical images. Addressing this, we propose MedXChat, a unified multimodal large model designed for seamless interactions between medical assistants and users. MedXChat encompasses three key functionalities: CXR(Chest X-ray)-to-Report generation, CXR-based visual question-answering (VQA), and Text-to-CXR synthesis. Our contributions are as follows. Firstly, our model showcases exceptional cross-task adaptability, displaying adeptness across all three defined tasks and outperforming the benchmark models on the MIMIC dataset in medical multimodal applications. Secondly, we introduce an innovative Text-to-CXR synthesis approach that utilizes instruction-following capabilities within the Stable Diffusion (SD) architecture. This technique integrates smoothly with the existing model framework, requiring no extra parameters, thereby maintaining the SD's generative strength while also bestowing upon it the capacity to render fine-grained medical images with high fidelity. Comprehensive experiments validate MedXChat's synergistic enhancement across all tasks. Our instruction data and model will be open-sourced.

Recent advancements in mixed-modal generative models have enabled flexible integration of information across image-text content. These models have opened new avenues for developing unified biomedical assistants capable of analyzing biomedical images, answering complex questions about them, and predicting the impact of medical procedures on a patient's health. However, existing resources face challenges such as limited data availability, narrow domain coverage, and restricted sources (e.g., medical papers). To address these gaps, we present MedMax, the first large-scale multimodal biomedical instruction-tuning dataset for mixed-modal foundation models. With 1.47 million instances, MedMax encompasses a diverse range of tasks, including multimodal content generation (interleaved image-text data), biomedical image captioning and generation, visual chatting, and report understanding. These tasks span diverse medical domains such as radiology and histopathology. Subsequently, we fine-tune a mixed-modal foundation model on the MedMax dataset, achieving significant performance improvements: a 26% gain over the Chameleon model and an 18.3% improvement over GPT-4o across 12 downstream biomedical visual question-answering tasks. Additionally, we introduce a unified evaluation suite for biomedical tasks, providing a robust framework to guide the development of next-generation mixed-modal biomedical AI assistants.

Excellence in a wide variety of medical applications poses considerable challenges for AI, requiring advanced reasoning, access to up-to-date medical knowledge and understanding of complex multimodal data. Gemini models, with strong general capabilities in multimodal and long-context reasoning, offer exciting possibilities in medicine. Building on these core strengths of Gemini, we introduce Med-Gemini, a family of highly capable multimodal models that are specialized in medicine with the ability to seamlessly use web search, and that can be efficiently tailored to novel modalities using custom encoders. We evaluate Med-Gemini on 14 medical benchmarks, establishing new state-of-the-art (SoTA) performance on 10 of them, and surpass the GPT-4 model family on every benchmark where a direct comparison is viable, often by a wide margin. On the popular MedQA (USMLE) benchmark, our best-performing Med-Gemini model achieves SoTA performance of 91.1% accuracy, using a novel uncertainty-guided search strategy. On 7 multimodal benchmarks including NEJM Image Challenges and MMMU (health & medicine), Med-Gemini improves over GPT-4V by an average relative margin of 44.5%. We demonstrate the effectiveness of Med-Gemini's long-context capabilities through SoTA performance on a needle-in-a-haystack retrieval task from long de-identified health records and medical video question answering, surpassing prior bespoke methods using only in-context learning. Finally, Med-Gemini's performance suggests real-world utility by surpassing human experts on tasks such as medical text summarization, alongside demonstrations of promising potential for multimodal medical dialogue, medical research and education. Taken together, our results offer compelling evidence for Med-Gemini's potential, although further rigorous evaluation will be crucial before real-world deployment in this safety-critical domain.

Automatic generation of graphic designs has recently received considerable attention. However, the state-of-the-art approaches are complex and rely on proprietary datasets, which creates reproducibility barriers. In this paper, we propose an open framework for automatic graphic design called OpenCOLE, where we build a modified version of the pioneering COLE and train our model exclusively on publicly available datasets. Based on GPT4V evaluations, our model shows promising performance comparable to the original COLE. We release the pipeline and training results to encourage open development.

Summaries of medical text shall be faithful by being consistent and factual with source inputs, which is an important but understudied topic for safety and efficiency in healthcare. In this paper, we investigate and improve faithfulness in summarization on a broad range of medical summarization tasks. Our investigation reveals that current summarization models often produce unfaithful outputs for medical input text. We then introduce FaMeSumm, a framework to improve faithfulness by fine-tuning pre-trained language models based on medical knowledge. FaMeSumm performs contrastive learning on designed sets of faithful and unfaithful summaries, and it incorporates medical terms and their contexts to encourage faithful generation of medical terms. We conduct comprehensive experiments on three datasets in two languages: health question and radiology report summarization datasets in English, and a patient-doctor dialogue dataset in Chinese. Results demonstrate that FaMeSumm is flexible and effective by delivering consistent improvements over mainstream language models such as BART, T5, mT5, and PEGASUS, yielding state-of-the-art performances on metrics for faithfulness and general quality. Human evaluation by doctors also shows that FaMeSumm generates more faithful outputs. Our code is available at https://github.com/psunlpgroup/FaMeSumm .

Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models pose significant obstacles for hospitals in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking the flexibility to perform well across both. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to four times longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MTF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field.

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

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.

Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets -- CovidDialog -- (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog tasks. We perform both automatic and human evaluation of responses generated by these models. The results show that the generated responses are promising in being doctor-like, relevant to the conversation history, and clinically informative. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue.

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.

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.

Curated datasets for healthcare are often limited due to the need of human annotations from experts. In this paper, we present MedEval, a multi-level, multi-task, and multi-domain medical benchmark to facilitate the development of language models for healthcare. MedEval is comprehensive and consists of data from several healthcare systems and spans 35 human body regions from 8 examination modalities. With 22,779 collected sentences and 21,228 reports, we provide expert annotations at multiple levels, offering a granular potential usage of the data and supporting a wide range of tasks. Moreover, we systematically evaluated 10 generic and domain-specific language models under zero-shot and finetuning settings, from domain-adapted baselines in healthcare to general-purposed state-of-the-art large language models (e.g., ChatGPT). Our evaluations reveal varying effectiveness of the two categories of language models across different tasks, from which we notice the importance of instruction tuning for few-shot usage of large language models. Our investigation paves the way toward benchmarking language models for healthcare and provides valuable insights into the strengths and limitations of adopting large language models in medical domains, informing their practical applications and future advancements.

To tackle the AVeriTeC shared task hosted by the FEVER-24, we introduce a system that only employs publicly available large language models (LLMs) for each step of automated fact-checking, dubbed the Herd of Open LLMs for verifying real-world claims (HerO). For evidence retrieval, a language model is used to enhance a query by generating hypothetical fact-checking documents. We prompt pretrained and fine-tuned LLMs for question generation and veracity prediction by crafting prompts with retrieved in-context samples. HerO achieved 2nd place on the leaderboard with the AVeriTeC score of 0.57, suggesting the potential of open LLMs for verifying real-world claims. For future research, we make our code publicly available at https://github.com/ssu-humane/HerO.

Extracting patient information from unstructured text is a critical task in health decision-support and clinical research. Large language models (LLMs) have shown the potential to accelerate clinical curation via few-shot in-context learning, in contrast to supervised learning which requires much more costly human annotations. However, despite drastic advances in modern LLMs such as GPT-4, they still struggle with issues regarding accuracy and interpretability, especially in mission-critical domains such as health. Here, we explore a general mitigation framework using self-verification, which leverages the LLM to provide provenance for its own extraction and check its own outputs. This is made possible by the asymmetry between verification and generation, where the latter is often much easier than the former. Experimental results show that our method consistently improves accuracy for various LLMs in standard clinical information extraction tasks. Additionally, self-verification yields interpretations in the form of a short text span corresponding to each output, which makes it very efficient for human experts to audit the results, paving the way towards trustworthy extraction of clinical information in resource-constrained scenarios. To facilitate future research in this direction, we release our code and prompts.

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