{"id":"https://openalex.org/W4285077493","doi":"https://doi.org/10.1109/tcbb.2022.3190266","title":"Explaining Black Box Drug Target Prediction Through Model Agnostic Counterfactual Samples","display_name":"Explaining Black Box Drug Target Prediction Through Model Agnostic Counterfactual Samples","publication_year":2022,"publication_date":"2022-07-12","ids":{"openalex":"https://openalex.org/W4285077493","doi":"https://doi.org/10.1109/tcbb.2022.3190266","pmid":"https://pubmed.ncbi.nlm.nih.gov/35820003"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3190266","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3190266","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":true,"oa_status":"green","oa_url":"https://figshare.com/articles/journal_contribution/Explaining_Black_Box_Drug_Target_Prediction_through_Model_Agnostic_Counterfactual_Samples/20582802","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100764745","display_name":"Tri Minh Nguyen","orcid":"https://orcid.org/0000-0002-9045-8589"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Tri Minh Nguyen","raw_affiliation_strings":["Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-9045-8589","affiliations":[{"raw_affiliation_string":"Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040230589","display_name":"Thomas P. Quinn","orcid":"https://orcid.org/0000-0003-3163-579X"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas P Quinn","raw_affiliation_strings":["Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100705489","display_name":"Thin Nguyen","orcid":"https://orcid.org/0000-0003-3467-8963"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thin Nguyen","raw_affiliation_strings":["Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0003-3467-8963","affiliations":[{"raw_affiliation_string":"Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia","institution_ids":["https://openalex.org/I149704539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085471517","display_name":"Truyen Tran","orcid":"https://orcid.org/0000-0001-6531-8907"},"institutions":[{"id":"https://openalex.org/I149704539","display_name":"Deakin University","ror":"https://ror.org/02czsnj07","country_code":"AU","type":"education","lineage":["https://openalex.org/I149704539"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Truyen Tran","raw_affiliation_strings":["Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0001-6531-8907","affiliations":[{"raw_affiliation_string":"Applied Artificial Intelligence Institute, Deakin University, Victoria, Australia","institution_ids":["https://openalex.org/I149704539"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100764745"],"corresponding_institution_ids":["https://openalex.org/I149704539"],"apc_list":null,"apc_paid":null,"fwci":1.6593,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.85703378,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"2","first_page":"1020","last_page":"1029"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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":0.9987999796867371,"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/T12026","display_name":"Explainable Artificial Intelligence (XAI)","score":0.9452999830245972,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9323999881744385,"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/counterfactual-thinking","display_name":"Counterfactual thinking","score":0.8970744609832764},{"id":"https://openalex.org/keywords/black-box","display_name":"Black box","score":0.5201588273048401},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.47882893681526184},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44188985228538513},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.31916284561157227},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.28944820165634155},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.20546630024909973},{"id":"https://openalex.org/keywords/social-psychology","display_name":"Social psychology","score":0.10564860701560974}],"concepts":[{"id":"https://openalex.org/C108650721","wikidata":"https://www.wikidata.org/wiki/Q1783253","display_name":"Counterfactual thinking","level":2,"score":0.8970744609832764},{"id":"https://openalex.org/C94966114","wikidata":"https://www.wikidata.org/wiki/Q29256","display_name":"Black box","level":2,"score":0.5201588273048401},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.47882893681526184},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44188985228538513},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31916284561157227},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28944820165634155},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.20546630024909973},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.10564860701560974}],"mesh":[{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2022.3190266","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3190266","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:35820003","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35820003","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:figshare.com:article/20582802","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Explaining_Black_Box_Drug_Target_Prediction_through_Model_Agnostic_Counterfactual_Samples/20582802","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/20582802","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Explaining_Black_Box_Drug_Target_Prediction_through_Model_Agnostic_Counterfactual_Samples/20582802","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.47999998927116394,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1542941925","https://openalex.org/W1641379095","https://openalex.org/W1976499671","https://openalex.org/W1993046136","https://openalex.org/W2082261506","https://openalex.org/W2086286404","https://openalex.org/W2092285329","https://openalex.org/W2099196192","https://openalex.org/W2116494521","https://openalex.org/W2171234651","https://openalex.org/W2198606573","https://openalex.org/W2259538443","https://openalex.org/W2332488709","https://openalex.org/W2486285194","https://openalex.org/W2562979205","https://openalex.org/W2740517540","https://openalex.org/W2785720803","https://openalex.org/W2785947426","https://openalex.org/W2895744665","https://openalex.org/W2911871527","https://openalex.org/W2913103105","https://openalex.org/W2945295328","https://openalex.org/W2946617578","https://openalex.org/W2962764565","https://openalex.org/W2962858109","https://openalex.org/W2963125461","https://openalex.org/W2972317931","https://openalex.org/W2973049920","https://openalex.org/W2977595407","https://openalex.org/W2978484973","https://openalex.org/W2979481854","https://openalex.org/W2989848927","https://openalex.org/W3005769002","https://openalex.org/W3016419862","https://openalex.org/W3032123378","https://openalex.org/W3088102389","https://openalex.org/W3092732263","https://openalex.org/W3096561213","https://openalex.org/W3099768690","https://openalex.org/W3104149808","https://openalex.org/W3104956673","https://openalex.org/W3175786839","https://openalex.org/W4211131469","https://openalex.org/W4214717370","https://openalex.org/W4285416263","https://openalex.org/W4297733535","https://openalex.org/W6674876905","https://openalex.org/W6677254318","https://openalex.org/W6730559633","https://openalex.org/W6739901393","https://openalex.org/W6747978776","https://openalex.org/W6748744355","https://openalex.org/W6754681716","https://openalex.org/W6755069753","https://openalex.org/W6755374895","https://openalex.org/W6758881193","https://openalex.org/W6761184903","https://openalex.org/W6767288045","https://openalex.org/W6785783176"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3201448254","https://openalex.org/W4286970243","https://openalex.org/W2066431708","https://openalex.org/W3025615835","https://openalex.org/W4384133558","https://openalex.org/W173210993","https://openalex.org/W2390660599","https://openalex.org/W3003410553","https://openalex.org/W3028847759"],"abstract_inverted_index":{"Many":[0],"high-performance":[1],"DTA":[2,24,168],"deep":[3,49],"learning":[4,78],"models":[5,25],"have":[6],"been":[7],"proposed,":[8],"but":[9],"they":[10],"are":[11],"mostly":[12],"black-box":[13],"and":[14,28,107,125,128,156],"thus":[15],"lack":[16],"human":[17],"interpretability.":[18],"Explainable":[19],"AI":[20],"(XAI)":[21],"can":[22,162],"make":[23],"more":[26,134],"trustworthy,":[27],"allows":[29],"to":[30,43,86,158],"distill":[31],"biological":[32],"knowledge":[33],"from":[34],"the":[35,45,57,61,66,91,104,113,118,123,164,171],"models.":[36],"Counterfactual":[37,81],"explanation":[38,141],"is":[39],"one":[40],"popular":[41],"approach":[42],"explaining":[44],"behaviour":[46,165],"of":[47,166],"a":[48,75,151,167],"neural":[50],"network,":[51],"which":[52],"works":[53],"by":[54,145],"systematically":[55],"answering":[56],"question":[58],"\"How":[59],"would":[60],"model":[62,169],"output":[63],"change":[64],"if":[65],"inputs":[67,176],"were":[68],"changed":[69],"in":[70,140,170,177],"this":[71],"way?\".":[72],"We":[73,116,148],"propose":[74],"multi-agent":[76],"reinforcement":[77],"framework,":[79],"Multi-Agent":[80],"Drug-target":[82],"binding":[83],"Affinity":[84],"(MACDA),":[85],"generate":[87],"counterfactual":[88,99,110],"explanations":[89,136],"for":[90,109],"drug-protein":[92],"complex.":[93],"Our":[94],"proposed":[95,119],"framework":[96,121,132],"provides":[97],"human-interpretable":[98],"instances":[100],"while":[101],"optimizing":[102],"both":[103],"input":[105],"drug":[106],"target":[108],"generation":[111],"at":[112],"same":[114],"time.":[115],"benchmark":[117],"MACDA":[120,161],"using":[122],"Davis":[124],"PDBBind":[126],"dataset":[127],"find":[129],"that":[130,182],"our":[131],"produces":[133],"parsimonious":[135],"with":[137,184],"no":[138],"loss":[139],"validity,":[142],"as":[143],"measured":[144],"encoding":[146],"similarity.":[147],"then":[149],"present":[150],"case":[152],"study":[153],"involving":[154],"ABL1":[155],"Nilotinib":[157],"demonstrate":[159],"how":[160],"explain":[163],"underlying":[172],"substructure":[173],"interaction":[174],"between":[175],"its":[178],"prediction,":[179],"revealing":[180],"mechanisms":[181],"align":[183],"prior":[185],"domain":[186],"knowledge.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
