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The massive scale and inherent complexity of these datasets pose significant challenges for data management, analysis, and interpretation in the field of bioinformatics. Concurrently, artificial intelligence (AI) techniques, particularly deep learning and reinforcement learning, have achieved groundbreaking advances in medical diagnostics, drug discovery, and genomic analyses, providing novel theoretical tools and analytical paradigms for bioinformatics research. AI techniques are now extensively applied to DNA, RNA, and protein sequence prediction and design, 3D structural elucidation, functional annotation, integrative analysis of multi-omics data, and personalized drug design for precision medicine, significantly advancing biological research. This review systematically summarizes recent research progress and representative applications of AI techniques in bioinformatics, specifically discussing suitable scenarios and advantages of traditional machine learning algorithms, deep learning models, and reinforcement learning methods. We highlight AI\u2019s transformative impact with quantitative metrics from landmark achievements: accurate near-atomic protein structure prediction (median 0.96 \u00c5 on CASP14), robust single-cell modeling (AvgBIO $\\approx $ 0.82), high protein design success rates (up to 92%), and sensitive cancer detection (Area Under Curve (AUC) $\\approx $ 0.93). Furthermore, the paper provides an in-depth analysis of the latest advancements of AI in specific tasks, including biomedical text mining, multimodal omics integration, and single-cell analyses, while highlighting current challenges such as data noise and sparsity, difficulties in modeling long biological sequences, complexities in multimodal data integration, insufficient model interpretability, and ethical and privacy concerns. Finally, the paper outlines promising future research directions, emphasizing large-scale data mining, cross-domain model generalization, innovations in drug design and personalized medicine, and advocates for establishing an open and collaborative research ecosystem.<\/jats:p>","DOI":"10.1093\/bib\/bbaf576","type":"journal-article","created":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T05:47:52Z","timestamp":1762667272000},"source":"Crossref","is-referenced-by-count":5,"title":["Artificial intelligence in bioinformatics: a survey"],"prefix":"10.1093","volume":"26","author":[{"given":"Jiyue","family":"Jiang","sequence":"first","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]},{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Sha Tin District, New Territories, 999077 Hong Kong SAR ,","place":["China"]}]},{"given":"Yunke","family":"Li","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]},{"name":"Guangzhou Medical University , Xinzao Town, Panyu District, Guangzhou, 511436 Guangdong Province ,","place":["China"]}]},{"given":"Shiwei","family":"Cao","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]},{"name":"ShanghaiTech University , 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210 ,","place":["China"]}]},{"given":"Yuheng","family":"Shan","sequence":"additional","affiliation":[{"name":"National University of Singapore , 21 Lower Kent Ridge Road, 119077 Singapore ,","place":["Singapore"]}]},{"given":"Yuexing","family":"Liu","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]}]},{"given":"Tianyi","family":"Fei","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]},{"name":"ShanghaiTech University , 393 Middle Huaxia Road, Pudong New Area, Shanghai 201210 ,","place":["China"]}]},{"given":"Yule","family":"Yu","sequence":"additional","affiliation":[{"name":"Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , Hangzhou 310024 ,","place":["China"]}]},{"given":"Yi","family":"Feng","sequence":"additional","affiliation":[{"name":"GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University , 511436 Guangzhou Province ,","place":["China"]}]},{"given":"Yu","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Sha Tin District, New Territories, 999077 Hong Kong SAR ,","place":["China"]},{"name":"The CUHK Shenzhen Research Institute , Hi-Tech Park, Nanshan, Shenzhen, 518057 Guangzhou Province ,","place":["China"]}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005 Guangzhou Province ,","place":["China"]},{"name":"GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University , 511436 Guangzhou Province 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