{"id":"https://openalex.org/W3213998394","doi":"https://doi.org/10.1093/bib/bbab451","title":"EGFI: drug\u2013drug interaction extraction and generation with fusion of enriched entity and sentence information","display_name":"EGFI: drug\u2013drug interaction extraction and generation with fusion of enriched entity and sentence information","publication_year":2021,"publication_date":"2021-11-02","ids":{"openalex":"https://openalex.org/W3213998394","doi":"https://doi.org/10.1093/bib/bbab451","mag":"3213998394","pmid":"https://pubmed.ncbi.nlm.nih.gov/34791012"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab451","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab451","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5100727472","display_name":"Lei Huang","orcid":"https://orcid.org/0000-0003-2458-5149"},"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":"Lei Huang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023725018","display_name":"Jiecong Lin","orcid":"https://orcid.org/0000-0003-3347-837X"},"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":"Jiecong Lin","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002127716","display_name":"Xiangtao Li","orcid":"https://orcid.org/0000-0001-9089-1799"},"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"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiangtao Li","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, China","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I4210100255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035185924","display_name":"Linqi Song","orcid":"https://orcid.org/0000-0003-2756-4984"},"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":"Linqi Song","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041264208","display_name":"Zetian Zheng","orcid":"https://orcid.org/0000-0002-7199-0051"},"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":"Zetian Zheng","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"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":true,"raw_author_name":"Ka-Chun Wong","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002127716","https://openalex.org/A5030015771"],"corresponding_institution_ids":["https://openalex.org/I168719708","https://openalex.org/I194450716","https://openalex.org/I4210100255"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.5543,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.83495659,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8194000124931335,"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":0.8194000124931335,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.06970000267028809,"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/T10028","display_name":"Topic Modeling","score":0.066600002348423,"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/computer-science","display_name":"Computer science","score":0.8596266508102417},{"id":"https://openalex.org/keywords/drugbank","display_name":"DrugBank","score":0.811416745185852},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6074064373970032},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6054728627204895},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5713810324668884},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5162291526794434},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.49723199009895325},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.4431452453136444},{"id":"https://openalex.org/keywords/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.4323877692222595},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.428035169839859},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.41479790210723877},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.1941944658756256},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.17697963118553162}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8596266508102417},{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.811416745185852},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6074064373970032},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6054728627204895},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5713810324668884},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5162291526794434},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.49723199009895325},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.4431452453136444},{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.4323877692222595},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.428035169839859},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.41479790210723877},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.1941944658756256},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.17697963118553162},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0}],"mesh":[{"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab451","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab451","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34791012","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34791012","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1697431053","display_name":null,"funder_award_id":"CityU 11202219","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G6784292314","display_name":null,"funder_award_id":"CityU 11203520","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320334123","display_name":"Hong Kong Institute for Data Science","ror":null},{"id":"https://openalex.org/F4320335055","display_name":"Health and Medical Research Fund","ror":"https://ror.org/03qh32912"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1018047830","https://openalex.org/W2013181441","https://openalex.org/W2036109829","https://openalex.org/W2075549063","https://openalex.org/W2101052193","https://openalex.org/W2131347449","https://openalex.org/W2170189740","https://openalex.org/W2250539671","https://openalex.org/W2417285541","https://openalex.org/W2485374661","https://openalex.org/W2558999090","https://openalex.org/W2612690371","https://openalex.org/W2767891136","https://openalex.org/W2768282280","https://openalex.org/W2770565711","https://openalex.org/W2781528640","https://openalex.org/W2785001576","https://openalex.org/W2790602452","https://openalex.org/W2794304292","https://openalex.org/W2805208465","https://openalex.org/W2891331614","https://openalex.org/W2900758217","https://openalex.org/W2907304305","https://openalex.org/W2911489562","https://openalex.org/W2913951776","https://openalex.org/W2915071810","https://openalex.org/W2924700250","https://openalex.org/W2959428074","https://openalex.org/W2964026782","https://openalex.org/W2971398276","https://openalex.org/W2974658886","https://openalex.org/W2984452801","https://openalex.org/W2987479113","https://openalex.org/W2995738274","https://openalex.org/W3027982260","https://openalex.org/W3033077186","https://openalex.org/W3088335873","https://openalex.org/W3094542104","https://openalex.org/W3105068956","https://openalex.org/W3113157522","https://openalex.org/W3167136668","https://openalex.org/W4206174637","https://openalex.org/W4239019441","https://openalex.org/W4250526791","https://openalex.org/W6626744847","https://openalex.org/W6784175220"],"related_works":["https://openalex.org/W2365158734","https://openalex.org/W2009313526","https://openalex.org/W2465211533","https://openalex.org/W2157969515","https://openalex.org/W129624489","https://openalex.org/W4387804095","https://openalex.org/W2767891136","https://openalex.org/W4388615774","https://openalex.org/W2137052779","https://openalex.org/W2176533785"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,177],"rapid":[2],"growth":[3,170],"in":[4,40,184],"literature":[5,61],"accumulates":[6],"diverse":[7],"and":[8,37,54,71,99,142,151,165,186],"yet":[9],"comprehensive":[10],"biomedical":[11,89],"knowledge":[12,29,39],"hidden":[13],"to":[14,25,30,102,160,172,195],"be":[15],"mined":[16],"such":[17,46],"as":[18],"drug":[19,56,198],"interactions.":[20],"However,":[21],"it":[22],"is":[23],"difficult":[24],"extract":[26],"the":[27,35,74,79,95,112,123,135,146,157,168,174,191],"heterogeneous":[28],"retrieve":[31],"or":[32],"even":[33],"discover":[34],"latest":[36],"novel":[38,197],"an":[41],"efficient":[42],"manner.":[43],"To":[44],"address":[45],"a":[47],"problem,":[48],"we":[49,93,155],"propose":[50,94],"EGFI":[51,65,77,115,194],"for":[52,107],"extracting":[53],"consolidating":[55],"interactions":[57],"from":[58],"large-scale":[59],"medical":[60],"text":[62],"data.":[63],"Specifically,":[64],"consists":[66],"of":[67,149,193],"two":[68],"parts:":[69],"classification":[70,75,136,158],"generation.":[72],"In":[73,91,111],"part,":[76,114],"encompasses":[78],"language":[80,119],"model":[81,120],"BioBERT":[82],"which":[83],"has":[84],"been":[85],"comprehensively":[86],"pretrained":[87,118],"on":[88,129,138],"corpus.":[90],"particular,":[92],"multihead":[96],"self-attention":[97],"mechanism":[98],"packed":[100],"BiGRU":[101],"fuse":[103],"multiple":[104],"semantic":[105],"information":[106],"rigorous":[108],"context":[109],"modeling.":[110],"generation":[113,124],"utilizes":[116],"another":[117],"BioGPT-2":[121],"where":[122],"sentences":[125,164,179],"are":[126,181,203],"selected":[127],"based":[128],"filtering":[130],"rules.":[131],"RESULTS:":[132],"We":[133],"evaluated":[134],"part":[137,159],"'DDIs":[139],"2013'":[140],"dataset":[141,189],"'DTIs'":[143],"dataset,":[144],"achieving":[145],"F1":[147],"scores":[148],"0.842":[150],"0.720":[152],"respectively.":[153],"Moreover,":[154],"applied":[156],"distinguish":[161],"high-quality":[162],"generated":[163,178],"verified":[166],"with":[167],"existing":[169],"truth":[171],"confirm":[173],"filtered":[175],"sentences.":[176],"that":[180],"not":[182],"recorded":[183],"DrugBank":[185],"DDIs":[187],"2013":[188],"demonstrated":[190],"potential":[192],"identify":[196],"relationships.":[199],"AVAILABILITY:":[200],"Source":[201],"code":[202],"publicly":[204],"available":[205],"at":[206],"https://github.com/Layne-Huang/EGFI.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
