{"id":"https://openalex.org/W4404809819","doi":"https://doi.org/10.1109/jbhi.2024.3507738","title":"TransformDDI: The Transformer-Based Joint Multi-Task Model for End-to-End Drug-Drug Interaction Extraction","display_name":"TransformDDI: The Transformer-Based Joint Multi-Task Model for End-to-End Drug-Drug Interaction Extraction","publication_year":2024,"publication_date":"2024-11-28","ids":{"openalex":"https://openalex.org/W4404809819","doi":"https://doi.org/10.1109/jbhi.2024.3507738","pmid":"https://pubmed.ncbi.nlm.nih.gov/40030324"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3507738","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3507738","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/A5014901230","display_name":"Dimitrios Zaikis","orcid":"https://orcid.org/0000-0002-0361-7060"},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Dimitrios Zaikis","raw_affiliation_strings":["School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece"],"raw_orcid":"https://orcid.org/0000-0002-0361-7060","affiliations":[{"raw_affiliation_string":"School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066340205","display_name":"Ioannis Vlahavas","orcid":"https://orcid.org/0000-0003-3477-8825"},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ioannis Vlahavas","raw_affiliation_strings":["School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece"],"raw_orcid":"https://orcid.org/0000-0003-3477-8825","affiliations":[{"raw_affiliation_string":"School of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I21370196"],"apc_list":null,"apc_paid":null,"fwci":1.4411,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.84317448,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"29","issue":"4","first_page":"3045","last_page":"3056"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7838000059127808,"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":0.7838000059127808,"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/T10429","display_name":"EEG and Brain-Computer Interfaces","score":0.7300999760627747,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.7089999914169312,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.6826733350753784},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6675952076911926},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5729299783706665},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5483525395393372},{"id":"https://openalex.org/keywords/drug-drug-interaction","display_name":"Drug-drug interaction","score":0.4158184826374054},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4100215435028076},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36572277545928955},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2120235562324524},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.16835430264472961},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.15578025579452515},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.09092888236045837}],"concepts":[{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.6826733350753784},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6675952076911926},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5729299783706665},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5483525395393372},{"id":"https://openalex.org/C2910466267","wikidata":"https://www.wikidata.org/wiki/Q718753","display_name":"Drug-drug interaction","level":3,"score":0.4158184826374054},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4100215435028076},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36572277545928955},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2120235562324524},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.16835430264472961},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.15578025579452515},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.09092888236045837},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"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":"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":"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":"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":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3507738","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3507738","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:40030324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40030324","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":[{"id":"https://openalex.org/G6129264207","display_name":"COMBATTING DIET RELATED NON-COMMUNICABLE DISEASE THROUGH ENHANCED SURVEILLANCE","funder_award_id":"101084642","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W2014849717","https://openalex.org/W2114361266","https://openalex.org/W2134033474","https://openalex.org/W2162251320","https://openalex.org/W2170189740","https://openalex.org/W2485374661","https://openalex.org/W2537411544","https://openalex.org/W2539469848","https://openalex.org/W2587809655","https://openalex.org/W2734608416","https://openalex.org/W2765742249","https://openalex.org/W2808142148","https://openalex.org/W2896457183","https://openalex.org/W2910406387","https://openalex.org/W2911489562","https://openalex.org/W2964167098","https://openalex.org/W2977316918","https://openalex.org/W2984582583","https://openalex.org/W3004541293","https://openalex.org/W3004844052","https://openalex.org/W3025257690","https://openalex.org/W3091311542","https://openalex.org/W3093844547","https://openalex.org/W3193463107","https://openalex.org/W3193719766","https://openalex.org/W3199422761","https://openalex.org/W3217710765","https://openalex.org/W4288086191","https://openalex.org/W4313527320","https://openalex.org/W4385075877","https://openalex.org/W4385245566","https://openalex.org/W4386215651","https://openalex.org/W6629460809","https://openalex.org/W6682007918","https://openalex.org/W6727690538","https://openalex.org/W6732946871","https://openalex.org/W6757817989","https://openalex.org/W6761672038","https://openalex.org/W6771959558"],"related_works":["https://openalex.org/W3082755771","https://openalex.org/W2395332729","https://openalex.org/W2407625558","https://openalex.org/W2485789143","https://openalex.org/W2040338448","https://openalex.org/W2415873281","https://openalex.org/W2463344692","https://openalex.org/W4403660838","https://openalex.org/W4248267070","https://openalex.org/W2341529717"],"abstract_inverted_index":{"Drug-Drug":[0],"Interactions":[1],"(DDI)":[2],"identification":[3],"is":[4],"a":[5,131,136,161,166],"part":[6],"of":[7,60,68],"the":[8,28,43,58,102,106,156,181,195],"drug":[9,18,86,138,158],"safety":[10],"process,":[11],"that":[12,20,126,188],"focuses":[13],"at":[14],"avoiding":[15],"potential":[16],"adverse":[17],"effects":[19],"can":[21,150],"lead":[22],"to":[23,38,98],"patient":[24],"health":[25],"risks.":[26],"With":[27],"exponential":[29],"growth":[30],"in":[31,78,135,160],"published":[32],"literature,":[33],"it":[34],"becomes":[35],"increasingly":[36],"difficult":[37],"extract":[39],"useful":[40],"information":[41],"from":[42,62],"most":[44],"relevant":[45],"research.":[46],"Therefore,":[47],"Machine":[48],"Learning":[49],"and":[50,73,88,130,141,174],"specifically":[51],"Relationship":[52,74],"Extraction":[53,183],"has":[54],"been":[55],"employed":[56],"for":[57,84],"extraction":[59,124,140],"DDIs":[61],"biomedical":[63],"literature.":[64],"This":[65],"task":[66],"consists":[67],"both":[69],"Named":[70],"Entity":[71],"Recognition":[72],"Classification":[75],"techniques":[76],"tackled":[77],"either":[79],"pipelined":[80],"or":[81],"joint":[82,121],"approaches":[83,95],"recognizing":[85],"mentions":[87],"classifying":[89],"their":[90],"interactions,":[91],"respectively.":[92],"However,":[93],"current":[94,196],"are":[96],"prone":[97],"error":[99],"propagation":[100],"between":[101,108],"tasks,":[103],"not":[104],"taking":[105],"relevance":[107],"them":[109],"into":[110],"account.":[111],"In":[112],"this":[113],"paper":[114],"we":[115],"propose":[116],"TransformDDI,":[117],"an":[118],"end-to-end":[119],"Transformer-based":[120],"multi-task":[122],"DDI":[123,182],"model":[125,149],"integrates":[127],"domain":[128],"knowledge":[129],"shared":[132],"parameter":[133],"layer":[134],"dynamic":[137,175],"entities":[139,159],"interaction":[142],"classification":[143],"Language":[144],"Model":[145],"architecture.":[146],"Our":[147],"proposed":[148],"generate":[151],"variable":[152],"outputs":[153],"based":[154],"on":[155,180],"recognized":[157],"single-model":[162],"architecture":[163],"by":[164],"implementing":[165],"Dynamic":[167],"Pair":[168],"Attention":[169],"Mechanism":[170],"with":[171],"task-specific":[172],"focus":[173],"loss":[176],"functions.":[177],"Experiments":[178],"conducted":[179],"2013":[184],"benchmark":[185],"corpus":[186],"indicate":[187],"our":[189],"methodology":[190],"offers":[191],"significant":[192],"improvements":[193],"over":[194],"state-of-the-art.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}
