{"id":"https://openalex.org/W7171484996","doi":"https://doi.org/10.1145/3807503.3819800","title":"Towards Optimal Prompt Design for Clinical Information Extraction using Large Language Models","display_name":"Towards Optimal Prompt Design for Clinical Information Extraction using Large Language Models","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171484996","doi":"https://doi.org/10.1145/3807503.3819800"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819800","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819800","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819800","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074855352","display_name":"Xinqi Su","orcid":"https://orcid.org/0009-0008-4581-1807"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinqi Su","raw_affiliation_strings":["Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0009-0008-4581-1807","affiliations":[{"raw_affiliation_string":"Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101249035","display_name":"Hanyun Yin","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanyun Yin","raw_affiliation_strings":["Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0009-0003-5302-5033","affiliations":[{"raw_affiliation_string":"Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109641625","display_name":"Yining Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yining Yang","raw_affiliation_strings":["Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0009-0000-2419-6106","affiliations":[{"raw_affiliation_string":"Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143796865","display_name":"Rongrong Wang","orcid":"https://orcid.org/0009-0002-6829-0633"},"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":"Rongrong Wang","raw_affiliation_strings":["University of Texas Health Science Center at Houston, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0009-0002-6829-0633","affiliations":[{"raw_affiliation_string":"University of Texas Health Science Center at Houston, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023436656","display_name":"Qiuhao Lu","orcid":"https://orcid.org/0000-0003-2368-8410"},"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":"Qiuhao Lu","raw_affiliation_strings":["University of Texas Health Science Center at Houston, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-2368-8410","affiliations":[{"raw_affiliation_string":"University of Texas Health Science Center at Houston, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032226587","display_name":"Sunyang Fu","orcid":"https://orcid.org/0000-0003-1691-5179"},"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":"Sunyang Fu","raw_affiliation_strings":["University of Texas Health Science Center at Houston, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-1691-5179","affiliations":[{"raw_affiliation_string":"University of Texas Health Science Center at Houston, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101585391","display_name":"Hongfang Liu","orcid":"https://orcid.org/0000-0003-2570-3741"},"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":"Hongfang Liu","raw_affiliation_strings":["University of Texas Health Science Center at Houston, Houston, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-2570-3741","affiliations":[{"raw_affiliation_string":"University of Texas Health Science Center at Houston, Houston, TX, USA","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101688218","display_name":"Ruihong Huang","orcid":"https://orcid.org/0000-0002-4639-7766"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruihong Huang","raw_affiliation_strings":["Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0000-0002-4639-7766","affiliations":[{"raw_affiliation_string":"Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5187000036239624},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3659999966621399},{"id":"https://openalex.org/keywords/information-model","display_name":"Information model","score":0.3285999894142151},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.32820001244544983},{"id":"https://openalex.org/keywords/information-system","display_name":"Information system","score":0.3240000009536743}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6636999845504761},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5187000036239624},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4991999864578247},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39100000262260437},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3659999966621399},{"id":"https://openalex.org/C21338462","wikidata":"https://www.wikidata.org/wiki/Q1662581","display_name":"Information model","level":2,"score":0.3285999894142151},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.32820001244544983},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32749998569488525},{"id":"https://openalex.org/C180198813","wikidata":"https://www.wikidata.org/wiki/Q121182","display_name":"Information system","level":2,"score":0.3240000009536743},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.3167000114917755},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26249998807907104},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.2531999945640564}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819800","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819800","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819800","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819800","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W2103330371","https://openalex.org/W2137407193","https://openalex.org/W2168041406","https://openalex.org/W2768488789","https://openalex.org/W2911489562","https://openalex.org/W2943638938","https://openalex.org/W2963716420","https://openalex.org/W3002784191","https://openalex.org/W3080429061","https://openalex.org/W3082330004","https://openalex.org/W4283318325","https://openalex.org/W4379379356","https://openalex.org/W4385571696","https://openalex.org/W4385573087","https://openalex.org/W4391292768","https://openalex.org/W4391809309","https://openalex.org/W4404239715","https://openalex.org/W4415540429","https://openalex.org/W4416542771","https://openalex.org/W7124316889"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"large":[1],"language":[2],"models":[3,135],"(LLMs)":[4],"can":[5],"be":[6],"applied":[7],"to":[8,24,163,175],"clinical":[9,32,44,187],"information":[10],"extraction":[11,53],"(IE)":[12],"through":[13],"zero-shot":[14],"or":[15],"few-shot":[16],"in-context":[17],"learning.":[18],"However,":[19],"LLMs":[20],"are":[21],"highly":[22],"sensitive":[23],"prompt":[25,40,99,156,166,184],"design,":[26],"which":[27],"remains":[28],"insufficiently":[29],"studied":[30],"for":[31,42,183],"IE.":[33],"In":[34],"this":[35],"paper,":[36],"we":[37,61,84],"systematically":[38],"investigate":[39],"design":[41,100,185],"two":[43,56],"IE":[45,103,188],"tasks:":[46],"named":[47],"entity":[48,77,119],"recognition":[49],"(NER)":[50],"and":[51,69,79,92,108,117,136,148,189,195],"relation":[52,88],"(RE)":[54],"on":[55,115,133],"benchmark":[57],"datasets.":[58],"For":[59,82,105,112],"NER,":[60,106],"evaluate":[62],"four":[63],"prompting":[64,128,194],"formats:":[65],"BIO,":[66],"TANL,":[67],"DICE,":[68],"SPAN,":[70],"representing":[71],"token":[72],"tagging,":[73],"text-to-text":[74],"generation,":[75],"descriptive":[76],"extraction,":[78],"span":[80],"labeling.":[81],"RE,":[83,113],"compare":[85,127],"three":[86],"paradigms:":[87],"prediction,":[89,91],"missing-entity":[90],"entity-pair":[93],"identification.":[94],"Experimental":[95],"results":[96],"show":[97],"that":[98,159],"significantly":[101],"affects":[102],"performance.":[104],"TANL":[107],"SPAN":[109],"outperform":[110],"BIO.":[111],"conditioning":[114],"relations":[116],"generating":[118],"pairs":[120],"is":[121],"most":[122],"effective":[123],"strategy.":[124],"We":[125,151],"further":[126],"with":[129,168],"fine-tuning":[130],"approaches":[131],"based":[132],"BERT-family":[134],"smaller":[137],"LLMs,":[138],"observing":[139],"a":[140],"substantial":[141],"gap":[142],"between":[143,193],"prompting,":[144],"general-purpose":[145],"LLM":[146,161],"fine-tuning,":[147],"domain-specific":[149,173],"fine-tuning.":[150,196],"also":[152],"propose":[153],"an":[154],"error-driven":[155],"optimization":[157],"approach":[158],"leverages":[160],"self-reflection":[162],"iteratively":[164],"refine":[165],"components":[167],"error":[169],"feedback,":[170],"providing":[171],"richer":[172],"guidance":[174,182],"LLMs.":[176],"Overall,":[177],"our":[178],"study":[179],"offers":[180],"practical":[181],"in":[186],"highlights":[190],"the":[191],"trade-offs":[192]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}