{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T11:42:30Z","timestamp":1774352550202,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,8,21]],"date-time":"2023-08-21T00:00:00Z","timestamp":1692576000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82003579"],"award-info":[{"award-number":["82003579"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81973172"],"award-info":[{"award-number":["81973172"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82173660"],"award-info":[{"award-number":["82173660"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LR21H300003"],"award-info":[{"award-number":["LR21H300003"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang Province","doi-asserted-by":"publisher","award":["LQ21H300005"],"award-info":[{"award-number":["LQ21H300005"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Program of Zhejiang Province","doi-asserted-by":"crossref","award":["2020C03010"],"award-info":[{"award-number":["2020C03010"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Program of Zhejiang Province","doi-asserted-by":"crossref","award":["2023C03111"],"award-info":[{"award-number":["2023C03111"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Predicting the biological properties of molecules is crucial in computer-aided drug development, yet it\u2019s often impeded by data scarcity and imbalance in many practical applications. Existing approaches are based on self-supervised learning or 3D data and using an increasing number of parameters to improve performance. These approaches may not take full advantage of established chemical knowledge and could inadvertently introduce noise into the respective model. In this study, we introduce a more elegant transformer-based framework with focused attention for molecular representation (TransFoxMol) to improve the understanding of artificial intelligence (AI) of molecular structure property relationships. TransFoxMol incorporates a multi-scale 2D molecular environment into a graph neural network\u2009+\u2009Transformer module and uses prior chemical maps to obtain a more focused attention landscape compared to that obtained using existing approaches. Experimental results show that TransFoxMol achieves state-of-the-art performance on MoleculeNet benchmarks and surpasses the performance of baselines that use self-supervised learning or geometry-enhanced strategies on small-scale datasets. Subsequent analyses indicate that TransFoxMol\u2019s predictions are highly interpretable and the clever use of chemical knowledge enables AI to perceive molecules in a simple but rational way, enhancing performance.<\/jats:p>","DOI":"10.1093\/bib\/bbad306","type":"journal-article","created":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T09:24:23Z","timestamp":1692696263000},"source":"Crossref","is-referenced-by-count":39,"title":["TransFoxMol: predicting molecular property with focused attention"],"prefix":"10.1093","volume":"24","author":[{"given":"Jian","family":"Gao","sequence":"first","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Zheyuan","family":"Shen","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Yufeng","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Software Technology, Zhejiang University , Hangzhou , China"}]},{"given":"Jialiang","family":"Lu","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Yang","family":"Lu","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Sikang","family":"Chen","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Qingyu","family":"Bian","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4498-1460","authenticated-orcid":false,"given":"Yue","family":"Guo","sequence":"additional","affiliation":[{"name":"Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University , Hangzhou , China"}]},{"given":"Liteng","family":"Shen","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"given":"Jian","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Software Technology, Zhejiang University , Hangzhou , China"}]},{"given":"Binbin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Computing, Zhejiang University City College , Hangzhou , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":false,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"State Key Lab of CAD&CG, College of Pharmaceutical Sciences, Zhejiang University , Zhejiang , China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University , Hangzhou , China"}]},{"given":"Qiaojun","family":"He","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, 310058 , PR China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University , Hangzhou , China"},{"name":"Centre for Drug Safety Evaluation and Research of ZJU , Hangzhou, 310058 , PR China"},{"name":"Cancer Center of Zhejiang University , Hangzhou , China"}]},{"given":"Jinxin","family":"Che","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2178-4372","authenticated-orcid":false,"given":"Xiaowu","family":"Dong","sequence":"additional","affiliation":[{"name":"Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China"},{"name":"Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University , Hangzhou , China"},{"name":"Cancer Center of Zhejiang University , Hangzhou , China"},{"name":"Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang , China"}]}],"member":"286","published-online":{"date-parts":[[2023,8,21]]},"reference":[{"key":"2023101811535203500_ref1","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1038\/534314a","article-title":"Can you teach old drugs new tricks?","volume":"534","author":"Nosengo","year":"2016","journal-title":"Nature"},{"key":"2023101811535203500_ref2","doi-asserted-by":"crossref","first-page":"10520","DOI":"10.1021\/acs.chemrev.8b00728","article-title":"Concepts of artificial intelligence for computer-assisted drug discovery","volume":"119","author":"Yang","year":"2019","journal-title":"Chem Rev"},{"key":"2023101811535203500_ref3","doi-asserted-by":"crossref","first-page":"bbab581","DOI":"10.1093\/bib\/bbab581","article-title":"A weighted bilinear neural collaborative filtering approach for drug repositioning","volume":"23","author":"Meng","year":"2022","journal-title":"Brief 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