{"id":"https://openalex.org/W1971752899","doi":"https://doi.org/10.4018/jkdb.2012070102","title":"Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics","display_name":"Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics","publication_year":2012,"publication_date":"2012-07-01","ids":{"openalex":"https://openalex.org/W1971752899","doi":"https://doi.org/10.4018/jkdb.2012070102","mag":"1971752899"},"language":"en","primary_location":{"id":"doi:10.4018/jkdb.2012070102","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jkdb.2012070102","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5046236337","display_name":"Evrim Acar","orcid":"https://orcid.org/0000-0002-3737-292X"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Evrim Acar","raw_affiliation_strings":["Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038936036","display_name":"G\u00f6zde G\u00fcrdeniz","orcid":"https://orcid.org/0000-0002-1169-6408"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Gozde Gurdeniz","raw_affiliation_strings":["Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050384418","display_name":"Morten Arendt Rasmussen","orcid":"https://orcid.org/0000-0001-7431-5206"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Morten A. Rasmussen","raw_affiliation_strings":["Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077496973","display_name":"Daniela Rago","orcid":"https://orcid.org/0000-0002-4442-5671"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Daniela Rago","raw_affiliation_strings":["Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074291379","display_name":"Lars Ove Dragsted","orcid":"https://orcid.org/0000-0003-0609-6317"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Lars O. Dragsted","raw_affiliation_strings":["Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Human Nutrition, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031999645","display_name":"Rasmus Bro","orcid":"https://orcid.org/0000-0002-7641-4854"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Rasmus Bro","raw_affiliation_strings":["Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046236337"],"corresponding_institution_ids":["https://openalex.org/I124055696"],"apc_list":null,"apc_paid":null,"fwci":1.8824,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.84803825,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"3","issue":"3","first_page":"22","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9940999746322632,"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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.970300018787384,"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":0.9574000239372253,"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/metabolomics","display_name":"Metabolomics","score":0.7928986549377441},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6302922964096069},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.6238070726394653},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.5328308343887329},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.5264754295349121},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.5130028128623962},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.48236697912216187},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46083763241767883},{"id":"https://openalex.org/keywords/sparse-matrix","display_name":"Sparse matrix","score":0.4426061511039734},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38209980726242065},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24183756113052368},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2034527063369751},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.19405201077461243},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.13661029934883118},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09356799721717834},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.08966368436813354},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08115643262863159}],"concepts":[{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.7928986549377441},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6302922964096069},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.6238070726394653},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.5328308343887329},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.5264754295349121},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.5130028128623962},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.48236697912216187},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46083763241767883},{"id":"https://openalex.org/C56372850","wikidata":"https://www.wikidata.org/wiki/Q1050404","display_name":"Sparse matrix","level":3,"score":0.4426061511039734},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38209980726242065},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24183756113052368},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2034527063369751},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.19405201077461243},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.13661029934883118},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09356799721717834},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.08966368436813354},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08115643262863159},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","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":[],"locations_count":3,"locations":[{"id":"doi:10.4018/jkdb.2012070102","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jkdb.2012070102","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:igg:jkdb00:v:3:y:2012:i:3:p:22-43","is_oa":false,"landing_page_url":"http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/jkdb.2012070102","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/5bc40ac3-2d01-4128-a52a-26c790118280","is_oa":false,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/5bc40ac3-2d01-4128-a52a-26c790118280","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Evrim , A A , G\u00fcrdeniz , G , Rasmussen , M A , Rago , D , Dragsted , L O & Bro , R 2012 , ' Coupled matrix factorization with sparse factors to identify potential biomarkers in metabolomics ' , International Journal of Knowledge Discovery in Bioinformatics , vol. 3 , no. 3 , pp. 22-43 . https://doi.org/10.4018/jkdb.2012070102","raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322928","display_name":"Danmarks Frie Forskningsfond","ror":"https://ror.org/02sptwz63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1632866817","https://openalex.org/W1921200167","https://openalex.org/W1999463926","https://openalex.org/W2025341678","https://openalex.org/W2038281828","https://openalex.org/W2043842833","https://openalex.org/W2046049351","https://openalex.org/W2052438487","https://openalex.org/W2054018124","https://openalex.org/W2071729267","https://openalex.org/W2079269074","https://openalex.org/W2080067882","https://openalex.org/W2099388546","https://openalex.org/W2117420919","https://openalex.org/W2119825970","https://openalex.org/W2121989412","https://openalex.org/W2126762950","https://openalex.org/W2130852547","https://openalex.org/W2135029798","https://openalex.org/W2135046866","https://openalex.org/W2138145347","https://openalex.org/W2138180870","https://openalex.org/W2140862024","https://openalex.org/W2142931933","https://openalex.org/W2146508253","https://openalex.org/W2152465918","https://openalex.org/W2158218920","https://openalex.org/W2163986851","https://openalex.org/W2798909945","https://openalex.org/W3029645440","https://openalex.org/W3143596294","https://openalex.org/W4246980425","https://openalex.org/W4301014524","https://openalex.org/W6680599301"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W34555840"],"abstract_inverted_index":{"Metabolomics":[0],"focuses":[1],"on":[2,91,124,141,187],"the":[3,34,72,92,127,134,155,158,178],"detection":[4],"of":[5,19,39,46,77,146,153,177],"chemical":[6],"substances":[7],"in":[8,37,138],"biological":[9],"fluids":[10],"such":[11],"as":[12,82],"urine":[13],"and":[14,28,51,167,175],"blood":[15,147],"using":[16,184],"a":[17,83,111,142,151],"number":[18],"analytical":[20],"techniques":[21],"including":[22],"Nuclear":[23],"Magnetic":[24],"Resonance":[25],"(NMR)":[26],"spectroscopy":[27],"Liquid":[29],"Chromatography-Mass":[30],"Spectrometry":[31],"(LC-MS).":[32],"Among":[33],"major":[35],"challenges":[36],"analysis":[38,45,76],"metabolomics":[40,164,188],"data":[41,47,78,144,165,189],"are":[42,181],"(i)":[43],"joint":[44,75],"from":[48,79,150],"multiple":[49,80],"platforms,":[50],"(ii)":[52],"capturing":[53],"easily":[54],"interpretable":[55],"underlying":[56,135],"patterns,":[57],"which":[58,109],"could":[59],"be":[60],"further":[61],"utilized":[62],"for":[63,116,171],"biomarker":[64],"discovery.":[65],"In":[66],"order":[67],"to":[68,161],"address":[69],"these":[70],"challenges,":[71],"authors":[73,128,156],"formulate":[74],"platforms":[81],"coupled":[84],"matrix":[85],"factorization":[86],"problem":[87],"with":[88,106],"sparsity":[89],"penalties":[90],"factor":[93,118],"matrices.":[94],"They":[95],"developed":[96],"an":[97],"all-at-once":[98],"optimization":[99,113],"algorithm,":[100],"called":[101],"CMF-SPOPT":[102,131],"(Coupled":[103],"Matrix":[104],"Factorization":[105],"SParse":[107],"OPTimization),":[108],"is":[110],"gradient-based":[112],"approach":[114,160,180],"solving":[115],"all":[117],"matrices":[119],"simultaneously.":[120],"Using":[121],"numerical":[122],"experiments":[123],"simulated":[125],"data,":[126],"demonstrate":[129],"that":[130],"can":[132],"capture":[133],"sparse":[136],"patterns":[137],"data.":[139],"Furthermore,":[140],"real":[143],"set":[145],"samples":[148],"collected":[149],"group":[152],"rats,":[154],"use":[157],"proposed":[159,179],"jointly":[162],"analyze":[163],"sets":[166],"identify":[168],"potential":[169],"biomarkers":[170],"apple":[172],"intake.":[173],"Advantages":[174],"limitations":[176],"also":[182],"discussed":[183],"illustrative":[185],"examples":[186],"sets.":[190]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}