{"id":"https://openalex.org/W4406259941","doi":"https://doi.org/10.1109/bibm62325.2024.10822260","title":"Efficient Knowledge Graph Embedding Framework to Alleviate Data Sparsity for Polypharmacy Side Effects Prediction","display_name":"Efficient Knowledge Graph Embedding Framework to Alleviate Data Sparsity for Polypharmacy Side Effects Prediction","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259941","doi":"https://doi.org/10.1109/bibm62325.2024.10822260"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822260","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822260","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5112011463","display_name":"Senbo Tu","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Senbo Tu","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051597671","display_name":"Zhihao Yang","orcid":"https://orcid.org/0000-0001-6186-2024"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Yang","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lei Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Wang","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100641142","display_name":"Wei Liu","orcid":"https://orcid.org/0000-0002-7409-0948"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Liu","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343737","display_name":"Yin Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yin Zhang","raw_affiliation_strings":["Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences,Institute of Health Service and Transfusion Medicine,Beijing,China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022604762","display_name":"Bo Xu","orcid":"https://orcid.org/0000-0003-4135-0683"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Xu","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100370452","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0002-4656-7446"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100603313","display_name":"Yumeng Yang","orcid":"https://orcid.org/0009-0009-1911-0780"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yumeng Yang","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042620633","display_name":"Zhehuan Zhao","orcid":"https://orcid.org/0000-0002-5001-1352"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhehuan Zhao","raw_affiliation_strings":["Dalian University of Technology,School of Software,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Software,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023931221","display_name":"Hongfei Lin","orcid":"https://orcid.org/0000-0003-0872-7688"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Lin","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"5127","last_page":"5134"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13970","display_name":"Pharmacy and Medical Practices","score":0.8827000260353088,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13970","display_name":"Pharmacy and Medical Practices","score":0.8827000260353088,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8693000078201294,"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/T10496","display_name":"Pharmaceutical Practices and Patient Outcomes","score":0.8529999852180481,"subfield":{"id":"https://openalex.org/subfields/2717","display_name":"Geriatrics and Gerontology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/polypharmacy","display_name":"Polypharmacy","score":0.8314274549484253},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7018328309059143},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.6852922439575195},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6566593647003174},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5514683127403259},{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.5037381052970886},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3894685208797455},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.386627733707428},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36608079075813293},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30015891790390015},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13060083985328674},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.08884751796722412}],"concepts":[{"id":"https://openalex.org/C36434225","wikidata":"https://www.wikidata.org/wiki/Q1895998","display_name":"Polypharmacy","level":2,"score":0.8314274549484253},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7018328309059143},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.6852922439575195},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6566593647003174},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5514683127403259},{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.5037381052970886},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3894685208797455},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.386627733707428},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36608079075813293},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30015891790390015},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13060083985328674},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.08884751796722412},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822260","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822260","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1979845492","https://openalex.org/W2009313526","https://openalex.org/W2029592334","https://openalex.org/W2046345054","https://openalex.org/W2086169342","https://openalex.org/W2091439417","https://openalex.org/W2094154229","https://openalex.org/W2109482131","https://openalex.org/W2134237567","https://openalex.org/W2136127280","https://openalex.org/W2151070626","https://openalex.org/W2184957013","https://openalex.org/W2234451305","https://openalex.org/W2625343706","https://openalex.org/W2759136286","https://openalex.org/W2786016794","https://openalex.org/W2802200505","https://openalex.org/W2962756421","https://openalex.org/W2963911286","https://openalex.org/W2972392269","https://openalex.org/W3003265726","https://openalex.org/W3089843526","https://openalex.org/W3096264553","https://openalex.org/W3108458441","https://openalex.org/W3138304638","https://openalex.org/W3152737236","https://openalex.org/W4212856313","https://openalex.org/W4230270846","https://openalex.org/W4252707176","https://openalex.org/W4283323543","https://openalex.org/W6608344535","https://openalex.org/W6631964550","https://openalex.org/W6678830454","https://openalex.org/W6682691769","https://openalex.org/W6718112784","https://openalex.org/W6769544757","https://openalex.org/W6778510123"],"related_works":["https://openalex.org/W2604454537","https://openalex.org/W2883748392","https://openalex.org/W2897702399","https://openalex.org/W4206028705","https://openalex.org/W2757431232","https://openalex.org/W2808284704","https://openalex.org/W2954554213","https://openalex.org/W2251363251","https://openalex.org/W4206547516","https://openalex.org/W4293236197"],"abstract_inverted_index":{"Polypharmacy":[0],"is":[1,52],"the":[2,9,25,34,56,131,154,160],"combined":[3],"use":[4],"of":[5,11,21,37,58,101,123,156],"multiple":[6,38],"drugs":[7],"for":[8,48,136],"treatment":[10],"diseases,":[12],"which":[13,87],"also":[14],"often":[15,53],"comes":[16],"with":[17,176],"a":[18,42,78],"higher":[19],"risk":[20],"side":[22,35,50,70,162],"effects.":[23],"In":[24,73],"medical":[26],"industry,":[27],"acquiring":[28],"rich":[29],"and":[30,94,110,192],"comprehensive":[31],"information":[32],"about":[33],"effects":[36,51,71,163],"drug":[39],"therapy":[40],"becomes":[41],"crucial":[43],"task.":[44,165],"However,":[45],"data":[46,60,157],"collection":[47],"many":[49],"sparse,":[54],"so":[55],"features":[57],"these":[59],"cannot":[61],"be":[62],"adequately":[63],"learned,":[64],"resulting":[65],"in":[66,69,159,186,195],"poor":[67],"performance":[68,174],"prediction.":[72],"this":[74],"paper,":[75],"we":[76],"propose":[77],"framework":[79],"based":[80],"on":[81,189,198],"knowledge":[82],"graph":[83],"embedding":[84,107],"(KGE)":[85],"models":[86],"improves":[88],"KGE":[89,111,137],"by":[90,184,193],"using":[91],"LTE":[92],"operations":[93],"subsampling":[95,112,134],"methods":[96,135],"(called":[97],"LTESampleKGE).":[98],"LTESampleKGE":[99,150,181],"consists":[100],"two":[102],"main":[103],"modules":[104],"i.e.,":[105],"Entity":[106],"enhancement":[108],"module":[109],"module.":[113],"The":[114],"former":[115],"applies":[116],"linear":[117],"transformation":[118],"to":[119,126,142,146],"entity":[120,128],"representation":[121],"instead":[122],"GCN":[124],"structure":[125],"enhance":[127],"embedding,":[129],"while":[130],"latter":[132],"utilizes":[133],"negative":[138],"sampling":[139],"(NS)":[140],"loss":[141],"pay":[143],"more":[144],"attention":[145],"sparse":[147],"data.":[148],"Thus,":[149],"can":[151],"effectively":[152],"alleviate":[153],"problem":[155],"sparsity":[158],"polypharmacy":[161],"prediction":[164],"Experimental":[166],"evaluations":[167],"indicate":[168],"that":[169],"our":[170],"method":[171],"demonstrates":[172],"superior":[173],"compared":[175],"baseline":[177],"models.":[178],"For":[179],"example,":[180],"outperforms":[182],"MSTE":[183],"1.20%":[185],"PR-AUC":[187],"score":[188,197],"TWOSIDES":[190],"dataset":[191],"0.46%":[194],"AP@n":[196],"Drugbank":[199],"dataset.":[200]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}