{"id":"https://openalex.org/W2777058570","doi":"https://doi.org/10.1186/s13040-017-0160-6","title":"Scalable non-negative matrix tri-factorization","display_name":"Scalable non-negative matrix tri-factorization","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2777058570","doi":"https://doi.org/10.1186/s13040-017-0160-6","mag":"2777058570","pmid":"https://pubmed.ncbi.nlm.nih.gov/29299064"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-017-0160-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0160-6","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13040-017-0160-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033514783","display_name":"Andrej \u010copar","orcid":"https://orcid.org/0000-0003-4309-9170"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Andrej \u010copar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086052373","display_name":"Marinka \u017ditnik","orcid":"https://orcid.org/0000-0001-8530-7228"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Marinka \u017eitnik","raw_affiliation_strings":["Department of Computer Science, Stanford University, Stanford, 94305 CA USA","Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stanford University, Stanford, 94305 CA USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073792028","display_name":"Bla\u017e Zupan","orcid":"https://orcid.org/0000-0002-5864-7056"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Bla\u017e Zupan","raw_affiliation_strings":["Baylor College of Medicine, Houston, 77030 TX USA","Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0002-5864-7056","affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Houston, 77030 TX USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033514783"],"corresponding_institution_ids":["https://openalex.org/I153976015"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.4905,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.60047847,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10","issue":"1","first_page":"41","last_page":"41"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12303","display_name":"Tensor decomposition and applications","score":0.29739999771118164,"subfield":{"id":"https://openalex.org/subfields/2605","display_name":"Computational Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12303","display_name":"Tensor decomposition and applications","score":0.29739999771118164,"subfield":{"id":"https://openalex.org/subfields/2605","display_name":"Computational Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.2540000081062317,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.04610000178217888,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6941061019897461},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5768646597862244},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5217878818511963},{"id":"https://openalex.org/keywords/factorization","display_name":"Factorization","score":0.5002415180206299},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.472371369600296},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.4350179135799408},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.259138286113739},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10741782188415527},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08121976256370544},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.06409552693367004}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6941061019897461},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5768646597862244},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5217878818511963},{"id":"https://openalex.org/C187834632","wikidata":"https://www.wikidata.org/wiki/Q188804","display_name":"Factorization","level":2,"score":0.5002415180206299},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.472371369600296},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.4350179135799408},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.259138286113739},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10741782188415527},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08121976256370544},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.06409552693367004},{"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-017-0160-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0160-6","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:29299064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29299064","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:1d3af326feb2487f9bbf5409188124f1","is_oa":true,"landing_page_url":"https://doaj.org/article/1d3af326feb2487f9bbf5409188124f1","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":"BioData Mining, Vol 10, Iss 1, Pp 1-16 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4665761","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5746986","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-017-0160-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-017-0160-6","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5769677123","display_name":"Artificial Intelligence and Intelligent Systems","funder_award_id":"P2-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W54780379","https://openalex.org/W74439177","https://openalex.org/W79478496","https://openalex.org/W206344101","https://openalex.org/W284798019","https://openalex.org/W1569505069","https://openalex.org/W1675515972","https://openalex.org/W1825216778","https://openalex.org/W1964904043","https://openalex.org/W1968580628","https://openalex.org/W1970357458","https://openalex.org/W1978642402","https://openalex.org/W1981409633","https://openalex.org/W1983157164","https://openalex.org/W1985462363","https://openalex.org/W2001032894","https://openalex.org/W2004143838","https://openalex.org/W2030848960","https://openalex.org/W2043545458","https://openalex.org/W2045156863","https://openalex.org/W2050561213","https://openalex.org/W2098176827","https://openalex.org/W2102140136","https://openalex.org/W2115632271","https://openalex.org/W2116542188","https://openalex.org/W2119487894","https://openalex.org/W2120128322","https://openalex.org/W2125972858","https://openalex.org/W2132692097","https://openalex.org/W2135007932","https://openalex.org/W2136637647","https://openalex.org/W2136897707","https://openalex.org/W2147003974","https://openalex.org/W2153398041","https://openalex.org/W2155830939","https://openalex.org/W2159789820","https://openalex.org/W2173213060","https://openalex.org/W2182055431","https://openalex.org/W2494655283","https://openalex.org/W2518567779","https://openalex.org/W2521492299","https://openalex.org/W2559655401","https://openalex.org/W2777058570","https://openalex.org/W2915079449","https://openalex.org/W2950082447","https://openalex.org/W2999905431","https://openalex.org/W3104030484","https://openalex.org/W3143596294","https://openalex.org/W4229632044","https://openalex.org/W4231451199","https://openalex.org/W4233299962","https://openalex.org/W4234842777","https://openalex.org/W4249138131","https://openalex.org/W4250331344","https://openalex.org/W6680012447","https://openalex.org/W6680022386","https://openalex.org/W6681753409","https://openalex.org/W6959794839"],"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":{"BACKGROUND:":[0],"Matrix":[1,30,108],"factorization":[2,31,58,100,175,248],"is":[3,66,84,91,184,239,243],"a":[4,33,39,46,67,87,114,122,126,147,160,173,193,212,251],"well":[5,205],"established":[6],"pattern":[7],"discovery":[8],"tool":[9],"that":[10,37,90,166,201,217],"has":[11],"seen":[12],"numerous":[13],"applications":[14],"in":[15,81,104,121,154,250,262],"biomedical":[16,141,197],"data":[17,35,40,102,123,142,161,271,276],"analytics,":[18],"such":[19],"as":[20],"gene":[21],"expression":[22],"co-clustering,":[23],"patient":[24],"stratification,":[25],"and":[26,42,54,63,125,170,208],"gene-disease":[27],"association":[28],"mining.":[29,143],"learns":[32],"latent":[34,47,106,116,127,151,266],"model":[36],"takes":[38],"matrix":[41,85,99,155,162,190,237,247],"transforms":[43],"it":[44],"into":[45,163,172],"feature":[48,55],"space":[49,117],"enabling":[50],"generalization,":[51],"noise":[52],"removal":[53],"discovery.":[56],"However,":[57],"algorithms":[59,73],"are":[60,167],"numerically":[61],"intensive,":[62],"hence":[64],"there":[65],"pressing":[68],"challenge":[69],"to":[70,74,279],"scale":[71],"current":[72],"work":[75],"with":[76,188],"large":[77,196,275],"datasets.":[78],"Our":[79],"focus":[80],"this":[82,111],"paper":[83],"tri-factorization,":[86],"popular":[88],"method":[89],"not":[92],"limited":[93],"by":[94,112],"the":[95,132,136,181,256],"assumption":[96],"of":[97,129,180],"standard":[98],"about":[101],"residing":[103],"one":[105],"space.":[107],"tri-factorization":[109,238],"solves":[110],"inferring":[113],"separate":[115],"for":[118,140,150,234,265,270],"each":[119],"dimension":[120],"matrix,":[124],"mapping":[128],"interactions":[130],"between":[131],"inferred":[133],"spaces,":[134],"making":[135],"approach":[137,149,158,183,203,219,233,242,258],"particularly":[138],"suitable":[139],"RESULTS:":[144],"We":[145,254],"developed":[146],"block-wise":[148],"factor":[152,267],"learning":[153],"tri-factorization.":[156,191],"The":[157,241],"partitions":[159],"disjoint":[164],"submatrices":[165],"treated":[168],"independently":[169],"fed":[171],"parallel":[174,246],"system.":[176],"An":[177],"appealing":[178],"property":[179],"proposed":[182],"its":[185,227],"mathematical":[186],"equivalence":[187],"serial":[189],"In":[192],"study":[194],"on":[195,206],"datasets":[198],"we":[199,215],"show":[200],"our":[202,218],"scales":[204],"multi-processor":[207],"multi-GPU":[209,252],"architectures.":[210],"On":[211],"four-GPU":[213],"system":[214],"demonstrate":[216],"can":[220],"be":[221,260,280],"more":[222],"than":[223,226],"100-times":[224],"faster":[225],"single-processor":[228],"counterpart.":[229],"CONCLUSIONS:":[230],"A":[231],"general":[232],"scaling":[235],"non-negative":[236],"proposed.":[240],"especially":[244],"useful":[245,261],"implemented":[249],"environment.":[253],"expect":[255],"new":[257],"will":[259],"emerging":[263],"procedures":[264],"analysis,":[268],"notably":[269],"integration,":[272],"where":[273],"many":[274],"matrices":[277],"need":[278],"collectively":[281],"factorized.":[282]},"counts_by_year":[{"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":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
