{"id":"https://openalex.org/W4391292768","doi":"https://doi.org/10.1093/jamia/ocad259","title":"Improving large language models for clinical named entity recognition via prompt engineering","display_name":"Improving large language models for clinical named entity recognition via prompt engineering","publication_year":2024,"publication_date":"2024-01-27","ids":{"openalex":"https://openalex.org/W4391292768","doi":"https://doi.org/10.1093/jamia/ocad259","pmid":"https://pubmed.ncbi.nlm.nih.gov/38281112"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocad259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocad259","pdf_url":"https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad259/56437671/ocad259.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad259/56437671/ocad259.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100715220","display_name":"Yan Hu","orcid":"https://orcid.org/0009-0008-2413-5918"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Hu","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":"https://orcid.org/0009-0008-2413-5918","affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042874172","display_name":"Qingyu Chen","orcid":"https://orcid.org/0000-0002-6036-1516"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qingyu Chen","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD, United States","Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD, United States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079546302","display_name":"Jingcheng Du","orcid":"https://orcid.org/0000-0002-0322-4566"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingcheng Du","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":"https://orcid.org/0000-0002-0322-4566","affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036053506","display_name":"Xueqing Peng","orcid":"https://orcid.org/0000-0002-3296-3472"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xueqing Peng","raw_affiliation_strings":["Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080240865","display_name":"Vipina K. Keloth","orcid":"https://orcid.org/0000-0001-6919-1122"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vipina Kuttichi Keloth","raw_affiliation_strings":["Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101472330","display_name":"Xu Zuo","orcid":"https://orcid.org/0000-0002-9713-4579"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu Zuo","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016388137","display_name":"Yujia Zhou","orcid":"https://orcid.org/0000-0003-0889-2261"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yujia Zhou","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":"https://orcid.org/0000-0003-0889-2261","affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034185112","display_name":"Zehan Li","orcid":"https://orcid.org/0000-0002-2955-6809"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zehan Li","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055458864","display_name":"Xiaoqian Jiang","orcid":"https://orcid.org/0000-0001-9933-2205"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoqian Jiang","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":"https://orcid.org/0000-0001-9933-2205","affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083081872","display_name":"Zhiyong Lu","orcid":"https://orcid.org/0000-0001-9998-916X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiyong Lu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD, United States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046709245","display_name":"Kirk Roberts","orcid":"https://orcid.org/0000-0001-6525-5213"},"institutions":[{"id":"https://openalex.org/I4210093798","display_name":"Museum of Fine Arts, Houston","ror":"https://ror.org/00n9dj543","country_code":"US","type":"archive","lineage":["https://openalex.org/I4210093798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kirk Roberts","raw_affiliation_strings":["McWilliams School of Biomedical Informatics , Houston, TX, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics , Houston, TX, United States","institution_ids":["https://openalex.org/I4210093798"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084072550","display_name":"Hua Xu","orcid":"https://orcid.org/0000-0002-5274-4672"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hua Xu","raw_affiliation_strings":["Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Biomedical Informatics and Data Science, School of Medicine, Yale University , New Haven, CT, United States","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5084072550"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":{"value":3967,"currency":"USD","value_usd":3967},"fwci":85.9348,"has_fulltext":true,"cited_by_count":279,"citation_normalized_percentile":{"value":0.99959442,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"31","issue":"9","first_page":"1812","last_page":"1820"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.5266000032424927,"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":0.5266000032424927,"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":0.14399999380111694,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.09229999780654907,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7695245742797852},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.7011972069740295},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6479517817497253},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.596562385559082},{"id":"https://openalex.org/keywords/baseline","display_name":"Baseline (sea)","score":0.5715410113334656},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.5471959114074707},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5177571177482605},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48898255825042725},{"id":"https://openalex.org/keywords/guideline","display_name":"Guideline","score":0.4383111000061035},{"id":"https://openalex.org/keywords/adverse-event-reporting-system","display_name":"Adverse Event Reporting System","score":0.4376063942909241},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40087053179740906},{"id":"https://openalex.org/keywords/adverse-effect","display_name":"Adverse effect","score":0.26457375288009644},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16640615463256836},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.0857137143611908}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7695245742797852},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.7011972069740295},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6479517817497253},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.596562385559082},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.5715410113334656},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.5471959114074707},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5177571177482605},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48898255825042725},{"id":"https://openalex.org/C2780182762","wikidata":"https://www.wikidata.org/wiki/Q1630279","display_name":"Guideline","level":2,"score":0.4383111000061035},{"id":"https://openalex.org/C2777105317","wikidata":"https://www.wikidata.org/wiki/Q4686710","display_name":"Adverse Event Reporting System","level":3,"score":0.4376063942909241},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40087053179740906},{"id":"https://openalex.org/C197934379","wikidata":"https://www.wikidata.org/wiki/Q2047938","display_name":"Adverse effect","level":2,"score":0.26457375288009644},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16640615463256836},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0857137143611908},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C111368507","wikidata":"https://www.wikidata.org/wiki/Q43518","display_name":"Oceanography","level":1,"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/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","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}],"mesh":[{"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":"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":"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":"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":"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":"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":"D009323","descriptor_name":"Natural Language Processing","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":"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":"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":"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":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/jamia/ocad259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocad259","pdf_url":"https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad259/56437671/ocad259.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:38281112","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38281112","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:pubmedcentral.nih.gov:11339492","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11339492","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11339492/pdf/ocad259.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":"J Am Med Inform Assoc","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:uthshis_docs-1197","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthshis_docs/197","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12478435","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12478435/","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":"ArXiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/jamia/ocad259","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocad259","pdf_url":"https://academic.oup.com/jamia/advance-article-pdf/doi/10.1093/jamia/ocad259/56437671/ocad259.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G184072500","display_name":null,"funder_award_id":"R01AG066749-03S1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3414687875","display_name":null,"funder_award_id":"R21AI164100","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4219384955","display_name":null,"funder_award_id":"RR180012","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G4324966325","display_name":null,"funder_award_id":"R01LM013712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4337381829","display_name":null,"funder_award_id":"R21EB029575","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5344341928","display_name":null,"funder_award_id":"1RF1AG072799","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G5373119292","display_name":null,"funder_award_id":"1RF1AG072799","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6071359385","display_name":null,"funder_award_id":"U01TR002062","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6247586359","display_name":null,"funder_award_id":"R01AG066749","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6391021328","display_name":null,"funder_award_id":"2124789","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6568267561","display_name":null,"funder_award_id":"R01LM011934","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7043769918","display_name":null,"funder_award_id":"1R01AG080429","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G8720705388","display_name":null,"funder_award_id":"1K99LM01402","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391292768.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2004910511","https://openalex.org/W2107435951","https://openalex.org/W2146089916","https://openalex.org/W2168041406","https://openalex.org/W2169818249","https://openalex.org/W2768488789","https://openalex.org/W2805211535","https://openalex.org/W2911489562","https://openalex.org/W3046375318","https://openalex.org/W3135084718","https://openalex.org/W4292779060","https://openalex.org/W4319460874","https://openalex.org/W4319662928","https://openalex.org/W4366563389","https://openalex.org/W4368340908","https://openalex.org/W4381480701","https://openalex.org/W4381587418","https://openalex.org/W4387356888","https://openalex.org/W4403515058","https://openalex.org/W6778883912","https://openalex.org/W6781031682"],"related_works":["https://openalex.org/W4377865234","https://openalex.org/W3180764077","https://openalex.org/W4281560212","https://openalex.org/W4210800588","https://openalex.org/W3116252395","https://openalex.org/W2769084352","https://openalex.org/W4385574021","https://openalex.org/W2887593177","https://openalex.org/W4386322467","https://openalex.org/W2757016069"],"abstract_inverted_index":{"IMPORTANCE:":[0],"The":[1,273,332],"study":[2,59,333],"highlights":[3],"the":[4,37,51,61,106,110,130,139,183,239,254,260,289,336,344],"potential":[5,310,385],"of":[6,63,198,228,241,251,291,329,338,348,357,366],"large":[7],"language":[8],"models,":[9],"specifically":[10],"GPT-3.5":[11,64,191,221],"and":[12,19,29,48,65,74,100,117,158,169,181,192,203,222,233,257,304,327,346,376],"GPT-4,":[13],"in":[14,105,129,280,311,350],"processing":[15],"complex":[16],"clinical":[17,45,68,91,103,146,284,351,361,386],"data":[18],"extracting":[20],"meaningful":[21],"information":[22],"with":[23,155,295],"minimal":[24],"training":[25,268,377],"data.":[26],"By":[27],"developing":[28],"refining":[30],"prompt-based":[31],"strategies,":[32],"we":[33,143],"can":[34],"significantly":[35,379],"enhance":[36],"models'":[38,141,382],"performance,":[39,142,368],"making":[40],"them":[41],"viable":[42],"tools":[43],"for":[44,67,173,201,206,231,236,253,259,283,301,384],"NER":[46,92,285,362],"tasks":[47,73,363],"possibly":[49],"reducing":[50],"reliance":[52],"on":[53,89],"extensive":[54],"annotated":[55,171],"datasets.":[56],"OBJECTIVES:":[57],"This":[58],"quantifies":[60],"capabilities":[62,345],"GPT-4":[66,193,223,308],"named":[69],"entity":[70],"recognition":[71],"(NER)":[72],"proposes":[75],"task-specific":[76,147,296,330,370],"prompts":[77,154],"to":[78,95,119,185,315,360],"improve":[79,138],"their":[80],"performance.":[81,214],"MATERIALS":[82],"AND":[83],"METHODS:":[84],"We":[85,176],"evaluated":[86],"these":[87,246],"models":[88,184,293,317,359],"2":[90],"tasks:":[93],"(1)":[94,152],"extract":[96],"medical":[97,374],"problems,":[98],"treatments,":[99],"tests":[101],"from":[102,126],"notes":[104],"MTSamples":[107,202,232,255],"corpus,":[108],"following":[109],"2010":[111],"i2b2":[112],"concept":[113],"extraction":[114],"shared":[115],"task,":[116],"(2)":[118,161],"identify":[120],"nervous":[121],"system":[122,135],"disorder-related":[123],"adverse":[124,132],"events":[125],"safety":[127],"reports":[128],"vaccine":[131],"event":[133],"reporting":[134],"(VAERS).":[136],"To":[137],"GPT":[140,292,358,381],"developed":[144],"a":[145,277,299],"prompt":[148,209,243,325,371],"framework":[149],"that":[150,341],"includes":[151],"baseline":[153,189],"task":[156],"description":[157],"format":[159],"specification,":[160],"annotation":[162],"guideline-based":[163],"prompts,":[164,190,297],"(3)":[165],"error":[166],"analysis-based":[167],"instructions,":[168],"(4)":[170],"samples":[172,269],"few-shot":[174],"learning.":[175],"assessed":[177],"each":[178],"prompt's":[179],"effectiveness":[180,240],"compared":[182],"BioClinicalBERT.":[186],"RESULTS:":[187],"Using":[188],"achieved":[194,224],"relaxed":[195,225],"F1":[196,226],"scores":[197],"0.634,":[199],"0.804":[200],"0.301,":[204],"0.593":[205],"VAERS.":[207],"Additional":[208],"components":[210,218],"consistently":[211],"improved":[212,294],"model":[213],"When":[215],"all":[216],"4":[217],"were":[219],"used,":[220],"socres":[227],"0.794,":[229],"0.861":[230],"0.676,":[234],"0.736":[235],"VAERS,":[237],"demonstrating":[238],"our":[242,369],"framework.":[244],"Although":[245],"results":[247],"trail":[248],"BioClinicalBERT":[249],"(F1":[250],"0.901":[252],"dataset":[256],"0.802":[258],"VAERS),":[261],"it":[262],"is":[263],"very":[264],"promising":[265,278],"considering":[266],"few":[267],"are":[270],"needed.":[271],"DISCUSSION:":[272],"study's":[274],"findings":[275],"suggest":[276],"direction":[279],"leveraging":[281],"LLMs":[282,306,349],"tasks.":[286],"However,":[287],"while":[288],"performance":[290,314,347],"there's":[298],"need":[300],"further":[302],"development":[303],"refinement.":[305],"like":[307,318],"show":[309],"achieving":[312],"close":[313],"state-of-the-art":[316],"BioClinicalBERT,":[319],"but":[320],"they":[321],"still":[322],"require":[323],"careful":[324],"engineering":[326],"understanding":[328],"knowledge.":[331],"also":[334],"underscores":[335],"importance":[337],"evaluation":[339],"schemas":[340],"accurately":[342],"reflect":[343],"settings.":[352],"CONCLUSION:":[353],"While":[354],"direct":[355],"application":[356],"falls":[364],"short":[365],"optimal":[367],"framework,":[372],"incorporating":[373],"knowledge":[375],"samples,":[378],"enhances":[380],"feasibility":[383],"applications.":[387]},"counts_by_year":[{"year":2026,"cited_by_count":42},{"year":2025,"cited_by_count":156},{"year":2024,"cited_by_count":81}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}