A Comprehensive Survey of Foundation Models in Medicine

Foundation models (FMs) are large-scale deep learning models that are developed using large datasets and self-supervised learning methods. These models serve as a base for different downstream tasks, including healthcare. FMs have been adopted with great success across various domains within healthcare. Existing healthcare-based surveys have not yet included all of these domains. Therefore, we provide a detailed survey 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. 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 open research issues and potential lessons learned to provide researchers and practitioners with insights into the capabilities of FMs in healthcare to advance their deployment and mitigate associated risks.