{"id":"https://openalex.org/W2985757832","doi":"https://doi.org/10.1093/bioinformatics/btz809","title":"Network-based multi-task learning models for biomarker selection and cancer outcome prediction","display_name":"Network-based multi-task learning models for biomarker selection and cancer outcome prediction","publication_year":2019,"publication_date":"2019-10-30","ids":{"openalex":"https://openalex.org/W2985757832","doi":"https://doi.org/10.1093/bioinformatics/btz809","mag":"2985757832","pmid":"https://pubmed.ncbi.nlm.nih.gov/31688914"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz809","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz809","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1814/32915569/btz809.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1814/32915569/btz809.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100422345","display_name":"Zhibo Wang","orcid":"https://orcid.org/0000-0002-5804-3279"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhibo Wang","raw_affiliation_strings":["Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA","Genomics and Bioinformatics Cluster, University of Central Florida , Orlando, FL 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Genomics and Bioinformatics Cluster, University of Central Florida , Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036755436","display_name":"Zhezhi He","orcid":"https://orcid.org/0000-0002-6357-236X"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhezhi He","raw_affiliation_strings":["School of Electrical, Computer and Energy Engineering, Arizona State University , Tempe, AZ 85287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical, Computer and Energy Engineering, Arizona State University , Tempe, AZ 85287, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101503338","display_name":"Milan Shah","orcid":"https://orcid.org/0000-0002-3572-7408"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milan Shah","raw_affiliation_strings":["Department of Computer Science, Duke University , Durham, NC, 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University , Durham, NC, 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372506","display_name":"Teng Zhang","orcid":"https://orcid.org/0000-0002-5310-8766"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teng Zhang","raw_affiliation_strings":["Department of Mathematics, University of Central Florida , Orlando, FL 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Central Florida , Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047916979","display_name":"Deliang Fan","orcid":"https://orcid.org/0000-0002-7989-6297"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deliang Fan","raw_affiliation_strings":["School of Electrical, Computer and Energy Engineering, Arizona State University , Tempe, AZ 85287, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical, Computer and Energy Engineering, Arizona State University , Tempe, AZ 85287, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100441789","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0003-3605-9373"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA","Genomics and Bioinformatics Cluster, University of Central Florida , Orlando, FL 32816, USA"],"raw_orcid":"https://orcid.org/0000-0003-3605-9373","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida , Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Genomics and Bioinformatics Cluster, University of Central Florida , Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100441789"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4525,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.82501868,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"6","first_page":"1814","last_page":"1822"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9179999828338623,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9179999828338623,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.028699999675154686,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.019500000402331352,"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/computational-biology","display_name":"Computational biology","score":0.5978841781616211},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.516054093837738},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.505406379699707},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4930374324321747},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.45771872997283936},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.45295441150665283},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.4417318105697632},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4305873513221741},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.41471806168556213},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36012396216392517},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32544708251953125},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.24269503355026245},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20408368110656738}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5978841781616211},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.516054093837738},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.505406379699707},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4930374324321747},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.45771872997283936},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.45295441150665283},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.4417318105697632},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4305873513221741},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.41471806168556213},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36012396216392517},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32544708251953125},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.24269503355026245},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20408368110656738}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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:10.1093/bioinformatics/btz809","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz809","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1814/32915569/btz809.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31688914","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31688914","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz809","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz809","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/6/1814/32915569/btz809.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.41999998688697815,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G7032288738","display_name":null,"funder_award_id":"FET 1908495","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7221860340","display_name":null,"funder_award_id":"IIS 1755761","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W131292521","https://openalex.org/W1491070134","https://openalex.org/W1496388003","https://openalex.org/W1520812622","https://openalex.org/W1965302838","https://openalex.org/W1974834178","https://openalex.org/W1989262738","https://openalex.org/W2016964184","https://openalex.org/W2027847194","https://openalex.org/W2035421116","https://openalex.org/W2069628816","https://openalex.org/W2073933425","https://openalex.org/W2086864109","https://openalex.org/W2106425267","https://openalex.org/W2109682960","https://openalex.org/W2114918651","https://openalex.org/W2116063398","https://openalex.org/W2119387367","https://openalex.org/W2128985829","https://openalex.org/W2131987814","https://openalex.org/W2135046866","https://openalex.org/W2143426320","https://openalex.org/W2144227498","https://openalex.org/W2150533948","https://openalex.org/W2150671673","https://openalex.org/W2158485828","https://openalex.org/W2167283581","https://openalex.org/W2170989872","https://openalex.org/W2520491400","https://openalex.org/W2527438532","https://openalex.org/W2539428289","https://openalex.org/W2555803041","https://openalex.org/W2739852640","https://openalex.org/W2771967647","https://openalex.org/W2804291108","https://openalex.org/W2951029718","https://openalex.org/W3104123570","https://openalex.org/W6746086544"],"related_works":["https://openalex.org/W1556453709","https://openalex.org/W3135849929","https://openalex.org/W2802217527","https://openalex.org/W2909382709","https://openalex.org/W4366245510","https://openalex.org/W2964663169","https://openalex.org/W3216867886","https://openalex.org/W2901652497","https://openalex.org/W2157872031","https://openalex.org/W4282973552"],"abstract_inverted_index":{"MOTIVATION:":[0],"Detecting":[1],"cancer":[2,26,41,89,100,118,135,160,182],"gene":[3,109,203],"expression":[4,50],"and":[5,22,78,112,133,164,180,191,199,202],"transcriptome":[6],"changes":[7,51],"with":[8,151,186],"mRNA-sequencing":[9],"or":[10,60],"array-based":[11],"data":[12,218],"are":[13,57,184,219],"important":[14],"for":[15],"understanding":[16],"the":[17,31,46,68,106,116,122,140,152,155,187],"molecular":[18,166],"mechanisms":[19,55],"underlying":[20,115],"carcinogenesis":[21],"cellular":[23],"events":[24],"during":[25],"progression.":[27],"In":[28],"previous":[29],"studies,":[30],"differentially":[32,83,94],"expressed":[33,84,95],"genes":[34,85,96,190],"were":[35],"detected":[36,168],"across":[37,87,158],"patients":[38],"in":[39,52,62,193],"one":[40],"type.":[42,101],"These":[43],"studies":[44],"ignored":[45],"role":[47],"of":[48,197],"mRNA":[49],"driving":[53],"tumorigenic":[54],"that":[56,139],"either":[58],"universal":[59],"specific":[61,97],"different":[63,88,125,159],"tumor":[64,126],"types.":[65,127,161],"To":[66],"address":[67],"problem,":[69],"we":[70],"introduce":[71],"two":[72],"network-based":[73,142],"multi-task":[74,143,170],"learning":[75,144,171],"frameworks,":[76],"NetML":[77],"NetSML,":[79],"to":[80,98,120],"discover":[81],"common":[82,107,163],"shared":[86],"types":[90],"as":[91,93],"well":[92],"each":[99],"The":[102,162,174],"proposed":[103,141],"frameworks":[104,145,172],"consider":[105],"latent":[108],"co-expression":[110],"modules":[111],"gene-sample":[113],"biclusters":[114],"multiple":[117],"datasets":[119,137,183],"learn":[121],"knowledge":[123,156],"crossing":[124],"RESULTS:":[128],"Large-scale":[129],"experiments":[130],"on":[131,173],"simulations":[132],"real":[134],"high-throughput":[136],"validate":[138],"perform":[146],"better":[147],"sample":[148],"classification":[149],"compared":[150],"models":[153],"without":[154],"sharing":[157],"cancer-specific":[165],"signatures":[167],"by":[169],"Cancer":[175],"Genome":[176,200],"Atlas":[177],"ovarian,":[178],"breast":[179],"prostate":[181],"correlated":[185],"known":[188],"marker":[189],"enriched":[192],"cancer-relevant":[194],"Kyoto":[195],"Encyclopedia":[196],"Genes":[198],"pathways":[201],"ontology":[204],"terms.":[205],"AVAILABILITY":[206],"AND":[207],"IMPLEMENTATION:":[208],"Source":[209],"code":[210],"is":[211],"available":[212,220],"at:":[213],"https://github.com/compbiolabucf/NetML.":[214],"SUPPLEMENTARY":[215],"INFORMATION:":[216],"Supplementary":[217],"at":[221],"Bioinformatics":[222],"online.":[223]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
