Foundation models in bioinformatics

With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs employed in a variety of downstream tasks, including genomics, transcriptomics, proteomics, drug discovery and single-cell analysis. Our aim is to assist scientists in selecting appropriate FMs in bioinformatics, according to four model types: language FMs, vision FMs, graph FMs and multimodal FMs. In addition to understanding molecular landscapes, AI technology can establish the theoretical and practical foundation for continued innovation in molecular biology.