{"id":"https://openalex.org/W3016041832","doi":"https://doi.org/10.1101/2020.04.10.036491","title":"Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model","display_name":"Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model","publication_year":2020,"publication_date":"2020-04-13","ids":{"openalex":"https://openalex.org/W3016041832","doi":"https://doi.org/10.1101/2020.04.10.036491","mag":"3016041832","pmid":"https://pubmed.ncbi.nlm.nih.gov/33936513","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8075535"},"language":"en","primary_location":{"id":"doi:10.1101/2020.04.10.036491","doi":"https://doi.org/10.1101/2020.04.10.036491","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.10.036491","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.10.036491.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.10.036491.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046080277","display_name":"Heming Zhang","orcid":"https://orcid.org/0000-0002-3171-5805","observed_orcids":["https://orcid.org/0000-0002-3171-5805"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heming Zhang","raw_affiliation_strings":["Computer Science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069049743","display_name":"Jiarui Feng","orcid":"https://orcid.org/0000-0002-3409-6819","observed_orcids":["https://orcid.org/0000-0002-3409-6819"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiarui Feng","raw_affiliation_strings":["Data science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Data science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063777597","display_name":"Amanda Zeng","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda Zeng","raw_affiliation_strings":["Data science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Data science, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071367198","display_name":"Philip Payne","orcid":"https://orcid.org/0000-0002-9532-2998","observed_orcids":["https://orcid.org/0000-0002-9532-2998"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip Payne","raw_affiliation_strings":["Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100780432","display_name":"Fuhai Li","orcid":"https://orcid.org/0000-0002-3773-146X","observed_orcids":["https://orcid.org/0000-0002-3773-146X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fuhai Li","raw_affiliation_strings":["Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Institute for Informatics (I2), Washington University School of Medicine, Washington University in St. Louis, St. Louis, MO, USA","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100780432"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2020","issue":null,"first_page":"1364","last_page":"1372"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":9.999999747378752e-05,"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/T11948","display_name":"Machine Learning in Materials Science","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tumor-cell-response","display_name":"tumor cell response","score":0.6819999814033508},{"id":"https://openalex.org/keywords/cancer-pathways","display_name":"cancer pathways","score":0.9330000281333923},{"id":"https://openalex.org/keywords/multi-omics-integration","display_name":"multi-omics integration","score":0.7440000176429749},{"id":"https://openalex.org/keywords/drug-resistance","display_name":"drug resistance","score":0.7049999833106995},{"id":"https://openalex.org/keywords/explainable-deep-learning","display_name":"explainable deep learning","score":0.703000009059906},{"id":"https://openalex.org/keywords/drug-target-identification","display_name":"drug target identification","score":0.34700000286102295}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5862106084823608},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5386528372764587},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5131036043167114},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4893311858177185},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.4844215214252472},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48382654786109924},{"id":"https://openalex.org/C2994119904","wikidata":"https://www.wikidata.org/wiki/Q1251001","display_name":"Drug response","level":3,"score":0.42413222789764404},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4214397370815277},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4107440710067749},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3639528155326843},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26427197456359863},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24954456090927124},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.17649880051612854},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000971","descriptor_name":"Antineoplastic Combined Chemotherapy Protocols","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1101/2020.04.10.036491","doi":"https://doi.org/10.1101/2020.04.10.036491","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.10.036491","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.10.036491.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:8075535","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8075535","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,"listed_in":[],"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":"AMIA Annu Symp Proc","raw_type":"Text"},{"id":"pmid:33936513","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33936513","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,"listed_in":[],"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":"AMIA ... Annual Symposium proceedings. AMIA Symposium","raw_type":"Journal Article"},{"id":"mag:3159462434","doi":null,"is_oa":false,"landing_page_url":"https://europepmc.org/article/MED/33936513","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1101/2020.04.10.036491","doi":"https://doi.org/10.1101/2020.04.10.036491","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.04.10.036491","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/04/13/2020.04.10.036491.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.8337000012397766,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3016041832.pdf","grobid_xml":"https://content.openalex.org/works/W3016041832.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2043398720","https://openalex.org/W2103017472","https://openalex.org/W2121604817","https://openalex.org/W2143152083","https://openalex.org/W2146416540","https://openalex.org/W2159482845","https://openalex.org/W2294516783","https://openalex.org/W2299417213","https://openalex.org/W2473876819","https://openalex.org/W2608863179","https://openalex.org/W2612467560","https://openalex.org/W2764045916","https://openalex.org/W2767891136","https://openalex.org/W2770878219","https://openalex.org/W2775061087","https://openalex.org/W2796153225","https://openalex.org/W2883248903","https://openalex.org/W2886526762","https://openalex.org/W2920097475","https://openalex.org/W2920147611","https://openalex.org/W2951449549","https://openalex.org/W2973526013","https://openalex.org/W3086347240"],"related_works":["https://openalex.org/W3086347240","https://openalex.org/W3136745296","https://openalex.org/W4311505031","https://openalex.org/W4401793664","https://openalex.org/W4395689586","https://openalex.org/W3159412124","https://openalex.org/W2775061087","https://openalex.org/W3080700490","https://openalex.org/W4205719393","https://openalex.org/W4376114038"],"abstract_inverted_index":{"Abstract":[0],"Drug":[1],"combinations":[2],"targeting":[3],"multiple":[4],"targets/pathways":[5],"are":[6,17],"believed":[7],"to":[8,11,142],"be":[9,140],"able":[10],"reduce":[12],"drug":[13,21,38,80,100,108,146],"resistance.":[14],"Computational":[15],"models":[16,44],"essential":[18],"for":[19,37],"novel":[20,144],"combination":[22,39,101,109],"discovery.":[23],"In":[24],"this":[25],"study,":[26],"we":[27,59],"proposed":[28],"a":[29,47,64,83,112],"new":[30,136],"simplified":[31],"deep":[32],"learning":[33],"model,":[34],"DeepSignalingSynergy":[35],",":[36],"prediction.":[40],"Compared":[41],"with":[42],"existing":[43],"that":[45,134],"use":[46],"large":[48],"number":[49],"of":[50,67,76,93,107,115,125,127],"chemical-structure":[51],"and":[52,79,87],"genomics":[53],"features":[54],"in":[55,82],"densely":[56],"connected":[57],"layers,":[58],"built":[60],"the":[61,74,94,97,105,119,123,128],"model":[62,95,120],"on":[63],"small":[65,113],"set":[66,114],"cancer":[68],"signaling":[69,116,130,137],"pathways,":[70,131],"which":[71,132],"can":[72],"mimic":[73],"integration":[75],"multi-omics":[77],"data":[78,103],"target/mechanism":[81],"more":[84],"biological":[85],"meaningful":[86],"explainable":[88],"manner.":[89],"The":[90],"evaluation":[91],"results":[92],"using":[96,111],"NCI":[98],"ALMANAC":[99],"screening":[102],"indicated":[104],"feasibility":[106],"prediction":[110],"pathways.":[117],"Interestingly,":[118],"analysis":[121],"suggested":[122],"importance":[124],"heterogeneity":[126],"46":[129],"indicates":[133],"some":[135],"pathways":[138],"should":[139],"targeted":[141],"discover":[143],"synergistic":[145],"combinations.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-04-17T00:00:00"}