{"id":"https://openalex.org/W4417498255","doi":"https://doi.org/10.1186/s12859-025-06350-7","title":"SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation","display_name":"SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation","publication_year":2025,"publication_date":"2025-12-17","ids":{"openalex":"https://openalex.org/W4417498255","doi":"https://doi.org/10.1186/s12859-025-06350-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/41408154"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06350-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06350-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06350-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067209491","display_name":"Jack Freeman","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jack Freeman","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086619052","display_name":"Robert J. Millikin","orcid":"https://orcid.org/0000-0001-7440-3695"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert J. Millikin","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052044401","display_name":"Liang Xu","orcid":"https://orcid.org/0000-0001-9196-4232"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leo Xu","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ishaan Sharma","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ishaan Sharma","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023482526","display_name":"Bethany B. Moore","orcid":"https://orcid.org/0000-0003-3051-745X"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bethany Moore","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090816556","display_name":"Cannon Lock","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cannon Lock","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083866127","display_name":"Kevin W. George","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin Shine George","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Aviral Bal","orcid":null},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aviral Bal","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055365054","display_name":"Chitrasen Mohanty","orcid":"https://orcid.org/0009-0008-0864-6371"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chitrasen Mohanty","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA","Morgridge Institute for Research, Madison, WI 53715 , USA"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA","institution_ids":["https://openalex.org/I29680605"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083447121","display_name":"Ron Stewart","orcid":"https://orcid.org/0000-0002-9041-1828"},"institutions":[{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ron Stewart","raw_affiliation_strings":["Morgridge Institute for Research, Madison WI, , 53715, USA. rstewart@morgridge.org","Morgridge Institute for Research, Madison, WI 53715 , USA. rstewart@morgridge.org"],"affiliations":[{"raw_affiliation_string":"Morgridge Institute for Research, Madison WI, , 53715, USA. rstewart@morgridge.org","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"Morgridge Institute for Research, Madison, WI 53715 , USA. rstewart@morgridge.org","institution_ids":["https://openalex.org/I29680605"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5067209491"],"corresponding_institution_ids":["https://openalex.org/I29680605"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35618976,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"16","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9674000144004822,"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":0.9674000144004822,"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/T10028","display_name":"Topic Modeling","score":0.00559999980032444,"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/T10206","display_name":"Meta-analysis and systematic reviews","score":0.00419999985024333,"subfield":{"id":"https://openalex.org/subfields/1804","display_name":"Statistics, Probability and Uncertainty"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5672000050544739},{"id":"https://openalex.org/keywords/transparency","display_name":"Transparency (behavior)","score":0.5644999742507935},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.4851999878883362},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.37119999527931213},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3693999946117401},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.3587000072002411},{"id":"https://openalex.org/keywords/biological-database","display_name":"Biological database","score":0.3231000006198883}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7646999955177307},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5672000050544739},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.5644999742507935},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5365999937057495},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.4851999878883362},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39250001311302185},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.37119999527931213},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3693999946117401},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.3587000072002411},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32820001244544983},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.3231000006198883},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.30219998955726624},{"id":"https://openalex.org/C180198813","wikidata":"https://www.wikidata.org/wiki/Q121182","display_name":"Information system","level":2,"score":0.2922999858856201},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.29030001163482666},{"id":"https://openalex.org/C2778571376","wikidata":"https://www.wikidata.org/wiki/Q1355821","display_name":"Frontier","level":2,"score":0.28999999165534973},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.27649998664855957},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.27160000801086426}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06350-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06350-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41408154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41408154","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:28a61ecc96524529928eb8c6146d3883","is_oa":true,"landing_page_url":"https://doaj.org/article/28a61ecc96524529928eb8c6146d3883","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-15 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12829140","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12829140/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06350-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06350-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W2032739348","https://openalex.org/W2061167720","https://openalex.org/W2133012565","https://openalex.org/W2164173383","https://openalex.org/W2327037637","https://openalex.org/W2411035889","https://openalex.org/W2616598798","https://openalex.org/W2786651430","https://openalex.org/W2896730986","https://openalex.org/W2921377602","https://openalex.org/W2970482702","https://openalex.org/W2974335753","https://openalex.org/W3017463390","https://openalex.org/W3027879771","https://openalex.org/W3034383590","https://openalex.org/W3211283825","https://openalex.org/W4221143046","https://openalex.org/W4287329731","https://openalex.org/W4362515116","https://openalex.org/W4388139915","https://openalex.org/W4388685661","https://openalex.org/W4388926373","https://openalex.org/W4389984066","https://openalex.org/W4390041933","https://openalex.org/W4390602555","https://openalex.org/W4393147129","https://openalex.org/W4395474395","https://openalex.org/W4399629030","https://openalex.org/W4400375223","https://openalex.org/W4402701703","https://openalex.org/W4404225840","https://openalex.org/W4404782812","https://openalex.org/W4405766390","https://openalex.org/W4406779522","https://openalex.org/W4407310644","https://openalex.org/W4409190866","https://openalex.org/W4410806538","https://openalex.org/W4411459644","https://openalex.org/W4416043407"],"related_works":[],"abstract_inverted_index":{"Generating":[0],"and":[1,20,110,168,193,223,242,252,262,301,313,318],"testing":[2],"hypotheses":[3,14,56,61,322],"is":[4,240,296],"a":[5,118,123,183,219,253,268,304],"critical":[6,94],"aspect":[7],"of":[8,31,54,135,151,163,271],"biomedical":[9,32,48,321],"science.":[10],"Typically,":[11],"researchers":[12,315],"generate":[13,58],"by":[15,160],"carefully":[16],"analyzing":[17],"available":[18,302],"information":[19,166],"making":[21],"logical":[22],"connections,":[23],"which":[24,80],"are":[25,158],"then":[26],"tested.":[27,66],"The":[28],"accelerating":[29],"growth":[30],"literature":[33],"makes":[34],"it":[35,244],"increasingly":[36],"difficult":[37],"to":[38,133,138,148,171,198,227,291,316],"keep":[39],"pace":[40],"with":[41,117,195,218,280],"connections":[42],"between":[43],"biological":[44,102],"entities":[45],"emerging":[46],"across":[47],"research.":[49],"Recently":[50],"developed":[51],"automated":[52],"means":[53],"generating":[55],"can":[57,63,106],"many":[59],"more":[60],"than":[62],"be":[64,134],"easily":[65],"One":[67],"such":[68,75],"approach":[69],"involves":[70],"literature\u2011based":[71],"discovery":[72],"(LBD)":[73],"systems":[74,91],"as":[76],"Serial":[77],"KinderMiner":[78],"(SKiM),":[79],"surfaces":[81],"putative":[82],"A\u2011B\u2011C":[83],"links":[84],"derived":[85],"from":[86],"term":[87],"co\u2011occurrence.":[88],"However,":[89],"LBD":[90,125],"leave":[92],"three":[93],"gaps:":[95],"(i)":[96],"they":[97,105,112],"find":[98],"statistical":[99],"associations,":[100],"not":[101,114,174],"relationships;":[103],"(ii)":[104],"produce":[107],"false\u2011positive":[108],"leads;":[109],"(iii)":[111],"do":[113],"assess":[115],"agreement":[116,279],"hypothesis":[119,250],"in":[120,165,176,259,264],"question.":[121],"As":[122],"result,":[124],"search":[126,192],"results":[127],"often":[128],"require":[129],"costly":[130],"manual":[131],"curation":[132,153],"practical":[136],"utility":[137],"the":[139,146,169,177,229,233,237,246,249,256,260],"researcher.":[140],"Large":[141],"language":[142],"models":[143],"(LLMs)":[144],"have":[145],"potential":[147],"automate":[149],"much":[150],"this":[152],"step,":[154],"but":[155],"standalone":[156],"LLMs":[157,197],"hampered":[159],"hallucinations,":[161],"lack":[162],"transparency":[164],"sources,":[167],"inability":[170],"reference":[172],"data":[173],"included":[175],"training":[178],"corpus.":[179],"We":[180],"introduce":[181],"SKiM-GPT,":[182],"retrieval-augmented":[184],"generation":[185],"(RAG)":[186],"system":[187,239],"that":[188],"combines":[189],"SKiM\u2019s":[190],"co-occurrence":[191],"retrieval":[194],"frontier":[196],"evaluate":[199,228,320],"user-defined":[200],"hypotheses.":[201],"For":[202],"every":[203],"chosen":[204],"A-B-C":[205],"SKiM":[206],"hit,":[207],"SKiM-GPT":[208,238,275,295],"retrieves":[209],"appropriate":[210],"PubMed":[211],"abstract":[212],"texts,":[213],"filters":[214],"out":[215],"irrelevant":[216],"abstracts":[217],"fine-tuned":[220],"relevance":[221],"model,":[222],"prompts":[224],"an":[225],"LLM":[226],"user\u2019s":[230],"hypothesis,":[231],"given":[232],"relevant":[234],"abstracts.":[235],"Importantly,":[236],"transparent":[241],"human-verifiable:":[243],"displays":[245],"retrieved":[247],"abstracts,":[248],"score,":[251],"justification":[254],"for":[255],"score":[257],"grounded":[258],"texts":[261],"written":[263],"natural":[265],"language.":[266],"On":[267],"benchmark":[269],"consisting":[270],"14":[272],"disease-gene-drug":[273],"hypotheses,":[274],"achieves":[276],"strong":[277],"ordinal":[278],"four":[281],"expert":[282,293],"biologists":[283],"(Cohen\u2019s":[284],"\u03ba":[285],"=":[286],"0.84),":[287],"demonstrating":[288],"its":[289],"ability":[290],"replicate":[292],"judgment.":[294],"open-source":[297],"(":[298,307],"https://github.com/stewart-lab/skimgpt":[299],")":[300],"through":[303],"web":[305],"interface":[306],"https://skim.morgridge.org":[308],"),":[309],"enabling":[310],"both":[311],"wet-lab":[312],"computational":[314],"systematically":[317],"efficiently":[319],"at":[323],"scale.":[324]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-12-17T00:00:00"}
