{"id":"https://openalex.org/W4389951503","doi":"https://doi.org/10.3389/frma.2023.1247094","title":"A metric learning-based method for biomedical entity linking","display_name":"A metric learning-based method for biomedical entity linking","publication_year":2023,"publication_date":"2023-12-19","ids":{"openalex":"https://openalex.org/W4389951503","doi":"https://doi.org/10.3389/frma.2023.1247094","pmid":"https://pubmed.ncbi.nlm.nih.gov/38173988"},"language":"en","primary_location":{"id":"doi:10.3389/frma.2023.1247094","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2023.1247094","pdf_url":"https://www.frontiersin.org/articles/10.3389/frma.2023.1247094/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/frma.2023.1247094/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104216555","display_name":"Ngoc D. Le","orcid":null},"institutions":[{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]},{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Ngoc D. Le","raw_affiliation_strings":["Faculty of Information Technology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050147609","display_name":"Nhung T. H. Nguyen","orcid":"https://orcid.org/0000-0001-5935-9235"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nhung T. H. Nguyen","raw_affiliation_strings":["Department of Computer Science, School of Engineering, University of Manchester, Manchester, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Engineering, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5104216555"],"corresponding_institution_ids":["https://openalex.org/I123565023","https://openalex.org/I23582244"],"apc_list":{"value":950,"currency":"USD","value_usd":950},"apc_paid":{"value":950,"currency":"USD","value_usd":950},"fwci":0.1685,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59210292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"8","issue":null,"first_page":"1247094","last_page":"1247094"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.995199978351593,"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":0.995199978351593,"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":0.9941999912261963,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.9873999953269958,"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/unified-medical-language-system","display_name":"Unified Medical Language System","score":0.7864100337028503},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7735496759414673},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6484798192977905},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5850717425346375},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5650320053100586},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5649213790893555},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5609256625175476},{"id":"https://openalex.org/keywords/ambiguity","display_name":"Ambiguity","score":0.5420880913734436},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5297414064407349},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.5213866829872131},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5188320875167847},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5124269127845764},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.5123528242111206},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5107972621917725},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5034567713737488},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43433359265327454}],"concepts":[{"id":"https://openalex.org/C69505689","wikidata":"https://www.wikidata.org/wiki/Q455338","display_name":"Unified Medical Language System","level":2,"score":0.7864100337028503},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7735496759414673},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6484798192977905},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5850717425346375},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5650320053100586},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5649213790893555},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5609256625175476},{"id":"https://openalex.org/C2780522230","wikidata":"https://www.wikidata.org/wiki/Q1140419","display_name":"Ambiguity","level":2,"score":0.5420880913734436},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5297414064407349},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.5213866829872131},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5188320875167847},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5124269127845764},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.5123528242111206},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5107972621917725},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5034567713737488},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43433359265327454},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","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},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/frma.2023.1247094","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2023.1247094","pdf_url":"https://www.frontiersin.org/articles/10.3389/frma.2023.1247094/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},{"id":"pmid:38173988","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38173988","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":"Frontiers in research metrics and analytics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10762861","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10762861","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10762861/pdf/frma-08-1247094.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Res Metr Anal","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:8da68e425f8c4a08b6da763e94145065","is_oa":true,"landing_page_url":"https://doaj.org/article/8da68e425f8c4a08b6da763e94145065","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Research Metrics and Analytics, Vol 8 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/frma.2023.1247094","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2023.1247094","pdf_url":"https://www.frontiersin.org/articles/10.3389/frma.2023.1247094/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389951503.pdf"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1546510067","https://openalex.org/W1993436046","https://openalex.org/W2033184625","https://openalex.org/W2061167720","https://openalex.org/W2096733369","https://openalex.org/W2122950138","https://openalex.org/W2123442489","https://openalex.org/W2154699792","https://openalex.org/W2159583324","https://openalex.org/W2169495281","https://openalex.org/W2331398706","https://openalex.org/W2346452181","https://openalex.org/W2593390416","https://openalex.org/W2600659824","https://openalex.org/W2606377603","https://openalex.org/W2810417023","https://openalex.org/W2892181857","https://openalex.org/W2894176037","https://openalex.org/W2908694412","https://openalex.org/W2936503027","https://openalex.org/W2943284727","https://openalex.org/W2948909602","https://openalex.org/W2950188904","https://openalex.org/W2953126493","https://openalex.org/W2962830213","https://openalex.org/W2963775347","https://openalex.org/W2970641574","https://openalex.org/W2986848299","https://openalex.org/W2987249037","https://openalex.org/W2998702515","https://openalex.org/W3091432621","https://openalex.org/W3109894131","https://openalex.org/W3120093105","https://openalex.org/W3128741952","https://openalex.org/W3164540570","https://openalex.org/W4236912465","https://openalex.org/W4286989061","https://openalex.org/W4287816908","https://openalex.org/W4293354637","https://openalex.org/W4295312788","https://openalex.org/W4297831742","https://openalex.org/W4323852640","https://openalex.org/W4385245566","https://openalex.org/W4385574140","https://openalex.org/W6631190155","https://openalex.org/W6683390034","https://openalex.org/W6692806008","https://openalex.org/W6730323794","https://openalex.org/W6739901393","https://openalex.org/W6750853375","https://openalex.org/W6755207826","https://openalex.org/W6766978945","https://openalex.org/W6775972400","https://openalex.org/W6791006740","https://openalex.org/W6794029143","https://openalex.org/W6801338492","https://openalex.org/W6810226671"],"related_works":["https://openalex.org/W2418017279","https://openalex.org/W2169373522","https://openalex.org/W1541691357","https://openalex.org/W2090135255","https://openalex.org/W2168409722","https://openalex.org/W2782437235","https://openalex.org/W2548972888","https://openalex.org/W2026505290","https://openalex.org/W1993715838","https://openalex.org/W2359088421"],"abstract_inverted_index":{"in":[0,42,157,191,203,258],"a":[1,170,176,183,199,206],"knowledge":[2],"base,":[3],"e.g.,":[4],"the":[5,13,18,23,106,119,124,128,133,138,145,148,153,187,192,211,238],"Unified":[6],"Medical":[7],"Language":[8],"System":[9],"(UMLS).":[10],"One":[11],"of":[12,17,25,55,127,140,147,155,186,189,213,240],"most":[14,82],"challenging":[15,221],"aspects":[16],"entity":[19,141,178],"linking":[20],"task":[21],"is":[22,116,161,234,267],"ambiguity":[24],"mentions,":[26],"i.e.,":[27,90,121,224],"(1)":[28],"mentions":[29,65,156,181,190,214],"whose":[30],"surface":[31],"forms":[32],"are":[33,102],"very":[34,162],"similar,":[35],"but":[36],"which":[37,160],"map":[38],"to":[39,63,112,117,122,131,150,209,236,244],"different":[40,43,158],"entities":[41,47,67],"contexts,":[44,159],"and":[45,66,179,215,226,243,261],"(2)":[46],"that":[48,72,174,230],"can":[49,75],"be":[50,76],"expressed":[51],"using":[52,78],"diverse":[53],"types":[54],"mentions.":[56],"Recent":[57],"studies":[58],"have":[59,93],"used":[60],"BERT-based":[61],"encoders":[62],"encode":[64],"into":[68],"distinguishable":[69],"representations":[70,154],"such":[71],"their":[73],"similarity":[74],"measured":[77],"distance":[79],"metrics.":[80],"However,":[81],"real-world":[83],"biomedical":[84,222],"datasets":[85],"suffer":[86],"from":[87,105],"severe":[88],"imbalance,":[89],"some":[91],"classes":[92,130],"many":[94],"instances":[95,126],"while":[96],"others":[97],"appear":[98],"only":[99],"once":[100],"or":[101],"completely":[103],"absent":[104],"training":[107,193,260],"data.":[108],"A":[109],"common":[110],"way":[111],"address":[113,237],"this":[114,166],"issue":[115,239],"down-sample":[118],"dataset,":[120],"reduce":[123],"number":[125,188],"majority":[129],"make":[132],"dataset":[134],"more":[135],"balanced.":[136],"In":[137],"context":[139],"linking,":[142],"down-sampling":[143],"reduces":[144,255],"ability":[146],"model":[149],"comprehensively":[151],"learn":[152,210],"important.":[163],"To":[164],"tackle":[165],"issue,":[167],"we":[168,228],"propose":[169],"metric-based":[171],"learning":[172],"method":[173,197,233,253],"treats":[175],"given":[177],"its":[180],"as":[182],"whole,":[184],"regardless":[185],"set.":[194],"Specifically,":[195],"our":[196,231,252],"uses":[198],"triplet":[200],"loss-based":[201],"function":[202],"conjunction":[204],"with":[205,247],"clustering":[207],"technique":[208],"representation":[212],"entities.":[216],"Through":[217],"evaluations":[218],"on":[219],"two":[220],"datasets,":[223],"MedMentions":[225],"BC5CDR,":[227],"show":[229],"proposed":[232],"able":[235],"imbalanced":[241],"data":[242],"perform":[245],"competitively":[246],"other":[248],"state-of-the-art":[249],"models.":[250],"Moreover,":[251],"significantly":[254],"computational":[256],"cost":[257],"both":[259],"inference":[262],"steps.":[263],"Our":[264],"source":[265],"code":[266],"publicly":[268],"available":[269],"here.":[270]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
