{"id":"https://openalex.org/W4387210603","doi":"https://doi.org/10.48550/arxiv.2309.16150","title":"AE-GPT: Using Large Language Models to Extract Adverse Events from Surveillance Reports-A Use Case with Influenza Vaccine Adverse Events","display_name":"AE-GPT: Using Large Language Models to Extract Adverse Events from Surveillance Reports-A Use Case with Influenza Vaccine Adverse Events","publication_year":2023,"publication_date":"2023-09-28","ids":{"openalex":"https://openalex.org/W4387210603","doi":"https://doi.org/10.48550/arxiv.2309.16150"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2309.16150","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2309.16150","pdf_url":"https://arxiv.org/pdf/2309.16150","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2309.16150","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113134285","display_name":"Yiming Li","orcid":"https://orcid.org/0000-0001-5871-2316"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li, Yiming","raw_affiliation_strings":[", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104594518","display_name":"Jianfu Li","orcid":"https://orcid.org/0000-0002-9949-7007"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li, Jianfu","raw_affiliation_strings":[", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083672597","display_name":"Jianping He","orcid":"https://orcid.org/0000-0002-4059-9455"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"He, Jianping","raw_affiliation_strings":[", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076058129","display_name":"Cui Tao","orcid":"https://orcid.org/0000-0002-4267-1924"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao, Cui","raw_affiliation_strings":[", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"],"affiliations":[{"raw_affiliation_string":", McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I919571938"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5113134285"],"corresponding_institution_ids":["https://openalex.org/I919571938"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10833","display_name":"Vaccine Coverage and Hesitancy","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/3306","display_name":"Health"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10654","display_name":"Pneumonia and Respiratory Infections","score":0.9775999784469604,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/adverse-effect","display_name":"Adverse effect","score":0.6724140048027039},{"id":"https://openalex.org/keywords/outbreak","display_name":"Outbreak","score":0.6348143815994263},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.5670410394668579},{"id":"https://openalex.org/keywords/adverse-event-reporting-system","display_name":"Adverse Event Reporting System","score":0.4791388213634491},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4314122498035431},{"id":"https://openalex.org/keywords/environmental-health","display_name":"Environmental health","score":0.3744562268257141},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.33437928557395935},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.314123272895813},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.28793731331825256},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2745439410209656},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.16220903396606445}],"concepts":[{"id":"https://openalex.org/C197934379","wikidata":"https://www.wikidata.org/wiki/Q2047938","display_name":"Adverse effect","level":2,"score":0.6724140048027039},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.6348143815994263},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.5670410394668579},{"id":"https://openalex.org/C2777105317","wikidata":"https://www.wikidata.org/wiki/Q4686710","display_name":"Adverse Event Reporting System","level":3,"score":0.4791388213634491},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4314122498035431},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.3744562268257141},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.33437928557395935},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.314123272895813},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.28793731331825256},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2745439410209656},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.16220903396606445}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2309.16150","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2309.16150","pdf_url":"https://arxiv.org/pdf/2309.16150","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2309.16150","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2309.16150","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2309.16150","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2309.16150","pdf_url":"https://arxiv.org/pdf/2309.16150","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8399999737739563,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387210603.pdf","grobid_xml":"https://content.openalex.org/works/W4387210603.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W979396035","https://openalex.org/W1845364899","https://openalex.org/W1918065319","https://openalex.org/W1975597036","https://openalex.org/W1976988340","https://openalex.org/W1983077458","https://openalex.org/W1998268789","https://openalex.org/W2008361529","https://openalex.org/W2116310281","https://openalex.org/W2136970311","https://openalex.org/W2320856077","https://openalex.org/W2546821105","https://openalex.org/W2781571133","https://openalex.org/W2906808750","https://openalex.org/W2986530058","https://openalex.org/W2988647680","https://openalex.org/W3002783676","https://openalex.org/W3058517477","https://openalex.org/W3135084718","https://openalex.org/W3169536731","https://openalex.org/W3172480024","https://openalex.org/W3177920269","https://openalex.org/W3178079110","https://openalex.org/W4212893806","https://openalex.org/W4212974972","https://openalex.org/W4225479391","https://openalex.org/W4243640523","https://openalex.org/W4287327402","https://openalex.org/W4292779060","https://openalex.org/W4293740214","https://openalex.org/W4318685230","https://openalex.org/W4322492760","https://openalex.org/W4324027515","https://openalex.org/W4327946446","https://openalex.org/W4360979863","https://openalex.org/W4361020574","https://openalex.org/W4361806442","https://openalex.org/W4362553921","https://openalex.org/W4366241052","https://openalex.org/W4372348374","https://openalex.org/W4379653093","https://openalex.org/W4382132333","https://openalex.org/W4384918448","https://openalex.org/W4384921136","https://openalex.org/W4385292160","https://openalex.org/W4385474113","https://openalex.org/W4385495736","https://openalex.org/W4385951095","https://openalex.org/W4386655575"],"related_works":["https://openalex.org/W1669499790","https://openalex.org/W4282838629","https://openalex.org/W3135769848","https://openalex.org/W1967736925","https://openalex.org/W4281861147","https://openalex.org/W4388132138","https://openalex.org/W2342267228","https://openalex.org/W3011938841","https://openalex.org/W2918034594","https://openalex.org/W4280493563"],"abstract_inverted_index":{"Though":[0],"Vaccines":[1],"are":[2],"instrumental":[3],"in":[4,29,119],"global":[5],"health,":[6],"mitigating":[7],"infectious":[8],"diseases":[9],"and":[10,32,75,105],"pandemic":[11],"outbreaks,":[12],"they":[13],"can":[14],"occasionally":[15],"lead":[16],"to":[17,50,58,134],"adverse":[18],"events":[19],"(AEs).":[20],"Recently,":[21],"Large":[22],"Language":[23],"Models":[24],"(LLMs)":[25],"have":[26],"shown":[27],"promise":[28],"effectively":[30],"identifying":[31],"cataloging":[33],"AEs":[34,57],"within":[35],"clinical":[36],"reports.":[37],"Utilizing":[38],"data":[39],"from":[40,48],"the":[41,114],"Vaccine":[42],"Adverse":[43],"Event":[44],"Reporting":[45],"System":[46],"(VAERS)":[47],"1990":[49],"2016,":[51],"this":[52],"study":[53],"particularly":[54],"focuses":[55],"on":[56],"evaluate":[59],"LLMs'":[60,117],"capability":[61],"for":[62,102,107],"AE":[63,129,136],"extraction.":[64],"A":[65],"variety":[66],"of":[67,113],"prevalent":[68],"LLMs,":[69],"including":[70],"GPT-2,":[71],"GPT-3":[72],"variants,":[73],"GPT-4,":[74],"Llama":[76],"2,":[77],"were":[78],"evaluated":[79],"using":[80],"Influenza":[81],"vaccine":[82],"as":[83],"a":[84,96,124],"use":[85],"case.":[86],"The":[87,110],"fine-tuned":[88],"GPT":[89],"3.5":[90],"model":[91],"(AE-GPT)":[92],"stood":[93],"out":[94],"with":[95],"0.704":[97],"averaged":[98],"micro":[99],"F1":[100],"score":[101],"strict":[103],"match":[104],"0.816":[106],"relaxed":[108],"match.":[109],"encouraging":[111],"performance":[112],"AE-GPT":[115],"underscores":[116],"potential":[118],"processing":[120],"medical":[121],"data,":[122],"indicating":[123],"significant":[125],"stride":[126],"towards":[127],"advanced":[128],"detection,":[130],"thus":[131],"presumably":[132],"generalizable":[133],"other":[135],"extraction":[137],"tasks.":[138]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
