{"id":"https://openalex.org/W4393092671","doi":"https://doi.org/10.1021/acs.jcim.3c01486","title":"CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction","display_name":"CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction","publication_year":2024,"publication_date":"2024-03-22","ids":{"openalex":"https://openalex.org/W4393092671","doi":"https://doi.org/10.1021/acs.jcim.3c01486","pmid":"https://pubmed.ncbi.nlm.nih.gov/38514966"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01486","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01486","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","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/A5076404110","display_name":"Fatemeh Rafiei","orcid":"https://orcid.org/0000-0002-1303-8660"},"institutions":[{"id":"https://openalex.org/I70640408","display_name":"Tehran University of Medical Sciences","ror":"https://ror.org/01c4pz451","country_code":"IR","type":"education","lineage":["https://openalex.org/I70640408"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Fatemeh Rafiei","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran","institution_ids":["https://openalex.org/I70640408"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057558544","display_name":"Hojjat Zeraati","orcid":"https://orcid.org/0000-0002-8635-4322"},"institutions":[{"id":"https://openalex.org/I70640408","display_name":"Tehran University of Medical Sciences","ror":"https://ror.org/01c4pz451","country_code":"IR","type":"education","lineage":["https://openalex.org/I70640408"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Hojjat Zeraati","raw_affiliation_strings":["Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran","institution_ids":["https://openalex.org/I70640408"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069064010","display_name":"Karim Abbasi","orcid":"https://orcid.org/0000-0003-2135-8864"},"institutions":[{"id":"https://openalex.org/I181744264","display_name":"Kharazmi University","ror":"https://ror.org/05hsgex59","country_code":"IR","type":"education","lineage":["https://openalex.org/I181744264"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Karim Abbasi","raw_affiliation_strings":["Laboratory of System Biology, Bioinformatics & Artificial Intelligence in Medicine (LBB&AI), Faculty of Mathematics and Computer Science, Kharazmi University, Tehran 14588-89694, Iran"],"raw_orcid":"https://orcid.org/0000-0003-2135-8864","affiliations":[{"raw_affiliation_string":"Laboratory of System Biology, Bioinformatics & Artificial Intelligence in Medicine (LBB&AI), Faculty of Mathematics and Computer Science, Kharazmi University, Tehran 14588-89694, Iran","institution_ids":["https://openalex.org/I181744264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018861719","display_name":"Parvin Razzaghi","orcid":"https://orcid.org/0000-0002-7031-4609"},"institutions":[{"id":"https://openalex.org/I161028277","display_name":"Institute for Advanced Studies in Basic Sciences","ror":"https://ror.org/00bzsst90","country_code":"IR","type":"education","lineage":["https://openalex.org/I161028277"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Parvin Razzaghi","raw_affiliation_strings":["Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran"],"raw_orcid":"https://orcid.org/0000-0002-7031-4609","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran","institution_ids":["https://openalex.org/I161028277"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021441524","display_name":"Jahan B. Ghasemi","orcid":"https://orcid.org/0000-0002-0380-8000"},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Jahan B Ghasemi","raw_affiliation_strings":["Chemistry Department, Faculty of Chemistry, School of Sciences, University of Tehran, Tehran 14174-66191, Iran"],"raw_orcid":"https://orcid.org/0000-0002-0380-8000","affiliations":[{"raw_affiliation_string":"Chemistry Department, Faculty of Chemistry, School of Sciences, University of Tehran, Tehran 14174-66191, Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088464143","display_name":"Mahboubeh Parsaeian","orcid":"https://orcid.org/0000-0003-1928-5424"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I70640408","display_name":"Tehran University of Medical Sciences","ror":"https://ror.org/01c4pz451","country_code":"IR","type":"education","lineage":["https://openalex.org/I70640408"]}],"countries":["GB","IR"],"is_corresponding":true,"raw_author_name":"Mahboubeh Parsaeian","raw_affiliation_strings":["Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, U.K","Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran"],"raw_orcid":"https://orcid.org/0000-0003-1928-5424","affiliations":[{"raw_affiliation_string":"Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, U.K","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, School of Health, Tehran University of Medical Sciences, Tehran 14167-53955, Iran","institution_ids":["https://openalex.org/I70640408"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030421501","display_name":"Ali Masoudi\u2010Nejad","orcid":"https://orcid.org/0000-0003-0659-5183"},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Ali Masoudi-Nejad","raw_affiliation_strings":["Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran 13145-1365, Iran"],"raw_orcid":"https://orcid.org/0000-0003-0659-5183","affiliations":[{"raw_affiliation_string":"Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran 13145-1365, Iran","institution_ids":["https://openalex.org/I23946033"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5030421501","https://openalex.org/A5088464143"],"corresponding_institution_ids":["https://openalex.org/I23946033","https://openalex.org/I40120149","https://openalex.org/I70640408"],"apc_list":null,"apc_paid":null,"fwci":12.5098,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.99186992,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"64","issue":"7","first_page":"2577","last_page":"2585"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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":0.994700014591217,"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/discriminative-model","display_name":"Discriminative model","score":0.6949257254600525},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6406230926513672},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.607047975063324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6051064729690552},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5903939008712769},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5082611441612244},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4870317578315735},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4115487039089203},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.0802045464515686}],"concepts":[{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6949257254600525},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6406230926513672},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.607047975063324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6051064729690552},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5903939008712769},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5082611441612244},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4870317578315735},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4115487039089203},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0802045464515686},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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/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":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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01486","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01486","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38514966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38514966","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7200000286102295,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G485015199","display_name":null,"funder_award_id":"IR.TUMS.MEDICINE.REC.1400.1398","funder_id":"https://openalex.org/F4320322670","funder_display_name":"Tehran University of Medical Sciences and Health Services"}],"funders":[{"id":"https://openalex.org/F4320322670","display_name":"Tehran University of Medical Sciences and Health Services","ror":"https://ror.org/01c4pz451"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W2090891622","https://openalex.org/W2115517051","https://openalex.org/W2299417213","https://openalex.org/W2344726805","https://openalex.org/W2469049024","https://openalex.org/W2517536022","https://openalex.org/W2739326744","https://openalex.org/W2775061087","https://openalex.org/W2893221764","https://openalex.org/W2949524414","https://openalex.org/W2959123242","https://openalex.org/W2960677646","https://openalex.org/W2981475131","https://openalex.org/W2982291409","https://openalex.org/W2982691277","https://openalex.org/W3006302308","https://openalex.org/W3032089175","https://openalex.org/W3084084616","https://openalex.org/W3092034553","https://openalex.org/W3160460047","https://openalex.org/W3167913840","https://openalex.org/W3172530361","https://openalex.org/W3196304395","https://openalex.org/W3202143517","https://openalex.org/W4205719393","https://openalex.org/W4206405364","https://openalex.org/W4206796410","https://openalex.org/W4212799760","https://openalex.org/W4220967131","https://openalex.org/W4288108355","https://openalex.org/W4293710115","https://openalex.org/W4308834336","https://openalex.org/W4367673946","https://openalex.org/W4378470974","https://openalex.org/W4378838672","https://openalex.org/W4380370418","https://openalex.org/W4380742954","https://openalex.org/W4384818885","https://openalex.org/W4388756595","https://openalex.org/W4389616450"],"related_works":["https://openalex.org/W4389116644","https://openalex.org/W2153315159","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W4205463238","https://openalex.org/W2761785940","https://openalex.org/W1482209366","https://openalex.org/W2110523656","https://openalex.org/W2521627374","https://openalex.org/W2981954115"],"abstract_inverted_index":{"Drug":[0],"synergy":[1,31],"prediction":[2],"plays":[3],"a":[4,84,97,123,176,202],"vital":[5],"role":[6],"in":[7,229,239],"cancer":[8],"treatment.":[9],"Because":[10],"experimental":[11],"approaches":[12,18],"are":[13,23,71,197],"labor-intensive":[14],"and":[15,34,51,68,75,105,146,160,170,182,190,220,246],"expensive,":[16],"computational-based":[17],"get":[19],"more":[20,45],"attention.":[21],"There":[22],"two":[24,92],"types":[25],"of":[26,215,236],"computational":[27],"methods":[28,228],"for":[29,102,115,167,179],"drug":[30,49],"prediction:":[32],"feature-based":[33,37,256],"similarity-based.":[35],"In":[36,60,81],"methods,":[38,62],"the":[39,57,63,78,129,133,142,147,155,164,187,191,213,234],"main":[40],"focus":[41],"is":[42,94,100,138],"to":[43,54,56,199,211],"extract":[44],"discriminative":[46,98],"features":[47,74,189,196],"from":[48,252],"pairs":[50],"cell":[52,69,106,118,135,149,171,183,247],"lines":[53,70,107,184],"pass":[55],"task":[58,79,203],"predictor.":[59,80,204],"similarity-based":[61,188,254],"similarities":[64],"among":[65],"all":[66],"drugs":[67,104,159,169,181,245],"utilized":[72,112],"as":[73,108,201],"fed":[76,198],"into":[77],"this":[82],"work,":[83],"novel":[85],"approach,":[86],"called":[87],"CFSSynergy,":[88],"that":[89],"combines":[90],"these":[91,195],"viewpoints":[93],"proposed.":[95],"First,":[96],"representation":[99,137,166,178],"extracted":[101],"paired":[103,168,180],"input.":[109],"We":[110],"have":[111,121],"transformer-based":[113],"architecture":[114],"drugs.":[116],"For":[117],"lines,":[119,248],"we":[120,153,174],"created":[122],"similarity":[124,144,156],"matrix":[125,145],"between":[126,157,244],"proteins":[127],"using":[128,163],"Node2Vec":[130],"algorithm.":[131],"Then,":[132,173],"new":[134,177],"line":[136,150],"computed":[139],"by":[140],"multiplying":[141],"protein-protein":[143],"initial":[148],"representation.":[151],"Next,":[152],"compute":[154,175],"unique":[158,161],"cells":[162],"learned":[165,192],"lines.":[172],"based":[185],"on":[186],"features.":[193],"Finally,":[194],"XGBoost":[200],"Two":[205],"well-known":[206],"data":[207],"sets":[208],"were":[209],"used":[210],"evaluate":[212],"performance":[214],"our":[216,237],"proposed":[217],"method:":[218],"DrugCombDB":[219],"OncologyScreen.":[221],"The":[222],"CFSSynergy":[223],"approach":[224,238],"consistently":[225],"outperformed":[226],"existing":[227],"comparative":[230],"evaluations.":[231],"This":[232],"substantiates":[233],"efficacy":[235],"capturing":[240],"complex":[241],"synergistic":[242],"interactions":[243],"setting":[249],"it":[250],"apart":[251],"conventional":[253],"or":[255],"methods.":[257]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":24}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
