{"id":"https://openalex.org/W4386304973","doi":"https://doi.org/10.1093/bib/bbad318","title":"InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data","display_name":"InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data","publication_year":2023,"publication_date":"2023-08-30","ids":{"openalex":"https://openalex.org/W4386304973","doi":"https://doi.org/10.1093/bib/bbad318","pmid":"https://pubmed.ncbi.nlm.nih.gov/37649392"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad318","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad318/51711768/bbad318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad318/51711768/bbad318.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022550580","display_name":"Hai Yang","orcid":"https://orcid.org/0000-0002-1161-4337"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hai Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China"],"raw_orcid":"https://orcid.org/0000-0002-1161-4337","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074247371","display_name":"Yawen Liu","orcid":"https://orcid.org/0000-0001-8165-6850"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yawen Liu","raw_affiliation_strings":["Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China"],"raw_orcid":"https://orcid.org/0000-0001-8165-6850","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060735481","display_name":"Yijing Yang","orcid":"https://orcid.org/0000-0003-4197-2570"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yijing Yang","raw_affiliation_strings":["Department of Computer Science, University of Illinois Urbana-Champaign , Champaign, Illinois , United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois Urbana-Champaign , Champaign, Illinois , United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100358079","display_name":"Dongdong Li","orcid":"https://orcid.org/0000-0002-1880-8054"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongdong Li","raw_affiliation_strings":["Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100621319","display_name":"Zhe Wang","orcid":"https://orcid.org/0000-0002-3759-2041"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhe Wang","raw_affiliation_strings":["Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China"],"raw_orcid":"https://orcid.org/0000-0002-3759-2041","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, East China University of Science and Technology , 200237, Shanghai , PR China","institution_ids":["https://openalex.org/I143593769"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100621319"],"corresponding_institution_ids":["https://openalex.org/I143593769"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.7268,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.72424432,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"24","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9976000189781189,"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":0.5509978532791138},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5420045256614685},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45703378319740295},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4387821555137634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4238031208515167},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4233379065990448},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35639023780822754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2278110682964325},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12819957733154297}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5509978532791138},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5420045256614685},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45703378319740295},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4387821555137634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4238031208515167},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4233379065990448},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35639023780822754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2278110682964325},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12819957733154297},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad318","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad318/51711768/bbad318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37649392","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37649392","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad318","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad318/51711768/bbad318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7249534290","display_name":null,"funder_award_id":"61902126","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386304973.pdf","grobid_xml":"https://content.openalex.org/works/W4386304973.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W953912505","https://openalex.org/W1867948347","https://openalex.org/W1966135244","https://openalex.org/W2002218976","https://openalex.org/W2018023891","https://openalex.org/W2022716620","https://openalex.org/W2025183726","https://openalex.org/W2034777892","https://openalex.org/W2040827479","https://openalex.org/W2044433401","https://openalex.org/W2059300459","https://openalex.org/W2070841378","https://openalex.org/W2071758665","https://openalex.org/W2075053675","https://openalex.org/W2097113581","https://openalex.org/W2103744931","https://openalex.org/W2114031931","https://openalex.org/W2119188775","https://openalex.org/W2121906867","https://openalex.org/W2124789022","https://openalex.org/W2139236349","https://openalex.org/W2159828795","https://openalex.org/W2160995259","https://openalex.org/W2168303063","https://openalex.org/W2318691537","https://openalex.org/W2344185956","https://openalex.org/W2436745791","https://openalex.org/W2442835468","https://openalex.org/W2470068589","https://openalex.org/W2528491735","https://openalex.org/W2532527181","https://openalex.org/W2557187647","https://openalex.org/W2592340788","https://openalex.org/W2740810575","https://openalex.org/W2750245257","https://openalex.org/W2765694924","https://openalex.org/W2771752959","https://openalex.org/W2772435237","https://openalex.org/W2796408191","https://openalex.org/W2890896123","https://openalex.org/W2906754611","https://openalex.org/W2912083425","https://openalex.org/W2914874661","https://openalex.org/W2915168078","https://openalex.org/W2946235775","https://openalex.org/W2958066336","https://openalex.org/W2986992501","https://openalex.org/W3004787903","https://openalex.org/W3039110853","https://openalex.org/W3042684909","https://openalex.org/W3047825284","https://openalex.org/W3102612616","https://openalex.org/W3128646645","https://openalex.org/W3156270925","https://openalex.org/W3164535579","https://openalex.org/W3195201018","https://openalex.org/W3206417123","https://openalex.org/W3209435229","https://openalex.org/W4205812412","https://openalex.org/W4210917993","https://openalex.org/W4301409532","https://openalex.org/W4306918625","https://openalex.org/W6726258750","https://openalex.org/W6734397981","https://openalex.org/W6737947904","https://openalex.org/W6770282681"],"related_works":["https://openalex.org/W2186113122","https://openalex.org/W1523310174","https://openalex.org/W2531913951","https://openalex.org/W2961085424","https://openalex.org/W4302381976","https://openalex.org/W4243634448","https://openalex.org/W4224009465","https://openalex.org/W2979752698","https://openalex.org/W4306674287","https://openalex.org/W4286629047"],"abstract_inverted_index":{"Cancer":[0],"driver":[1,36,110,123,132,138,160,171,198,206,235],"genes":[2,14,37,111,130,133,194,207,236],"are":[3,48],"critical":[4],"in":[5,17],"driving":[6],"tumor":[7],"cell":[8],"growth,":[9],"and":[10,24,51,91,116,134,156,215,237],"precisely":[11],"identifying":[12,170,233],"these":[13],"is":[15,53,80],"crucial":[16],"advancing":[18],"our":[19],"understanding":[20],"of":[21,108,246],"cancer":[22,27,35,137,225,234,241,248],"pathogenesis":[23],"developing":[25],"targeted":[26,247],"drugs.":[28,249],"Despite":[29],"the":[30,57,114,136,153,165,180,183,190,244],"current":[31],"methods":[32],"for":[33,168,212,232],"discovering":[34,216],"that":[38,95,128,186],"mainly":[39],"rely":[40],"on":[41,76,88,152],"integrating":[42],"multi-omics":[43,101],"data,":[44,102],"many":[45],"existing":[46],"models":[47],"overly":[49],"complex,":[50],"it":[52],"difficult":[54],"to":[55,63,148,202,240],"interpret":[56],"results":[58],"accurately.":[59],"This":[60,220],"study":[61],"aims":[62],"address":[64],"this":[65],"issue":[66],"by":[67,227],"introducing":[68],"InDEP,":[69],"an":[70,229],"interpretable":[71,230],"machine":[72],"learning":[73],"framework":[74,120,184,221],"based":[75,87],"cascade":[77,85],"forests.":[78],"InDEP":[79,103,146],"designed":[81],"with":[82,143,173],"easy-to-interpret":[83],"features,":[84],"forests":[86],"decision":[89],"trees":[90],"a":[92],"KernelSHAP":[93],"module":[94],"enables":[96],"fine-grained":[97],"post-hoc":[98],"interpretation.":[99],"Integrating":[100],"can":[104,222],"identify":[105,203],"essential":[106],"features":[107,163,176],"classified":[109],"at":[112],"both":[113],"gene":[115,139,181],"cancer-type":[117],"levels.":[118],"The":[119],"accurately":[121],"identifies":[122],"genes,":[124,172],"discovers":[125],"new":[126,210,217],"patterns":[127],"make":[129],"as":[131,197],"refines":[135],"catalog.":[140],"In":[141],"comparison":[142],"state-of-the-art":[144],"methods,":[145],"proved":[147],"be":[149],"more":[150],"accurate":[151],"test":[154],"set":[155],"identified":[157,196],"reliable":[158,204],"candidate":[159,205],"genes.":[161,199],"Mutational":[162],"were":[164,189,195],"primary":[166],"drivers":[167],"InDEP's":[169,200],"other":[174],"omics":[175],"also":[177],"contributing.":[178],"At":[179],"level,":[182],"concluded":[185],"substitution-type":[187],"mutations":[188],"main":[191],"reason":[192],"most":[193],"ability":[201],"opens":[208],"up":[209],"avenues":[211],"precision":[213],"oncology":[214],"biomedical":[218],"knowledge.":[219],"help":[223],"advance":[224],"research":[226],"providing":[228],"method":[231],"their":[238],"contribution":[239],"pathogenesis,":[242],"facilitating":[243],"development":[245]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
