{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T14:01:45Z","timestamp":1785333705659,"version":"3.55.0"},"reference-count":49,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"6","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Comput. Biol. Bioinform."],"published-print":{"date-parts":[[2025,11]]},"DOI":"10.1109\/tcbbio.2025.3617331","type":"journal-article","created":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:36:03Z","timestamp":1759772163000},"page":"3224-3235","source":"Crossref","is-referenced-by-count":2,"title":["Learning Universal Knowledge Graph Embedding for Predicting Biomedical Pairwise Interactions"],"prefix":"10.1109","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1139-487X","authenticated-orcid":false,"given":"Siyu","family":"Tao","sequence":"first","affiliation":[{"name":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5348-6029","authenticated-orcid":false,"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0433-6444","authenticated-orcid":false,"given":"Xin","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8389-2223","authenticated-orcid":false,"given":"Yimiao","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6774-9786","authenticated-orcid":false,"given":"Jie","family":"Zheng","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1038\/468851a"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12033-007-0069-2","volume":"38","author":"Skrabanek","year":"2008","journal-title":"Mol. Biotechnol."},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.7150\/thno.63416"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-023-01960-3"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac476"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/s42256-022-00605-1","volume":"5","author":"Bai","year":"2023","journal-title":"Nature Mach. Intell."},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab271"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04948-5"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0062866"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-023-00640-6"},{"key":"ref11","article-title":"Semi-supervised classification with graph convolutional networks","volume-title":"Proc. Int. Conf. Learn. Representations","author":"Kipf"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1016\/j.artint.2024.104129"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1109\/TKDE.2024.3524627"},{"key":"ref14","first-page":"2641","article-title":"Learning conjoint attentions for graph neural nets","volume-title":"Proc. Adv. Neural Inf. Process. Syst.","author":"He"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1109\/TNNLS.2024.3370918"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1016\/j.patcog.2024.111340"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1109\/TKDE.2024.3389966"},{"key":"ref18","article-title":"How powerful are graph neural networks?","volume-title":"Proc. Int. Conf. Learn. Representations","author":"Xu"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa211"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2022.1103092"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1109\/JBHI.2023.3306768"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad015"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2024.04.010"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1126\/article.64313"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac100"},{"key":"ref26","article-title":"Strategies for pre-training graph neural networks","volume-title":"Proc. Int. Conf. Learn. Representations","author":"Hu"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad400"},{"key":"ref28","article-title":"To transfer or not to transfer","volume-title":"Proc. Adv. Neural Inf. Process. Syst. Workshop Transfer Learn.","author":"Rosenstein"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.10.017"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s13721-018-0180-2","volume":"8","author":"Amala","year":"2019","journal-title":"Netw. Model. Anal. Health Informat. Bioinf."},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1272"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giae001"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1145\/3366423.3380027"},{"key":"ref34","first-page":"249","article-title":"Understanding the difficulty of training deep feedforward neural networks","volume-title":"Proc. 13th Int. Conf. Artif. Intell. Statist. JMLR Workshop Conf. Proc.","author":"Glorot"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1109\/CVPR.2016.90"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baac030"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3834"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-022-01131-2"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad764"},{"issue":"20","key":"ref40","first-page":"10","article-title":"Graph attention networks","volume":"1050","author":"Velickovic","year":"2017","journal-title":"Stat"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-93417-4_38"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1145\/3394486.3403168"},{"key":"ref43","article-title":"Adam: A method for stochastic optimization","author":"Kingma","year":"2014"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1016\/j.trecan.2018.08.003"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad806"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3799"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1002\/path.4912"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.08.058"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2764"}],"container-title":["IEEE Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/10723156\/11296745\/11189877.pdf?arnumber=11189877","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T18:45:17Z","timestamp":1765478717000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/11189877\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":49,"journal-issue":{"issue":"6"},"URL":"https:\/\/doi.org\/10.1109\/tcbbio.2025.3617331","relation":{},"ISSN":["2998-4165"],"issn-type":[{"value":"2998-4165","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11]]}}}