{"id":"https://openalex.org/W2598533412","doi":null,"title":"Set-level gene expression data analysis with machine learning","display_name":"Set-level gene expression data analysis with machine learning","publication_year":2014,"publication_date":"2014-09-18","ids":{"openalex":"https://openalex.org/W2598533412","mag":"2598533412"},"language":"en","primary_location":{"id":"pmh:oai:dspace.cvut.cz:10467/58997","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10467/58997","pdf_url":null,"source":{"id":"https://openalex.org/S4306400739","display_name":"Cvut DSpace (Czech Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I44504214","host_organization_name":"Czech Technical University in Prague","host_organization_lineage":["https://openalex.org/I44504214"],"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":"diserta\u010dn\u00ed pr\u00e1ce"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5006920882","display_name":"Mat\u011bj Holec","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mat\u011bj Holec","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5006920882"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9848999977111816,"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":0.9848999977111816,"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":0.014499999582767487,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":9.999999747378752e-05,"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/gene-sets","display_name":"gene sets","score":0.6600000262260437},{"id":"https://openalex.org/keywords/prior-knowledge-integration","display_name":"prior knowledge incorporation","score":0.6510000228881836},{"id":"https://openalex.org/keywords/cross-platform-data-integration","display_name":"cross-platform data integration","score":0.6790000200271606},{"id":"https://openalex.org/keywords/cross-species-data-integration","display_name":"cross-species data integration","score":0.9419999718666077},{"id":"https://openalex.org/keywords/overfitting","display_name":"overfitting","score":0.9179999828338623},{"id":"https://openalex.org/keywords/gene-expression-classification","display_name":"gene expression classification","score":0.6779999732971191}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.8539822101593018},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6275600790977478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5957851409912109},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.5569062829017639},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5211560726165771},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.49892139434814453},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.4817800223827362},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.46798110008239746},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4460674524307251},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.44022130966186523},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.43605396151542664},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3586732745170593},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2493574619293213},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16121497750282288},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11345899105072021},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.10901609063148499},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.1014464795589447},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09649065136909485},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:dspace.cvut.cz:10467/58997","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10467/58997","pdf_url":null,"source":{"id":"https://openalex.org/S4306400739","display_name":"Cvut DSpace (Czech Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I44504214","host_organization_name":"Czech Technical University in Prague","host_organization_lineage":["https://openalex.org/I44504214"],"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":"diserta\u010dn\u00ed pr\u00e1ce"},{"id":"mag:2598533412","doi":null,"is_oa":false,"landing_page_url":"http://cyber.felk.cvut.cz/teaching/radaUIB/Holec%20Matej%20disertace.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":128,"referenced_works":["https://openalex.org/W190535922","https://openalex.org/W598396932","https://openalex.org/W1480333175","https://openalex.org/W1480376833","https://openalex.org/W1486784550","https://openalex.org/W1523843467","https://openalex.org/W1551731376","https://openalex.org/W1565746575","https://openalex.org/W1570448133","https://openalex.org/W1570713908","https://openalex.org/W1607317395","https://openalex.org/W1786866761","https://openalex.org/W1906461790","https://openalex.org/W1913179380","https://openalex.org/W1971445167","https://openalex.org/W1972909920","https://openalex.org/W1973268693","https://openalex.org/W1978336444","https://openalex.org/W1978984420","https://openalex.org/W1981509058","https://openalex.org/W1983463159","https://openalex.org/W1987283311","https://openalex.org/W1987951940","https://openalex.org/W1989277387","https://openalex.org/W1992045522","https://openalex.org/W1997805746","https://openalex.org/W2012332881","https://openalex.org/W2017426710","https://openalex.org/W2020541351","https://openalex.org/W2021129827","https://openalex.org/W2026012474","https://openalex.org/W2029441111","https://openalex.org/W2032580087","https://openalex.org/W2032717553","https://openalex.org/W2039172942","https://openalex.org/W2039616495","https://openalex.org/W2044545767","https://openalex.org/W2047218894","https://openalex.org/W2050113778","https://openalex.org/W2058451329","https://openalex.org/W2063040754","https://openalex.org/W2072708674","https://openalex.org/W2075411161","https://openalex.org/W2081076969","https://openalex.org/W2082081674","https://openalex.org/W2084533385","https://openalex.org/W2089658797","https://openalex.org/W2091947792","https://openalex.org/W2093255090","https://openalex.org/W2093711185","https://openalex.org/W2098264959","https://openalex.org/W2100980426","https://openalex.org/W2101117089","https://openalex.org/W2103626657","https://openalex.org/W2106471679","https://openalex.org/W2107798086","https://openalex.org/W2107914050","https://openalex.org/W2109044536","https://openalex.org/W2109363337","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2111413836","https://openalex.org/W2113242816","https://openalex.org/W2113387206","https://openalex.org/W2113582979","https://openalex.org/W2113629891","https://openalex.org/W2114972221","https://openalex.org/W2115580179","https://openalex.org/W2118069309","https://openalex.org/W2119756816","https://openalex.org/W2120865735","https://openalex.org/W2120965285","https://openalex.org/W2121111814","https://openalex.org/W2121365413","https://openalex.org/W2122084873","https://openalex.org/W2123099342","https://openalex.org/W2123106337","https://openalex.org/W2124704116","https://openalex.org/W2127823872","https://openalex.org/W2127952499","https://openalex.org/W2129099812","https://openalex.org/W2129972555","https://openalex.org/W2130365699","https://openalex.org/W2130730559","https://openalex.org/W2132589078","https://openalex.org/W2133990480","https://openalex.org/W2134736660","https://openalex.org/W2134787419","https://openalex.org/W2135891958","https://openalex.org/W2136482257","https://openalex.org/W2136629313","https://openalex.org/W2136746865","https://openalex.org/W2136913687","https://openalex.org/W2138040987","https://openalex.org/W2138543194","https://openalex.org/W2138862313","https://openalex.org/W2139036189","https://openalex.org/W2139135974","https://openalex.org/W2139837606","https://openalex.org/W2141055671","https://openalex.org/W2141946210","https://openalex.org/W2142237411","https://openalex.org/W2143119085","https://openalex.org/W2143426320","https://openalex.org/W2145259857","https://openalex.org/W2146995322","https://openalex.org/W2150926065","https://openalex.org/W2154947819","https://openalex.org/W2157132621","https://openalex.org/W2157503003","https://openalex.org/W2157795344","https://openalex.org/W2158217645","https://openalex.org/W2158224118","https://openalex.org/W2158384363","https://openalex.org/W2159835316","https://openalex.org/W2160697532","https://openalex.org/W2165342893","https://openalex.org/W2166406453","https://openalex.org/W2167119716","https://openalex.org/W2168113705","https://openalex.org/W2168264491","https://openalex.org/W2168639800","https://openalex.org/W2168850532","https://openalex.org/W2331384579","https://openalex.org/W2592188805","https://openalex.org/W2621000931","https://openalex.org/W2760732609","https://openalex.org/W4239510810"],"related_works":["https://openalex.org/W7019234235","https://openalex.org/W6983548826","https://openalex.org/W7048716672","https://openalex.org/W7030340517","https://openalex.org/W2248753035","https://openalex.org/W797765068","https://openalex.org/W746817859","https://openalex.org/W7018105720","https://openalex.org/W2966044465","https://openalex.org/W2236731548"],"abstract_inverted_index":{"Gene":[0],"expression":[1,36,135,201,379],"data":[2,37,62,66,136,147,151,202,271],"analysis":[3,132,309,345,380],"methods":[4],"that":[5,68,111,249,296],"exploit":[6],"formalized":[7],"prior":[8,24,262],"knowledge":[9,25],"have":[10],"expanded":[11],"significantly":[12,313],"in":[13,22,302,315,371,384],"the":[14,30,33,52,60,82,103,107,112,119,122,128,139,171,176,179,187,192,213,219,225,229,239,253,267,282,286,289,305,334,367,391,403,406],"last":[15],"10":[16],"years.":[17],"This":[18],"thesis":[19,400],"explores":[20],"strategies":[21],"which":[23,45,99,235,330,372],"is":[26,291,366],"used":[27],"to":[28,70,127,154,184,197,212,333,358,402],"support":[29],"transformation":[31,58,114],"of":[32,54,92,96,121,133,158,175,191,228,242,261,269,307,317,327,336,346,353,363,393,395,405],"original":[34,83],"gene":[35,84,104,134,200,264,299,328,378],"into":[38],"a":[39,93,166,343],"so":[40],"called":[41],"set-level":[42,162,180,254,377],"representation,":[43],"on":[44,118,342],"machine-learning":[46,124,230],"algorithms":[47],"are":[48,100,236],"applied":[49],"usually":[50],"for":[51,224],"sake":[53],"predictive":[55,308,396],"classification.":[56,337],"The":[57,160],"generalizes":[59],"input":[61],"towards":[63],"\u201cmore":[64],"abstract\u201d":[65],"dimensions":[67],"correspond":[69],"various":[71],"biological":[72],"functional":[73,257],"or":[74,276],"structural":[75],"properties":[76],"rather":[77],"than":[78],"genes.":[79],"For":[80,285],"example,":[81],"expressions":[85,105],"may":[86],"be":[87,312,382],"replaced":[88],"by":[89,252,273],"activity":[90],"levels":[91],"specific":[94],"set":[95],"regulatory":[97],"pathways,":[98],"estimated":[101],"from":[102,138,375,390],"during":[106,218],"transformation.":[108,220],"We":[109,246,294],"hypothesize":[110],"outlined":[113],"has":[115,165],"positive":[116],"influence":[117],"outcome":[120],"subsequent":[123],"experiments":[125],"due":[126],"following":[129],"intuition.":[130],"Typically,":[131],"suffers":[137],"well-known":[140],"\u201clarge":[141,172],"p,":[142],"small":[143],"n\u201d":[144,189],"problem":[145],"(large":[146],"dimension":[148],"and":[149,387,412],"few":[150],"samples)":[152],"leading":[153],"an":[155,385],"increased":[156],"risk":[157],"overfitting.":[159],"transformed":[161],"representation":[163],"typically":[164],"smaller":[167],"dimension,":[168],"thereby":[169],"mitigating":[170],"p\u201d":[173],"part":[174,190],"problem.":[177],"Interestingly,":[178],"approach":[181],"enables":[182],"us":[183],"address":[185],"also":[186],"\u201csmall":[188],"problem,":[193],"since":[194],"it":[195],"allows":[196,266],"merge":[198],"several":[199],"sets":[203,208,265,300,329],"originally":[204],"using":[205,297],"different":[206,274],"feature":[207],"(genes)":[209],"but":[210],"unified":[211],"same":[214],"more":[215,292,324],"abstract":[216],"units":[217],"These":[221,338],"two":[222,233],"reasons":[223],"suspected":[226],"boost":[227],"performance":[231,306],"represent":[232,349],"hypotheses":[234],"tested":[237],"as":[238],"main":[240],"contribution":[241,352,362],"this":[243,354,364,399],"dissertation":[244],"work.":[245],"successfully":[247],"prove":[248],"generalization":[250],"caused":[251],"techniques":[255,374],"exploiting":[256],"relationships":[258],"among":[259],"genes":[260],"defined":[263],"integration":[268],"additional":[270],"obtained":[272],"platforms":[275],"even":[277],"species,":[278],"i.e.,":[279],"we":[280,321],"confirm":[281],"latter":[283],"hypothesis.":[284],"former":[287],"hypothesis,":[288],"situation":[290],"subtle.":[293],"show":[295],"standard":[298],"proposed":[301],"state-of-the-art":[303,376],"research,":[304],"will":[310],"not":[311],"improved":[314],"terms":[316],"classification":[318],"accuracy.":[319,397],"However,":[320],"propose":[322],"some":[323],"sophisticated":[325],"definitions":[326,340],"indeed":[331],"lead":[332],"improvement":[335],"new":[339],"based":[341],"careful":[344],"gene-regulatory":[347],"principles":[348],"another":[350],"significant":[351],"thesis,":[355],"albeit":[356],"limited":[357],"prokaryotes.":[359],"A":[360],"lateral":[361],"work":[365],"designed":[368],"evaluation":[369],"framework":[370],"numerous":[373],"can":[381],"compared":[383],"unbiased":[386],"objective":[388],"manner,":[389],"point":[392],"view":[394],"Lastly,":[398],"contributed":[401],"development":[404],"public":[407],"web-based":[408],"software":[409],"tools":[410],"XGENE.ORG":[411],"its":[413],"successor":[414],"miXGENE.":[415]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2017-04-07T00:00:00"}