Foundation models (FMs) are large-scale deep-learning models trained on extensive datasets using self-supervised techniques. These models serve as a base for various downstream tasks, including healthcare. FMs have been adopted with great success across various domains within healthcare, including natural language processing (NLP), computer vision, graph learning, biology, and omics. Existing healthcare-based surveys have not yet included all of these domains. Therefore, this survey provides a comprehensive overview of FMs in healthcare. We focus on the history, learning strategies, flagship models, applications, and challenges of FMs. We explore how FMs such as the BERT and GPT families are reshaping various healthcare domains, including clinical large language models, medical image analysis, and omics data. Furthermore, we provide a detailed taxonomy of healthcare applications facilitated by FMs, such as clinical NLP, medical computer vision, graph learning, and other biology-related tasks. Despite the promising opportunities FMs provide, they also have several associated challenges, which are explained in detail. We also outline potential future directions to provide researchers and practitioners with insights into the potential and limitations of FMs in healthcare to advance their deployment and mitigate associated risks.

基于自我监督方法使用大规模数据集训练的基础模型（FMs）被广泛应用于各个领域，包括医疗保健领域，特别在自然语言处理、医学图像分析、临床大型语言模型和病理组学数据等方面。该综述论文全面概述了FMs在医疗保健领域的历史、学习策略、旗舰模型、应用和挑战，并提供了详细的医疗应用分类，同时讨论了FMs所面临的挑战和未来研究方向。

医学基础模型综述