{"id":"https://openalex.org/W4379382575","doi":"https://doi.org/10.1109/tcbb.2023.3280557","title":"Optimal Supervised Reduction of High Dimensional Transcription Data","display_name":"Optimal Supervised Reduction of High Dimensional Transcription Data","publication_year":2023,"publication_date":"2023-06-05","ids":{"openalex":"https://openalex.org/W4379382575","doi":"https://doi.org/10.1109/tcbb.2023.3280557","pmid":"https://pubmed.ncbi.nlm.nih.gov/37276117"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3280557","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/tcbb.2023.3280557","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/A5008174658","display_name":"Richard Bailey","orcid":"https://orcid.org/0000-0002-1608-4961"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Bailey","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-1608-4961","affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022471155","display_name":"Aisharjya Sarkar","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aisharjya Sarkar","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0001-9469-1022","affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102781536","display_name":"Aaditya Singh","orcid":"https://orcid.org/0009-0004-5461-9594"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Aaditya Singh","raw_affiliation_strings":["Indian Institute of Technology, Kharagpur, West Bengal, India"],"raw_orcid":"https://orcid.org/0009-0004-5461-9594","affiliations":[{"raw_affiliation_string":"Indian Institute of Technology, Kharagpur, West Bengal, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008335723","display_name":"Alin Dobra","orcid":"https://orcid.org/0000-0003-2033-9952"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alin Dobra","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0003-2033-9952","affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-4403-8612","affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2273,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.68937261,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"20","issue":"5","first_page":"3093","last_page":"3105"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.9959999918937683,"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":0.9940999746322632,"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":0.7008078098297119},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.6394209861755371},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.5847830176353455},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5427821278572083},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4512471556663513},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4271474778652191},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4069632589817047},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37774285674095154},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33540844917297363}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7008078098297119},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.6394209861755371},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.5847830176353455},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5427821278572083},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4512471556663513},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4271474778652191},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4069632589817047},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37774285674095154},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33540844917297363},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3280557","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/tcbb.2023.3280557","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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:37276117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37276117","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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W798726819","https://openalex.org/W1587559447","https://openalex.org/W1647221522","https://openalex.org/W1800724332","https://openalex.org/W1996311090","https://openalex.org/W2009242103","https://openalex.org/W2015933146","https://openalex.org/W2051895207","https://openalex.org/W2054216349","https://openalex.org/W2067761476","https://openalex.org/W2076610093","https://openalex.org/W2082290707","https://openalex.org/W2092472450","https://openalex.org/W2092939357","https://openalex.org/W2101234009","https://openalex.org/W2113095561","https://openalex.org/W2118423420","https://openalex.org/W2134695923","https://openalex.org/W2137234026","https://openalex.org/W2149772057","https://openalex.org/W2153795693","https://openalex.org/W2154941270","https://openalex.org/W2207020174","https://openalex.org/W2412589610","https://openalex.org/W2599547448","https://openalex.org/W2735419231","https://openalex.org/W2755502262","https://openalex.org/W2758907677","https://openalex.org/W2791975514","https://openalex.org/W2792199558","https://openalex.org/W2802799492","https://openalex.org/W2889326414","https://openalex.org/W2902652978","https://openalex.org/W2903552149","https://openalex.org/W2904854274","https://openalex.org/W2921982558","https://openalex.org/W2943199409","https://openalex.org/W2963437321","https://openalex.org/W2980387214","https://openalex.org/W2998065416","https://openalex.org/W3092803354","https://openalex.org/W3124903422","https://openalex.org/W4301807748","https://openalex.org/W4388297464","https://openalex.org/W6622747680","https://openalex.org/W6675354045","https://openalex.org/W6757718351"],"related_works":["https://openalex.org/W1995622179","https://openalex.org/W1484111231","https://openalex.org/W1552543208","https://openalex.org/W2074396517","https://openalex.org/W2166963679","https://openalex.org/W2187269125","https://openalex.org/W1641615907","https://openalex.org/W3089231081","https://openalex.org/W2093956241","https://openalex.org/W2354420595"],"abstract_inverted_index":{"The":[0],"plight":[1],"of":[2,32,41,56,63,100,122,131],"navigating":[3],"high-dimensional":[4],"transcription":[5],"datasets":[6,58],"remains":[7],"a":[8,49,82,105],"persistent":[9],"problem.":[10],"This":[11],"problem":[12],"is":[13,166,185],"further":[14],"amplified":[15],"for":[16,71,76,134],"complex":[17,77],"disorders,":[18],"such":[19],"as":[20,22,125],"cancer":[21],"these":[23],"disorders":[24],"are":[25,45],"often":[26,46],"multigenic":[27,78],"traits":[28],"with":[29,48,153],"multiple":[30],"subsets":[31],"genes":[33],"collectively":[34],"affecting":[35],"the":[36,42,54,61,98,101,114,128,167],"type,":[37],"stage,":[38],"and":[39,59,147,160,172],"severity":[40],"trait.":[43],"We":[44,149],"faced":[47],"trade":[50],"off":[51],"between":[52,113],"reducing":[53,97],"dimensionality":[55,99],"our":[57,64,151],"maintaining":[60],"integrity":[62],"data.":[65],"To":[66],"accomplish":[67],"both":[68,92,158],"tasks":[69,93],"simultaneously":[70,94],"very":[72],"high":[73],"dimensional":[74],"transcriptome":[75],"traits,":[79],"we":[80],"propose":[81],"new":[83],"supervised":[84],"technique,":[85],"Class":[86],"Separation":[87],"Transformation":[88],"(CST).":[89],"CST":[90,118,165],"accomplishes":[91],"by":[95],"significantly":[96],"input":[102],"space":[103,108],"into":[104],"one-dimensional":[106],"transformed":[107],"that":[109,164],"provides":[110],"optimal":[111],"separation":[112],"differing":[115],"classes.":[116],"Furthermore,":[117],"offers":[119],"an":[120],"means":[121],"explainable":[123],"ML,":[124],"it":[126],"computes":[127],"relative":[129,176],"importance":[130],"each":[132],"feature":[133],"its":[135],"contribution":[136],"to":[137,144,177],"class":[138],"distinction,":[139],"which":[140],"can":[141],"thus":[142],"lead":[143],"deeper":[145],"insights":[146],"discovery.":[148],"compare":[150],"method":[152],"existing":[154,178],"state-of-the-art":[155],"methods":[156],"using":[157],"real":[159],"synthetic":[161],"datasets,":[162],"demonstrating":[163],"more":[168],"accurate,":[169],"robust,":[170],"scalable,":[171],"computationally":[173],"advantageous":[174],"technique":[175],"methods.":[179],"Code":[180],"used":[181],"in":[182],"this":[183],"paper":[184],"available":[186],"on":[187],"https://github.com/richiebailey74/CST.":[188]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
