{"id":"https://openalex.org/W3201023666","doi":"https://doi.org/10.1093/bioinformatics/btab671","title":"Continual knowledge infusion into pre-trained biomedical language models","display_name":"Continual knowledge infusion into pre-trained biomedical language models","publication_year":2021,"publication_date":"2021-09-20","ids":{"openalex":"https://openalex.org/W3201023666","doi":"https://doi.org/10.1093/bioinformatics/btab671","mag":"3201023666","pmid":"https://pubmed.ncbi.nlm.nih.gov/34554186"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab671","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/494/49007514/btab671.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/494/49007514/btab671.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021740848","display_name":"Kishlay Jha","orcid":"https://orcid.org/0000-0003-0826-445X"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kishlay Jha","raw_affiliation_strings":["Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013588572","display_name":"Aidong Zhang","orcid":"https://orcid.org/0000-0001-9723-3246"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aidong Zhang","raw_affiliation_strings":["Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Virginia , Charlottesville, VA 22903, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021740848"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2597,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.83906605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"494","last_page":"502"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9926000237464905,"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":0.9872000217437744,"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":0.8557785749435425},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5782553553581238},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5739670991897583},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.5528398156166077},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5416067838668823},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5184104442596436},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.5112223625183105},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4925151765346527},{"id":"https://openalex.org/keywords/question-answering","display_name":"Question answering","score":0.49168282747268677},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.46772658824920654},{"id":"https://openalex.org/keywords/fidelity","display_name":"Fidelity","score":0.4520381689071655},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.44766685366630554},{"id":"https://openalex.org/keywords/natural-language-understanding","display_name":"Natural language understanding","score":0.44556817412376404},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4218611419200897},{"id":"https://openalex.org/keywords/knowledge-representation-and-reasoning","display_name":"Knowledge representation and reasoning","score":0.4139788746833801},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4091145098209381},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.3722519874572754},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.17757117748260498}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8557785749435425},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5782553553581238},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5739670991897583},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5528398156166077},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5416067838668823},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5184104442596436},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.5112223625183105},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4925151765346527},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.49168282747268677},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.46772658824920654},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.4520381689071655},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.44766685366630554},{"id":"https://openalex.org/C2779439875","wikidata":"https://www.wikidata.org/wiki/Q1078276","display_name":"Natural language understanding","level":3,"score":0.44556817412376404},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4218611419200897},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.4139788746833801},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4091145098209381},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.3722519874572754},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.17757117748260498},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab671","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/494/49007514/btab671.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34554186","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34554186","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab671","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab671","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/494/49007514/btab671.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.7799999713897705}],"awards":[{"id":"https://openalex.org/G1378635745","display_name":null,"funder_award_id":"IIS-2008208","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2167990707","display_name":null,"funder_award_id":"1955151","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3770367615","display_name":null,"funder_award_id":"1934600","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8562946007","display_name":null,"funder_award_id":"1938167","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3201023666.pdf","grobid_xml":"https://content.openalex.org/works/W3201023666.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1997057722","https://openalex.org/W2102343050","https://openalex.org/W2136437513","https://openalex.org/W2143448637","https://openalex.org/W2149151184","https://openalex.org/W2150838562","https://openalex.org/W2154142897","https://openalex.org/W2250539671","https://openalex.org/W2473930607","https://openalex.org/W2509884321","https://openalex.org/W2560647685","https://openalex.org/W2563185281","https://openalex.org/W2740815822","https://openalex.org/W2788388592","https://openalex.org/W2808838104","https://openalex.org/W2895296143","https://openalex.org/W2908082115","https://openalex.org/W2911489562","https://openalex.org/W2917968119","https://openalex.org/W2920882081","https://openalex.org/W2944400536","https://openalex.org/W2951538941","https://openalex.org/W2953356739","https://openalex.org/W2954929116","https://openalex.org/W2964242047","https://openalex.org/W2970986510","https://openalex.org/W2991612931","https://openalex.org/W3005970824","https://openalex.org/W3023802502","https://openalex.org/W3035021780","https://openalex.org/W3035153870","https://openalex.org/W3035763680","https://openalex.org/W3046375318","https://openalex.org/W3098115739","https://openalex.org/W3098749216","https://openalex.org/W3112340563","https://openalex.org/W3126891849","https://openalex.org/W3170316419","https://openalex.org/W4294170691","https://openalex.org/W4295883599","https://openalex.org/W4385245566","https://openalex.org/W6675257112","https://openalex.org/W6681188176","https://openalex.org/W6682691769","https://openalex.org/W6684408796","https://openalex.org/W6691431627","https://openalex.org/W6724881955","https://openalex.org/W6739901393","https://openalex.org/W6741087337","https://openalex.org/W6742071618","https://openalex.org/W6758479261","https://openalex.org/W6761724051","https://openalex.org/W6762503438","https://openalex.org/W6762867720","https://openalex.org/W6764513019","https://openalex.org/W6767002648","https://openalex.org/W6767038488","https://openalex.org/W6770565238","https://openalex.org/W6779433498","https://openalex.org/W6780237715","https://openalex.org/W6781031682","https://openalex.org/W6784807622","https://openalex.org/W6785309951","https://openalex.org/W6797000528"],"related_works":["https://openalex.org/W1984061923","https://openalex.org/W2152164004","https://openalex.org/W3004288456","https://openalex.org/W4362496998","https://openalex.org/W4285410103","https://openalex.org/W3113264705","https://openalex.org/W2184397297","https://openalex.org/W1663435917","https://openalex.org/W2810079151","https://openalex.org/W2572241437"],"abstract_inverted_index":{"We":[0],"propose":[1,44],"a":[2,45,56],"new":[3,46,73],"representation":[4],"learning":[5,63,95],"approach":[6,87,109],"that":[7,50],"progressively":[8],"fuses":[9],"the":[10,17,25,28,40,60,67,72,77,85,104,107],"semantic":[11],"information":[12],"from":[13],"multiple":[14],"KBs":[15,26,42],"into":[16],"pretrained":[18],"biomedical":[19,29],"language":[20,82],"models.":[21,83],"Since":[22],"most":[23],"of":[24,80,106],"in":[27,114],"domain":[30],"are":[31],"expressed":[32],"as":[33],"parent-child":[34],"hierarchies,":[35],"we":[36],"choose":[37],"to":[38,70],"model":[39],"hierarchical":[41],"and":[43,94,110],"knowledge":[47,74],"modeling":[48],"strategy":[49],"encodes":[51],"their":[52],"topological":[53],"properties":[54],"at":[55],"granular":[57],"level.":[58],"Moreover,":[59],"proposed":[61,86,108],"continual":[62],"technique":[64],"efficiently":[65],"updates":[66],"concepts":[68],"representations":[69],"accommodate":[71],"while":[75],"preserving":[76],"memory":[78],"efficiency":[79],"contextualized":[81],"Altogether,":[84],"generates":[88],"knowledge-powered":[89],"embeddings":[90],"with":[91],"high":[92],"fidelity":[93],"efficiency.":[96],"Extensive":[97],"experiments":[98],"conducted":[99],"on":[100],"bioNLP":[101],"tasks":[102],"validate":[103],"efficacy":[105],"demonstrates":[111],"its":[112],"capability":[113],"generating":[115],"robust":[116],"concept":[117],"representations.":[118]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
