{"id":"https://openalex.org/W2116882627","doi":"https://doi.org/10.1093/bioinformatics/btg399","title":"Is cross-validation better than resubstitution for ranking genes?","display_name":"Is cross-validation better than resubstitution for ranking genes?","publication_year":2004,"publication_date":"2004-01-20","ids":{"openalex":"https://openalex.org/W2116882627","doi":"https://doi.org/10.1093/bioinformatics/btg399","mag":"2116882627","pmid":"https://pubmed.ncbi.nlm.nih.gov/14734317"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg399","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/253/48905291/bioinformatics_20_2_253.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/20/2/253/48905291/bioinformatics_20_2_253.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026990034","display_name":"Ulisses Braga-Neto","orcid":"https://orcid.org/0000-0002-1210-2173"},"institutions":[{"id":"https://openalex.org/I4210145812","display_name":"Cancer Genetics (United States)","ror":"https://ror.org/05feyya22","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145812"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ulisses Braga-Neto","raw_affiliation_strings":["Section of Clinical Cancer Genetics, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA","Section of Clinical Cancer Genetics#TAB#"],"affiliations":[{"raw_affiliation_string":"Section of Clinical Cancer Genetics, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA","institution_ids":[]},{"raw_affiliation_string":"Section of Clinical Cancer Genetics#TAB#","institution_ids":["https://openalex.org/I4210145812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001183500","display_name":"Ronaldo F. Hashimoto","orcid":"https://orcid.org/0000-0002-6399-8790"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ronaldo Hashimoto","raw_affiliation_strings":["Departamento de Ciencia de Computa\u00e7\u00e3o, Instituto de Matem\u00e1tica e Estat\u00edstica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil,#TAB#"],"affiliations":[{"raw_affiliation_string":"Departamento de Ciencia de Computa\u00e7\u00e3o, Instituto de Matem\u00e1tica e Estat\u00edstica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil,#TAB#","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112221423","display_name":"Edward R. Dougherty","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"funder","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward R. Dougherty","raw_affiliation_strings":["Dept. of Pathology, Univ. of Texas M. D. Anderson Cancer Center, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Pathology, Univ. of Texas M. D. Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055319271","display_name":"Danh V. Nguyen","orcid":"https://orcid.org/0000-0002-4025-8239"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danh V. Nguyen","raw_affiliation_strings":["Department of Statistics, Texas A&M University, College Station, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000822072","display_name":"Raymond J. Carroll","orcid":"https://orcid.org/0000-0002-5465-9682"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raymond J. Carroll","raw_affiliation_strings":["Department of Statistics, Texas A&M University, College Station, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026990034"],"corresponding_institution_ids":["https://openalex.org/I4210145812"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3389,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.88246577,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"20","issue":"2","first_page":"253","last_page":"258"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9961000084877014,"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":0.7348160743713379},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.7088199853897095},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.679474949836731},{"id":"https://openalex.org/keywords/word-error-rate","display_name":"Word error rate","score":0.5579534769058228},{"id":"https://openalex.org/keywords/probabilistic-classification","display_name":"Probabilistic classification","score":0.546176552772522},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.5301775932312012},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5049038529396057},{"id":"https://openalex.org/keywords/linear-discriminant-analysis","display_name":"Linear discriminant analysis","score":0.50401371717453},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4766153395175934},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4314185380935669},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.42334768176078796},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.42141833901405334},{"id":"https://openalex.org/keywords/linear-classifier","display_name":"Linear classifier","score":0.4122299551963806},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.2916357219219208},{"id":"https://openalex.org/keywords/naive-bayes-classifier","display_name":"Naive Bayes classifier","score":0.20674651861190796}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7348160743713379},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.7088199853897095},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.679474949836731},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.5579534769058228},{"id":"https://openalex.org/C189119545","wikidata":"https://www.wikidata.org/wiki/Q5128022","display_name":"Probabilistic classification","level":4,"score":0.546176552772522},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.5301775932312012},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5049038529396057},{"id":"https://openalex.org/C69738355","wikidata":"https://www.wikidata.org/wiki/Q1228929","display_name":"Linear discriminant analysis","level":2,"score":0.50401371717453},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4766153395175934},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4314185380935669},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.42334768176078796},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.42141833901405334},{"id":"https://openalex.org/C139532973","wikidata":"https://www.wikidata.org/wiki/Q2679259","display_name":"Linear classifier","level":3,"score":0.4122299551963806},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.2916357219219208},{"id":"https://openalex.org/C52001869","wikidata":"https://www.wikidata.org/wiki/Q812530","display_name":"Naive Bayes classifier","level":3,"score":0.20674651861190796}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg399","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/253/48905291/bioinformatics_20_2_253.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:14734317","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14734317","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg399","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg399","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/2/253/48905291/bioinformatics_20_2_253.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":[{"score":0.6200000047683716,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116882627.pdf","grobid_xml":"https://content.openalex.org/works/W2116882627.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1564947197","https://openalex.org/W1995386082","https://openalex.org/W2051265608","https://openalex.org/W2108020239","https://openalex.org/W2137721361","https://openalex.org/W2160533336"],"related_works":["https://openalex.org/W66535911","https://openalex.org/W2118882708","https://openalex.org/W2371425310","https://openalex.org/W2998259334","https://openalex.org/W2239966463","https://openalex.org/W2408521075","https://openalex.org/W2641936149","https://openalex.org/W2903240209","https://openalex.org/W2155435857","https://openalex.org/W2029097651"],"abstract_inverted_index":{"A":[0],"model-based":[1,85],"approach":[2],"is":[3,37,52,80,91,100],"used":[4],"to":[5,64,83,96,103],"compare":[6,65],"the":[7,25,47,55,76,84,104],"ranking":[8,67,73,97],"performances":[9],"of":[10,27,57],"resubstitution":[11,90],"and":[12,21,46],"cross-validation":[13,94],"for":[14,22],"classification":[15,41,49],"based":[16,68,74],"on":[17,69,75],"real-valued":[18],"feature":[19],"sets":[20],"prediction":[23],"in":[24,54,101,107],"context":[26],"probabilistic":[28],"Boolean":[29],"networks":[30],"(PBNs).":[31],"For":[32],"classification,":[33],"a":[34,58],"Gaussian":[35],"model":[36],"considered,":[38],"along":[39],"with":[40,72,93],"via":[42],"linear":[43],"discriminant":[44],"analysis":[45],"3-nearest-neighbor":[48],"rule.":[50],"Prediction":[51],"examined":[53],"steady-distribution":[56],"PBN.":[59],"Three":[60],"metrics":[61],"are":[62],"proposed":[63],"feature-set":[66],"error":[70],"estimation":[71],"true":[77],"error,":[78],"which":[79],"known":[81],"owing":[82],"approach.":[86],"In":[87],"all":[88],"cases,":[89],"competitive":[92],"relative":[95],"accuracy.":[98],"This":[99],"addition":[102],"enormous":[105],"savings":[106],"computation":[108],"time":[109],"afforded":[110],"by":[111],"resubstitution.":[112]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":6}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}