{"id":"https://openalex.org/W3147562045","doi":"https://doi.org/10.1145/3448016.3457328","title":"Medical Entity Disambiguation Using Graph Neural Networks","display_name":"Medical Entity Disambiguation Using Graph Neural Networks","publication_year":2021,"publication_date":"2021-06-09","ids":{"openalex":"https://openalex.org/W3147562045","doi":"https://doi.org/10.1145/3448016.3457328","mag":"3147562045"},"language":"en","primary_location":{"id":"doi:10.1145/3448016.3457328","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3448016.3457328","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2021 International Conference on Management of Data","raw_type":"proceedings-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2104.01488","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Alina Vretinaris","orcid":null},"institutions":[{"id":"https://openalex.org/I4210095996","display_name":"IBM (Germany)","ror":"https://ror.org/00pm7rm97","country_code":"DE","type":"company","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210095996"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alina Vretinaris","raw_affiliation_strings":["IBM Germany &amp; IBM Research, Ehningen, Germany"],"affiliations":[{"raw_affiliation_string":"IBM Germany &amp; IBM Research, Ehningen, Germany","institution_ids":["https://openalex.org/I4210095996"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Chuan Lei","orcid":null},"institutions":[{"id":"https://openalex.org/I4210085935","display_name":"IBM Research - Almaden","ror":"https://ror.org/005w8dd04","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210085935","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chuan Lei","raw_affiliation_strings":["IBM Research - Almaden, San Jose, CA, USA"],"affiliations":[{"raw_affiliation_string":"IBM Research - Almaden, San Jose, CA, USA","institution_ids":["https://openalex.org/I4210085935"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Vasilis Efthymiou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vasilis Efthymiou","raw_affiliation_strings":["FORTH-ICS &amp; IBM Research, Heraklion, Greece"],"affiliations":[{"raw_affiliation_string":"FORTH-ICS &amp; IBM Research, Heraklion, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xiao Qin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210085935","display_name":"IBM Research - Almaden","ror":"https://ror.org/005w8dd04","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210085935","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Qin","raw_affiliation_strings":["IBM Research - Almaden, San Jose, CA, USA"],"affiliations":[{"raw_affiliation_string":"IBM Research - Almaden, San Jose, CA, USA","institution_ids":["https://openalex.org/I4210085935"]}]},{"author_position":"last","author":{"id":null,"display_name":"Fatma \u00d6zcan","orcid":null},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fatma \u00d6zcan","raw_affiliation_strings":["Google &amp; IBM Research, Mountain View, CA, USA"],"affiliations":[{"raw_affiliation_string":"Google &amp; IBM Research, Mountain View, CA, USA","institution_ids":["https://openalex.org/I1291425158"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210095996"],"apc_list":null,"apc_paid":null,"fwci":3.2196,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.93024549,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"2310","last_page":"2318"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9994999766349792,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9983000159263611,"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/T11719","display_name":"Data Quality and Management","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.580299973487854},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.548799991607666},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4896000027656555},{"id":"https://openalex.org/keywords/word-sense-disambiguation","display_name":"Word-sense disambiguation","score":0.4661000072956085},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.4214000105857849},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.38420000672340393},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3801000118255615}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8023999929428101},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.580299973487854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.569599986076355},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.548799991607666},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4896000027656555},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46709999442100525},{"id":"https://openalex.org/C51646954","wikidata":"https://www.wikidata.org/wiki/Q48522","display_name":"Word-sense disambiguation","level":3,"score":0.4661000072956085},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.4214000105857849},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.41019999980926514},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.38420000672340393},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.383899986743927},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3801000118255615},{"id":"https://openalex.org/C3019150057","wikidata":"https://www.wikidata.org/wiki/Q92779279","display_name":"Medical information","level":2,"score":0.3709000051021576},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.3619999885559082},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.3465999960899353},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.34439998865127563},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.3043000102043152},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2906000018119812},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.27230000495910645},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2718999981880188},{"id":"https://openalex.org/C2985722590","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medical knowledge","level":2,"score":0.25279998779296875}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3448016.3457328","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3448016.3457328","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2021 International Conference on Management of Data","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2104.01488","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2104.01488","pdf_url":"https://arxiv.org/pdf/2104.01488","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2104.01488","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2104.01488","pdf_url":"https://arxiv.org/pdf/2104.01488","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1541691357","https://openalex.org/W1547612978","https://openalex.org/W1579584928","https://openalex.org/W1904153218","https://openalex.org/W1964189668","https://openalex.org/W2012459404","https://openalex.org/W2054745418","https://openalex.org/W2104511295","https://openalex.org/W2109005707","https://openalex.org/W2123442489","https://openalex.org/W2143902665","https://openalex.org/W2146089916","https://openalex.org/W2153579005","https://openalex.org/W2169099542","https://openalex.org/W2177768736","https://openalex.org/W2239231358","https://openalex.org/W2274308990","https://openalex.org/W2296283641","https://openalex.org/W2396881363","https://openalex.org/W2505532336","https://openalex.org/W2519887557","https://openalex.org/W2604314403","https://openalex.org/W2624431344","https://openalex.org/W2736776866","https://openalex.org/W2774837955","https://openalex.org/W2796167946","https://openalex.org/W2798649495","https://openalex.org/W2798768860","https://openalex.org/W2807021761","https://openalex.org/W2888634710","https://openalex.org/W2905267911","https://openalex.org/W2911286998","https://openalex.org/W2911489562","https://openalex.org/W2942259124","https://openalex.org/W2942692776","https://openalex.org/W2945266622","https://openalex.org/W2948709946","https://openalex.org/W2949182780","https://openalex.org/W2965857891","https://openalex.org/W2970119293","https://openalex.org/W3004507689","https://openalex.org/W3012892971","https://openalex.org/W6601487527","https://openalex.org/W6631190155","https://openalex.org/W6690815549","https://openalex.org/W6697244413","https://openalex.org/W6745537798","https://openalex.org/W6752795476"],"related_works":[],"abstract_inverted_index":{"Medical":[0],"knowledge":[1],"bases":[2],"(KBs),":[3],"distilled":[4],"from":[5],"biomedical":[6],"literature":[7],"and":[8,63,82,106,119],"regulatory":[9],"actions,":[10],"are":[11,50,132],"expected":[12],"to":[13,17,26,54,78,117,128,154,161],"provide":[14,83],"high-quality":[15],"information":[16],"facilitate":[18],"clinical":[19],"decision":[20],"making.":[21],"Entity":[22],"disambiguation":[23,48,158],"(also":[24],"referred":[25],"as":[27,32,137],"entity":[28,47,110],"linking)":[29],"is":[30],"considered":[31],"an":[33,144,170],"essential":[34],"task":[35],"in":[36,60,67,134,175],"unlocking":[37],"the":[38,58,61,64,68,156,162],"wealth":[39],"of":[40,173,177],"such":[41],"medical":[42,46,109],"KBs.":[43],"However,":[44],"existing":[45],"methods":[49],"not":[51],"adequate":[52],"due":[53],"word":[55],"discrepancies":[56],"between":[57],"entities":[59,130],"KB":[62],"text":[65,135],"snippets":[66,136],"source":[69],"documents.":[70],"Recently,":[71],"graph":[72],"neural":[73],"networks":[74],"(GNNs)":[75],"have":[76],"proven":[77],"be":[79],"very":[80],"effective":[81,145],"state-of-the-art":[84,165],"results":[85],"for":[86,108],"many":[87],"real-world":[88,182],"applications":[89],"with":[90],"graph-structured":[91],"data.":[92],"In":[93],"this":[94],"paper,":[95],"we":[96,123,142],"introduce":[97,124],"ED-GNN":[98,168],"based":[99],"on":[100,180],"three":[101],"representative":[102],"GNNs":[103],"(GraphSAGE,":[104],"R-GCN,":[105],"MAGNN)":[107],"disambiguation.":[111],"We":[112],"develop":[113],"two":[114],"optimization":[115],"techniques":[116],"fine-tune":[118],"improve":[120,155],"ED-GNN.":[121],"First,":[122],"a":[125,138],"novel":[126],"strategy":[127,148],"represent":[129],"that":[131,149],"mentioned":[133],"query":[139],"graph.":[140],"Second,":[141],"design":[143],"negative":[146,152],"sampling":[147],"identifies":[150],"hard":[151],"samples":[153],"model's":[157],"capability.":[159],"Compared":[160],"best":[163],"performing":[164],"solutions,":[166],"our":[167],"offers":[169],"average":[171],"improvement":[172],"7.3%":[174],"terms":[176],"F1":[178],"score":[179],"five":[181],"datasets.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2021-04-13T00:00:00"}
