{"id":"https://openalex.org/W3037979089","doi":"https://doi.org/10.1093/bib/bbaa110","title":"Enriching contextualized language model from knowledge graph for biomedical information extraction","display_name":"Enriching contextualized language model from knowledge graph for biomedical information extraction","publication_year":2020,"publication_date":"2020-05-07","ids":{"openalex":"https://openalex.org/W3037979089","doi":"https://doi.org/10.1093/bib/bbaa110","mag":"3037979089","pmid":"https://pubmed.ncbi.nlm.nih.gov/32591802"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa110","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa110","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/A5002241280","display_name":"Fei Hao","orcid":"https://orcid.org/0000-0001-5288-5523"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hao Fei","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055938662","display_name":"Yafeng Ren","orcid":"https://orcid.org/0000-0002-0291-4733"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yafeng Ren","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100333738","display_name":"Yue Zhang","orcid":"https://orcid.org/0000-0002-6327-5023"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yue Zhang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101801149","display_name":"Donghong Ji","orcid":"https://orcid.org/0000-0003-4020-983X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Donghong Ji","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5037727301","display_name":"Xiaohui Liang","orcid":"https://orcid.org/0000-0001-6351-2538"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiaohui Liang","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002241280"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":10.7374,"has_fulltext":false,"cited_by_count":169,"citation_normalized_percentile":{"value":0.98679121,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9980999827384949,"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":0.991100013256073,"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":0.7293109893798828},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.6051887273788452},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5805547833442688},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.565876305103302},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.48698553442955017},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4603429138660431},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.45366743206977844},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.43321534991264343},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3993096649646759},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35325390100479126},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1408710479736328}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7293109893798828},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.6051887273788452},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5805547833442688},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.565876305103302},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.48698553442955017},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4603429138660431},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.45366743206977844},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.43321534991264343},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3993096649646759},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35325390100479126},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1408710479736328}],"mesh":[{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa110","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa110","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:32591802","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32591802","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":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.7900000214576721}],"awards":[{"id":"https://openalex.org/G3753909773","display_name":null,"funder_award_id":"18JZD015","funder_id":"https://openalex.org/F4320321106","funder_display_name":"Ministry of Education of the People's Republic of China"},{"id":"https://openalex.org/G6442732870","display_name":null,"funder_award_id":"61772378","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6595826518","display_name":null,"funder_award_id":"61702121","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321106","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":97,"referenced_works":["https://openalex.org/W1533230146","https://openalex.org/W1614298861","https://openalex.org/W1850865022","https://openalex.org/W1989277387","https://openalex.org/W2047782770","https://openalex.org/W2117446654","https://openalex.org/W2127795553","https://openalex.org/W2129767020","https://openalex.org/W2136437513","https://openalex.org/W2148004186","https://openalex.org/W2157331557","https://openalex.org/W2158028897","https://openalex.org/W2184957013","https://openalex.org/W2187089797","https://openalex.org/W2251713149","https://openalex.org/W2252226131","https://openalex.org/W2283196293","https://openalex.org/W2346452181","https://openalex.org/W2507883388","https://openalex.org/W2518463060","https://openalex.org/W2567619939","https://openalex.org/W2593581739","https://openalex.org/W2596567068","https://openalex.org/W2597601064","https://openalex.org/W2599674900","https://openalex.org/W2600659824","https://openalex.org/W2602856279","https://openalex.org/W2607662938","https://openalex.org/W2728003555","https://openalex.org/W2739999456","https://openalex.org/W2772102631","https://openalex.org/W2800535933","https://openalex.org/W2804477062","https://openalex.org/W2884668708","https://openalex.org/W2885911173","https://openalex.org/W2887358545","https://openalex.org/W2888043489","https://openalex.org/W2890830728","https://openalex.org/W2891328459","https://openalex.org/W2910243263","https://openalex.org/W2911489562","https://openalex.org/W2912758732","https://openalex.org/W2913327674","https://openalex.org/W2915128308","https://openalex.org/W2915667579","https://openalex.org/W2925863688","https://openalex.org/W2932592714","https://openalex.org/W2938830017","https://openalex.org/W2941868238","https://openalex.org/W2945453987","https://openalex.org/W2948947170","https://openalex.org/W2949176808","https://openalex.org/W2950813464","https://openalex.org/W2953356739","https://openalex.org/W2963339489","https://openalex.org/W2963403868","https://openalex.org/W2964242047","https://openalex.org/W2970597249","https://openalex.org/W2971277756","https://openalex.org/W2972498556","https://openalex.org/W2977943755","https://openalex.org/W3004514756","https://openalex.org/W3105491236","https://openalex.org/W3145013517","https://openalex.org/W4237335579","https://openalex.org/W4288631803","https://openalex.org/W4385245566","https://openalex.org/W6631964550","https://openalex.org/W6636510571","https://openalex.org/W6662590293","https://openalex.org/W6678830454","https://openalex.org/W6686133869","https://openalex.org/W6691431627","https://openalex.org/W6691599004","https://openalex.org/W6691914602","https://openalex.org/W6695596964","https://openalex.org/W6704842505","https://openalex.org/W6718112784","https://openalex.org/W6739901393","https://openalex.org/W6741278343","https://openalex.org/W6741592336","https://openalex.org/W6748634344","https://openalex.org/W6750348125","https://openalex.org/W6750626944","https://openalex.org/W6750755720","https://openalex.org/W6751287528","https://openalex.org/W6753908009","https://openalex.org/W6754350045","https://openalex.org/W6755207826","https://openalex.org/W6757635932","https://openalex.org/W6757883768","https://openalex.org/W6758293299","https://openalex.org/W6758922096","https://openalex.org/W6760821579","https://openalex.org/W6761260114","https://openalex.org/W6761724051","https://openalex.org/W6763701032"],"related_works":["https://openalex.org/W842810586","https://openalex.org/W4319940250","https://openalex.org/W2352298027","https://openalex.org/W2092919065","https://openalex.org/W3138801416","https://openalex.org/W4236762297","https://openalex.org/W2444550338","https://openalex.org/W2369351710","https://openalex.org/W2594363579","https://openalex.org/W2169232658"],"abstract_inverted_index":{"Biomedical":[0],"information":[1,18,54,64,89],"extraction":[2,73,90,97,153],"(BioIE)":[3],"is":[4,10],"an":[5],"important":[6],"task.":[7],"The":[8],"aim":[9],"to":[11,44,55,104,123,138],"analyze":[12],"biomedical":[13,63,88,116,167],"texts":[14],"and":[15,23,60,82,98,133],"extract":[16],"structured":[17],"such":[19],"as":[20],"named":[21,93],"entities":[22],"semantic":[24],"relations":[25,165],"between":[26,166],"them.":[27],"In":[28,66,121],"recent":[29],"years,":[30],"pre-trained":[31,83],"language":[32,80,85,108],"models":[33,81,86],"have":[34],"largely":[35],"improved":[36],"the":[37,57,163],"performance":[38],"of":[39,115],"BioIE.":[40,174],"However,":[41],"they":[42],"neglect":[43],"incorporate":[45],"external":[46],"structural":[47],"knowledge,":[48,126],"which":[49,170],"can":[50,161],"provide":[51],"rich":[52],"factual":[53],"support":[56],"underlying":[58,164],"understanding":[59],"reasoning":[61],"for":[62,173],"extraction.":[65,100],"this":[67],"paper,":[68],"we":[69,127],"first":[70],"evaluate":[71],"current":[72],"methods,":[74],"including":[75,92],"vanilla":[76],"neural":[77],"networks,":[78],"general":[79],"contextualized":[84,107],"on":[87,144],"tasks,":[91],"entity":[94],"recognition,":[95],"relation":[96],"event":[99],"We":[101],"then":[102],"propose":[103],"enrich":[105],"a":[106,112,129],"model":[109],"by":[110],"integrating":[111],"large":[113],"scale":[114],"knowledge":[117,140,168],"graphs":[118],"(namely,":[119],"BioKGLM).":[120],"order":[122],"effectively":[124],"encode":[125],"explore":[128],"three-stage":[130],"training":[131],"procedure":[132],"introduce":[134],"different":[135],"fusion":[136],"strategies":[137],"facilitate":[139],"injection.":[141],"Experimental":[142],"results":[143],"multiple":[145],"tasks":[146],"show":[147],"that":[148,159],"BioKGLM":[149,160],"consistently":[150],"outperforms":[151],"state-of-the-art":[152],"models.":[154],"A":[155],"further":[156],"analysis":[157],"proves":[158],"capture":[162],"concepts,":[169],"are":[171],"crucial":[172]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":31},{"year":2024,"cited_by_count":55},{"year":2023,"cited_by_count":49},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
