{"id":"https://openalex.org/W3095092693","doi":"https://doi.org/10.1093/jamia/ocaa189","title":"Clinical concept extraction using transformers","display_name":"Clinical concept extraction using transformers","publication_year":2020,"publication_date":"2020-07-25","ids":{"openalex":"https://openalex.org/W3095092693","doi":"https://doi.org/10.1093/jamia/ocaa189","mag":"3095092693","pmid":"https://pubmed.ncbi.nlm.nih.gov/33120431"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocaa189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocaa189","pdf_url":"https://academic.oup.com/jamia/article-pdf/27/12/1935/34838661/ocaa189.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/jamia/article-pdf/27/12/1935/34838661/ocaa189.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103133745","display_name":"Xi Yang","orcid":"https://orcid.org/0000-0003-2981-3972"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I4390039331","display_name":"UF Health Cancer Center","ror":"https://ror.org/044vhe029","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xi Yang","raw_affiliation_strings":["Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030951014","display_name":"Jiang Bian","orcid":"https://orcid.org/0000-0002-2238-5429"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I4390039331","display_name":"UF Health Cancer Center","ror":"https://ror.org/044vhe029","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiang Bian","raw_affiliation_strings":["Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076610873","display_name":"William R. Hogan","orcid":"https://orcid.org/0000-0002-9881-1017"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William R Hogan","raw_affiliation_strings":["Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA"],"raw_orcid":"https://orcid.org/0000-0002-9881-1017","affiliations":[{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010253402","display_name":"Yonghui Wu","orcid":"https://orcid.org/0000-0002-6780-6135"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I4390039331","display_name":"UF Health Cancer Center","ror":"https://ror.org/044vhe029","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yonghui Wu","raw_affiliation_strings":["Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Informatics and eHealth core, University of Florida Health Cancer Center, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I4390039331"]},{"raw_affiliation_string":"Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010253402"],"corresponding_institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I33213144","https://openalex.org/I4390039331"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":null,"fwci":11.9011,"has_fulltext":true,"cited_by_count":155,"citation_normalized_percentile":{"value":0.98852782,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"27","issue":"12","first_page":"1935","last_page":"1942"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.5605999827384949,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.5605999827384949,"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":0.13989999890327454,"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/T10028","display_name":"Topic Modeling","score":0.11760000139474869,"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/transformer","display_name":"Transformer","score":0.7789229154586792},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7380651235580444},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.6751915812492371},{"id":"https://openalex.org/keywords/crfs","display_name":"CRFS","score":0.674322783946991},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.548639714717865},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4826262891292572},{"id":"https://openalex.org/keywords/clinical-practice","display_name":"Clinical Practice","score":0.4290602207183838},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.41870224475860596},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39130282402038574},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.11078619956970215},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09828701615333557}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.7789229154586792},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7380651235580444},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6751915812492371},{"id":"https://openalex.org/C2775953691","wikidata":"https://www.wikidata.org/wiki/Q5013874","display_name":"CRFS","level":3,"score":0.674322783946991},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.548639714717865},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4826262891292572},{"id":"https://openalex.org/C2779974597","wikidata":"https://www.wikidata.org/wiki/Q28448986","display_name":"Clinical Practice","level":2,"score":0.4290602207183838},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.41870224475860596},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39130282402038574},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11078619956970215},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09828701615333557},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C512399662","wikidata":"https://www.wikidata.org/wiki/Q3505712","display_name":"Family medicine","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/jamia/ocaa189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocaa189","pdf_url":"https://academic.oup.com/jamia/article-pdf/27/12/1935/34838661/ocaa189.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:33120431","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33120431","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":"Journal of the American Medical Informatics Association : JAMIA","raw_type":null},{"id":"pmh:oai:europepmc.org:7438915","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7727351","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7727351","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7727351","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/jamia/ocaa189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocaa189","pdf_url":"https://academic.oup.com/jamia/article-pdf/27/12/1935/34838661/ocaa189.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.6299999952316284}],"awards":[{"id":"https://openalex.org/G1237233325","display_name":null,"funder_award_id":"NIA R21AG062884","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G1473873222","display_name":null,"funder_award_id":"R21AG062884","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G1758891718","display_name":null,"funder_award_id":"R33 AG062884","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G19436128","display_name":null,"funder_award_id":"P30 AG028740","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G2213090008","display_name":null,"funder_award_id":"1R01CA246418","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G37493133","display_name":null,"funder_award_id":"1R01CA246418 R01","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5326816645","display_name":null,"funder_award_id":"00129436","funder_id":"https://openalex.org/F4320310009","funder_display_name":"University of Florida"},{"id":"https://openalex.org/G579819645","display_name":null,"funder_award_id":"R01-CA246418","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320309360","display_name":"Florida Department of Health","ror":"https://ror.org/03e1xkn26"},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320310009","display_name":"University of Florida","ror":"https://ror.org/02y3ad647"},{"id":"https://openalex.org/F4320332659","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88"},{"id":"https://openalex.org/F4320334287","display_name":"Clinical and Translational Science Institute, University of Florida","ror":null},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3095092693.pdf","grobid_xml":"https://content.openalex.org/works/W3095092693.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W100623710","https://openalex.org/W131094782","https://openalex.org/W567831624","https://openalex.org/W898365131","https://openalex.org/W1637593105","https://openalex.org/W1739897536","https://openalex.org/W2104381725","https://openalex.org/W2114668172","https://openalex.org/W2121227244","https://openalex.org/W2122402213","https://openalex.org/W2137407193","https://openalex.org/W2146089916","https://openalex.org/W2155276279","https://openalex.org/W2161563551","https://openalex.org/W2163922914","https://openalex.org/W2168041406","https://openalex.org/W2270070752","https://openalex.org/W2396881363","https://openalex.org/W2412299847","https://openalex.org/W2413905792","https://openalex.org/W2467995757","https://openalex.org/W2625625371","https://openalex.org/W2651948199","https://openalex.org/W2768488789","https://openalex.org/W2769851464","https://openalex.org/W2911489562","https://openalex.org/W2915128229","https://openalex.org/W2917662859","https://openalex.org/W2940685834","https://openalex.org/W2955483668","https://openalex.org/W2970198438","https://openalex.org/W2976476443","https://openalex.org/W2979250794","https://openalex.org/W2993873509","https://openalex.org/W2994689047","https://openalex.org/W2996388935","https://openalex.org/W3005237274","https://openalex.org/W3023154087","https://openalex.org/W3027260829","https://openalex.org/W3104523752","https://openalex.org/W4212774754","https://openalex.org/W4245100404","https://openalex.org/W6624194647","https://openalex.org/W6636672007","https://openalex.org/W6678277124","https://openalex.org/W6719402147","https://openalex.org/W6762060370","https://openalex.org/W6772397405","https://openalex.org/W6777507432"],"related_works":["https://openalex.org/W2055466819","https://openalex.org/W50079190","https://openalex.org/W2356597680","https://openalex.org/W182104056","https://openalex.org/W2111726165","https://openalex.org/W2011251309","https://openalex.org/W2796133761","https://openalex.org/W3088215229","https://openalex.org/W2511246383","https://openalex.org/W2184553228"],"abstract_inverted_index":{"OBJECTIVE:":[0],"The":[1,137,204],"goal":[2],"of":[3,66,152,186],"this":[4,220],"study":[5,182],"is":[6,213],"to":[7,31,159,200],"explore":[8],"transformer-based":[9,54,128,187],"models":[10,30,89,100,129,188,212],"(eg,":[11],"Bidirectional":[12],"Encoder":[13],"Representations":[14],"from":[15,73],"Transformers":[16],"[BERT])":[17],"for":[18,62,189],"clinical":[19,29,67,98,104,127,146,190,202,205,211,227],"concept":[20,33,147,191,228],"extraction":[21,34,148,229],"and":[22,35,60,76,80,106,155,172,177,195,230],"develop":[23],"an":[24,131],"open-source":[25,132],"package":[26,207,221],"with":[27,109,150,208],"pretrained":[28,90,101,210],"facilitate":[32],"other":[36,201,231],"downstream":[37],"natural":[38],"language":[39],"processing":[40],"(NLP)":[41],"tasks":[42,232],"in":[43,233],"the":[44,74,81,125,160,167,175,184,234],"medical":[45,235],"domain.":[46,236],"METHODS:":[47],"We":[48,85,218],"systematically":[49],"explored":[50],"4":[51,126,209],"widely":[52],"used":[53],"architectures,":[55],"including":[56],"BERT,":[57],"RoBERTa,":[58],"ALBERT,":[59],"ELECTRA,":[61],"extracting":[63],"various":[64],"types":[65],"concepts":[68],"using":[69,91,102],"3":[70,144],"public":[71,145],"datasets":[72,149],"2010":[75,176],"2012":[77,178],"i2b2":[78,179],"challenges":[79],"2018":[82],"n2c2":[83],"challenge.":[84],"examined":[86],"general":[87,92],"transformer":[88,99,206],"English":[93],"corpora":[94],"as":[95,97,119],"well":[96],"a":[103,110,120],"corpus":[105],"compared":[107],"them":[108],"long":[111],"short-term":[112],"memory":[113],"conditional":[114],"random":[115],"fields":[116],"(LSTM-CRFs)":[117],"mode":[118],"baseline.":[121],"Furthermore,":[122],"we":[123],"integrated":[124],"into":[130],"package.":[133],"RESULTS":[134],"AND":[135],"CONCLUSION:":[136],"RoBERTa-MIMIC":[138,164],"model":[139],"achieved":[140],"state-of-the-art":[141],"performance":[142],"on":[143,174,226],"F1-scores":[151],"0.8994,":[153],"0.8053,":[154],"0.8907,":[156],"respectively.":[157],"Compared":[158],"baseline":[161],"LSTM-CRFs":[162],"model,":[163],"remarkably":[165],"improved":[166],"F1-score":[168],"by":[169],"approximately":[170],"4%":[171],"6%":[173],"datasets.":[180],"This":[181],"demonstrated":[183],"efficiency":[185],"extraction.":[192],"Our":[193],"methods":[194],"systems":[196],"can":[197],"be":[198],"applied":[199],"tasks.":[203],"publicly":[214],"available":[215],"at":[216],"https://github.com/uf-hobi-informatics-lab/ClinicalTransformerNER.":[217],"believe":[219],"will":[222],"improve":[223],"current":[224],"practice":[225]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":34},{"year":2023,"cited_by_count":35},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}