{"id":"https://openalex.org/W4399752207","doi":"https://doi.org/10.1142/s2972335324500054","title":"Iterative Prompt Refinement for Mining Gene Relationships from ChatGPT","display_name":"Iterative Prompt Refinement for Mining Gene Relationships from ChatGPT","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399752207","doi":"https://doi.org/10.1142/s2972335324500054"},"language":"en","primary_location":{"id":"doi:10.1142/s2972335324500054","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s2972335324500054","pdf_url":null,"source":{"id":"https://openalex.org/S5407039934","display_name":"International Journal of Artificial Intelligence and Robotics Research","issn_l":"2972-3353","issn":["2972-3353","2972-3361"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Artificial Intelligence and Robotics Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104806027","display_name":"Yibo Chen","orcid":"https://orcid.org/0000-0002-3969-2679"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yibo Chen","raw_affiliation_strings":["Institute for Data Science and Informatics, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0002-3969-2679","affiliations":[{"raw_affiliation_string":"Institute for Data Science and Informatics, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104329798","display_name":"Jeffrey Gao","orcid":"https://orcid.org/0009-0001-4878-3978"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeffrey Gao","raw_affiliation_strings":["Marriotts Ridge High School, Marriottsville, MD 21104, USA"],"raw_orcid":"https://orcid.org/0009-0001-4878-3978","affiliations":[{"raw_affiliation_string":"Marriotts Ridge High School, Marriottsville, MD 21104, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057923227","display_name":"Marius Petruc","orcid":"https://orcid.org/0000-0002-6022-2620"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marius Petruc","raw_affiliation_strings":["Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0002-6022-2620","affiliations":[{"raw_affiliation_string":"Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028252532","display_name":"Richard Hammer","orcid":"https://orcid.org/0000-0002-7173-9414"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard D. Hammer","raw_affiliation_strings":["Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0002-7173-9414","affiliations":[{"raw_affiliation_string":"Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060329217","display_name":"Mihail Popescu","orcid":"https://orcid.org/0000-0002-6145-8096"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihail Popescu","raw_affiliation_strings":["Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0002-6145-8096","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0002-4809-0514","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.5623,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.83948461,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"01","issue":"02","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9907000064849854,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9886000156402588,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.607204258441925},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6013464331626892},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5757319927215576},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49280503392219543},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.47028449177742004},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44114604592323303},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.4191848933696747},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.389708936214447},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37732890248298645},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3299662470817566},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2367440164089203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21429774165153503},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.19474411010742188},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14104527235031128},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.14005997776985168},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13866430521011353}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.607204258441925},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6013464331626892},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5757319927215576},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49280503392219543},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.47028449177742004},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44114604592323303},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.4191848933696747},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.389708936214447},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37732890248298645},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3299662470817566},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2367440164089203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21429774165153503},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.19474411010742188},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14104527235031128},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.14005997776985168},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13866430521011353},{"id":"https://openalex.org/C180747234","wikidata":"https://www.wikidata.org/wiki/Q23373","display_name":"Cognitive psychology","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1142/s2972335324500054","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s2972335324500054","pdf_url":null,"source":{"id":"https://openalex.org/S5407039934","display_name":"International Journal of Artificial Intelligence and Robotics Research","issn_l":"2972-3353","issn":["2972-3353","2972-3361"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Artificial Intelligence and Robotics Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2856240588","display_name":null,"funder_award_id":"R01-LM013392","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2011835017","https://openalex.org/W2103397879","https://openalex.org/W2137881949","https://openalex.org/W3173777717","https://openalex.org/W4205730624","https://openalex.org/W4285796263","https://openalex.org/W4307425304","https://openalex.org/W4308834893","https://openalex.org/W4381805620","https://openalex.org/W4385607534"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"ChatGPT":[0,24],"has":[1],"demonstrated":[2],"its":[3],"potential":[4],"as":[5,81,114,151,161],"a":[6,43,129],"surrogate":[7],"knowledge":[8],"graph.":[9],"Trained":[10],"on":[11,27],"extensive":[12],"data":[13],"sources,":[14],"including":[15],"open-access":[16],"publications,":[17],"peer-reviewed":[18],"research":[19],"articles,":[20],"and":[21,30,57,73,97,118,155],"biomedical":[22],"websites,":[23],"extracted":[25],"information":[26],"gene":[28,68,92,142,148,152],"relationships":[29,69,93],"biological":[31],"pathways":[32,156],"so":[33],"that":[34,49],"it":[35],"can":[36],"be":[37,187],"used":[38,188],"to":[39,158],"predict":[40],"them.":[41],"However,":[42],"major":[44],"challenge":[45],"is":[46],"model":[47],"hallucination,":[48],"is,":[50],"high":[51],"false":[52],"positive":[53],"rates.":[54],"To":[55],"assess":[56],"address":[58],"this":[59,184],"challenge,":[60],"we":[61,85,144],"systematically":[62],"evaluated":[63],"ChatGPT\u2019s":[64],"capacity":[65],"for":[66,177,189],"predicting":[67],"using":[70,111],"GPT-3.5-turbo,":[71],"GPT-4,":[72],"GPT-4o.":[74],"Benchmarking":[75],"against":[76],"the":[77,82,137],"KEGG":[78],"Pathway":[79],"Database":[80],"ground":[83],"truth,":[84],"experimented":[86],"with":[87,132],"diverse":[88],"prompting":[89,173],"strategies,":[90],"targeting":[91],"of":[94],"activation,":[95],"inhibition,":[96],"phosphorylation.":[98],"We":[99],"introduced":[100],"an":[101],"innovative":[102],"iterative":[103],"prompt":[104,109],"refinement":[105],"technique.":[106],"By":[107],"assessing":[108],"efficacy":[110],"metrics":[112],"such":[113,150,160,178],"F-1":[115],"score,":[116],"precision,":[117],"recall,":[119],"GPT-4":[120],"suggested":[121],"improved":[122],"prompts.":[123],"A":[124],"refined":[125],"prompt,":[126],"which":[127],"combines":[128],"specialized":[130],"role":[131],"explanatory":[133],"text,":[134],"significantly":[135],"enhanced":[136],"performance.":[138],"Going":[139],"beyond":[140],"pairwise":[141],"relationships,":[143],"also":[145],"deciphered":[146],"complex":[147],"interplays,":[149],"interaction":[153],"chains":[154],"pertinent":[157],"diseases":[159],"non-small":[162],"cell":[163],"lung":[164],"cancer.":[165],"Direct":[166],"prompts":[167],"showed":[168],"limited":[169],"success,":[170],"but":[171],"\u201cleast-to-most\u201d":[172],"exhibited":[174],"significant":[175],"potentials":[176],"network":[179],"constructions.":[180],"The":[181],"methods":[182],"in":[183],"study":[185],"may":[186],"other":[190],"bioinformatics":[191],"prediction":[192],"problems.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
