{"id":"https://openalex.org/W4409683733","doi":"https://doi.org/10.1109/jbhi.2025.3563289","title":"When East Meets West: Cross-Domain Drug Interaction Annotations With Large Language Models and Bidirectional Neural Networks","display_name":"When East Meets West: Cross-Domain Drug Interaction Annotations With Large Language Models and Bidirectional Neural Networks","publication_year":2025,"publication_date":"2025-04-22","ids":{"openalex":"https://openalex.org/W4409683733","doi":"https://doi.org/10.1109/jbhi.2025.3563289","pmid":"https://pubmed.ncbi.nlm.nih.gov/40261770"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3563289","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3563289","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055599076","display_name":"Ruoxuan Zhang","orcid":"https://orcid.org/0009-0006-2451-2862"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Ruoxuan Zhang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062106534","display_name":"Weidun Xie","orcid":"https://orcid.org/0000-0001-9009-2647"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB","HK"],"is_corresponding":false,"raw_author_name":"Weidun Xie","raw_affiliation_strings":["Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K","Department of Computer Science, City University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066935890","display_name":"Qiuzhen Lin","orcid":"https://orcid.org/0000-0003-2415-0401"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuzhen Lin","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102718214","display_name":"Xiangtao Li","orcid":"https://orcid.org/0000-0002-8716-9823"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Li","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030015771","display_name":"Ka\u2010Chun Wong","orcid":"https://orcid.org/0000-0001-6062-733X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ka-Chun Wong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5055599076"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":null,"apc_paid":null,"fwci":0.8073,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.71198921,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"29","issue":"10","first_page":"7694","last_page":"7703"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.987500011920929,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.987500011920929,"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/T10028","display_name":"Topic Modeling","score":0.9796000123023987,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9768000245094299,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7037618160247803},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5259901881217957},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5182821154594421},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4644472897052765},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4576084315776825}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7037618160247803},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5259901881217957},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5182821154594421},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4644472897052765},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4576084315776825},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3563289","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3563289","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40261770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40261770","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1956185323","https://openalex.org/W2026375486","https://openalex.org/W2082836881","https://openalex.org/W2155277441","https://openalex.org/W2578877719","https://openalex.org/W2597646117","https://openalex.org/W2802200505","https://openalex.org/W2901504064","https://openalex.org/W2912758732","https://openalex.org/W2913015533","https://openalex.org/W2962876161","https://openalex.org/W2969485917","https://openalex.org/W3019826089","https://openalex.org/W3088680691","https://openalex.org/W3094497296","https://openalex.org/W3122870545","https://openalex.org/W3130412740","https://openalex.org/W3160967194","https://openalex.org/W3193463107","https://openalex.org/W3205082786","https://openalex.org/W4200253720","https://openalex.org/W4220967131","https://openalex.org/W4228996904","https://openalex.org/W4229033742","https://openalex.org/W4253028564","https://openalex.org/W4293492272","https://openalex.org/W4297253404","https://openalex.org/W4298255586","https://openalex.org/W4302286406","https://openalex.org/W4307093167","https://openalex.org/W4313405519","https://openalex.org/W4321020983","https://openalex.org/W4321460049","https://openalex.org/W4361244537","https://openalex.org/W4366824201","https://openalex.org/W4386033873","https://openalex.org/W4386576685","https://openalex.org/W4390245896","https://openalex.org/W4399011591","https://openalex.org/W4399553339","https://openalex.org/W4399746375","https://openalex.org/W4401918320","https://openalex.org/W4403123186","https://openalex.org/W4403369693","https://openalex.org/W4403655554","https://openalex.org/W4408126010"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Drug":[0],"combination":[1,288],"therapy":[2],"is":[3,133,150],"a":[4,66,83,146,234],"promising":[5],"strategy":[6],"for":[7,65,100,109,141,154,192,243,286],"managing":[8],"complex":[9],"and":[10,35,90,116,158,180,186],"co-existing":[11],"diseases.":[12],"However,":[13],"drug-drug":[14],"interactions":[15,29],"(DDIs)":[16],"can":[17,231,278],"result":[18],"in":[19,237,270,290],"unexpected":[20],"adverse":[21,32],"effects,":[22],"making":[23],"it":[24],"crucial":[25],"to":[26,30,72,96,112,123,137,221],"understand":[27],"such":[28],"prevent":[31],"drug":[33,53,111,241,287],"reactions":[34],"develop":[36],"new":[37],"therapeutic":[38],"strategies.":[39],"Current":[40],"DDI":[41,101,162,200,262],"annotation":[42,163,189,201,263],"methods":[43,61],"heavily":[44],"rely":[45],"on":[46,182],"atom-level":[47],"graph":[48],"structural":[49],"features,":[50],"overlooking":[51],"valuable":[52,235],"contextual":[54,88,107,130],"representations":[55,89],"within":[56],"medical":[57,74,142,273],"literature.":[58],"Additionally,":[59],"these":[60,78,128],"are":[62],"typically":[63],"designed":[64],"specific":[67],"task,":[68],"limiting":[69],"their":[70],"scalability":[71],"diverse":[73],"scenarios.":[75],"To":[76],"address":[77],"limitations,":[79],"we":[80,104],"propose":[81],"TEmbed-DDI,":[82],"novel":[84],"framework":[85,136,256],"that":[86,168,229],"leverages":[87],"pre-trained":[91,118],"large":[92,119],"language":[93,120],"model":[94,121],"embeddings":[95,122,140],"enhance":[97],"feature":[98],"extraction":[99],"annotations.":[102,144],"Specifically,":[103],"retrieve":[105],"meaningful":[106],"texts":[108],"each":[110],"enrich":[113],"semantic":[114],"features":[115,126],"adopt":[117],"capture":[124],"rich":[125],"from":[127],"long-range":[129],"representations.":[131],"TEmbed-DDI":[132,153,169,203,230],"the":[134,155,174,183,193,247,254,268,280,291],"first":[135,255],"incorporate":[138],"LLM-powered":[139,284],"interaction":[143,188],"Furthermore,":[145,252],"bidirectional":[147],"neural":[148],"network":[149],"integrated":[151],"into":[152,261],"integrative":[156],"Western":[157,184],"traditional":[159,258],"Chinese":[160,197,259],"medicine":[161,260],"tasks.":[164],"Comparative":[165],"results":[166],"demonstrate":[167],"achieves":[170],"state-of-the-art":[171],"performance,":[172],"with":[173],"highest":[175],"AUC":[176,211],"scores":[177],"of":[178,212,249,282],"0.992":[179],"0.95":[181],"CHCH":[185],"DEEP":[187],"benchmarks.":[190],"Even":[191],"newly":[194],"constructed":[195],"Traditional":[196],"Medicine":[198],"(TCM)":[199],"benchmark,":[202],"consistently":[204],"exhibits":[205],"outstanding":[206],"generalization":[207],"capability,":[208],"achieving":[209],"an":[210],"0.956.":[213],"Moreover,":[214],"case":[215],"studies":[216],"further":[217],"validate":[218],"TEmbed-DDI's":[219,275],"capability":[220],"annotate":[222],"previously":[223,239],"unknown":[224,240],"interactions.":[225],"These":[226],"findings":[227],"suggest":[228],"serve":[232],"as":[233,253],"tool":[236],"annotating":[238],"combinations":[242],"real-world":[244],"applications,":[245],"facilitating":[246],"development":[248,281],"efficacious":[250],"therapies.":[251],"combining":[257],"tasks,":[264],"its":[265],"adaptability":[266],"highlights":[267],"potential":[269],"supporting":[271],"cross-domain":[272],"research.":[274],"design":[276],"principles":[277],"inspire":[279],"flexible":[283],"frameworks":[285],"discovery":[289],"future.":[292]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
