2023/02/13 by Zhiye Guo, Guo, Zhiye, Jian Liu +11 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Artificial Intelligence (cs.AI) #Bioinformatics and Genomic Networks #FOS: Biological sciences #FOS: Computer and information sciences #Gene expression and cancer classification #I.2.1 #J.3 #Machine Learning (cs.LG) #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.2302.10907
openalex publication_date 2023/02/13 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Denoising diffusion models have emerged as one of the most powerful generative models in recent years. They have achieved remarkable success in many fields, such as computer vision, natural language processing (NLP), and bioinformatics. Although there are a few excellent reviews on diffusion models and their applications in computer vision and NLP, there is a lack of an overview of their applications in bioinformatics. This review aims to provide a rather thorough overview of the applications of diffusion models in bioinformatics to aid their further development in bioinformatics and computational biology. We start with an introduction of the key concepts and theoretical foundations of three cornerstone diffusion modeling frameworks (denoising diffusion probabilistic models, noise-conditioned scoring networks, and stochastic differential equations), followed by a comprehensive description of diffusion models employed in the different domains of bioinformatics, including cryo-EM data enhancement, single-cell data analysis, protein design and generation, drug and small molecule design, and protein-ligand interaction. The review is concluded with a summary of the potential new development and applications of diffusion models in bioinformatics.