{"id":"https://openalex.org/W7118407843","doi":"https://doi.org/10.3389/fbinf.2025.1727953","title":"KG2ML: integrating knowledge graphs and positive unlabeled learning for identifying disease-associated genes","display_name":"KG2ML: integrating knowledge graphs and positive unlabeled learning for identifying disease-associated genes","publication_year":2026,"publication_date":"2026-01-08","ids":{"openalex":"https://openalex.org/W7118407843","doi":"https://doi.org/10.3389/fbinf.2025.1727953","pmid":"https://pubmed.ncbi.nlm.nih.gov/41584517"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1727953","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1727953","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1727953/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1727953/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122254736","display_name":"Praveen Kumar","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Praveen Kumar","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068126807","display_name":"Vincent T. Metzger","orcid":"https://orcid.org/0000-0002-8041-0370"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vincent T. Metzger","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Swastika T. Purushotham","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swastika T. Purushotham","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055037751","display_name":"Priyansh Kedia","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Priyansh Kedia","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053220470","display_name":"Cristian Bologa","orcid":"https://orcid.org/0000-0003-2232-4244"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cristian G. Bologa","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122278050","display_name":"Christophe G. Lambert","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christophe G. Lambert","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5122200865","display_name":"Jeremy J. Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeremy J. Yang","raw_affiliation_strings":["Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States"],"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, Translational Informatics Division, School of Medicine, University of New Mexico (UNM), Albuquerque, NM, United States","institution_ids":["https://openalex.org/I169521973"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5122200865"],"corresponding_institution_ids":["https://openalex.org/I169521973"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02941428,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1727953","last_page":"1727953"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7311999797821045,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7311999797821045,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.16279999911785126,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.051600001752376556,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6334999799728394},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5245000123977661},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.42980000376701355},{"id":"https://openalex.org/keywords/subject","display_name":"Subject (documents)","score":0.3598000109195709},{"id":"https://openalex.org/keywords/inclusion","display_name":"Inclusion (mineral)","score":0.3580999970436096},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.3569999933242798},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31520000100135803}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6334999799728394},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6262000203132629},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5421000123023987},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5245000123977661},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5218999981880188},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.42980000376701355},{"id":"https://openalex.org/C2777855551","wikidata":"https://www.wikidata.org/wiki/Q12310021","display_name":"Subject (documents)","level":2,"score":0.3598000109195709},{"id":"https://openalex.org/C109359841","wikidata":"https://www.wikidata.org/wiki/Q728944","display_name":"Inclusion (mineral)","level":2,"score":0.3580999970436096},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3569999933242798},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33489999175071716},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31520000100135803},{"id":"https://openalex.org/C2777220311","wikidata":"https://www.wikidata.org/wiki/Q6423340","display_name":"Knowledge acquisition","level":2,"score":0.29010000824928284},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.28029999136924744},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.2775999903678894},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2689000070095062},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.26030001044273376},{"id":"https://openalex.org/C115925183","wikidata":"https://www.wikidata.org/wiki/Q1412694","display_name":"Knowledge-based systems","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2558000087738037},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2524000108242035}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3389/fbinf.2025.1727953","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1727953","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1727953/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41584517","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41584517","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12823822","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12823822/","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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1727953","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1727953","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1727953/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3569758468","display_name":null,"funder_award_id":"OT2OD030546","funder_id":"https://openalex.org/F4320337349","funder_display_name":"NIH Office of the Director"},{"id":"https://openalex.org/G4586743802","display_name":null,"funder_award_id":"R01MH129764","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G7470883805","display_name":null,"funder_award_id":"3OT2OD030546-01S3","funder_id":"https://openalex.org/F4320337349","funder_display_name":"NIH Office of the Director"},{"id":"https://openalex.org/G7713933513","display_name":null,"funder_award_id":"OT2OD030546","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"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337349","display_name":"NIH Office of the Director","ror":"https://ror.org/00fj8a872"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7118407843.pdf","grobid_xml":"https://content.openalex.org/works/W7118407843.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W2097532544","https://openalex.org/W2110684048","https://openalex.org/W2123958887","https://openalex.org/W2159583324","https://openalex.org/W2187413858","https://openalex.org/W2295598076","https://openalex.org/W2608690367","https://openalex.org/W2788085070","https://openalex.org/W2934871562","https://openalex.org/W2937762029","https://openalex.org/W3021393704","https://openalex.org/W3096932862","https://openalex.org/W3129792448","https://openalex.org/W3209094369","https://openalex.org/W4211123915","https://openalex.org/W4221048327","https://openalex.org/W4297004340","https://openalex.org/W4307432689","https://openalex.org/W4309400074","https://openalex.org/W4361278700","https://openalex.org/W4367626561","https://openalex.org/W4386254278","https://openalex.org/W4391365195","https://openalex.org/W4396944462","https://openalex.org/W4400009256","https://openalex.org/W4404082263","https://openalex.org/W4405270630","https://openalex.org/W4408398233"],"related_works":[],"abstract_inverted_index":{"The":[0],"observed":[1],"improvement":[2],"in":[3],"classification":[4],"performance":[5],"after":[6],"the":[7,17,24,69],"inclusion":[8],"of":[9,23,72],"PULSCAR-imputed":[10],"genes":[11,28],"as":[12],"positive":[13],"examples,":[14],"along":[15],"with":[16,51],"subject":[18],"matter":[19],"experts'":[20],"(SME)":[21],"evaluations":[22],"top":[25],"15":[26],"imputed":[27],"for":[29],"12":[30],"diseases,":[31],"suggests":[32],"that":[33],"PU":[34],"learning":[35],"can":[36],"effectively":[37],"uncover":[38],"disease-gene":[39],"associations":[40],"missing":[41],"from":[42],"existing":[43],"knowledge":[44],"graphs":[45],"(KGs).":[46],"By":[47],"integrating":[48],"KG":[49],"data":[50],"ML-based":[52],"inference,":[53],"our":[54],"KG2ML":[55],"pipeline":[56],"provides":[57],"a":[58],"scalable":[59],"and":[60],"interpretable":[61],"framework":[62],"to":[63],"advance":[64],"biomedical":[65],"research":[66],"while":[67],"addressing":[68],"inherent":[70],"limitations":[71],"current":[73],"KGs.":[74]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-01-08T00:00:00"}
