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However, only a small fraction of potential drug combinations exhibit true synergistic effects, making the prediction of drug synergy a critical yet challenging task. In this study, we propose BridgeSyn, a novel bridge fusion framework for drug synergy prediction. BridgeSyn leverages the knowledge from pretrained biological language models to enrich both drug compound and cell line representations. We introduce a bridging fusion mechanism that employs a set of shared latent tokens derived from global features, serving as a semantic interface to effectively fuse the representations of drug pairs and cell lines. By combining biological prior knowledge with this fusion strategy, BridgeSyn can capture complex biological interactions and achieve superior prediction results. Extensive experiments on two public datasets demonstrate that BridgeSyn consistently outperforms existing computation methods.<\/jats:p>","DOI":"10.1093\/bib\/bbaf624","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T15:02:51Z","timestamp":1763737371000},"source":"Crossref","is-referenced-by-count":1,"title":["BridgeSyn: a bridging fusion framework for drug combination synergy prediction"],"prefix":"10.1093","volume":"26","author":[{"given":"Qingyu","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Medical Informatics , School of Biomedical Engineering and Informatics, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166 Jiangsu,","place":["China"]}]},{"given":"Suwan","family":"Mao","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics , School of Biomedical Engineering and Informatics, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166 Jiangsu,","place":["China"]}]},{"given":"Xiaoyan","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Computing , Harbin Institute of Technology, 92 West Dazhi Street, Nangang District, Harbin, 150001 Heilongjiang,","place":["China"]}]},{"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Yangtze Delta Region Institute (Quzhou) , University of Electronic Science and Technology of China, 1 Chengdian Road, Kecheng District, Quzhou, 324000 Zhejiang,","place":["China"]},{"name":"Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China, 2006 Xiyuan Avenue, West Hi-tech Zone, Chengdu, 611731 Sichuan,","place":["China"]}]},{"given":"Qing","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Anesthesiology , Hospital (T.C.M) Affiliated To Southwest Medical University, 182 Chunhui Road, Longmatan District, Luzhou, 646000 Sichuan,","place":["China"]}]},{"given":"Xi","family":"Su","sequence":"additional","affiliation":[{"name":"The Affiliated Foshan Women and Children Hospital , Guangdong Medical University, 11 Renmin West Road, Chancheng District, Foshan, 528000 Guangdong,","place":["China"]}]},{"given":"Junjie","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics , School of Biomedical Engineering and Informatics, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, 211166 Jiangsu,","place":["China"]}]},{"given":"Wen","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Oncology , The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Gulou District, Nanjing, 210029 Jiangsu,","place":["China"]}]},{"given":"Ximei","family":"Luo","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China, 2006 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