{"id":"https://openalex.org/W4389879592","doi":"https://doi.org/10.1109/tcbb.2023.3343808","title":"Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance","display_name":"Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance","publication_year":2023,"publication_date":"2023-12-18","ids":{"openalex":"https://openalex.org/W4389879592","doi":"https://doi.org/10.1109/tcbb.2023.3343808","pmid":"https://pubmed.ncbi.nlm.nih.gov/38109236"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3343808","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3343808","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5052818218","display_name":"Eric J. Barnett","orcid":"https://orcid.org/0000-0003-2493-2251"},"institutions":[{"id":"https://openalex.org/I20388574","display_name":"SUNY Upstate Medical University","ror":"https://ror.org/040kfrw16","country_code":"US","type":"education","lineage":["https://openalex.org/I20388574"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric J. Barnett","raw_affiliation_strings":["Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA"],"raw_orcid":"https://orcid.org/0000-0003-2493-2251","affiliations":[{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA","institution_ids":["https://openalex.org/I20388574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052478277","display_name":"Daniel G. Onete","orcid":null},"institutions":[{"id":"https://openalex.org/I20388574","display_name":"SUNY Upstate Medical University","ror":"https://ror.org/040kfrw16","country_code":"US","type":"education","lineage":["https://openalex.org/I20388574"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel G. Onete","raw_affiliation_strings":["College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Medicine, MD Program, SUNY Upstate Medical University, Syracuse, NY, USA","institution_ids":["https://openalex.org/I20388574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065842715","display_name":"Asif Salekin","orcid":"https://orcid.org/0000-0002-0807-8967"},"institutions":[{"id":"https://openalex.org/I70983195","display_name":"Syracuse University","ror":"https://ror.org/025r5qe02","country_code":"US","type":"education","lineage":["https://openalex.org/I70983195"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Asif Salekin","raw_affiliation_strings":["Laboratory for Ubiquitous and Intelligent Sensing, Department of Electrical Engineering and Computer Science, Syracuse University, Syracuse, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-0807-8967","affiliations":[{"raw_affiliation_string":"Laboratory for Ubiquitous and Intelligent Sensing, Department of Electrical Engineering and Computer Science, Syracuse University, Syracuse, NY, USA","institution_ids":["https://openalex.org/I70983195"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052145058","display_name":"Stephen V. Faraone","orcid":"https://orcid.org/0000-0002-9217-3982"},"institutions":[{"id":"https://openalex.org/I20388574","display_name":"SUNY Upstate Medical University","ror":"https://ror.org/040kfrw16","country_code":"US","type":"education","lineage":["https://openalex.org/I20388574"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen V. Faraone","raw_affiliation_strings":["Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-9217-3982","affiliations":[{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA","institution_ids":["https://openalex.org/I20388574"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.5953,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.90693886,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"169","last_page":"177"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9865999817848206,"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/T11660","display_name":"Blood groups and transfusion","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.7432939410209656},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.7169650793075562},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.6813136339187622},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6736642122268677},{"id":"https://openalex.org/keywords/univariate","display_name":"Univariate","score":0.6614488959312439},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6421548128128052},{"id":"https://openalex.org/keywords/multivariate-statistics","display_name":"Multivariate statistics","score":0.5046101808547974},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.47619760036468506},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3542299270629883},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2062605321407318},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11291876435279846}],"concepts":[{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.7432939410209656},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.7169650793075562},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.6813136339187622},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6736642122268677},{"id":"https://openalex.org/C199163554","wikidata":"https://www.wikidata.org/wiki/Q1681619","display_name":"Univariate","level":3,"score":0.6614488959312439},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6421548128128052},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.5046101808547974},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.47619760036468506},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3542299270629883},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2062605321407318},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11291876435279846}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3343808","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3343808","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38109236","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38109236","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1247537706","display_name":null,"funder_award_id":"R01MH116037","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G2048465227","display_name":null,"funder_award_id":"U01 AR076092","funder_id":"https://openalex.org/F4320337362","funder_display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases"},{"id":"https://openalex.org/G5734088670","display_name":null,"funder_award_id":"R01NS128535","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"}],"funders":[{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337362","display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","ror":"https://ror.org/006zn3t30"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":95,"referenced_works":["https://openalex.org/W1492273171","https://openalex.org/W1505191356","https://openalex.org/W1802506671","https://openalex.org/W1971141173","https://openalex.org/W1971376634","https://openalex.org/W1972057415","https://openalex.org/W1973956579","https://openalex.org/W1984407806","https://openalex.org/W1990700240","https://openalex.org/W1997899395","https://openalex.org/W2002466929","https://openalex.org/W2017695531","https://openalex.org/W2017826413","https://openalex.org/W2020663825","https://openalex.org/W2032840557","https://openalex.org/W2042308063","https://openalex.org/W2058338438","https://openalex.org/W2060307480","https://openalex.org/W2060319981","https://openalex.org/W2067206919","https://openalex.org/W2079023204","https://openalex.org/W2093120748","https://openalex.org/W2094173563","https://openalex.org/W2101357408","https://openalex.org/W2102986375","https://openalex.org/W2105092596","https://openalex.org/W2110633408","https://openalex.org/W2121514846","https://openalex.org/W2122886214","https://openalex.org/W2123231396","https://openalex.org/W2125895642","https://openalex.org/W2133752646","https://openalex.org/W2137514719","https://openalex.org/W2150965754","https://openalex.org/W2151554678","https://openalex.org/W2154776925","https://openalex.org/W2160630750","https://openalex.org/W2166059093","https://openalex.org/W2166336042","https://openalex.org/W2174579634","https://openalex.org/W2271387649","https://openalex.org/W2339719595","https://openalex.org/W2346599948","https://openalex.org/W2395294369","https://openalex.org/W2411938957","https://openalex.org/W2564048406","https://openalex.org/W2601418911","https://openalex.org/W2614911760","https://openalex.org/W2736287575","https://openalex.org/W2738836339","https://openalex.org/W2751739125","https://openalex.org/W2757581422","https://openalex.org/W2759066107","https://openalex.org/W2798787647","https://openalex.org/W2808011097","https://openalex.org/W2889960200","https://openalex.org/W2892268143","https://openalex.org/W2895654086","https://openalex.org/W2902380111","https://openalex.org/W2922073769","https://openalex.org/W2944540884","https://openalex.org/W2959750635","https://openalex.org/W2964136462","https://openalex.org/W2976096265","https://openalex.org/W2979349116","https://openalex.org/W2986688311","https://openalex.org/W2992152394","https://openalex.org/W3008720068","https://openalex.org/W3020176164","https://openalex.org/W3047586714","https://openalex.org/W3083095031","https://openalex.org/W3090495773","https://openalex.org/W3091334831","https://openalex.org/W3132258074","https://openalex.org/W3137972473","https://openalex.org/W3155566609","https://openalex.org/W3166407793","https://openalex.org/W3170452754","https://openalex.org/W3174053279","https://openalex.org/W3177240533","https://openalex.org/W3184344090","https://openalex.org/W3206602242","https://openalex.org/W3207277428","https://openalex.org/W3217314753","https://openalex.org/W4200206783","https://openalex.org/W4210397775","https://openalex.org/W4211064437","https://openalex.org/W4212877577","https://openalex.org/W4214905369","https://openalex.org/W4220931598","https://openalex.org/W4223920832","https://openalex.org/W4240484632","https://openalex.org/W4241421973","https://openalex.org/W6682981795","https://openalex.org/W6810284068"],"related_works":["https://openalex.org/W1828158523","https://openalex.org/W2049578243","https://openalex.org/W2000145235","https://openalex.org/W2122079181","https://openalex.org/W1985848810","https://openalex.org/W2889939530","https://openalex.org/W2399195672","https://openalex.org/W3121881699","https://openalex.org/W2748838164","https://openalex.org/W2066015000"],"abstract_inverted_index":{"Many":[0],"studies":[1],"have":[2],"been":[3],"conducted":[4],"with":[5,134],"the":[6,17,59,95,112,179,188],"goal":[7],"of":[8,13,19,33,114,183],"correctly":[9],"predicting":[10,78],"diagnostic":[11],"status":[12],"a":[14,34,46,143],"disorder":[15,130],"using":[16],"combination":[18],"genomic":[20,67,165],"data":[21,107,118,148,160,184],"and":[22,40,62,85,126,150,181],"machine":[23,68,166],"learning.":[24],"It":[25],"is":[26],"often":[27],"hard":[28],"to":[29,37,106,121,159],"judge":[30],"which":[31],"components":[32],"study":[35],"led":[36],"better":[38,42],"results":[39,44,154],"whether":[41],"reported":[43,138,172],"represent":[45],"true":[47],"improvement":[48],"or":[49],"an":[50,128,135],"uncorrected":[51],"bias":[52],"inflating":[53],"performance.":[54,80,140,173],"We":[55,71,81,141],"extracted":[56],"information":[57],"about":[58],"methods":[60,102,157],"used":[61,72,99],"other":[63],"differentiating":[64],"features":[65,74],"in":[66,75,137,170],"learning":[69,167],"models.":[70],"these":[73],"linear":[76],"regressions":[77],"model":[79,124,139],"tested":[82],"for":[83],"univariate":[84],"multivariate":[86],"associations":[87],"as":[88,90],"well":[89],"interactions":[91],"between":[92,147],"features.":[93],"Of":[94],"models":[96],"reviewed,":[97],"46%":[98],"feature":[100,122],"selection":[101],"that":[103,156,177],"can":[104],"lead":[105],"leakage.":[108],"Across":[109],"our":[110],"models,":[111],"number":[113],"hyperparameter":[115],"optimizations":[116],"reported,":[117],"leakage":[119,149,161,185],"due":[120],"selection,":[123],"type,":[125],"modeling":[127],"autoimmune":[129],"were":[131],"significantly":[132],"associated":[133],"increase":[136],"found":[142],"significant,":[144],"negative":[145],"interaction":[146],"training":[151],"size.":[152],"Our":[153],"suggest":[155],"susceptible":[158],"are":[162],"prevalent":[163],"among":[164],"research,":[168],"resulting":[169],"inflated":[171],"Best":[174],"practice":[175],"guidelines":[176],"promote":[178],"avoidance":[180],"recognition":[182],"may":[186],"help":[187],"field":[189],"avoid":[190],"biased":[191],"results.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}