{"id":"https://openalex.org/W4408521042","doi":"https://doi.org/10.1109/bhi62660.2024.10913581","title":"ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways","display_name":"ReguloGPT: Harnessing GPT for End-to-End Knowledge Graph Construction of Molecular Regulatory Pathways","publication_year":2024,"publication_date":"2024-11-10","ids":{"openalex":"https://openalex.org/W4408521042","doi":"https://doi.org/10.1109/bhi62660.2024.10913581"},"language":"en","primary_location":{"id":"doi:10.1109/bhi62660.2024.10913581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi62660.2024.10913581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-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/A5044454140","display_name":"Xidong Wu","orcid":"https://orcid.org/0000-0001-8796-4272"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xidong Wu","raw_affiliation_strings":["University of Pittsburgh,Electrical and Computer Engineering,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh,Electrical and Computer Engineering,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047651401","display_name":"Sumin Jo","orcid":"https://orcid.org/0000-0003-1445-9392"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumin Jo","raw_affiliation_strings":["University of Pittsburgh,Electrical and Computer Engineering,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh,Electrical and Computer Engineering,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036955542","display_name":"Yiming Zeng","orcid":"https://orcid.org/0000-0001-6429-0682"},"institutions":[{"id":"https://openalex.org/I4210134769","display_name":"University of Pittsburgh Medical Center","ror":"https://ror.org/04ehecz88","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210098814","https://openalex.org/I4210134769"]},{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiming Zeng","raw_affiliation_strings":["University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I4210134769","https://openalex.org/I4210128526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059680425","display_name":"Arun Das","orcid":"https://orcid.org/0000-0001-7512-0523"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arun Das","raw_affiliation_strings":["University of Pittsburgh School of Medicine,Department of Medicine,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh School of Medicine,Department of Medicine,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057799604","display_name":"Tinghe Zhang","orcid":"https://orcid.org/0000-0002-4595-6167"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ting-He Zhang","raw_affiliation_strings":["University of Pittsburgh School of Medicine,Department of Medicine,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh School of Medicine,Department of Medicine,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057913623","display_name":"Parth Patel","orcid":"https://orcid.org/0000-0003-0257-1408"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Parth Patel","raw_affiliation_strings":["The University of Texas at San Antonio,Electrical and Computer Engineering,San Antonio,TX,USA"],"affiliations":[{"raw_affiliation_string":"The University of Texas at San Antonio,Electrical and Computer Engineering,San Antonio,TX,USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103918508","display_name":"Y F Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuanjing Wei","raw_affiliation_strings":["Language Technologies Institute, Carnegie Mellon University,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, Carnegie Mellon University,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100440407","display_name":"Lei Li","orcid":"https://orcid.org/0000-0003-3095-9776"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Li","raw_affiliation_strings":["Language Technologies Institute, Carnegie Mellon University,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, Carnegie Mellon University,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010896860","display_name":"Shou\u2010Jiang Gao","orcid":"https://orcid.org/0000-0001-6194-1742"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shou-Jiang Gao","raw_affiliation_strings":["University of California San Diego,Department of Medicine,La Jolla,CA,USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego,Department of Medicine,La Jolla,CA,USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103256015","display_name":"Jianqiu Zhang","orcid":"https://orcid.org/0000-0003-2592-6195"},"institutions":[{"id":"https://openalex.org/I45438204","display_name":"The University of Texas at San Antonio","ror":"https://ror.org/01kd65564","country_code":"US","type":"education","lineage":["https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianqiu Zhang","raw_affiliation_strings":["The University of Texas at San Antonio,Electrical and Computer Engineering,San Antonio,TX,USA"],"affiliations":[{"raw_affiliation_string":"The University of Texas at San Antonio,Electrical and Computer Engineering,San Antonio,TX,USA","institution_ids":["https://openalex.org/I45438204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038117263","display_name":"Dexter Pratt","orcid":"https://orcid.org/0000-0002-1471-9513"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dexter Pratt","raw_affiliation_strings":["University of Pittsburgh School of Medicine,Department of Microbiology and Molecular Genetics,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh School of Medicine,Department of Microbiology and Molecular Genetics,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028190064","display_name":"Yu\u2010Chiao Chiu","orcid":"https://orcid.org/0000-0003-1647-8634"},"institutions":[{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]},{"id":"https://openalex.org/I4210134769","display_name":"University of Pittsburgh Medical Center","ror":"https://ror.org/04ehecz88","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210098814","https://openalex.org/I4210134769"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Chiao Chiu","raw_affiliation_strings":["University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I4210134769","https://openalex.org/I4210128526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068887242","display_name":"Yufei Huang","orcid":"https://orcid.org/0000-0001-6268-5357"},"institutions":[{"id":"https://openalex.org/I4210128526","display_name":"UPMC Hillman Cancer Center","ror":"https://ror.org/03bw34a45","country_code":"US","type":"facility","lineage":["https://openalex.org/I170201317","https://openalex.org/I4210128526"]},{"id":"https://openalex.org/I4210134769","display_name":"University of Pittsburgh Medical Center","ror":"https://ror.org/04ehecz88","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210098814","https://openalex.org/I4210134769"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yufei Huang","raw_affiliation_strings":["University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh Medical Center,Hillman Cancer Center,Pittsburgh,PA,USA","institution_ids":["https://openalex.org/I4210134769","https://openalex.org/I4210128526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5044454140"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":0.7502,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.72952902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.953499972820282,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.953499972820282,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9498999714851379,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.941100001335144,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.7045656442642212},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4837682247161865},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.13226717710494995}],"concepts":[{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.7045656442642212},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4837682247161865},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.13226717710494995}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bhi62660.2024.10913581","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bhi62660.2024.10913581","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1998402534","https://openalex.org/W2097352005","https://openalex.org/W2098201295","https://openalex.org/W2250724656","https://openalex.org/W2329659234","https://openalex.org/W2563912688","https://openalex.org/W2617283576","https://openalex.org/W2769630486","https://openalex.org/W2787901052","https://openalex.org/W2894374770","https://openalex.org/W3035370585","https://openalex.org/W3038003025","https://openalex.org/W3177287302","https://openalex.org/W3184509920","https://openalex.org/W3212193424","https://openalex.org/W4220865439","https://openalex.org/W4223491992","https://openalex.org/W4283689228","https://openalex.org/W4285041540","https://openalex.org/W4285153328","https://openalex.org/W4294216483","https://openalex.org/W4294921120","https://openalex.org/W4313638908","https://openalex.org/W4327900239","https://openalex.org/W4380323810","https://openalex.org/W4387619038","https://openalex.org/W4389403907","https://openalex.org/W4390692489","https://openalex.org/W4393238126","https://openalex.org/W4399978597","https://openalex.org/W4401043863","https://openalex.org/W4404783854","https://openalex.org/W6776868103","https://openalex.org/W6809646742","https://openalex.org/W6857640506"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2151749779","https://openalex.org/W3179968364","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"Molecular":[0],"Regulatory":[1],"Pathways":[2],"(MRPs)":[3],"are":[4,224],"key":[5],"to":[6,89,176],"understanding":[7],"biological":[8,208],"functions.":[9],"Knowledge":[10],"Graphs":[11],"(KGs)":[12],"help":[13],"organize":[14],"and":[15,34,74,94,141,183,219],"analyze":[16],"MRPs":[17],"by":[18,98,173],"structuring":[19],"complex":[20],"interactions.":[21,82],"Current":[22],"methods":[23],"for":[24,51,66,153,206],"extracting":[25],"KGs":[26],"from":[27,76],"biomedical":[28],"literature":[29],"struggle":[30],"with":[31,160],"hierarchical":[32,92],"relationships":[33],"context.":[35],"Large":[36],"Language":[37],"Models":[38],"(LLMs)":[39],"like":[40],"GPT-4":[41,60,152],"show":[42],"promise":[43],"in":[44,187],"addressing":[45],"these":[46],"issues":[47],"but":[48],"remain":[49],"underexplored":[50],"end-to-end":[52,68],"KG":[53],"construction.":[54],"We":[55,106,144],"present":[56],"reguloGPT,":[57],"a":[58,71,77,85,108,147],"novel":[59,148],"based":[61],"in-context":[62],"learning":[63],"prompt":[64],"designed":[65],"the":[67,103,132,163],"extraction":[69],"of":[70,129,195],"regulatory":[72,81],"graph":[73,88],"context":[75,100],"sentence":[78],"that":[79,157],"describes":[80],"reguloGPT":[83,130,175,212],"employs":[84],"context-aware":[86],"relational":[87,104],"capture":[90],"MRPs'":[91],"structure":[93],"resolves":[95],"semantic":[96],"inconsistencies":[97],"embedding":[99],"directly":[101],"within":[102],"edges.":[105],"created":[107],"benchmark":[109,133,164,217],"dataset":[110,134],"comprising":[111],"four":[112],"hundred":[113],"annotated":[114],"PubMed":[115],"titles":[116,182],"on":[117,131,162],"N<sup":[118],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[119,123,170,179,190,221],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">6</sup>":[120,124,171,180,191,222],"-methyladenosine":[121],"(m<sup":[122],"A)":[125],"regulations.":[126],"Rigorous":[127],"evaluations":[128,161],"showed":[135],"marked":[136],"improvements":[137],"over":[138],"existing":[139],"algorithms":[140],"other":[142],"LLMs.":[143],"further":[145],"developed":[146],"G-Eval":[149],"scheme,":[150],"leveraging":[151],"annotation-free":[154],"performance":[155],"evaluation":[156],"demonstrated":[158,184],"agreement":[159],"dataset.":[165],"Lastly,":[166],"we":[167],"constructed":[168],"m<sup":[169,178,189,220],"A-KG":[172,223],"applying":[174],"1,396":[177],"A-related":[181],"its":[185],"utility":[186],"elucidating":[188],"A's":[192],"reg-ulatory":[193],"mechanisms":[194],"cancer":[196],"phenotypes":[197],"across":[198],"various":[199],"cancers.":[200],"These":[201],"results":[202],"underscore":[203],"reguloGPT's":[204],"potential":[205],"advancing":[207],"knowledge":[209],"extraction.":[210],"All":[211],"works":[213],"including":[214],"source":[215],"code,":[216],"datasets,":[218],"available":[225],"at":[226],"https://github.com/Huang-AI4Medicine-Lab/reguloGPt.":[227]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2025-12-21T23:12:01.093139","created_date":"2025-10-10T00:00:00"}
