{"id":"https://openalex.org/W2773619566","doi":"https://doi.org/10.1186/s12918-017-0480-7","title":"Identifying drug-pathway association pairs based on L2,1-integrative penalized matrix decomposition","display_name":"Identifying drug-pathway association pairs based on L2,1-integrative penalized matrix decomposition","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2773619566","doi":"https://doi.org/10.1186/s12918-017-0480-7","mag":"2773619566","pmid":"https://pubmed.ncbi.nlm.nih.gov/29297378"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-017-0480-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0480-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0480-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0480-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073144090","display_name":"Jin\u2010Xing Liu","orcid":"https://orcid.org/0000-0001-6104-2149"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin-Xing Liu","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034004890","display_name":"Dongqin Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Qin Wang","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064185915","display_name":"Chun-Hou Zheng","orcid":"https://orcid.org/0000-0002-2695-1926"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China. zhengch99@126.com","School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China. zhengch99@126.com","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026569643","display_name":"Ying-Lian Gao","orcid":"https://orcid.org/0000-0003-0483-5622"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ying-Lian Gao","raw_affiliation_strings":["Library of Qufu Normal University, Qufu Normal University, Rizhao, China. yinliangao@126.com","Library of Qufu Normal University, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Library of Qufu Normal University, Qufu Normal University, Rizhao, China. yinliangao@126.com","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"Library of Qufu Normal University, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103014265","display_name":"Shasha Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sha-Sha Wu","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007539735","display_name":"Junliang Shang","orcid":"https://orcid.org/0000-0002-8488-2228"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun-Liang Shang","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5026569643","https://openalex.org/A5064185915"],"corresponding_institution_ids":["https://openalex.org/I202126657"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.2746,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.82704079,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"S6","first_page":"119","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9871000051498413,"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":0.9853000044822693,"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":0.7023290991783142},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.5073878169059753},{"id":"https://openalex.org/keywords/norm","display_name":"Norm (philosophy)","score":0.5045195817947388},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.4867124855518341},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3880424499511719},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.331412136554718}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7023290991783142},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.5073878169059753},{"id":"https://openalex.org/C191795146","wikidata":"https://www.wikidata.org/wiki/Q3878446","display_name":"Norm (philosophy)","level":2,"score":0.5045195817947388},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.4867124855518341},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3880424499511719},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.331412136554718},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12918-017-0480-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0480-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0480-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:29297378","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29297378","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:ed8537d5b70b443689c1e3728091b23d","is_oa":false,"landing_page_url":"https://doaj.org/article/ed8537d5b70b443689c1e3728091b23d","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 11, Iss S6, Pp 63-73 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5770056","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5770056","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-017-0480-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0480-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0480-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2773619566.pdf","grobid_xml":"https://content.openalex.org/works/W2773619566.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W25961052","https://openalex.org/W1533908463","https://openalex.org/W1969369049","https://openalex.org/W1989654707","https://openalex.org/W2002889167","https://openalex.org/W2011250979","https://openalex.org/W2016843909","https://openalex.org/W2023221658","https://openalex.org/W2033591223","https://openalex.org/W2039050532","https://openalex.org/W2043080272","https://openalex.org/W2050344998","https://openalex.org/W2053090063","https://openalex.org/W2075529464","https://openalex.org/W2085034490","https://openalex.org/W2089744178","https://openalex.org/W2100929382","https://openalex.org/W2102096225","https://openalex.org/W2105709960","https://openalex.org/W2108933868","https://openalex.org/W2112384360","https://openalex.org/W2130410032","https://openalex.org/W2133807576","https://openalex.org/W2135194391","https://openalex.org/W2139292387","https://openalex.org/W2146130798","https://openalex.org/W2150535767","https://openalex.org/W2157751286","https://openalex.org/W2162280103","https://openalex.org/W2162316550","https://openalex.org/W2167010218","https://openalex.org/W2240799214","https://openalex.org/W2259538443","https://openalex.org/W2296721019","https://openalex.org/W2344784208","https://openalex.org/W2402014506","https://openalex.org/W2402683807","https://openalex.org/W2418858918","https://openalex.org/W2486650429","https://openalex.org/W2495942494","https://openalex.org/W2586284062","https://openalex.org/W2601530120","https://openalex.org/W2617875283","https://openalex.org/W2621325907","https://openalex.org/W4247924304"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2317200988","https://openalex.org/W2052122378","https://openalex.org/W2544423928","https://openalex.org/W2053286651","https://openalex.org/W2181743346","https://openalex.org/W2187401768","https://openalex.org/W2181413294","https://openalex.org/W2947381795"],"abstract_inverted_index":{"Traditional":[0],"drug":[1],"identification":[2,25],"methods":[3,12,26],"follow":[4],"the":[5,14,36,47,53,65,76,79,97,104,111,117,128,134,142,155,171,181],"\u201cone":[6],"drug-one":[7],"target\u201d":[8],"thought.":[9],"But":[10],"those":[11],"ignore":[13],"natural":[15],"characters":[16],"of":[17,27,78,144,164],"human":[18],"diseases.":[19],"To":[20],"overcome":[21],"this":[22],"limitation,":[23],"many":[24],"drug-pathway":[28,94,167],"association":[29,168],"pairs":[30,169],"have":[31,59],"been":[32],"developed,":[33],"such":[34],"as":[35],"integrative":[37],"penalized":[38],"matrix":[39],"decomposition":[40],"(iPaD)":[41],"method.":[42],"The":[43,178],"iPaD":[44,80,172],"method":[45,86,132,148,157,173,188],"imposes":[46],"L":[48,88,98,105,112,118,129,145],"1":[49,113],"-norm":[50,107,114,120],"penalty":[51,108,115,121],"on":[52,180],"regularization":[54],"term.":[55],"However,":[56],"lasso-type":[57],"penalties":[58],"an":[60],"obvious":[61],"disadvantage,":[62],"that":[63,141,186],"is,":[64],"sparsity":[66],"produced":[67],"by":[68,174],"them":[69],"is":[70,149,189],"too":[71],"dispersive.":[72],"Therefore,":[73],"to":[74,91,109,133,151],"improve":[75],"performance":[77,143],"method,":[81],"we":[82,102,139],"propose":[83],"a":[84],"novel":[85],"named":[87],"2,1":[89,99,106,119,130,146],"-iPaD":[90,100,131,147],"identify":[92],"paired":[93],"associations.":[95],"In":[96],"model,":[101],"use":[103],"replace":[110],"since":[116],"can":[122,158],"produce":[123],"row":[124],"sparsity.":[125],"By":[126],"applying":[127],"CCLE":[135],"and":[136],"NCI-60":[137],"datasets,":[138],"demonstrate":[140],"superior":[150],"existing":[152],"methods.":[153],"And":[154],"proposed":[156],"achieve":[159],"better":[160],"enrichment":[161],"in":[162],"terms":[163],"discovering":[165],"validated":[166],"than":[170],"performing":[175],"permutation":[176],"test.":[177],"results":[179],"two":[182],"real":[183],"datasets":[184],"prove":[185],"our":[187],"effective.":[190]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2017-12-22T00:00:00"}
