Daily Papers

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.

A radiology report comprises several sections, including the Findings and Impression of the diagnosis. Automatically generating the Impression from the Findings is crucial for reducing radiologists' workload and improving diagnostic accuracy. Pretrained models that excel in common abstractive summarization problems encounter challenges when applied to specialized medical domains largely due to the complex terminology and the necessity for accurate clinical context. Such tasks in medical domains demand extracting core information, avoiding context shifts, and maintaining proper flow. Misuse of medical terms can lead to drastic clinical errors. To address these issues, we introduce a sequential transfer learning that ensures key content extraction and coherent summarization. Sequential transfer learning often faces challenges like initial parameter decay and knowledge loss, which we resolve with the Fisher matrix regularization. Using MIMIC-CXR and Open-I datasets, our model, CSTRL - Context-driven Sequential TRansfer Learning - achieved state-of-the-art performance, showing 56.2% improvement in BLEU-1, 40.5% in BLEU-2, 84.3% in BLEU-3, 28.9% in ROUGE-1, 41.0% in ROUGE-2 and 26.5% in ROGUE-3 score over benchmark studies. We also analyze factual consistency scores while preserving the medical context. Our code is publicly available at https://github.com/fahmidahossain/Report_Summarization.

The advancement of natural language processing (NLP) systems in healthcare hinges on language model ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient's medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba, with 130 million and 2.8 billion parameters, demonstrates a superior performance in modeling clinical language across extended text lengths compared to Mamba and clinical Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and accuracy, outperforming existing clinical language models and general domain large models like GPT-4 in longitudinal clinical notes information extraction tasks.

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can struggle in specialized domains such as medicine, where unique domain-specific terminologies, domain-specific abbreviations, and varying document structures are common. This paper explores strategies for adapting these models to domain-specific requirements, primarily through continuous pre-training on domain-specific data. We pre-trained several German medical language models on 2.4B tokens derived from translated public English medical data and 3B tokens of German clinical data. The resulting models were evaluated on various German downstream tasks, including named entity recognition (NER), multi-label classification, and extractive question answering. Our results suggest that models augmented by clinical and translation-based pre-training typically outperform general domain models in medical contexts. We conclude that continuous pre-training has demonstrated the ability to match or even exceed the performance of clinical models trained from scratch. Furthermore, pre-training on clinical data or leveraging translated texts have proven to be reliable methods for domain adaptation in medical NLP tasks.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

Large Language Models (LLMs) have demonstrated significant potential in transforming clinical applications. In this study, we investigate the efficacy of four techniques in adapting LLMs for clinical use-cases: continuous pretraining, instruct fine-tuning, NEFTune, and prompt engineering. We employ these methods on Mistral 7B and Mixtral 8x7B models, leveraging a large-scale clinical pretraining dataset of 50 billion tokens and an instruct fine-tuning dataset of 500 million tokens. Our evaluation across various clinical tasks reveals the impact of each technique. While continuous pretraining beyond 250 billion tokens yields marginal improvements on its own, it establishes a strong foundation for instruct fine-tuning. Notably, NEFTune, designed primarily to enhance generation quality, surprisingly demonstrates additional gains on our benchmark. Complex prompt engineering methods further enhance performance. These findings show the importance of tailoring fine-tuning strategies and exploring innovative techniques to optimize LLM performance in the clinical domain.

The use of large pretrained neural networks to create contextualized word embeddings has drastically improved performance on several natural language processing (NLP) tasks. These computationally expensive models have begun to be applied to domain-specific NLP tasks such as re-hospitalization prediction from clinical notes. This paper demonstrates that using large pretrained models produces excellent results on common learning analytics tasks. Pre-training deep language models using student forum data from a wide array of online courses improves performance beyond the state of the art on three text classification tasks. We also show that a smaller, distilled version of our model produces the best results on two of the three tasks while limiting computational cost. We make both models available to the research community at large.

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

Multimodal in-context learning (ICL) remains underexplored despite significant potential for domains such as medicine. Clinicians routinely encounter diverse, specialized tasks requiring adaptation from limited examples, such as drawing insights from a few relevant prior cases or considering a constrained set of differential diagnoses. While multimodal large language models (MLLMs) have shown advances in medical visual question answering (VQA), their ability to learn multimodal tasks from context is largely unknown. We introduce SMMILE, the first expert-driven multimodal ICL benchmark for medical tasks. Eleven medical experts curated problems, each including a multimodal query and multimodal in-context examples as task demonstrations. SMMILE encompasses 111 problems (517 question-image-answer triplets) covering 6 medical specialties and 13 imaging modalities. We further introduce SMMILE++, an augmented variant with 1038 permuted problems. A comprehensive evaluation of 15 MLLMs demonstrates that most models exhibit moderate to poor multimodal ICL ability in medical tasks. In open-ended evaluations, ICL contributes only 8% average improvement over zero-shot on SMMILE and 9.4% on SMMILE++. We observe a susceptibility for irrelevant in-context examples: even a single noisy or irrelevant example can degrade performance by up to 9.5%. Moreover, example ordering exhibits a recency bias, i.e., placing the most relevant example last can lead to substantial performance improvements by up to 71%. Our findings highlight critical limitations and biases in current MLLMs when learning multimodal medical tasks from context.

Contextual word embedding models such as ELMo (Peters et al., 2018) and BERT (Devlin et al., 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such as clinical text; moreover, in the clinical domain, no publicly-available pre-trained BERT models yet exist. In this work, we address this need by exploring and releasing BERT models for clinical text: one for generic clinical text and another for discharge summaries specifically. We demonstrate that using a domain-specific model yields performance improvements on three common clinical NLP tasks as compared to nonspecific embeddings. These domain-specific models are not as performant on two clinical de-identification tasks, and argue that this is a natural consequence of the differences between de-identified source text and synthetically non de-identified task text.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

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

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.

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.

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

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

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

Pretrained language models have been used in various natural language processing applications. In the mental health domain, domain-specific language models are pretrained and released, which facilitates the early detection of mental health conditions. Social posts, e.g., on Reddit, are usually long documents. However, there are no domain-specific pretrained models for long-sequence modeling in the mental health domain. This paper conducts domain-specific continued pretraining to capture the long context for mental health. Specifically, we train and release MentalXLNet and MentalLongformer based on XLNet and Longformer. We evaluate the mental health classification performance and the long-range ability of these two domain-specific pretrained models. Our models are released in HuggingFace.

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

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

The use of deep neural models for diagnosis prediction from clinical text has shown promising results. However, in clinical practice such models must not only be accurate, but provide doctors with interpretable and helpful results. We introduce ProtoPatient, a novel method based on prototypical networks and label-wise attention with both of these abilities. ProtoPatient makes predictions based on parts of the text that are similar to prototypical patients - providing justifications that doctors understand. We evaluate the model on two publicly available clinical datasets and show that it outperforms existing baselines. Quantitative and qualitative evaluations with medical doctors further demonstrate that the model provides valuable explanations for clinical decision support.

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

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.

Since the emergence of the Transformer architecture, language model development has increased, driven by their promising potential. However, releasing these models into production requires properly understanding their behavior, particularly in sensitive domains such as medicine. Despite this need, the medical literature still lacks technical assessments of pre-trained language models, which are especially valuable in resource-constrained settings in terms of computational power or limited budget. To address this gap, we provide a comprehensive survey of language models in the medical domain. In addition, we selected a subset of these models for thorough evaluation, focusing on classification and text generation tasks. Our subset encompasses 53 models, ranging from 110 million to 13 billion parameters, spanning the three families of Transformer-based models and from diverse knowledge domains. This study employs a series of approaches for text classification together with zero-shot prompting instead of model training or fine-tuning, which closely resembles the limited resource setting in which many users of language models find themselves. Encouragingly, our findings reveal remarkable performance across various tasks and datasets, underscoring the latent potential of certain models to contain medical knowledge, even without domain specialization. Consequently, our study advocates for further exploration of model applications in medical contexts, particularly in resource-constrained settings. The code is available on https://github.com/anpoc/Language-models-in-medicine.

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

Large language models (LLMs) hold great promise for medical applications and are evolving rapidly, with new models being released at an accelerated pace. However, current evaluations of LLMs in clinical contexts remain limited. Most existing benchmarks rely on medical exam-style questions or PubMed-derived text, failing to capture the complexity of real-world electronic health record (EHR) data. Others focus narrowly on specific application scenarios, limiting their generalizability across broader clinical use. To address this gap, we present BRIDGE, a comprehensive multilingual benchmark comprising 87 tasks sourced from real-world clinical data sources across nine languages. We systematically evaluated 52 state-of-the-art LLMs (including DeepSeek-R1, GPT-4o, Gemini, and Llama 4) under various inference strategies. With a total of 13,572 experiments, our results reveal substantial performance variation across model sizes, languages, natural language processing tasks, and clinical specialties. Notably, we demonstrate that open-source LLMs can achieve performance comparable to proprietary models, while medically fine-tuned LLMs based on older architectures often underperform versus updated general-purpose models. The BRIDGE and its corresponding leaderboard serve as a foundational resource and a unique reference for the development and evaluation of new LLMs in real-world clinical text understanding.

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.

A long-running goal of the clinical NLP community is the extraction of important variables trapped in clinical notes. However, roadblocks have included dataset shift from the general domain and a lack of public clinical corpora and annotations. In this work, we show that large language models, such as InstructGPT, perform well at zero- and few-shot information extraction from clinical text despite not being trained specifically for the clinical domain. Whereas text classification and generation performance have already been studied extensively in such models, here we additionally demonstrate how to leverage them to tackle a diverse set of NLP tasks which require more structured outputs, including span identification, token-level sequence classification, and relation extraction. Further, due to the dearth of available data to evaluate these systems, we introduce new datasets for benchmarking few-shot clinical information extraction based on a manual re-annotation of the CASI dataset for new tasks. On the clinical extraction tasks we studied, the GPT-3 systems significantly outperform existing zero- and few-shot baselines.

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

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when performed on clinical named entity recognition and natural language inference tasks. One of the core limitations of these transformers is the substantial memory consumption due to their full self-attention mechanism. To overcome this, long sequence transformer models, e.g. Longformer and BigBird, were proposed with the idea of sparse attention mechanism to reduce the memory usage from quadratic to the sequence length to a linear scale. These models extended the maximum input sequence length from 512 to 4096, which enhanced the ability of modeling long-term dependency and consequently achieved optimal results in a variety of tasks. Inspired by the success of these long sequence transformer models, we introduce two domain enriched language models, namely Clinical-Longformer and Clinical-BigBird, which are pre-trained from large-scale clinical corpora. We evaluate both pre-trained models using 10 baseline tasks including named entity recognition, question answering, and document classification tasks. The results demonstrate that Clinical-Longformer and Clinical-BigBird consistently and significantly outperform ClinicalBERT as well as other short-sequence transformers in all downstream tasks. We have made our source code available at [https://github.com/luoyuanlab/Clinical-Longformer] the pre-trained models available for public download at: [https://huggingface.co/yikuan8/Clinical-Longformer].

Clinical Question Answering (QA) systems enable doctors to quickly access patient information from electronic health records (EHRs). However, training these systems requires significant annotated data, which is limited due to the expertise needed and the privacy concerns associated with clinical data. This paper explores generating Clinical QA data using large language models (LLMs) in a zero-shot setting. We find that naive prompting often results in easy questions that do not reflect the complexity of clinical scenarios. To address this, we propose two prompting strategies: 1) instructing the model to generate questions that do not overlap with the input context, and 2) summarizing the input record using a predefined schema to scaffold question generation. Experiments on two Clinical QA datasets demonstrate that our method generates more challenging questions, significantly improving fine-tuning performance over baselines. We compare synthetic and gold data and find a gap between their training efficacy resulting from the quality of synthetically generated answers.

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

Large Language Models (LLMs) hold great promise to revolutionize current clinical systems for their superior capacities on medical text processing tasks and medical licensing exams. Meanwhile, traditional ML models such as SVM and XGBoost have still been mainly adopted in clinical prediction tasks. An emerging question is Can LLMs beat traditional ML models in clinical prediction? Thus, we build a new benchmark ClinicalBench to comprehensively study the clinical predictive modeling capacities of both general-purpose and medical LLMs, and compare them with traditional ML models. ClinicalBench embraces three common clinical prediction tasks, two databases, 14 general-purpose LLMs, 8 medical LLMs, and 11 traditional ML models. Through extensive empirical investigation, we discover that both general-purpose and medical LLMs, even with different model scales, diverse prompting or fine-tuning strategies, still cannot beat traditional ML models in clinical prediction yet, shedding light on their potential deficiency in clinical reasoning and decision-making. We call for caution when practitioners adopt LLMs in clinical applications. ClinicalBench can be utilized to bridge the gap between LLMs' development for healthcare and real-world clinical practice.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

The rapid development of Large Language Models (LLMs) for healthcare applications has spurred calls for holistic evaluation beyond frequently-cited benchmarks like USMLE, to better reflect real-world performance. While real-world assessments are valuable indicators of utility, they often lag behind the pace of LLM evolution, likely rendering findings obsolete upon deployment. This temporal disconnect necessitates a comprehensive upfront evaluation that can guide model selection for specific clinical applications. We introduce MEDIC, a framework assessing LLMs across five critical dimensions of clinical competence: medical reasoning, ethics and bias, data and language understanding, in-context learning, and clinical safety. MEDIC features a novel cross-examination framework quantifying LLM performance across areas like coverage and hallucination detection, without requiring reference outputs. We apply MEDIC to evaluate LLMs on medical question-answering, safety, summarization, note generation, and other tasks. Our results show performance disparities across model sizes, baseline vs medically finetuned models, and have implications on model selection for applications requiring specific model strengths, such as low hallucination or lower cost of inference. MEDIC's multifaceted evaluation reveals these performance trade-offs, bridging the gap between theoretical capabilities and practical implementation in healthcare settings, ensuring that the most promising models are identified and adapted for diverse healthcare applications.

Mental health is a critical issue in modern society, and mental disorders could sometimes turn to suicidal ideation without adequate treatment. Early detection of mental disorders and suicidal ideation from social content provides a potential way for effective social intervention. Recent advances in pretrained contextualized language representations have promoted the development of several domain-specific pretrained models and facilitated several downstream applications. However, there are no existing pretrained language models for mental healthcare. This paper trains and release two pretrained masked language models, i.e., MentalBERT and MentalRoBERTa, to benefit machine learning for the mental healthcare research community. Besides, we evaluate our trained domain-specific models and several variants of pretrained language models on several mental disorder detection benchmarks and demonstrate that language representations pretrained in the target domain improve the performance of mental health detection tasks.

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.

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.

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.

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity Recognition (NER). Recent research in biomedical language processing has offered a number of biomedical LMs pre-trained using different methods and techniques that advance results on many BioNLP tasks, including NER. However, there is still a lack of a comprehensive comparison of pre-training approaches that would work more optimally in the biomedical domain. This paper aims to investigate different pre-training methods, such as pre-training the biomedical LM from scratch and pre-training it in a continued fashion. We compare existing methods with our proposed pre-training method of initializing weights for new tokens by distilling existing weights from the BERT model inside the context where the tokens were found. The method helps to speed up the pre-training stage and improve performance on NER. In addition, we compare how masking rate, corruption strategy, and masking strategies impact the performance of the biomedical LM. Finally, using the insights from our experiments, we introduce a new biomedical LM (BIOptimus), which is pre-trained using Curriculum Learning (CL) and contextualized weight distillation method. Our model sets new states of the art on several biomedical Named Entity Recognition (NER) tasks. We release our code and all pre-trained models

Foundation Models (FMs) trained on Electronic Health Records (EHRs) have achieved state-of-the-art results on numerous clinical prediction tasks. However, most existing EHR FMs have context windows of <1k tokens. This prevents them from modeling full patient EHRs which can exceed 10k's of events. Recent advancements in subquadratic long-context architectures (e.g., Mamba) offer a promising solution. However, their application to EHR data has not been well-studied. We address this gap by presenting the first systematic evaluation of the effect of context length on modeling EHR data. We find that longer context models improve predictive performance -- our Mamba-based model surpasses the prior state-of-the-art on 9/14 tasks on the EHRSHOT prediction benchmark. For clinical applications, however, model performance alone is insufficient -- robustness to the unique properties of EHR is crucial. Thus, we also evaluate models across three previously underexplored properties of EHR data: (1) the prevalence of "copy-forwarded" diagnoses which creates artificial repetition of tokens within EHR sequences; (2) the irregular time intervals between EHR events which can lead to a wide range of timespans within a context window; and (3) the natural increase in disease complexity over time which makes later tokens in the EHR harder to predict than earlier ones. Stratifying our EHRSHOT results, we find that higher levels of each property correlate negatively with model performance, but that longer context models are more robust to more extreme levels of these properties. Our work highlights the potential for using long-context architectures to model EHR data, and offers a case study for identifying new challenges in modeling sequential data motivated by domains outside of natural language. We release our models and code at: https://github.com/som-shahlab/long_context_clues

Large Language Models (LLMs) are at the forefront of NLP achievements but fall short in dealing with shortcut learning, factual inconsistency, and vulnerability to adversarial inputs.These shortcomings are especially critical in medical contexts, where they can misrepresent actual model capabilities. Addressing this, we present SemEval-2024 Task 2: Safe Biomedical Natural Language Inference for ClinicalTrials. Our contributions include the refined NLI4CT-P dataset (i.e., Natural Language Inference for Clinical Trials - Perturbed), designed to challenge LLMs with interventional and causal reasoning tasks, along with a comprehensive evaluation of methods and results for participant submissions. A total of 106 participants registered for the task contributing to over 1200 individual submissions and 25 system overview papers. This initiative aims to advance the robustness and applicability of NLI models in healthcare, ensuring safer and more dependable AI assistance in clinical decision-making. We anticipate that the dataset, models, and outcomes of this task can support future research in the field of biomedical NLI. The dataset, competition leaderboard, and website are publicly available.

Many cognitive approaches to well-being, such as recognizing and reframing unhelpful thoughts, have received considerable empirical support over the past decades, yet still lack truly widespread adoption in self-help format. A barrier to that adoption is a lack of adequately specific and diverse dedicated practice material. This work examines whether current language models can be leveraged to both produce a virtually unlimited quantity of practice material illustrating standard unhelpful thought patterns matching specific given contexts, and generate suitable positive reframing proposals. We propose PATTERNREFRAME, a novel dataset of about 10k examples of thoughts containing unhelpful thought patterns conditioned on a given persona, accompanied by about 27k positive reframes. By using this dataset to train and/or evaluate current models, we show that existing models can already be powerful tools to help generate an abundance of tailored practice material and hypotheses, with no or minimal additional model training required.

The advancement of large language models (LLMs) has opened new frontiers in natural language processing, particularly in specialized domains like healthcare. In this paper, we propose the Incremental Curriculum-Based Fine-Tuning (ICFT) framework to enhance the generative capabilities of medical large language models (MLLMs). ICFT combines curriculum-based learning, dual-stage memory coordination, and parameter-efficient fine-tuning to enable a progressive transition from general linguistic knowledge to strong domain-specific expertise. Experimental results across diverse medical NLP tasks, including question answering, preference classification, and response generation, demonstrate that ICFT consistently outperforms state-of-the-art baselines, achieving improvements in both accuracy and efficiency. Further analysis reveals the framework's ability to generalize to unseen data, reduce errors, and deliver diverse, contextually relevant medical responses. These findings establish ICFT as a robust and scalable solution for adapting LLMs to the medical domain, offering practical benefits for real-world healthcare applications.

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.

Multiple Instance Learning (MIL) is a cornerstone approach in computational pathology (CPath) for generating clinically meaningful slide-level embeddings from gigapixel tissue images. However, MIL often struggles with small, weakly supervised clinical datasets. In contrast to fields such as NLP and conventional computer vision, where transfer learning is widely used to address data scarcity, the transferability of MIL models remains poorly understood. In this study, we systematically evaluate the transfer learning capabilities of pretrained MIL models by assessing 11 models across 21 pretraining tasks for morphological and molecular subtype prediction. Our results show that pretrained MIL models, even when trained on different organs than the target task, consistently outperform models trained from scratch. Moreover, pretraining on pancancer datasets enables strong generalization across organs and tasks, outperforming slide foundation models while using substantially less pretraining data. These findings highlight the robust adaptability of MIL models and demonstrate the benefits of leveraging transfer learning to boost performance in CPath. Lastly, we provide a resource which standardizes the implementation of MIL models and collection of pretrained model weights on popular CPath tasks, available at https://github.com/mahmoodlab/MIL-Lab

Recent advances in large language models have led to renewed interest in natural language processing in healthcare using the free text of clinical notes. One distinguishing characteristic of clinical notes is their long time span over multiple long documents. The unique structure of clinical notes creates a new design choice: when the context length for a language model predictor is limited, which part of clinical notes should we choose as the input? Existing studies either choose the inputs with domain knowledge or simply truncate them. We propose a framework to analyze the sections with high predictive power. Using MIMIC-III, we show that: 1) predictive power distribution is different between nursing notes and discharge notes and 2) combining different types of notes could improve performance when the context length is large. Our findings suggest that a carefully selected sampling function could enable more efficient information extraction from clinical notes.

We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.

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.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

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

Large language models offer transformative potential for healthcare, yet their responsible and equitable development depends critically on a deeper understanding of how training data characteristics influence model behavior, including the potential for bias. Current practices in dataset curation and bias assessment often lack the necessary transparency, creating an urgent need for comprehensive evaluation frameworks to foster trust and guide improvements. In this study, we present an in-depth analysis of potential downstream biases in clinical language models, with a focus on differential opioid prescription tendencies across diverse demographic groups, such as ethnicity, gender, and age. As part of this investigation, we introduce HC4: Healthcare Comprehensive Commons Corpus, a novel and extensively curated pretraining dataset exceeding 89 billion tokens. Our evaluation leverages both established general benchmarks and a novel, healthcare-specific methodology, offering crucial insights to support fairness and safety in clinical AI applications.

Background: General-purpose large language models that utilize both text and images have not been evaluated on a diverse array of challenging medical cases. Methods: Using 934 cases from the NEJM Image Challenge published between 2005 and 2023, we evaluated the accuracy of the recently released Generative Pre-trained Transformer 4 with Vision model (GPT-4V) compared to human respondents overall and stratified by question difficulty, image type, and skin tone. We further conducted a physician evaluation of GPT-4V on 69 NEJM clinicopathological conferences (CPCs). Analyses were conducted for models utilizing text alone, images alone, and both text and images. Results: GPT-4V achieved an overall accuracy of 61% (95% CI, 58 to 64%) compared to 49% (95% CI, 49 to 50%) for humans. GPT-4V outperformed humans at all levels of difficulty and disagreement, skin tones, and image types; the exception was radiographic images, where performance was equivalent between GPT-4V and human respondents. Longer, more informative captions were associated with improved performance for GPT-4V but similar performance for human respondents. GPT-4V included the correct diagnosis in its differential for 80% (95% CI, 68 to 88%) of CPCs when using text alone, compared to 58% (95% CI, 45 to 70%) of CPCs when using both images and text. Conclusions: GPT-4V outperformed human respondents on challenging medical cases and was able to synthesize information from both images and text, but performance deteriorated when images were added to highly informative text. Overall, our results suggest that multimodal AI models may be useful in medical diagnostic reasoning but that their accuracy may depend heavily on context.

We focus on the Source Free Object Detection (SFOD) problem, when source data is unavailable during adaptation, and the model must adapt to the unlabeled target domain. In medical imaging, several approaches have leveraged a semi-supervised student-teacher architecture to bridge domain discrepancy. Context imbalance in labeled training data and significant domain shifts between domains can lead to biased teacher models that produce inaccurate pseudolabels, degrading the student model's performance and causing a mode collapse. Class imbalance, particularly when one class significantly outnumbers another, leads to contextual bias. To tackle the problem of context bias and the significant performance drop of the student model in the SFOD setting, we introduce Grounded Teacher (GT) as a standard framework. In this study, we model contextual relationships using a dedicated relational context module and leverage it to mitigate inherent biases in the model. This approach enables us to apply augmentations to closely related classes, across and within domains, enhancing the performance of underrepresented classes while keeping the effect on dominant classes minimal. We further improve the quality of predictions by implementing an expert foundational branch to supervise the student model. We validate the effectiveness of our approach in mitigating context bias under the SFOD setting through experiments on three medical datasets supported by comprehensive ablation studies. All relevant resources, including preprocessed data, trained model weights, and code, are publicly available at this https://github.com/Tajamul21/Grounded_Teacher.

In this paper, we introduce a unified and generalist Biomedical Generative Pre-trained Transformer (BiomedGPT) model, which leverages self-supervision on large and diverse datasets to accept multi-modal inputs and perform a range of downstream tasks. Our experiments demonstrate that BiomedGPT delivers expansive and inclusive representations of biomedical data, outperforming the majority of preceding state-of-the-art models across five distinct tasks with 20 public datasets spanning over 15 unique biomedical modalities. Through the ablation study, we also showcase the efficacy of our multi-modal and multi-task pretraining approach in transferring knowledge to previously unseen data. Overall, our work presents a significant step forward in developing unified and generalist models for biomedicine, with far-reaching implications for improving healthcare outcomes.

Adapting pretrained language models to novel domains, such as clinical applications, traditionally involves retraining their entire set of parameters. Parameter-Efficient Fine-Tuning (PEFT) techniques for fine-tuning language models significantly reduce computational requirements by selectively fine-tuning small subsets of parameters. In this study, we propose a two-step PEFT framework and evaluate it in the clinical domain. Our approach combines a specialised PEFT adapter layer designed for clinical domain adaptation with another adapter specialised for downstream tasks. We evaluate the framework on multiple clinical outcome prediction datasets, comparing it to clinically trained language models. Our framework achieves a better AUROC score averaged across all clinical downstream tasks compared to clinical language models. In particular, we observe large improvements of 4-5% AUROC in large-scale multilabel classification tasks, such as diagnoses and procedures classification. To our knowledge, this study is the first to provide an extensive empirical analysis of the interplay between PEFT techniques and domain adaptation in an important real-world domain of clinical applications.

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

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

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

Clinical notes in Electronic Health Records (EHR) present rich documented information of patients to inference phenotype for disease diagnosis and study patient characteristics for cohort selection. Unsupervised user embedding aims to encode patients into fixed-length vectors without human supervisions. Medical concepts extracted from the clinical notes contain rich connections between patients and their clinical categories. However, existing unsupervised approaches of user embeddings from clinical notes do not explicitly incorporate medical concepts. In this study, we propose a concept-aware unsupervised user embedding that jointly leverages text documents and medical concepts from two clinical corpora, MIMIC-III and Diabetes. We evaluate user embeddings on both extrinsic and intrinsic tasks, including phenotype classification, in-hospital mortality prediction, patient retrieval, and patient relatedness. Experiments on the two clinical corpora show our approach exceeds unsupervised baselines, and incorporating medical concepts can significantly improve the baseline performance.

Objectives: We aim to dynamically retrieve informative demonstrations, enhancing in-context learning in multimodal large language models (MLLMs) for disease classification. Methods: We propose a Retrieval-Augmented In-Context Learning (RAICL) framework, which integrates retrieval-augmented generation (RAG) and in-context learning (ICL) to adaptively select demonstrations with similar disease patterns, enabling more effective ICL in MLLMs. Specifically, RAICL examines embeddings from diverse encoders, including ResNet, BERT, BioBERT, and ClinicalBERT, to retrieve appropriate demonstrations, and constructs conversational prompts optimized for ICL. We evaluated the framework on two real-world multi-modal datasets (TCGA and IU Chest X-ray), assessing its performance across multiple MLLMs (Qwen, Llava, Gemma), embedding strategies, similarity metrics, and varying numbers of demonstrations. Results: RAICL consistently improved classification performance. Accuracy increased from 0.7854 to 0.8368 on TCGA and from 0.7924 to 0.8658 on IU Chest X-ray. Multi-modal inputs outperformed single-modal ones, with text-only inputs being stronger than images alone. The richness of information embedded in each modality will determine which embedding model can be used to get better results. Few-shot experiments showed that increasing the number of retrieved examples further enhanced performance. Across different similarity metrics, Euclidean distance achieved the highest accuracy while cosine similarity yielded better macro-F1 scores. RAICL demonstrated consistent improvements across various MLLMs, confirming its robustness and versatility. Conclusions: RAICL provides an efficient and scalable approach to enhance in-context learning in MLLMs for multimodal disease classification.

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

Brief hospital course (BHC) summaries are common clinical documents generated by summarizing clinical notes. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as BHC synthesis have not been shown. To enable the adaptation of LLMs for BHC synthesis, we introduce a novel benchmark consisting of a pre-processed dataset extracted from MIMIC-IV notes, encapsulating clinical note, and brief hospital course (BHC) pairs. We assess the performance of two general-purpose LLMs and three healthcare-adapted LLMs to improve BHC synthesis from clinical notes. Using clinical notes as input for generating BHCs, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to three open-source LLMs (Clinical-T5-Large, Llama2-13B, FLAN-UL2) and two proprietary LLMs (GPT-3.5, GPT-4). We quantitatively evaluate the performance of these LLMs across varying context-length inputs using conventional natural language similarity metrics. We further perform a qualitative study where five diverse clinicians blindly compare clinician-written BHCs and two LLM-generated BHCs for 30 samples across metrics of comprehensiveness, conciseness, factual correctness, and fluency. Overall, we present a new benchmark and pre-processed dataset for using LLMs in BHC synthesis from clinical notes. We observe high-quality summarization performance for both in-context proprietary and fine-tuned open-source LLMs using both quantitative metrics and a qualitative clinical reader study. We propose our work as a benchmark to motivate future works to adapt and assess the performance of LLMs in BHC synthesis.

High-quality and carefully curated data is a cornerstone of training medical large language models, as it directly impacts both generalization and robustness to unseen clinical tasks. We investigate strategies for training and data curation to develop a robust multimodal reasoning model in the medical domain. Our work focuses on supervised fine-tuning (SFT) and explores data recipes that leverage structured reasoning traces. Using our proposed data recipe, we scale experiments to a dataset of over 8 million examples and 6.8 billion response tokens, achieving state-of-the-art performance among open-source models across diverse out-of-distribution medical benchmark tasks. Our results further indicate that curating a high-quality, diverse training dataset with varying structured reasoning trace lengths enables the fine-tuned model to self-calibrate its reasoning trajectory lengths based on the downstream task, without explicit supervision. We present key insights, describe the data curation strategy, and outline next steps toward developing robust medical vision-language reasoning system.

Medical decision-making requires integrating diverse medical information, from imaging to clinical narratives. These medical modalities are often acquired in a many-to-many manner. However, current medical vision-language pretraining models (Med-VLPMs) fail to directly account for this many-to-many mapping in their model training and embeddings. To address this, we present Probabilistic Modality-Enhanced Diagnosis (ProbMED), a multimodal Med-VLPM that employs probabilistic contrastive learning to model distributions over embeddings rather than deterministic estimates. ProbMED aligns four distinct modalities -- chest X-rays, electrocardiograms, echocardiograms, and clinical text -- into a unified probabilistic embedding space. We use InfoNCE loss with Hellinger distance to integrate inter-modality distributions. We introduce a probabilistic synthetic sampling loss that captures modality-specific mean and variance to improve intra-modality binding. Extensive experiments across 13 medical datasets demonstrate that our model outperforms current Med-VLPMs in cross-modality retrieval, zero-shot, and few-shot classification. We also demonstrate the robust integration of multiple modalities for prognostication, showing improved intra- and inter-medical modality binding.

The recent surge of foundation models in computer vision and natural language processing opens up perspectives in utilizing multi-modal clinical data to train large models with strong generalizability. Yet pathological image datasets often lack biomedical text annotation and enrichment. Guiding data-efficient image diagnosis from the use of biomedical text knowledge becomes a substantial interest. In this paper, we propose to Connect Image and Text Embeddings (CITE) to enhance pathological image classification. CITE injects text insights gained from language models pre-trained with a broad range of biomedical texts, leading to adapt foundation models towards pathological image understanding. Through extensive experiments on the PatchGastric stomach tumor pathological image dataset, we demonstrate that CITE achieves leading performance compared with various baselines especially when training data is scarce. CITE offers insights into leveraging in-domain text knowledge to reinforce data-efficient pathological image classification. Code is available at https://github.com/Yunkun-Zhang/CITE.

Training models on low-resource named entity recognition tasks has been shown to be a challenge, especially in industrial applications where deploying updated models is a continuous effort and crucial for business operations. In such cases there is often an abundance of unlabeled data, while labeled data is scarce or unavailable. Pre-trained language models trained to extract contextual features from text were shown to improve many natural language processing (NLP) tasks, including scarcely labeled tasks, by leveraging transfer learning. However, such models impose a heavy memory and computational burden, making it a challenge to train and deploy such models for inference use. In this work-in-progress we combined the effectiveness of transfer learning provided by pre-trained masked language models with a semi-supervised approach to train a fast and compact model using labeled and unlabeled examples. Preliminary evaluations show that the compact models can achieve competitive accuracy with 36x compression rate when compared with a state-of-the-art pre-trained language model, and run significantly faster in inference, allowing deployment of such models in production environments or on edge devices.

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

Recent advancements in Large Multimodal Models (LMMs) have attracted interest in their generalization capability with only a few samples in the prompt. This progress is particularly relevant to the medical domain, where the quality and sensitivity of data pose unique challenges for model training and application. However, the dependency on high-quality data for effective in-context learning raises questions about the feasibility of these models when encountering with the inevitable variations and errors inherent in real-world medical data. In this paper, we introduce MID-M, a novel framework that leverages the in-context learning capabilities of a general-domain Large Language Model (LLM) to process multimodal data via image descriptions. MID-M achieves a comparable or superior performance to task-specific fine-tuned LMMs and other general-domain ones, without the extensive domain-specific training or pre-training on multimodal data, with significantly fewer parameters. This highlights the potential of leveraging general-domain LLMs for domain-specific tasks and offers a sustainable and cost-effective alternative to traditional LMM developments. Moreover, the robustness of MID-M against data quality issues demonstrates its practical utility in real-world medical domain applications.

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

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

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

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

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

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

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

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.

Leveraging pre-trained models with tailored prompts for in-context learning has proven highly effective in NLP tasks. Building on this success, recent studies have applied a similar approach to the Segment Anything Model (SAM) within a ``one-shot" framework, where only a single reference image and its label are employed. However, these methods face limitations in the medical domain, primarily due to SAM's essential requirement for visual prompts and the over-reliance on pixel similarity for generating them. This dependency may lead to (1) inaccurate prompt generation and (2) clustering of point prompts, resulting in suboptimal outcomes. To address these challenges, we introduce Med-PerSAM, a novel and straightforward one-shot framework designed for the medical domain. Med-PerSAM uses only visual prompt engineering and eliminates the need for additional training of the pretrained SAM or human intervention, owing to our novel automated prompt generation process. By integrating our lightweight warping-based prompt tuning model with SAM, we enable the extraction and iterative refinement of visual prompts, enhancing the performance of the pre-trained SAM. This advancement is particularly meaningful in the medical domain, where creating visual prompts poses notable challenges for individuals lacking medical expertise. Our model outperforms various foundational models and previous SAM-based approaches across diverse 2D medical imaging datasets.

Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.

Clinical Natural Language Processing (NLP) has become an emerging technology in healthcare that leverages a large amount of free-text data in electronic health records (EHRs) to improve patient care, support clinical decisions, and facilitate clinical and translational science research. Recently, deep learning has achieved state-of-the-art performance in many clinical NLP tasks. However, training deep learning models usually requires large annotated datasets, which are normally not publicly available and can be time-consuming to build in clinical domains. Working with smaller annotated datasets is typical in clinical NLP and therefore, ensuring that deep learning models perform well is crucial for the models to be used in real-world applications. A widely adopted approach is fine-tuning existing Pre-trained Language Models (PLMs), but these attempts fall short when the training dataset contains only a few annotated samples. Few-Shot Learning (FSL) has recently been investigated to tackle this problem. Siamese Neural Network (SNN) has been widely utilized as an FSL approach in computer vision, but has not been studied well in NLP. Furthermore, the literature on its applications in clinical domains is scarce. In this paper, we propose two SNN-based FSL approaches for clinical NLP, including Pre-Trained SNN (PT-SNN) and SNN with Second-Order Embeddings (SOE-SNN). We evaluated the proposed approaches on two clinical tasks, namely clinical text classification and clinical named entity recognition. We tested three few-shot settings including 4-shot, 8-shot, and 16-shot learning. Both clinical NLP tasks were benchmarked using three PLMs, including BERT,BioBERT, and BioClinicalBERT. The experimental results verified the effectiveness of the proposed SNN-based FSL approaches in both NLP tasks.

This study assesses deep learning models for audio classification in a clinical setting with the constraint of small datasets reflecting real-world prospective data collection. We analyze CNNs, including DenseNet and ConvNeXt, alongside transformer models like ViT, SWIN, and AST, and compare them against pre-trained audio models such as YAMNet and VGGish. Our method highlights the benefits of pre-training on large datasets before fine-tuning on specific clinical data. We prospectively collected two first-of-their-kind patient audio datasets from stroke patients. We investigated various preprocessing techniques, finding that RGB and grayscale spectrogram transformations affect model performance differently based on the priors they learn from pre-training. Our findings indicate CNNs can match or exceed transformer models in small dataset contexts, with DenseNet-Contrastive and AST models showing notable performance. This study highlights the significance of incremental marginal gains through model selection, pre-training, and preprocessing in sound classification; this offers valuable insights for clinical diagnostics that rely on audio classification.

The rapid progress in Large Language Models (LLMs) has prompted the creation of numerous benchmarks to evaluate their capabilities.This study focuses on the Comprehensive Medical Benchmark in Chinese (CMB), showcasing how dataset diversity and distribution in supervised fine-tuning (SFT) may enhance LLM performance.Remarkably, We successfully trained a smaller base model to achieve scores comparable to larger models, indicating that a diverse and well-distributed dataset can optimize performance regardless of model size.This study suggests that even smaller models may reach high performance levels with carefully curated and varied datasets.By integrating a wide range of instructional content, our approach addresses potential issues such as data quality inconsistencies. Our results imply that a broader spectrum of training data may enhance a model's ability to generalize and perform effectively across different medical scenarios, highlighting the importance of dataset quality and diversity in fine-tuning processes.

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

We introduce a novel contextual embedding model med-gte-hybrid that was derived from the gte-large sentence transformer to extract information from unstructured clinical narratives. Our model tuning strategy for med-gte-hybrid combines contrastive learning and a denoising autoencoder. To evaluate the performance of med-gte-hybrid, we investigate several clinical prediction tasks in large patient cohorts extracted from the MIMIC-IV dataset, including Chronic Kidney Disease (CKD) patient prognosis, estimated glomerular filtration rate (eGFR) prediction, and patient mortality prediction. Furthermore, we demonstrate that the med-gte-hybrid model improves patient stratification, clustering, and text retrieval, thus outperforms current state-of-the-art models on the Massive Text Embedding Benchmark (MTEB). While some of our evaluations focus on CKD, our hybrid tuning of sentence transformers could be transferred to other medical domains and has the potential to improve clinical decision-making and personalised treatment pathways in various healthcare applications.

Multimodal large language models (MLLMs) have demonstrated promising prospects in healthcare, particularly for addressing complex medical tasks, supporting multidisciplinary treatment (MDT), and enabling personalized precision medicine. However, their practical deployment faces critical challenges in resource efficiency, diagnostic accuracy, clinical considerations, and ethical privacy. To address these limitations, we propose Infi-Med, a comprehensive framework for medical MLLMs that introduces three key innovations: (1) a resource-efficient approach through curating and constructing high-quality supervised fine-tuning (SFT) datasets with minimal sample requirements, with a forward-looking design that extends to both pretraining and posttraining phases; (2) enhanced multimodal reasoning capabilities for cross-modal integration and clinical task understanding; and (3) a systematic evaluation system that assesses model performance across medical modalities and task types. Our experiments demonstrate that Infi-Med achieves state-of-the-art (SOTA) performance in general medical reasoning while maintaining rapid adaptability to clinical scenarios. The framework establishes a solid foundation for deploying MLLMs in real-world healthcare settings by balancing model effectiveness with operational constraints.

Large language models exhibit promising general capabilities but often lack specialized knowledge for domain-specific tasks. Developing domain experts from a base model enables a range of applications without prohibitive training costs. This work demonstrates a method using continuous training and instruction fine-tuning to rapidly adapt Llama 2 base models to the Chinese medical domain. We first conduct continuous training on 1B tokens from Chinese medical references to teach relevant vocabulary and knowledge. The models are then fine-tuned on 54K examples sourced from the Chinese National Medical Licensing Examination. Experiments on Chinese medical data confirm the effectiveness of this approach, producing a model comparable to GPT-3.5-turbo while using way less computational resource. The resulting domain-specific model could be useful for various Chinese medical applications. More broadly, this provides a template for domain-specific training of large language models in areas where pre-trained models lack the required expertise, such as law, science, and engineering.

In-context learning, where pre-trained language models learn to perform tasks from task examples and instructions in their contexts, has attracted much attention in the NLP community. However, the ability of in-context learning is not fully exploited because language models are not explicitly trained to learn in context. To this end, we propose PICL (Pre-training for In-Context Learning), a framework to enhance the language models' in-context learning ability by pre-training the model on a large collection of "intrinsic tasks" in the general plain-text corpus using the simple language modeling objective. PICL encourages the model to infer and perform tasks by conditioning on the contexts while maintaining task generalization of pre-trained models. We evaluate the in-context learning performance of the model trained with PICL on seven widely-used text classification datasets and the Super-NaturalInstrctions benchmark, which contains 100+ NLP tasks formulated to text generation. Our experiments show that PICL is more effective and task-generalizable than a range of baselines, outperforming larger language models with nearly 4x parameters. The code is publicly available at https://github.com/thu-coai/PICL.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks. This also benefits biomedical domain: researchers from informatics, medicine, and computer science (CS) communities propose various PLMs trained on biomedical datasets, e.g., biomedical text, electronic health records, protein, and DNA sequences for various biomedical tasks. However, the cross-discipline characteristics of biomedical PLMs hinder their spreading among communities; some existing works are isolated from each other without comprehensive comparison and discussions. It expects a survey that not only systematically reviews recent advances of biomedical PLMs and their applications but also standardizes terminology and benchmarks. In this paper, we summarize the recent progress of pre-trained language models in the biomedical domain and their applications in biomedical downstream tasks. Particularly, we discuss the motivations and propose a taxonomy of existing biomedical PLMs. Their applications in biomedical downstream tasks are exhaustively discussed. At last, we illustrate various limitations and future trends, which we hope can provide inspiration for the future research of the research community.

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

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

Medical Vision-Language Pretraining (MedVLP) shows promise in learning generalizable and transferable visual representations from paired and unpaired medical images and reports. MedVLP can provide useful features to downstream tasks and facilitate adapting task-specific models to new setups using fewer examples. However, existing MedVLP methods often differ in terms of datasets, preprocessing, and finetuning implementations. This pose great challenges in evaluating how well a MedVLP method generalizes to various clinically-relevant tasks due to the lack of unified, standardized, and comprehensive benchmark. To fill this gap, we propose BenchX, a unified benchmark framework that enables head-to-head comparison and systematical analysis between MedVLP methods using public chest X-ray datasets. Specifically, BenchX is composed of three components: 1) Comprehensive datasets covering nine datasets and four medical tasks; 2) Benchmark suites to standardize data preprocessing, train-test splits, and parameter selection; 3) Unified finetuning protocols that accommodate heterogeneous MedVLP methods for consistent task adaptation in classification, segmentation, and report generation, respectively. Utilizing BenchX, we establish baselines for nine state-of-the-art MedVLP methods and found that the performance of some early MedVLP methods can be enhanced to surpass more recent ones, prompting a revisiting of the developments and conclusions from prior works in MedVLP. Our code are available at https://github.com/yangzhou12/BenchX.

Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was performed in two ways: i) connecting words that have the same underlying `concept' in UMLS, and ii) leveraging semantic group knowledge in UMLS to create clinically meaningful input embeddings. By applying these two strategies, UmlsBERT can encode clinical domain knowledge into word embeddings and outperform existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference clinical NLP tasks.

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.

Clinical notes contain rich data, which is unexploited in predictive modeling compared to structured data. In this work, we developed a new text representation Clinical XLNet for clinical notes which also leverages the temporal information of the sequence of the notes. We evaluated our models on prolonged mechanical ventilation prediction problem and our experiments demonstrated that Clinical XLNet outperforms the best baselines consistently.

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Knowledge Distillation (KD), it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from 15 million to 65 million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including Natural Language Inference, Relation Extraction, Named Entity Recognition, and Sequence Classification. To our knowledge, this is the first comprehensive study specifically focused on creating efficient and compact transformers for clinical NLP tasks. The models and code used in this study can be found on our Huggingface profile at https://huggingface.co/nlpie and Github page at https://github.com/nlpie-research/Lightweight-Clinical-Transformers, respectively, promoting reproducibility of our results.

Existing pre-trained models are generally geared towards a particular class of problems. To date, there seems to be still no consensus on what the right architecture and pre-training setup should be. This paper presents a unified framework for pre-training models that are universally effective across datasets and setups. We begin by disentangling architectural archetypes with pre-training objectives -- two concepts that are commonly conflated. Next, we present a generalized & unified perspective for self-supervision in NLP and show how different pre-training objectives can be cast as one another and how interpolating between different objectives can be effective. We then propose Mixture-of-Denoisers (MoD), a pre-training objective that combines diverse pre-training paradigms together. We furthermore introduce a notion of mode switching, wherein downstream fine-tuning is associated with specific pre-training schemes. We conduct extensive ablative experiments to compare multiple pre-training objectives and find that our method pushes the Pareto-frontier by outperforming T5 & GPT-like models across multiple diverse setups. By scaling our model up to 20B parameters, we achieve SOTA performance on 50 well-established supervised finetuning based NLP tasks. Our model also achieve strong results at in-context learning, outperforming 175B GPT-3 on zero-shot SuperGLUE and tripling the performance of T5-XXL on one-shot summarization. On 0-shot MMLU, UL2 20B outperforms T0 and T5 models. UL2 20B also works well with chain-of-thought prompting and reasoning, making it an appealing choice for research into reasoning at a small to medium scale of 20B parameters. Finally, we apply FLAN instruction tuning to the UL2 20B model, achieving MMLU and Big-Bench scores competitive to FLAN-PaLM 62B. We release Flax-based T5X checkpoints for the UL2 20B & Flan-UL2 20B.

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

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

With the proliferation of Large Language Models (LLMs) in diverse domains, there is a particular need for unified evaluation standards in clinical medical scenarios, where models need to be examined very thoroughly. We present CliMedBench, a comprehensive benchmark with 14 expert-guided core clinical scenarios specifically designed to assess the medical ability of LLMs across 7 pivot dimensions. It comprises 33,735 questions derived from real-world medical reports of top-tier tertiary hospitals and authentic examination exercises. The reliability of this benchmark has been confirmed in several ways. Subsequent experiments with existing LLMs have led to the following findings: (i) Chinese medical LLMs underperform on this benchmark, especially where medical reasoning and factual consistency are vital, underscoring the need for advances in clinical knowledge and diagnostic accuracy. (ii) Several general-domain LLMs demonstrate substantial potential in medical clinics, while the limited input capacity of many medical LLMs hinders their practical use. These findings reveal both the strengths and limitations of LLMs in clinical scenarios and offer critical insights for medical research.

Domain-specific text embeddings are critical for clinical natural language processing, yet systematic comparisons across model architectures remain limited. This study evaluates ten transformer-based embedding models adapted for cardiology through Low-Rank Adaptation (LoRA) fine-tuning on 106,535 cardiology text pairs derived from authoritative medical textbooks. Results demonstrate that encoder-only architectures, particularly BioLinkBERT, achieve superior domain-specific performance (separation score: 0.510) compared to larger decoder-based models, while requiring significantly fewer computational resources. The findings challenge the assumption that larger language models necessarily produce better domain-specific embeddings and provide practical guidance for clinical NLP system development. All models, training code, and evaluation datasets are publicly available to support reproducible research in medical informatics.

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.

We present a new dataset for machine comprehension in the medical domain. Our dataset uses clinical case reports with around 100,000 gap-filling queries about these cases. We apply several baselines and state-of-the-art neural readers to the dataset, and observe a considerable gap in performance (20% F1) between the best human and machine readers. We analyze the skills required for successful answering and show how reader performance varies depending on the applicable skills. We find that inferences using domain knowledge and object tracking are the most frequently required skills, and that recognizing omitted information and spatio-temporal reasoning are the most difficult for the machines.

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.

We present MedHal, a novel large-scale dataset specifically designed to evaluate if models can detect hallucinations in medical texts. Current hallucination detection methods face significant limitations when applied to specialized domains like medicine, where they can have disastrous consequences. Existing medical datasets are either too small, containing only a few hundred samples, or focus on a single task like Question Answering or Natural Language Inference. MedHal addresses these gaps by: (1) incorporating diverse medical text sources and tasks; (2) providing a substantial volume of annotated samples suitable for training medical hallucination detection models; and (3) including explanations for factual inconsistencies to guide model learning. We demonstrate MedHal's utility by training and evaluating a baseline medical hallucination detection model, showing improvements over general-purpose hallucination detection approaches. This resource enables more efficient evaluation of medical text generation systems while reducing reliance on costly expert review, potentially accelerating the development of medical AI research.

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 this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.

The integration of large language models (LLMs) into medical practice holds transformative potential, yet their real-world clinical utility remains limited by critical alignment challenges: (1) a disconnect between static evaluation benchmarks and dynamic clinical cognitive needs, (2) difficulties in adapting to evolving, multi-source medical standards, and (3) the inability of conventional reward models to capture nuanced, multi-dimensional medical quality criteria. To address these gaps, we propose MR-RML (Multidimensional Rubric-oriented Reward Model Learning) via GPRC (Geometric Projection Reference Constraints), a novel alignment framework that integrates medical standards into a structured "Dimensions-Scenarios-Disciplines" matrix to guide data generation and model optimization. MR-RML introduces three core innovations: (1) a "Dimensions-Scenarios-Disciplines" medical standard system that embeds domain standards into the full training pipeline; (2) an independent multi-dimensional reward model that decomposes evaluation criteria, shifting from real-time rubric-based scoring to internalized reward modeling for improved consistency and cost-efficiency; (3) geometric projection reference constraints that transform medical cognitive logic into mathematical regularization, aligning scoring gradients with clinical reasoning and enabling synthetic data-driven training. Through extensive evaluations on the authoritative medical benchmark Healthbench, our method yields substantial performance gains over the base LLM Qwen-32B (45% on the full subset and 85% on Hard subset, respectively). It achieves a SOTA among open-source LLMs with scores of 62.7 (full subset) and 44.7 (hard subset), while also outperforming the majority of closed-source models.

Vision-language pre-training has recently gained popularity as it allows learning rich feature representations using large-scale data sources. This paradigm has quickly made its way into the medical image analysis community. In particular, there is an impressive amount of recent literature developing vision-language models for radiology. However, the available medical datasets with image-text supervision are scarce, and medical concepts are fine-grained, involving expert knowledge that existing vision-language models struggle to encode. In this paper, we propose to take a prudent step back from the literature and revisit supervised, unimodal pre-training, using fine-grained labels instead. We conduct an extensive comparison demonstrating that unimodal pre-training is highly competitive and better suited to integrating heterogeneous data sources. Our results also question the potential of recent vision-language models for open-vocabulary generalization, which have been evaluated using optimistic experimental settings. Finally, we study novel alternatives to better integrate fine-grained labels and noisy text supervision.

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

In-context learning (ICL) improves language models' performance on a variety of NLP tasks by simply demonstrating a handful of examples at inference time. It is not well understood why ICL ability emerges, as the model has never been specifically trained on such demonstrations. Unlike prior work that explores implicit mechanisms behind ICL, we study ICL via investigating the pretraining data. Specifically, we first adapt an iterative, gradient-based approach to find a small subset of pretraining data that supports ICL. We observe that a continued pretraining on this small subset significantly improves the model's ICL ability, by up to 18%. We then compare the supportive subset constrastively with random subsets of pretraining data and discover: (1) The supportive pretraining data to ICL do not have a higher domain relevance to downstream tasks. (2) The supportive pretraining data have a higher mass of rarely occurring, long-tail tokens. (3) The supportive pretraining data are challenging examples where the information gain from long-range context is below average, indicating learning to incorporate difficult long-range context encourages ICL. Our work takes a first step towards understanding ICL via analyzing instance-level pretraining data. Our insights have a potential to enhance the ICL ability of language models by actively guiding the construction of pretraining data in the future.

Objective: Using natural language processing (NLP) to find sentences that state treatment plans in a clinical note, would automate plan extraction and would further enable their use in tools that help providers and care managers. However, as in the most NLP tasks on clinical text, creating gold standard to train and test NLP models is tedious and expensive. Fortuitously, sometimes but not always clinical notes contain sections with a heading that identifies the section as a plan. Leveraging contents of such labeled sections as a noisy training data, we assessed accuracy of NLP models trained with the data. Methods: We used common variations of plan headings and rule-based heuristics to find plan sections with headings in clinical notes, and we extracted sentences from them and formed a noisy training data of plan sentences. We trained Support Vector Machine (SVM) and Convolutional Neural Network (CNN) models with the data. We measured accuracy of the trained models on the noisy dataset using ten-fold cross validation and separately on a set-aside manually annotated dataset. Results: About 13% of 117,730 clinical notes contained treatment plans sections with recognizable headings in the 1001 longitudinal patient records that were obtained from Cleveland Clinic under an IRB approval. We were able to extract and create a noisy training data of 13,492 plan sentences from the clinical notes. CNN achieved best F measures, 0.91 and 0.97 in the cross-validation and set-aside evaluation experiments respectively. SVM slightly underperformed with F measures of 0.89 and 0.96 in the same experiments. Conclusion: Our study showed that the training supervised learning models using noisy plan sentences was effective in identifying them in all clinical notes. More broadly, sections with informal headings in clinical notes can be a good source for generating effective training data.

We propose MedicalNarratives, a dataset curated from medical pedagogical videos similar in nature to data collected in Think-Aloud studies and inspired by Localized Narratives, which collects grounded image-text data by curating instructors' speech and mouse cursor movements synchronized in time. MedicalNarratives enables pretraining of both semantic and dense objectives, alleviating the need to train medical semantic and dense tasks disparately due to the lack of reasonably sized datasets. Our dataset contains 4.7M image-text pairs from videos and articles, with 1M samples containing dense annotations in the form of traces and bounding boxes. To evaluate the utility of MedicalNarratives, we train GenMedClip based on the CLIP architecture using our dataset spanning 12 medical domains and demonstrate that it outperforms previous state-of-the-art models on a newly constructed medical imaging benchmark that comprehensively evaluates performance across all modalities. Data, demo, code and models available at https://medical-narratives.github.io

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large language models (LLMs) that can be used to solve diverse table tasks such as semantic parsing, question answering as well as classification problems. Traditionally, there existed separate models specialized for each task individually. It raises the question of how far can we go to build a unified model that works well on some table tasks without significant degradation on others. To that end, we attempt at creating a shared modeling approach in the pretraining stage with encoder-decoder style LLMs that can cater to diverse tasks. We evaluate our approach that continually pretrains and finetunes different model families of T5 with data from tables and surrounding context, on these downstream tasks at different model scales. Through multiple ablation studies, we observe that our pretraining with self-supervised objectives can significantly boost the performance of the models on these tasks. As an example of one improvement, we observe that the instruction finetuned public models which come specialized on text question answering (QA) and have been trained on table data still have room for improvement when it comes to table specific QA. Our work is the first attempt at studying the advantages of a unified approach to table specific pretraining when scaled from 770M to 11B sequence to sequence models while also comparing the instruction finetuned variants of the models.

The availability of different pre-trained semantic models enabled the quick development of machine learning components for downstream applications. Despite the availability of abundant text data for low resource languages, only a few semantic models are publicly available. Publicly available pre-trained models are usually built as a multilingual version of semantic models that can not fit well for each language due to context variations. In this work, we introduce different semantic models for Amharic. After we experiment with the existing pre-trained semantic models, we trained and fine-tuned nine new different models using a monolingual text corpus. The models are build using word2Vec embeddings, distributional thesaurus (DT), contextual embeddings, and DT embeddings obtained via network embedding algorithms. Moreover, we employ these models for different NLP tasks and investigate their impact. We find that newly trained models perform better than pre-trained multilingual models. Furthermore, models based on contextual embeddings from RoBERTA perform better than the word2Vec models.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

Despite the proven effectiveness of Transformer neural networks across multiple domains, their performance with Electronic Health Records (EHR) can be nuanced. The unique, multidimensional sequential nature of EHR data can sometimes make even simple linear models with carefully engineered features more competitive. Thus, the advantages of Transformers, such as efficient transfer learning and improved scalability are not always fully exploited in EHR applications. Addressing these challenges, we introduce SANSformer, an attention-free sequential model designed with specific inductive biases to cater for the unique characteristics of EHR data. In this work, we aim to forecast the demand for healthcare services, by predicting the number of patient visits to healthcare facilities. The challenge amplifies when dealing with divergent patient subgroups, like those with rare diseases, which are characterized by unique health trajectories and are typically smaller in size. To address this, we employ a self-supervised pretraining strategy, Generative Summary Pretraining (GSP), which predicts future summary statistics based on past health records of a patient. Our models are pretrained on a health registry of nearly one million patients, then fine-tuned for specific subgroup prediction tasks, showcasing the potential to handle the multifaceted nature of EHR data. In evaluation, SANSformer consistently surpasses robust EHR baselines, with our GSP pretraining method notably amplifying model performance, particularly within smaller patient subgroups. Our results illuminate the promising potential of tailored attention-free models and self-supervised pretraining in refining healthcare utilization predictions across various patient demographics.

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.