{"id":"https://openalex.org/W3164087725","doi":"https://doi.org/10.1109/tcbb.2021.3086702","title":"MatchMaker: A Deep Learning Framework for Drug Synergy Prediction","display_name":"MatchMaker: A Deep Learning Framework for Drug Synergy Prediction","publication_year":2021,"publication_date":"2021-06-04","ids":{"openalex":"https://openalex.org/W3164087725","doi":"https://doi.org/10.1109/tcbb.2021.3086702","mag":"3164087725","pmid":"https://pubmed.ncbi.nlm.nih.gov/34086576"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3086702","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3086702","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":"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/A5068218826","display_name":"Halil \u0130brahim Kuru","orcid":"https://orcid.org/0000-0003-4356-8846"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Halil Ibrahim Kuru","raw_affiliation_strings":["Computer Engineering Department, Bilkent University, Ankara, Turkey"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051657734","display_name":"\u00d6znur Ta\u015ftan","orcid":"https://orcid.org/0000-0001-7058-5372"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Oznur Tastan","raw_affiliation_strings":["Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey"],"affiliations":[{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey","institution_ids":["https://openalex.org/I134235054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090836372","display_name":"A. Erc\u00fcment \u00c7i\u00e7ek","orcid":"https://orcid.org/0000-0001-8613-6619"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["TR","US"],"is_corresponding":false,"raw_author_name":"A. Ercument Cicek","raw_affiliation_strings":["Computer Engineering Department, Bilkent University, Ankara, Turkey","Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068218826"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":null,"apc_paid":null,"fwci":16.3559,"has_fulltext":false,"cited_by_count":158,"citation_normalized_percentile":{"value":0.99383984,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"19","issue":"4","first_page":"2334","last_page":"2344"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9962999820709229,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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":0.6200607419013977},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5624957084655762},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5501079559326172},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4894832372665405},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4830677807331085},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.4421808123588562},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1500825583934784},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.12108859419822693},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11421114206314087},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11308497190475464}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6200607419013977},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5624957084655762},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5501079559326172},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4894832372665405},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4830677807331085},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.4421808123588562},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1500825583934784},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.12108859419822693},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11421114206314087},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11308497190475464}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","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":"D004357","descriptor_name":"Drug Synergism","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2021.3086702","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3086702","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:34086576","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34086576","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:repository.bilkent.edu.tr:11693/111331","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/111331","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"Article"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/76852","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/76852","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.800000011920929}],"awards":[{"id":"https://openalex.org/G1179340234","display_name":null,"funder_award_id":"BAGEP","funder_id":"https://openalex.org/F4320325520","funder_display_name":"Bilim Akademisi"}],"funders":[{"id":"https://openalex.org/F4320308943","display_name":"Microsoft Research","ror":"https://ror.org/00d0nc645"},{"id":"https://openalex.org/F4320310207","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33"},{"id":"https://openalex.org/F4320310281","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666"},{"id":"https://openalex.org/F4320323792","display_name":"Bilkent \u00dcniversitesi","ror":"https://ror.org/02vh8a032"},{"id":"https://openalex.org/F4320324280","display_name":"ASELSAN","ror":"https://ror.org/04knh8e66"},{"id":"https://openalex.org/F4320325520","display_name":"Bilim Akademisi","ror":null},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1435191252","https://openalex.org/W1522301498","https://openalex.org/W1533861849","https://openalex.org/W1546436101","https://openalex.org/W1569935772","https://openalex.org/W1696775091","https://openalex.org/W2025678613","https://openalex.org/W2034978228","https://openalex.org/W2036291018","https://openalex.org/W2036654087","https://openalex.org/W2060737851","https://openalex.org/W2061061337","https://openalex.org/W2095705004","https://openalex.org/W2098924854","https://openalex.org/W2100563036","https://openalex.org/W2101234009","https://openalex.org/W2105536900","https://openalex.org/W2113551867","https://openalex.org/W2122825543","https://openalex.org/W2140595402","https://openalex.org/W2146416540","https://openalex.org/W2165863045","https://openalex.org/W2177317049","https://openalex.org/W2267040404","https://openalex.org/W2295598076","https://openalex.org/W2299417213","https://openalex.org/W2323328911","https://openalex.org/W2335854816","https://openalex.org/W2461427403","https://openalex.org/W2471562228","https://openalex.org/W2608863179","https://openalex.org/W2609325838","https://openalex.org/W2610860012","https://openalex.org/W2612467560","https://openalex.org/W2618398196","https://openalex.org/W2767891136","https://openalex.org/W2775061087","https://openalex.org/W2803581864","https://openalex.org/W2811415290","https://openalex.org/W2898321887","https://openalex.org/W2906092989","https://openalex.org/W2911964244","https://openalex.org/W2938214930","https://openalex.org/W2950182476","https://openalex.org/W2950860419","https://openalex.org/W2951449549","https://openalex.org/W2953384591","https://openalex.org/W2960677646","https://openalex.org/W2972008107","https://openalex.org/W2984763239","https://openalex.org/W2999554466","https://openalex.org/W3014482292","https://openalex.org/W6631190155","https://openalex.org/W6631943919","https://openalex.org/W6674330103","https://openalex.org/W6675354045","https://openalex.org/W6703221619","https://openalex.org/W6713134421","https://openalex.org/W6738373677","https://openalex.org/W6751697710","https://openalex.org/W6769964198"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W2939353110","https://openalex.org/W4321369474","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3046775127"],"abstract_inverted_index":{"Drug":[0],"combination":[1,98],"therapies":[2],"have":[3],"been":[4],"a":[5,83],"viable":[6],"strategy":[7],"for":[8,31],"the":[9,50,88,94,105,110,129,135],"treatment":[10],"of":[11,52,79,107],"complex":[12],"diseases":[13],"such":[14],"as":[15],"cancer":[16],"due":[17,40],"to":[18,41,54,100,116,145],"increased":[19],"efficacy":[20],"and":[21,75,113,120,138,147,155],"reduced":[22],"side":[23],"effects.":[24],"However,":[25],"experimentally":[26,57],"validating":[27],"all":[28],"possible":[29],"combinations":[30,53],"synergistic":[32],"interaction":[33],"even":[34],"with":[35,109],"high-throughout":[36],"screens":[37],"is":[38,153],"intractable":[39],"vast":[42],"combinatorial":[43],"search":[44],"space.":[45],"Computational":[46],"techniques":[47],"can":[48],"reduce":[49],"number":[51],"be":[55],"evaluated":[56],"by":[58],"prioritizing":[59],"promising":[60],"candidates.":[61],"We":[62,103,133],"present":[63,148],"MatchMaker":[64,108,152],"that":[65,141],"predicts":[66],"drug":[67,71,97,139],"synergy":[68],"scores":[69],"using":[70],"chemical":[72],"structure":[73],"information":[74],"gene":[76],"expression":[77],"profiles":[78],"cell":[80,136],"lines":[81],"in":[82],"deep":[84],"learning":[85],"framework.":[86],"For":[87],"first":[89],"time,":[90],"our":[91],"model":[92],"utilizes":[93],"largest":[95],"known":[96],"dataset":[99],"date,":[101],"DrugComb.":[102],"compare":[104],"performance":[106],"state-of-the-art":[111],"models":[112],"observe":[114],"up":[115],"\u223c":[117,121],"15%":[118],"correlation":[119],"33%":[122],"mean":[123],"squared":[124],"error":[125],"(MSE)":[126],"improvements":[127],"over":[128],"next":[130],"best":[131],"method.":[132],"investigate":[134],"types":[137],"pairs":[140],"are":[142],"relatively":[143],"harder":[144],"predict":[146],"novel":[149],"candidate":[150],"pairs.":[151],"built":[154],"available":[156],"at":[157],"https://github.com/tastanlab/matchmaker.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":50},{"year":2024,"cited_by_count":47},{"year":2023,"cited_by_count":32},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":5}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
