Daily Papers

Kolmogorov-Arnold Networks (KANs) have inspired numerous works exploring their applications across a wide range of scientific problems, with the potential to replace Multilayer Perceptrons (MLPs). While many KANs are designed using basis and polynomial functions, such as B-splines, ReLU-KAN utilizes a combination of ReLU functions to mimic the structure of B-splines and take advantage of ReLU's speed. However, ReLU-KAN is not built for multiple inputs, and its limitations stem from ReLU's handling of negative values, which can restrict feature extraction. To address these issues, we introduce Activation Function-Based Kolmogorov-Arnold Networks (AF-KAN), expanding ReLU-KAN with various activations and their function combinations. This novel KAN also incorporates parameter reduction methods, primarily attention mechanisms and data normalization, to enhance performance on image classification datasets. We explore different activation functions, function combinations, grid sizes, and spline orders to validate the effectiveness of AF-KAN and determine its optimal configuration. In the experiments, AF-KAN significantly outperforms MLP, ReLU-KAN, and other KANs with the same parameter count. It also remains competitive even when using fewer than 6 to 10 times the parameters while maintaining the same network structure. However, AF-KAN requires a longer training time and consumes more FLOPs. The repository for this work is available at https://github.com/hoangthangta/All-KAN.

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.

As large language models (LLMs) continue to evolve, the need for robust and standardized evaluation benchmarks becomes paramount. Evaluating the performance of these models is a complex challenge that requires careful consideration of various linguistic tasks, model architectures, and benchmarking methodologies. In recent years, various frameworks have emerged as noteworthy contributions to the field, offering comprehensive evaluation tests and benchmarks for assessing the capabilities of LLMs across diverse domains. This paper provides an exploration and critical analysis of some of these evaluation methodologies, shedding light on their strengths, limitations, and impact on advancing the state-of-the-art in natural language processing.

Med42-v2 introduces a suite of clinical large language models (LLMs) designed to address the limitations of generic models in healthcare settings. These models are built on Llama3 architecture and fine-tuned using specialized clinical data. They underwent multi-stage preference alignment to effectively respond to natural prompts. While generic models are often preference-aligned to avoid answering clinical queries as a precaution, Med42-v2 is specifically trained to overcome this limitation, enabling its use in clinical settings. Med42-v2 models demonstrate superior performance compared to the original Llama3 models in both 8B and 70B parameter configurations and GPT-4 across various medical benchmarks. These LLMs are developed to understand clinical queries, perform reasoning tasks, and provide valuable assistance in clinical environments. The models are now publicly available at https://huggingface.co/m42-health{https://huggingface.co/m42-health}.

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

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

Large Language Models (LLMs) have 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.

This paper investigates the challenges of developing large language models (LLMs) proficient in both multilingual understanding and medical knowledge. We demonstrate that simply translating medical data does not guarantee strong performance on clinical tasks in the target language. Our experiments reveal that the optimal language mix in training data varies significantly across different medical tasks. We find that larger models with carefully calibrated language ratios achieve superior performance on native-language clinical tasks. Furthermore, our results suggest that relying solely on fine-tuning may not be the most effective approach for incorporating new language knowledge into LLMs. Instead, data and computationally intensive pretraining methods may still be necessary to achieve optimal performance in multilingual medical settings. These findings provide valuable guidance for building effective and inclusive medical AI systems for diverse linguistic communities.

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.

Self-supervised representation learning is heavily dependent on data augmentations to specify the invariances encoded in representations. Previous work has shown that applying diverse data augmentations is crucial to downstream performance, but augmentation techniques remain under-explored. In this work, we propose a new family of local transformations based on Gaussian random fields to generate image augmentations for self-supervised representation learning. These transformations generalize the well-established affine and color transformations (translation, rotation, color jitter, etc.) and greatly increase the space of augmentations by allowing transformation parameter values to vary from pixel to pixel. The parameters are treated as continuous functions of spatial coordinates, and modeled as independent Gaussian random fields. Empirical results show the effectiveness of the new transformations for self-supervised representation learning. Specifically, we achieve a 1.7% top-1 accuracy improvement over baseline on ImageNet downstream classification, and a 3.6% improvement on out-of-distribution iNaturalist downstream classification. However, due to the flexibility of the new transformations, learned representations are sensitive to hyperparameters. While mild transformations improve representations, we observe that strong transformations can degrade the structure of an image, indicating that balancing the diversity and strength of augmentations is important for improving generalization of learned representations.

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

For the first time, we explore few-shot tuning of vision foundation models for class-incremental learning. Unlike existing few-shot class incremental learning (FSCIL) methods, which train an encoder on a base session to ensure forward compatibility for future continual learning, foundation models are generally trained on large unlabelled data without such considerations. This renders prior methods from traditional FSCIL incompatible for FSCIL with the foundation model. To this end, we propose Consistency-guided Asynchronous Contrastive Tuning (CoACT), a new approach to continually tune foundation models for new classes in few-shot settings. CoACT comprises three components: (i) asynchronous contrastive tuning, which learns new classes by including LoRA modules in the pre-trained encoder, while enforcing consistency between two asynchronous encoders; (ii) controlled fine-tuning, which facilitates effective tuning of a subset of the foundation model; and (iii) consistency-guided incremental tuning, which enforces additional regularization during later sessions to reduce forgetting of the learned classes. We perform an extensive study on 16 diverse datasets and demonstrate the effectiveness of CoACT, outperforming the best baseline method by 2.47% on average and with up to 12.52% on individual datasets. Additionally, CoACT shows reduced forgetting and robustness in low-shot experiments. As an added bonus, CoACT shows up to 13.5% improvement in standard FSCIL over the current SOTA on benchmark evaluations. We make our code publicly available at https://github.com/ShuvenduRoy/CoACT-FSCIL.

Compound figures, which are multi-panel composites containing diverse subfigures, are ubiquitous in biomedical literature, yet large-scale subfigure extraction remains largely unaddressed. Prior work on subfigure extraction has been limited in both dataset size and generalizability, leaving a critical open question: How does high-fidelity image-text alignment via large-scale subfigure extraction impact representation learning in vision-language models? We address this gap by introducing a scalable subfigure extraction pipeline based on transformer-based object detection, trained on a synthetic corpus of 500,000 compound figures, and achieving state-of-the-art performance on both ImageCLEF 2016 and synthetic benchmarks. Using this pipeline, we release OPEN-PMC-18M, a large-scale high quality biomedical vision-language dataset comprising 18 million clinically relevant subfigure-caption pairs spanning radiology, microscopy, and visible light photography. We train and evaluate vision-language models on our curated datasets and show improved performance across retrieval, zero-shot classification, and robustness benchmarks, outperforming existing baselines. We release our dataset, models, and code to support reproducible benchmarks and further study into biomedical vision-language modeling and representation learning.

Despite the growing scale of medical Vision-Language datasets, the impact of dataset quality on model performance remains under-explored. We introduce Open-PMC, a high-quality medical dataset from PubMed Central, containing 2.2 million image-text pairs, enriched with image modality annotations, subfigures, and summarized in-text references. Notably, the in-text references provide richer medical context, extending beyond the abstract information typically found in captions. Through extensive experiments, we benchmark Open-PMC against larger datasets across retrieval and zero-shot classification tasks. Our results show that dataset quality-not just size-drives significant performance gains. We complement our benchmark with an in-depth analysis of feature representation. Our findings highlight the crucial role of data curation quality in advancing multimodal medical AI. We release Open-PMC, along with the trained models and our codebase.

We perform a comprehensive benchmarking of contrastive frameworks for learning multimodal representations in the medical domain. Through this study, we aim to answer the following research questions: (i) How transferable are general-domain representations to the medical domain? (ii) Is multimodal contrastive training sufficient, or does it benefit from unimodal training as well? (iii) What is the impact of feature granularity on the effectiveness of multimodal medical representation learning? To answer these questions, we investigate eight contrastive learning approaches under identical training setups, and train them on 2.8 million image-text pairs from four datasets, and evaluate them on 25 downstream tasks, including classification (zero-shot and linear probing), image-to-text and text-to-image retrieval, and visual question-answering. Our findings suggest a positive answer to the first question, a negative answer to the second question, and the benefit of learning fine-grained features. Finally, we make our code publicly available.