{"id":"https://openalex.org/W4415386728","doi":"https://doi.org/10.3389/fbinf.2025.1649337","title":"Enhancing drug-target interaction prediction with graph representation learning and knowledge-based regularization","display_name":"Enhancing drug-target interaction prediction with graph representation learning and knowledge-based regularization","publication_year":2025,"publication_date":"2025-10-21","ids":{"openalex":"https://openalex.org/W4415386728","doi":"https://doi.org/10.3389/fbinf.2025.1649337","pmid":"https://pubmed.ncbi.nlm.nih.gov/41195325"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1649337","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1649337","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1649337/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1649337/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068243522","display_name":"Qiuyan Yao","orcid":"https://orcid.org/0000-0001-8753-6489"},"institutions":[{"id":"https://openalex.org/I4210135988","display_name":"Shanghai Traditional Chinese Medicine Hospital","ror":"https://ror.org/03p31hk68","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210135988"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qihuan Yao","raw_affiliation_strings":["Department of Traditional Chinese Medicine, Kongjiang Hospital, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Department of Traditional Chinese Medicine, Kongjiang Hospital, Shanghai, China","institution_ids":["https://openalex.org/I4210135988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100457758","display_name":"Zhen Chen","orcid":"https://orcid.org/0000-0003-2590-0307"},"institutions":[{"id":"https://openalex.org/I4210127380","display_name":"Pudong Medical Center","ror":"https://ror.org/02nptez24","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Chen","raw_affiliation_strings":["Department of Medical Laboratory, Shidong Hospital, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Laboratory, Shidong Hospital, Shanghai, China","institution_ids":["https://openalex.org/I4210127380"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054290599","display_name":"Ye Cao","orcid":"https://orcid.org/0000-0002-7365-7447"},"institutions":[{"id":"https://openalex.org/I2800570007","display_name":"Renji Hospital","ror":"https://ror.org/03ypbx660","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2800570007"]},{"id":"https://openalex.org/I4210164062","display_name":"YangPu Geriatric Hospital","ror":"https://ror.org/05hawxe81","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164062"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ye Cao","raw_affiliation_strings":["Department of Geriatrics, Renhe Hospital, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Department of Geriatrics, Renhe Hospital, Shanghai, China","institution_ids":["https://openalex.org/I4210164062","https://openalex.org/I2800570007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5119063652","display_name":"Huijing Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210135988","display_name":"Shanghai Traditional Chinese Medicine Hospital","ror":"https://ror.org/03p31hk68","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210135988"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huijing Hu","raw_affiliation_strings":["Department of Traditional Chinese Medicine, Shidong Hospital, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Department of Traditional Chinese Medicine, Shidong Hospital, Shanghai, China","institution_ids":["https://openalex.org/I4210135988"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054290599","https://openalex.org/A5119063652"],"corresponding_institution_ids":["https://openalex.org/I2800570007","https://openalex.org/I4210135988","https://openalex.org/I4210164062"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":4.7062,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.95493066,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"5","issue":null,"first_page":"1649337","last_page":"1649337"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9828000068664551,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.5383999943733215},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4918999969959259},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46230000257492065},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.3700000047683716},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.3327000141143799},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.28610000014305115}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5981000065803528},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.586899995803833},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.5383999943733215},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5134999752044678},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4918999969959259},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46230000257492065},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3700000047683716},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3327000141143799},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2937000095844269},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.28610000014305115},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.28060001134872437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2727999985218048},{"id":"https://openalex.org/C119247159","wikidata":"https://www.wikidata.org/wiki/Q1366192","display_name":"System identification","level":3,"score":0.2727000117301941},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.27219998836517334},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.2648000121116638},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C136389625","wikidata":"https://www.wikidata.org/wiki/Q334384","display_name":"Supervised learning","level":3,"score":0.2572000026702881},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.25690001249313354}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1649337","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1649337","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1649337/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41195325","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41195325","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:cff96c13740744b19e0931c8f81e261e","is_oa":true,"landing_page_url":"https://doaj.org/article/cff96c13740744b19e0931c8f81e261e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11392406","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12583218","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1649337","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1649337","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1649337/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415386728.pdf","grobid_xml":"https://content.openalex.org/works/W4415386728.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W2145578524","https://openalex.org/W2755129445","https://openalex.org/W2952522777","https://openalex.org/W3033099853","https://openalex.org/W3125008742","https://openalex.org/W3162048269","https://openalex.org/W3175599101","https://openalex.org/W3177721890","https://openalex.org/W3191852652","https://openalex.org/W3195848388","https://openalex.org/W4200022036","https://openalex.org/W4206078729","https://openalex.org/W4206419503","https://openalex.org/W4214499951","https://openalex.org/W4214940877","https://openalex.org/W4220837717","https://openalex.org/W4223985366","https://openalex.org/W4229451481","https://openalex.org/W4281648410","https://openalex.org/W4284681524","https://openalex.org/W4296293027","https://openalex.org/W4307425304","https://openalex.org/W4308834893","https://openalex.org/W4317951595","https://openalex.org/W4318014921","https://openalex.org/W4322588028","https://openalex.org/W4323036511","https://openalex.org/W4385330534","https://openalex.org/W4385441991","https://openalex.org/W4387219655","https://openalex.org/W4387804083","https://openalex.org/W4388455891","https://openalex.org/W4388615774","https://openalex.org/W4391640585","https://openalex.org/W4391824669","https://openalex.org/W4400079607","https://openalex.org/W4400618691","https://openalex.org/W4401622079","https://openalex.org/W4403210286","https://openalex.org/W4404878706","https://openalex.org/W4406887519","https://openalex.org/W4412567252"],"related_works":[],"abstract_inverted_index":{"We":[0],"validated":[1],"the":[2,32,37],"practical":[3],"utility":[4],"by":[5],"predicting":[6],"novel":[7],"DTIs":[8],"for":[9,28],"FDA-approved":[10],"drugs":[11],"and":[12,25,43],"experimentally":[13],"confirming":[14],"a":[15,23],"high":[16],"proportion":[17],"of":[18,39],"predictions.":[19],"Our":[20],"framework":[21],"offers":[22],"powerful":[24],"interpretable":[26],"solution":[27],"DTI":[29],"prediction":[30],"with":[31],"potential":[33],"to":[34],"substantially":[35],"accelerate":[36],"identification":[38],"new":[40],"drug":[41],"candidates":[42],"therapeutic":[44],"targets.":[45]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-22T00:00:00"}
