MedViT: A Robust Vision Transformer for Generalized Medical Image Classification

Large AI models, or foundation models, are models recently emerging with massive scales both parameter-wise and data-wise, the magnitudes of which often reach beyond billions. Once pretrained, large AI models demonstrate impressive performance in various downstream tasks. A concrete example is the recent debut of ChatGPT, whose capability has compelled people's imagination about the far-reaching influence that large AI models can have and their potential to transform different domains of our life. In health informatics, the advent of large AI models has brought new paradigms for the design of methodologies. The scale of multimodality data in the biomedical and health domain has been ever-expanding especially since the community embraced the era of deep learning, which provides the ground to develop, validate, and advance large AI models for breakthroughs in health-related areas. This article presents an up-to-date comprehensive review of large AI models, from background to their applications. We identify seven key sectors that large AI models are applicable and might have substantial influence, including 1) molecular biology and drug discovery; 2) medical diagnosis and decision-making; 3) medical imaging and vision; 4) medical informatics; 5) medical education; 6) public health; and 7) medical robotics. We examine their challenges in health informatics, followed by a critical discussion about potential future directions and pitfalls of large AI models in transforming the field of health informatics.

pdf/large-ai-models-in-health-informatics-applications-2z4em8ms.pdf

Large AI Models in Health Informatics: Applications, Challenges, and the Future

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.

pdf/biomedgpt-a-unified-and-generalist-biomedical-generative-pre-nm9ptb2c.pdf

BiomedGPT: A Unified and Generalist Biomedical Generative Pre-trained Transformer for Vision, Language, and Multimodal Tasks

The transformer is primarily used in the field of natural language processing. Recently, it has been adopted and shows promise in the computer vision (CV) field. Medical image analysis (MIA), as a critical branch of CV, also greatly benefits from this state-of-the-art technique. In this review, we first recap the core component of the transformer, the attention mechanism, and the detailed structures of the transformer. After that, we depict the recent progress of the transformer in the field of MIA. We organize the applications in a sequence of different tasks, including classification, segmentation, captioning, registration, detection, enhancement, localization, and synthesis. The mainstream classification and segmentation tasks are further divided into eleven medical image modalities. A large number of experiments studied in this review illustrate that the transformer-based method outperforms existing methods through comparisons with multiple evaluation metrics. Finally, we discuss the open challenges and future opportunities in this field. This task-modality review with the latest contents, detailed information, and comprehensive comparison may greatly benefit the broad MIA community.

pdf/recent-progress-in-transformer-based-medical-image-analysis-39313l3c.pdf

Recent progress in transformer-based medical image analysis

SwinCup: Cascaded swin transformer for histopathological structures segmentation in colorectal cancer

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

pdf/medmnist-v2-a-large-scale-lightweight-benchmark-for-2d-and-3rxeevxtqu.pdf

MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification

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MedMNIST v2: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification