{"id":"https://openalex.org/W3004127313","doi":"https://doi.org/10.1093/bioinformatics/btaa046","title":"Consensus features nested cross-validation","display_name":"Consensus features nested cross-validation","publication_year":2020,"publication_date":"2020-01-20","ids":{"openalex":"https://openalex.org/W3004127313","doi":"https://doi.org/10.1093/bioinformatics/btaa046","mag":"3004127313","pmid":"https://pubmed.ncbi.nlm.nih.gov/31985777"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa046","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/3093/48990620/btaa046.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/3093/48990620/btaa046.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047842287","display_name":"Saeid Parvandeh","orcid":"https://orcid.org/0000-0003-0917-2784"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I87208437","display_name":"University of Tulsa","ror":"https://ror.org/04wn28048","country_code":"US","type":"education","lineage":["https://openalex.org/I87208437"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saeid Parvandeh","raw_affiliation_strings":["Department of Molecular and Human Genetics , Baylor College of Medicine, Houston, TX, USA","Tandy School of Computer Science , University of Tulsa, Tulsa, OK, USA"],"raw_orcid":"https://orcid.org/0000-0003-0917-2784","affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics , Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Tandy School of Computer Science , University of Tulsa, Tulsa, OK, USA","institution_ids":["https://openalex.org/I87208437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081458605","display_name":"Hung\u2010Wen Yeh","orcid":"https://orcid.org/0000-0002-9904-3275"},"institutions":[{"id":"https://openalex.org/I1328594524","display_name":"Children's Mercy Hospital","ror":"https://ror.org/04zfmcq84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328594524"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hung-Wen Yeh","raw_affiliation_strings":["Health Services and Outcomes Research , Children\u2019s Mercy Hospital, Kansas City, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Health Services and Outcomes Research , Children\u2019s Mercy Hospital, Kansas City, MO, USA","institution_ids":["https://openalex.org/I1328594524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081736253","display_name":"Martin P. Paulus","orcid":"https://orcid.org/0000-0002-0825-3606"},"institutions":[{"id":"https://openalex.org/I4210159521","display_name":"Laureate Institute for Brain Research","ror":"https://ror.org/05e6pjy56","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210159521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin P Paulus","raw_affiliation_strings":["Laureate Institute for Brain Research , Tulsa, OK, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laureate Institute for Brain Research , Tulsa, OK, USA","institution_ids":["https://openalex.org/I4210159521"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049579672","display_name":"Brett A. McKinney","orcid":"https://orcid.org/0000-0002-9494-8833"},"institutions":[{"id":"https://openalex.org/I87208437","display_name":"University of Tulsa","ror":"https://ror.org/04wn28048","country_code":"US","type":"education","lineage":["https://openalex.org/I87208437"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brett A McKinney","raw_affiliation_strings":["Department of Mathematics , University of Tulsa, Tulsa, OK, USA","Tandy School of Computer Science , University of Tulsa, Tulsa, OK, USA"],"raw_orcid":"https://orcid.org/0000-0002-9494-8833","affiliations":[{"raw_affiliation_string":"Department of Mathematics , University of Tulsa, Tulsa, OK, USA","institution_ids":["https://openalex.org/I87208437"]},{"raw_affiliation_string":"Tandy School of Computer Science , University of Tulsa, Tulsa, OK, USA","institution_ids":["https://openalex.org/I87208437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5049579672"],"corresponding_institution_ids":["https://openalex.org/I87208437"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":9.3365,"has_fulltext":true,"cited_by_count":218,"citation_normalized_percentile":{"value":0.98788527,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"36","issue":"10","first_page":"3093","last_page":"3098"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.476500004529953,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.476500004529953,"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/T10764","display_name":"Privacy-Preserving Technologies in Data","score":0.22100000083446503,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.028200000524520874,"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":0.6563885807991028}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6563885807991028}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003865","descriptor_name":"Depressive Disorder, Major","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003865","descriptor_name":"Major Depressive Disorder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003865","descriptor_name":"Depressive Disorder, Major","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa046","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/3093/48990620/btaa046.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31985777","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31985777","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:6739685","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7776094","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7776094","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7776094","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa046","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa046","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/10/3093/48990620/btaa046.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.6499999761581421}],"awards":[{"id":"https://openalex.org/G2085657225","display_name":null,"funder_award_id":"GM103456","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4239674792","display_name":null,"funder_award_id":"GM121312","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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004127313.pdf","grobid_xml":"https://content.openalex.org/works/W3004127313.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1517808374","https://openalex.org/W1555759181","https://openalex.org/W1808644423","https://openalex.org/W1969198439","https://openalex.org/W2027595342","https://openalex.org/W2043235003","https://openalex.org/W2090790364","https://openalex.org/W2105981176","https://openalex.org/W2112081648","https://openalex.org/W2119590375","https://openalex.org/W2122825543","https://openalex.org/W2141007997","https://openalex.org/W2149199519","https://openalex.org/W2154776925","https://openalex.org/W2421101021","https://openalex.org/W2537679995","https://openalex.org/W2610276113","https://openalex.org/W2810040115","https://openalex.org/W2903328825","https://openalex.org/W2921256913","https://openalex.org/W2953267417","https://openalex.org/W2964278775","https://openalex.org/W2998216295","https://openalex.org/W2998678080","https://openalex.org/W2999299543","https://openalex.org/W4205228770","https://openalex.org/W4285719527","https://openalex.org/W6630956611","https://openalex.org/W6682981795","https://openalex.org/W7066667914"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"SUMMARY:":[0],"Feature":[1,91],"selection":[2,92,144,260],"can":[3],"improve":[4],"the":[5,28,44,81,100,139,147,205,240],"accuracy":[6,141,188,229],"of":[7,83,102,112,118,146,177,216],"machine-learning":[8],"models,":[9],"but":[10,191],"appropriate":[11],"steps":[12],"must":[13],"be":[14],"taken":[15],"to":[16,33,54,63,137,189,230,242],"avoid":[17,55],"overfitting.":[18],"Nested":[19],"cross-validation":[20,77],"(nCV)":[21],"is":[22,50,93,107,122,251],"a":[23,35,51,59,110,175,212,244],"common":[24],"approach":[25,256],"that":[26,42,57,66,79,249],"chooses":[27,211],"classification":[29,119,140],"model":[30],"and":[31,71,99,135,142,160,186,232,254],"features":[32,41,65,104,217,236],"represent":[34],"given":[36],"outer":[37],"fold":[38,98],"based":[39],"on":[40],"give":[43],"maximum":[45],"inner-fold":[46],"accuracy.":[47],"Differential":[48],"privacy":[49,88,159,245],"related":[52],"technique":[53],"overfitting":[56],"uses":[58],"privacy-preserving":[60],"noise":[61],"mechanism":[62],"identify":[64],"are":[67,274],"stable":[68,235],"between":[69,237],"training":[70,185],"holdout":[72],"sets.We":[73],"develop":[74],"consensus":[75,101],"nested":[76],"(cnCV)":[78],"combines":[80],"idea":[82],"feature":[84,113,143,259],"stability":[85,114],"from":[86,174],"differential":[87,158],"with":[89,131,150,218,261],"nCV.":[90,126,223],"applied":[94],"in":[95,124,204],"each":[96],"inner":[97,206],"top":[103],"across":[105],"folds":[106,238],"used":[108,123],"as":[109],"measure":[111],"or":[115],"reliability":[116],"instead":[117],"accuracy,":[120],"which":[121],"standard":[125,151],"We":[127,165,247],"use":[128],"simulated":[129],"data":[130,173,273],"main":[132],"effects,":[133],"correlation":[134],"interactions":[136],"compare":[138,167],"performance":[145],"new":[148],"cnCV":[149,181,192,209,225,233,250],"nCV,":[152,190],"Elastic":[153],"Net":[154],"optimized":[155],"by":[156],"cross-validation,":[157],"private":[161],"evaporative":[162],"cooling":[163],"(pEC).":[164],"also":[166],"these":[168],"methods":[169],"using":[170],"real":[171],"RNA-seq":[172],"study":[176],"major":[178],"depressive":[179],"disorder.The":[180],"method":[182,210,226],"has":[183,193,227],"similar":[184,228],"validation":[187],"much":[194],"shorter":[195],"run":[196],"times":[197],"because":[198],"it":[199],"does":[200],"not":[201],"construct":[202],"classifiers":[203],"folds.":[207],"The":[208,224],"more":[213],"parsimonious":[214],"set":[215],"fewer":[219],"false":[220],"positives":[221],"than":[222],"pEC":[231],"selects":[234],"without":[239],"need":[241],"specify":[243],"threshold.":[246],"show":[248],"an":[252],"effective":[253],"efficient":[255],"for":[257],"combining":[258],"classification.":[262],"AVAILABILITY":[263],"AND":[264],"IMPLEMENTATION:":[265],"Code":[266],"available":[267,275],"at":[268,276],"https://github.com/insilico/cncv.":[269],"SUPPLEMENTARY":[270],"INFORMATION:":[271],"Supplementary":[272],"Bioinformatics":[277],"online.":[278]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":40},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":41},{"year":2022,"cited_by_count":39},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":4}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}