{"id":"https://openalex.org/W4390971277","doi":"https://doi.org/10.1109/bibm58861.2023.10385533","title":"Joint Learning-based Multiple Documents Heterogeneous Graph Inference for Biomedical Entity Linking","display_name":"Joint Learning-based Multiple Documents Heterogeneous Graph Inference for Biomedical Entity Linking","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971277","doi":"https://doi.org/10.1109/bibm58861.2023.10385533"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385533","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385533","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 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/A5088459106","display_name":"Qizhu Dai","orcid":"https://orcid.org/0000-0003-1072-7847"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qizhu Dai","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039180924","display_name":"Jiang Zhong","orcid":"https://orcid.org/0000-0001-9614-6730"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiang Zhong","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100337582","display_name":"Chen Wang","orcid":"https://orcid.org/0000-0002-4630-0805"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Wang","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009992128","display_name":"Hong Yin","orcid":"https://orcid.org/0000-0002-3854-9686"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Yin","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029862133","display_name":"Qin Lei","orcid":"https://orcid.org/0000-0002-1340-5969"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Lei","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372201","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-4515-6792"},"institutions":[{"id":"https://openalex.org/I160993911","display_name":"Queensland University of Technology","ror":"https://ror.org/03pnv4752","country_code":"AU","type":"education","lineage":["https://openalex.org/I160993911"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["The University of Queensland,School of Information Technology and Electronic Engineering,Brisbane,Australia","School of Information Technology and Electronic Engineering, The University of Queensland, Brisbane, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Queensland,School of Information Technology and Electronic Engineering,Brisbane,Australia","institution_ids":["https://openalex.org/I160993911","https://openalex.org/I165143802"]},{"raw_affiliation_string":"School of Information Technology and Electronic Engineering, The University of Queensland, Brisbane, Australia","institution_ids":["https://openalex.org/I160993911","https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033869703","display_name":"Rongzhen Li","orcid":"https://orcid.org/0000-0003-0306-3982"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rongzhen Li","raw_affiliation_strings":["Chongqing University,College of Computer Science,Chongqing,China","College of Computer Science, Chongqing University, Chongqing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing University,College of Computer Science,Chongqing,China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"College of Computer Science, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"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":"abs/2002.10640","issue":null,"first_page":"2967","last_page":"2974"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9988999962806702,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9979000091552734,"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":0.8672848343849182},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.7608861923217773},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6101792454719543},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.544407844543457},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5283632874488831},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.5042175054550171},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5022127628326416},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.497238427400589},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48830723762512207},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4601583480834961},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4518274664878845},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42251163721084595},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.1955036222934723},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.15254685282707214},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08242407441139221}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8672848343849182},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.7608861923217773},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6101792454719543},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.544407844543457},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5283632874488831},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.5042175054550171},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5022127628326416},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.497238427400589},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48830723762512207},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4601583480834961},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4518274664878845},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42251163721084595},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.1955036222934723},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.15254685282707214},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08242407441139221},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385533","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385533","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7099999785423279,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W11298561","https://openalex.org/W174427690","https://openalex.org/W1522301498","https://openalex.org/W1852412531","https://openalex.org/W1924770834","https://openalex.org/W2039438423","https://openalex.org/W2133564696","https://openalex.org/W2169099542","https://openalex.org/W2251406901","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2740109156","https://openalex.org/W2757369719","https://openalex.org/W2771873754","https://openalex.org/W2798442412","https://openalex.org/W2888236192","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2938843701","https://openalex.org/W2945214661","https://openalex.org/W2952826391","https://openalex.org/W2953126493","https://openalex.org/W2963863453","https://openalex.org/W2967884905","https://openalex.org/W2970986510","https://openalex.org/W3014318675","https://openalex.org/W3034229721","https://openalex.org/W3104748221","https://openalex.org/W3164540570","https://openalex.org/W3170822064","https://openalex.org/W4286989061","https://openalex.org/W4287865052","https://openalex.org/W6600479677","https://openalex.org/W6607091552","https://openalex.org/W6631190155","https://openalex.org/W6638754787","https://openalex.org/W6640212811","https://openalex.org/W6679434410","https://openalex.org/W6755207826","https://openalex.org/W6759960650","https://openalex.org/W6771997646","https://openalex.org/W6775558341","https://openalex.org/W6801338492"],"related_works":["https://openalex.org/W1541691357","https://openalex.org/W2090135255","https://openalex.org/W2168409722","https://openalex.org/W2026505290","https://openalex.org/W2782437235","https://openalex.org/W1993715838","https://openalex.org/W2359088421","https://openalex.org/W2515501281","https://openalex.org/W2181629536","https://openalex.org/W2119465010"],"abstract_inverted_index":{"Biomedical":[0],"Entity":[1],"Linking(BEL)":[2],"is":[3,60],"the":[4,84,115,123,149],"task":[5],"of":[6],"linking":[7,81,142,161,175],"biomedical":[8,29,58,79,159],"mentions":[9,64,121],"in":[10,22,55,105,148],"natural":[11],"language":[12],"corpora":[13],"such":[14],"as":[15],"diseases":[16],"and":[17,39,99,102,122,127,165],"drugs":[18],"to":[19,129,140],"standard":[20],"entities":[21,67],"a":[23,56,94,106,131,137,152],"given":[24],"knowledge":[25],"base.":[26],"The":[27],"same":[28],"entity":[30,80,128,160,174],"can":[31],"have":[32],"multiple":[33,89],"mentions,":[34],"including":[35],"synonyms,":[36],"morphological":[37],"variations":[38],"names":[40],"with":[41,51,151],"different":[42],"word":[43],"order.":[44],"Thus,":[45],"making":[46],"predictions":[47],"for":[48,78],"each":[49,146],"mention":[50,126,147],"an":[52,75],"insufficient":[53],"context":[54],"single":[57],"document":[59],"challenging,":[61],"especially":[62],"when":[63],"or":[65],"linked":[66],"are":[68],"unseen":[69],"during":[70],"training.":[71],"This":[72],"paper":[73],"proposes":[74],"inference":[76],"method":[77,98,139,170],"based":[82],"on":[83,88,111,157],"heterogeneous":[85,132],"graph":[86],"constructed":[87],"documents.":[90],"We":[91],"first":[92],"design":[93],"joint":[95],"representation":[96],"learning":[97],"compute":[100],"mention-mention":[101],"mention-entity":[103],"similarity":[104],"unified":[107],"semantic":[108],"space.":[109],"Based":[110],"them,":[112],"we":[113,135],"utilize":[114],"mutual":[116],"nearest":[117],"neighbors":[118],"relationship":[119,124],"between":[120,125],"construct":[130],"graph.":[133],"Finally,":[134],"apply":[136],"clustering-based":[138],"make":[141],"predictions,":[143],"which":[144],"associates":[145],"documents":[150],"unique":[153],"entity.":[154],"Extensive":[155],"experiments":[156],"three":[158],"benchmarks":[162],"(MedMentions,":[163],"BC5CDR":[164],"NCBI)":[166],"demonstrate":[167],"that":[168],"our":[169],"outperforms":[171],"other":[172],"state-of-the-art":[173],"models.":[176]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
