{"id":"https://openalex.org/W3082830593","doi":"https://doi.org/10.1186/s12859-020-03718-9","title":"binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions","display_name":"binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions","publication_year":2020,"publication_date":"2020-08-28","ids":{"openalex":"https://openalex.org/W3082830593","doi":"https://doi.org/10.1186/s12859-020-03718-9","mag":"3082830593","pmid":"https://pubmed.ncbi.nlm.nih.gov/32859146"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03718-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03718-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03718-9","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://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03718-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076114786","display_name":"Samir Rachid Zaim","orcid":"https://orcid.org/0009-0007-9256-2324"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samir Rachid Zaim","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","institution_ids":[]},{"raw_affiliation_string":"The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084359412","display_name":"Colleen Kenost","orcid":null},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colleen Kenost","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031514900","display_name":"Joanne Berghout","orcid":"https://orcid.org/0000-0002-9250-9159"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joanne Berghout","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045042673","display_name":"Wesley Chiu","orcid":"https://orcid.org/0009-0007-0629-9305"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wesley Chiu","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108537301","display_name":"Liam Wilson","orcid":"https://orcid.org/0009-0007-8631-0358"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liam Wilson","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080955712","display_name":"Hao Helen Zhang","orcid":"https://orcid.org/0000-0001-8873-3329"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]},{"id":"https://openalex.org/I2800531696","display_name":"Arizona Science Center","ror":"https://ror.org/05g3rxr48","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2800531696"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hao Helen Zhang","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","Department of Mathematics, College of Sciences, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","institution_ids":["https://openalex.org/I138006243","https://openalex.org/I2800531696"]},{"raw_affiliation_string":"Department of Mathematics, College of Sciences, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. hzhang@math.arizona.edu","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074706648","display_name":"Yves A. Lussier","orcid":"https://orcid.org/0000-0001-9854-1005"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]},{"id":"https://openalex.org/I2800531696","display_name":"Arizona Science Center","ror":"https://ror.org/05g3rxr48","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2800531696"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Yves A. Lussier","raw_affiliation_strings":["Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","The Center for Applied Genetic and Genomic Medicine, 1295 N. Martin, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","The University of Arizona BIO5 Institute, 1657 E. Helen Street, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","The University of Arizona Cancer Center, 3838 N. Campbell Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA"],"raw_orcid":"https://orcid.org/0000-0001-9854-1005","affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I2800531696"]},{"raw_affiliation_string":"College of Medicine, Tucson, 1501 N. Campbell Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The Center for Applied Genetic and Genomic Medicine, 1295 N. Martin, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I4210151238"]},{"raw_affiliation_string":"The Graduate Interdisciplinary Program in Statistics, The University of Arizona, 617 N. Santa Rita Ave., Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The University of Arizona BIO5 Institute, 1657 E. Helen Street, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The University of Arizona Cancer Center, 3838 N. Campbell Ave, Tucson, AZ, 85721, USA. Lussier.Y@gmail.com","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Center for Biomedical Informatics and Biostatistics, University of Arizona Health Sciences, 1230 N. Cherry Ave, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074706648","https://openalex.org/A5080955712"],"corresponding_institution_ids":["https://openalex.org/I138006243","https://openalex.org/I2800531696","https://openalex.org/I4210151238"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3253,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.56594047,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"1","first_page":"374","last_page":"374"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.4731999933719635,"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/T10885","display_name":"Gene expression and cancer classification","score":0.4731999933719635,"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":0.39969998598098755,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.05640000104904175,"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/random-forest","display_name":"Random forest","score":0.8255023956298828},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.7011328935623169},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.681751012802124},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5736240744590759},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5420658588409424},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5006747245788574},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.45069509744644165},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4030546247959137},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12350654602050781}],"concepts":[{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.8255023956298828},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.7011328935623169},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.681751012802124},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5736240744590759},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5420658588409424},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5006747245788574},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.45069509744644165},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4030546247959137},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12350654602050781},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"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":"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":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"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":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007680","descriptor_name":"Kidney Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-020-03718-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03718-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03718-9","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:32859146","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32859146","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:repository.arizona.edu:10150/657479","is_oa":true,"landing_page_url":"http://hdl.handle.net/10150/657479","pdf_url":null,"source":{"id":"https://openalex.org/S4306400271","display_name":"UA Campus Repository (The University of Arizona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138006243","host_organization_name":"University of Arizona","host_organization_lineage":["https://openalex.org/I138006243"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"BMC BIOINFORMATICS","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:f79d3e96648b4b87a411af504b84c054","is_oa":true,"landing_page_url":"https://doaj.org/article/f79d3e96648b4b87a411af504b84c054","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-22 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7456085","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7456085","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/s12859-020-03718-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03718-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03718-9","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":[{"score":0.6000000238418579,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1796955875","display_name":null,"funder_award_id":"NCI P30CA023074","funder_id":"https://openalex.org/F4320310160","funder_display_name":"University of Arizona"},{"id":"https://openalex.org/G1931859731","display_name":null,"funder_award_id":"U01 AI122275","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2802122546","display_name":null,"funder_award_id":"P30CA023074","funder_id":"https://openalex.org/F4320310160","funder_display_name":"University of Arizona"},{"id":"https://openalex.org/G4383076684","display_name":"TRIPODS: UA-TRIPODS - Building Theoretical Foundations for Data Sciences","funder_award_id":"1740858","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5504591015","display_name":null,"funder_award_id":"P30CA023074","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5764817389","display_name":null,"funder_award_id":"U01AI122275","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6166548772","display_name":null,"funder_award_id":"P30CA023074","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6451618877","display_name":null,"funder_award_id":"P30 CA023074","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6882453022","display_name":null,"funder_award_id":"NCI P30CA023074","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7880695246","display_name":null,"funder_award_id":"1UG3OD023171","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8231805625","display_name":null,"funder_award_id":"U01AI122275","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G863747742","display_name":null,"funder_award_id":"UG3 OD023171","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310160","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334288","display_name":"Health Sciences, University of Arizona","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3082830593.pdf","grobid_xml":"https://content.openalex.org/works/W3082830593.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W147186041","https://openalex.org/W273955616","https://openalex.org/W1480376833","https://openalex.org/W1520812622","https://openalex.org/W1596515083","https://openalex.org/W1659523443","https://openalex.org/W1884291487","https://openalex.org/W1884926395","https://openalex.org/W1896022307","https://openalex.org/W1964459994","https://openalex.org/W1965944404","https://openalex.org/W1966116114","https://openalex.org/W1966363110","https://openalex.org/W1973065043","https://openalex.org/W1985372952","https://openalex.org/W1996031526","https://openalex.org/W2005330159","https://openalex.org/W2024800283","https://openalex.org/W2032617530","https://openalex.org/W2033803508","https://openalex.org/W2042036632","https://openalex.org/W2059909509","https://openalex.org/W2077653218","https://openalex.org/W2091374137","https://openalex.org/W2101250437","https://openalex.org/W2102636708","https://openalex.org/W2103017472","https://openalex.org/W2111611237","https://openalex.org/W2114973325","https://openalex.org/W2125697820","https://openalex.org/W2126292488","https://openalex.org/W2127356329","https://openalex.org/W2133277699","https://openalex.org/W2135046866","https://openalex.org/W2156665896","https://openalex.org/W2158416439","https://openalex.org/W2159187228","https://openalex.org/W2245213139","https://openalex.org/W2252976504","https://openalex.org/W2319197375","https://openalex.org/W2557117995","https://openalex.org/W2559655401","https://openalex.org/W2725273399","https://openalex.org/W2736783104","https://openalex.org/W2766438525","https://openalex.org/W2768645605","https://openalex.org/W2789630305","https://openalex.org/W2789970635","https://openalex.org/W2810511505","https://openalex.org/W2911964244","https://openalex.org/W2921763762","https://openalex.org/W2945976633","https://openalex.org/W2951454365","https://openalex.org/W2954061370","https://openalex.org/W2991138092","https://openalex.org/W2999615587","https://openalex.org/W3000554433","https://openalex.org/W3005805959","https://openalex.org/W3016727862","https://openalex.org/W3025501838","https://openalex.org/W3028541575","https://openalex.org/W3099006712","https://openalex.org/W6853427780"],"related_works":["https://openalex.org/W3193043704","https://openalex.org/W4386259002","https://openalex.org/W1546989560","https://openalex.org/W4388745254","https://openalex.org/W2980082554","https://openalex.org/W1517228774","https://openalex.org/W2767419625","https://openalex.org/W2389704471","https://openalex.org/W2117019857","https://openalex.org/W4385192698"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1,77,144,183],"this":[2,268],"era":[3],"of":[4,68],"data":[5],"science-driven":[6],"bioinformatics,":[7],"machine":[8],"learning":[9],"research":[10],"has":[11],"focused":[12],"on":[13],"feature":[14,119,276],"selection":[15,120,260,277],"as":[16,54,206,208],"users":[17],"want":[18],"more":[19,31],"interpretation":[20,128],"and":[21,64,98,136,147,155,174,181,201,226,247,261],"post-hoc":[22],"analyses":[23],"for":[24,129,220],"biomarker":[25,51],"detection.":[26],"However,":[27],"when":[28],"there":[29],"are":[30,58,84],"features":[32,70,130,204,223],"(i.e.,":[33,37],"transcripts)":[34],"than":[35],"samples":[36],"mice":[38],"or":[39],"human":[40],"samples)":[41],"in":[42,50,60,122,176,224,251],"a":[43,72,118,132,231],"study,":[44],"it":[45],"poses":[46],"major":[47],"statistical":[48,56,211],"challenges":[49],"detection":[52],"tasks":[53],"traditional":[55],"techniques":[57],"underpowered":[59],"high":[61,198],"dimension.":[62],"Second":[63],"third":[65],"order":[66],"interactions":[67,212],"these":[69],"pose":[71],"substantial":[73],"combinatoric":[74],"dimensional":[75],"challenge.":[76],"computational":[78,160,254],"biology,":[79],"random":[80],"forest":[81],"(RF)":[82],"classifiers":[83],"widely":[85],"used":[86],"due":[87],"to":[88,95,101,139,163,165,235,270],"their":[89,93,99,210],"flexibility,":[90],"powerful":[91],"performance,":[92],"ability":[94],"rank":[96],"features,":[97],"robustness":[100],"the":[102,153,187],"\"P":[103],">":[104,105],"N\"":[106],"high-dimensional":[107],"limitation":[108],"that":[109,124,242,273],"many":[110],"matrix":[111],"regression":[112],"algorithms":[113],"face.":[114],"We":[115],"propose":[116],"binomialRF,":[117],"technique":[121],"RFs":[123,225],"provides":[125],"an":[126,237],"alternative":[127],"using":[131,150,203],"correlated":[133,232],"binomial":[134,233],"distribution":[135,234],"scales":[137],"efficiently":[138],"analyze":[140],"multiway":[141],"interactions.":[142,182,248],"RESULTS:":[143],"both":[145],"simulations":[146,252],"validation":[148],"studies":[149],"datasets":[151],"from":[152,278],"TCGA":[154],"UCI":[156],"repositories,":[157],"binomialRF":[158,188,215],"showed":[159],"gains":[161,255],"(up":[162],"5":[164],"300":[166],"times":[167],"faster)":[168],"while":[169,256],"maintaining":[170],"competitive":[171,258],"variable":[172],"precision":[173,200],"recall":[175,202],"identifying":[177,221],"biomarkers'":[178,244],"main":[179,245],"effects":[180,246],"two":[184],"clinical":[185],"studies,":[186],"algorithm":[189,241],"prioritizes":[190],"previously-published":[191],"relevant":[192],"pathological":[193],"molecular":[194],"mechanisms":[195],"(features)":[196],"with":[197,209],"classification":[199,262],"alone,":[205],"well":[207],"alone.":[213],"CONCLUSION:":[214],"extends":[216],"upon":[217],"previous":[218],"methods":[219],"interpretable":[222],"brings":[227],"them":[228],"together":[229],"under":[230],"create":[236],"efficient":[238],"hypothesis":[239],"testing":[240],"identifies":[243],"Preliminary":[249],"results":[250],"demonstrate":[253],"retaining":[257],"model":[259],"accuracies.":[263],"Future":[264],"work":[265],"will":[266],"extend":[267],"framework":[269],"incorporate":[271],"ontologies":[272],"provide":[274],"pathway-level":[275],"gene":[279],"expression":[280],"input":[281],"data.":[282]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2020-09-08T00:00:00"}
