{"id":"https://openalex.org/W3175303525","doi":"https://doi.org/10.1109/tcbb.2021.3091814","title":"Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization","display_name":"Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization","publication_year":2021,"publication_date":"2021-06-23","ids":{"openalex":"https://openalex.org/W3175303525","doi":"https://doi.org/10.1109/tcbb.2021.3091814","mag":"3175303525","pmid":"https://pubmed.ncbi.nlm.nih.gov/34166199"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3091814","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3091814","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"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/A5074094001","display_name":"Pietro Pinoli","orcid":"https://orcid.org/0000-0001-9786-2851"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Pietro Pinoli","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057146676","display_name":"Gaia Ceddia","orcid":"https://orcid.org/0000-0001-9512-7781"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gaia Ceddia","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048332811","display_name":"Stefano Ceri","orcid":"https://orcid.org/0000-0003-0671-2415"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Ceri","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085346183","display_name":"Marco Masseroli","orcid":"https://orcid.org/0000-0003-2574-1174"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Masseroli","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074094001"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":0.724,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.68650234,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"4","first_page":"1956","last_page":"1967"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9984999895095825,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.6100730895996094},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5826343297958374},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5826002955436707},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5708724856376648},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.49054306745529175},{"id":"https://openalex.org/keywords/correlation-coefficient","display_name":"Correlation coefficient","score":0.4322204291820526},{"id":"https://openalex.org/keywords/line","display_name":"Line (geometry)","score":0.42704901099205017},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.41004830598831177},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38786035776138306},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38394105434417725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33684277534484863},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.28210365772247314},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26078805327415466},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13554039597511292},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.12064811587333679}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6100730895996094},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5826343297958374},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5826002955436707},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5708724856376648},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.49054306745529175},{"id":"https://openalex.org/C2780092901","wikidata":"https://www.wikidata.org/wiki/Q3433612","display_name":"Correlation coefficient","level":2,"score":0.4322204291820526},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.42704901099205017},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.41004830598831177},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38786035776138306},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38394105434417725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33684277534484863},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28210365772247314},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26078805327415466},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13554039597511292},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.12064811587333679},{"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004357","descriptor_name":"Drug Synergism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004357","descriptor_name":"Drug Synergism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004357","descriptor_name":"Drug Synergism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2021.3091814","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3091814","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34166199","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34166199","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:re.public.polimi.it:11311/1184595","is_oa":false,"landing_page_url":"http://hdl.handle.net/11311/1184595","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W82942351","https://openalex.org/W1696775091","https://openalex.org/W1823184461","https://openalex.org/W1975455559","https://openalex.org/W1980181290","https://openalex.org/W2027001671","https://openalex.org/W2036291018","https://openalex.org/W2043545458","https://openalex.org/W2045156863","https://openalex.org/W2072871705","https://openalex.org/W2096439168","https://openalex.org/W2146416540","https://openalex.org/W2155626151","https://openalex.org/W2157852151","https://openalex.org/W2165863045","https://openalex.org/W2214074259","https://openalex.org/W2473876819","https://openalex.org/W2520902279","https://openalex.org/W2571957366","https://openalex.org/W2608863179","https://openalex.org/W2950182476","https://openalex.org/W2960677646","https://openalex.org/W2969182594","https://openalex.org/W2972948942","https://openalex.org/W2982291409","https://openalex.org/W3014482292","https://openalex.org/W3022121690","https://openalex.org/W3032089175","https://openalex.org/W3105523772"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W2037504162","https://openalex.org/W4390394189","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2539013788","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W2075222291"],"abstract_inverted_index":{"Traditional":[0],"drug":[1,6,34,61,80,105,116,194],"experiments":[2],"to":[3,13,22,136,149,155],"find":[4],"synergistic":[5,33,60,104,166],"pairs":[7,62,106,117],"are":[8,36,172],"time-consuming":[9],"and":[10,107,110,162,185],"expensive":[11],"due":[12],"the":[14,52,94,128,137,182,187,198],"numerous":[15],"possible":[16],"combinations":[17],"of":[18,37,54,76,96,130,193,200],"drugs":[19,167],"that":[20,28,50],"have":[21],"be":[23],"examined.":[24],"Thus,":[25],"computational":[26,69],"methods":[27],"can":[29],"give":[30],"suggestions":[31],"for":[32,58],"investigations":[35],"great":[38],"interest.":[39],"Here,":[40],"we":[41,126,175],"propose":[42],"a":[43,73,119,169,190],"Non-negative":[44],"Matrix":[45],"Tri-Factorization":[46],"(NMTF)":[47],"based":[48],"approach":[49,140],"leverages":[51],"integration":[53],"different":[55],"data":[56,78,135,161,164],"types":[57],"predicting":[59],"in":[63,99,111,118,168,181,186],"multiple":[64],"specific":[65,120],"cell":[66,89,108,121,132,158,170],"lines.":[67,90],"Our":[68,139],"framework":[70],"relies":[71],"on":[72],"network-based":[74],"representation":[75],"available":[77,183],"about":[79,88,165],"synergism,":[81],"which":[82],"also":[83],"allows":[84],"integrating":[85],"genomic":[86,134,160],"information":[87],"We":[91],"computationally":[92],"evaluate":[93],"performances":[95],"our":[97,178,201],"method":[98],"finding":[100],"missing":[101],"relationships":[102],"between":[103,115],"lines,":[109],"computing":[112],"synergy":[113],"scores":[114],"line,":[122],"as":[123,125],"well":[124],"estimate":[127],"benefit":[129],"adding":[131],"line":[133,159,171],"network.":[138],"obtains":[141],"very":[142],"good":[143],"performance":[144],"(Average":[145],"Precision":[146],"Score":[147],"equal":[148,154],"0.937,":[150],"Pearson's":[151],"correlation":[152],"coefficient":[153],"0.760)":[156],"when":[157],"rich":[163],"considered.":[173],"Finally,":[174],"systematically":[176],"searched":[177],"top-scored":[179],"predictions":[180],"literature":[184],"NCI":[188],"ALMANAC,":[189],"well-known":[191],"database":[192],"combination":[195],"experiments,":[196],"proving":[197],"goodness":[199],"findings.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-02-27T16:54:17.756197","created_date":"2025-10-10T00:00:00"}
