{"id":"https://openalex.org/W4387251816","doi":"https://doi.org/10.1371/journal.pcbi.1011476","title":"XA4C: eXplainable representation learning via Autoencoders revealing Critical genes","display_name":"XA4C: eXplainable representation learning via Autoencoders revealing Critical genes","publication_year":2023,"publication_date":"2023-10-02","ids":{"openalex":"https://openalex.org/W4387251816","doi":"https://doi.org/10.1371/journal.pcbi.1011476","pmid":"https://pubmed.ncbi.nlm.nih.gov/37782668"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011476","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011476","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011476","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100404194","display_name":"Qing Li","orcid":"https://orcid.org/0009-0005-1327-4347"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Qing Li","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025770046","display_name":"Yang Yu","orcid":"https://orcid.org/0000-0003-2125-3229"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Yang Yu","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012401410","display_name":"Pathum Kossinna","orcid":"https://orcid.org/0000-0002-4621-2557"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Pathum Kossinna","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092985153","display_name":"Theodore Lun","orcid":null},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Theodore Lun","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027271308","display_name":"Wenyuan Liao","orcid":"https://orcid.org/0000-0002-6566-9341"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Wenyuan Liao","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072745510","display_name":"Qingrun Zhang","orcid":"https://orcid.org/0000-0003-2701-0711"},"institutions":[{"id":"https://openalex.org/I2802127220","display_name":"Alberta Children's Hospital","ror":"https://ror.org/00sx29x36","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2802127220"]},{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]},{"id":"https://openalex.org/I4210090991","display_name":"Institute of Cancer Research","ror":"https://ror.org/00dpztj76","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210090991"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Qingrun Zhang","raw_affiliation_strings":["Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada","Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada","Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada","Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I2802127220","https://openalex.org/I168635309"]},{"raw_affiliation_string":"Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I4210090991","https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5012401410","https://openalex.org/A5025770046","https://openalex.org/A5027271308","https://openalex.org/A5072745510","https://openalex.org/A5092985153","https://openalex.org/A5100404194"],"corresponding_institution_ids":["https://openalex.org/I168635309","https://openalex.org/I2802127220","https://openalex.org/I4210090991"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0114,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.86799802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"19","issue":"10","first_page":"e1011476","last_page":"e1011476"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9955999851226807,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9919000267982483,"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/representation","display_name":"Representation (politics)","score":0.6050862073898315},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5735195279121399},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5492579340934753},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49642688035964966},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43467432260513306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3191456198692322},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20732268691062927}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6050862073898315},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5735195279121399},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5492579340934753},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49642688035964966},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43467432260513306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3191456198692322},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20732268691062927},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011476","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011476","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37782668","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37782668","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10569512","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10569512","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10569512/pdf/pcbi.1011476.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ff21dbc9cb7c4b5db15a779be0d15d97","is_oa":true,"landing_page_url":"https://doaj.org/article/ff21dbc9cb7c4b5db15a779be0d15d97","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 10, p e1011476 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011476","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011476","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1005683155","display_name":null,"funder_award_id":"RTI-2021-00675","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G1304196372","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2417676328","display_name":null,"funder_award_id":"RGPIN-2018-0","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2980479518","display_name":null,"funder_award_id":"RGPIN-2018","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2998137668","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3216283581","display_name":null,"funder_award_id":"RGPIN-201","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3255232291","display_name":null,"funder_award_id":"RGPIN-2018-05147","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G400116904","display_name":null,"funder_award_id":"unknow","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6260179710","display_name":null,"funder_award_id":"JELF grant (36605)","funder_id":"https://openalex.org/F4320319952","funder_display_name":"Canada Foundation for Innovation"},{"id":"https://openalex.org/G6541501743","display_name":null,"funder_award_id":"NSERC, Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G717623787","display_name":null,"funder_award_id":"222300769","funder_id":"https://openalex.org/F4320325651","funder_display_name":"Alberta Innovates"},{"id":"https://openalex.org/G72083225","display_name":null,"funder_award_id":"VPR Catalyst grant","funder_id":"https://openalex.org/F4320310537","funder_display_name":"University of Calgary"},{"id":"https://openalex.org/G7471108959","display_name":null,"funder_award_id":"CRDPJ","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G7825491502","display_name":null,"funder_award_id":"CRD Grant","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320310537","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39"},{"id":"https://openalex.org/F4320319952","display_name":"Canada Foundation for Innovation","ror":"https://ror.org/000az4664"},{"id":"https://openalex.org/F4320325651","display_name":"Alberta Innovates","ror":null},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1537947034","https://openalex.org/W1923068721","https://openalex.org/W1966327575","https://openalex.org/W1986911601","https://openalex.org/W2034543587","https://openalex.org/W2064769568","https://openalex.org/W2095898243","https://openalex.org/W2101234009","https://openalex.org/W2109521384","https://openalex.org/W2119034410","https://openalex.org/W2126652700","https://openalex.org/W2128728535","https://openalex.org/W2144086069","https://openalex.org/W2158485828","https://openalex.org/W2166574880","https://openalex.org/W2179438025","https://openalex.org/W2295598076","https://openalex.org/W2418020448","https://openalex.org/W2561960501","https://openalex.org/W2618851150","https://openalex.org/W2620547470","https://openalex.org/W2791235391","https://openalex.org/W2797287022","https://openalex.org/W2809388839","https://openalex.org/W2884551085","https://openalex.org/W2891597765","https://openalex.org/W2945183595","https://openalex.org/W2946173685","https://openalex.org/W2951381561","https://openalex.org/W2962862931","https://openalex.org/W2967663220","https://openalex.org/W2970971581","https://openalex.org/W2980070874","https://openalex.org/W2995523160","https://openalex.org/W3006265958","https://openalex.org/W3016178978","https://openalex.org/W3081106993","https://openalex.org/W3083281037","https://openalex.org/W3092136373","https://openalex.org/W3097649106","https://openalex.org/W3130814454","https://openalex.org/W3164535579","https://openalex.org/W3195201018","https://openalex.org/W3196807348","https://openalex.org/W3200632075","https://openalex.org/W4210898159","https://openalex.org/W4226080084","https://openalex.org/W4295312788","https://openalex.org/W4295313945","https://openalex.org/W4301478443","https://openalex.org/W4318677254","https://openalex.org/W4365140800","https://openalex.org/W4366990879","https://openalex.org/W4385254289","https://openalex.org/W4399647672","https://openalex.org/W6631190155","https://openalex.org/W6632264627","https://openalex.org/W6675354045","https://openalex.org/W6722226382","https://openalex.org/W6810979106","https://openalex.org/W6869608176","https://openalex.org/W6910681941"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Machine":[0],"Learning":[1,12],"models":[2],"have":[3],"been":[4],"frequently":[5],"used":[6],"in":[7,18,22,32,50,111,137,178,206,235,247],"transcriptome":[8],"analyses.":[9],"Particularly,":[10],"Representation":[11],"(RL),":[13],"e.g.,":[14,28],"autoencoders,":[15],"are":[16,35,170],"effective":[17],"learning":[19],"critical":[20],"representations":[21,133],"noisy":[23],"data.":[24],"However,":[25,95],"learned":[26,132],"representations,":[27],"the":[29,70,77,89,96,236,268],"\"latent":[30],"variables\"":[31],"an":[33,105,138,227],"autoencoder,":[34],"difficult":[36],"to":[37,40,131,162,174,221],"interpret,":[38],"not":[39],"mention":[41],"prioritizing":[42],"essential":[43,186],"genes":[44,57,103,127,155,169,184,192,233,262],"for":[45,107,153],"functional":[46],"follow-up.":[47],"In":[48,252],"contrast,":[49],"traditional":[51],"analyses,":[52],"one":[53],"may":[54,74],"identify":[55],"important":[56],"such":[58],"as":[59,126],"Differentially":[60,63],"Expressed":[61],"(DiffEx),":[62],"Co-Expressed":[64],"(DiffCoEx),":[65],"and":[66,86,100,117,213,249,260],"Hub":[67,197],"genes.":[68],"Intuitively,":[69],"complex":[71,271],"gene-gene":[72],"interactions":[73],"be":[75],"beyond":[76],"capture":[78,185],"of":[79,91,98,238,270],"marginal":[80],"effects":[81],"(DiffEx)":[82],"or":[83,198],"correlations":[84],"(DiffCoEx":[85],"Hub),":[87],"indicating":[88],"need":[90],"powerful":[92],"RL":[93,259,266],"models.":[94],"lack":[97],"interpretability":[99],"individual":[101],"target":[102],"is":[104],"obstacle":[106],"RL's":[108],"broad":[109],"use":[110],"practice.":[112],"To":[113],"facilitate":[114],"interpretable":[115],"analysis":[116,257],"gene-identification":[118],"using":[119,258],"RL,":[120],"we":[121,149,229],"propose":[122],"\"Critical":[123],"genes\",":[124],"defined":[125],"that":[128,157,182],"contribute":[129],"highly":[130],"(e.g.,":[134],"latent":[135,163],"variables":[136],"autoencoder).":[139],"As":[140,226],"a":[141,203,207,214],"proof-of-concept,":[142],"supported":[143],"by":[144,264],"eXplainable":[145,151],"Artificial":[146],"Intelligence":[147],"(XAI),":[148],"implemented":[150],"Autoencoder":[152],"Critical":[154,168,183,191,232,261],"(XA4C)":[156],"quantifies":[158],"each":[159],"gene's":[160],"contribution":[161],"variables,":[164],"based":[165],"on":[166],"which":[167],"prioritized.":[171],"Applying":[172],"XA4C":[173,254],"gene":[175,210],"expression":[176],"data":[177],"six":[179],"cancers":[180],"showed":[181],"pathways":[187],"underlying":[188],"cancers.":[189],"Remarkably,":[190],"has":[193,202],"little":[194],"overlap":[195],"with":[196],"DiffEx":[199],"genes,":[200],"however,":[201],"higher":[204],"enrichment":[205],"comprehensive":[208],"disease":[209],"database":[211,216],"(DisGeNET)":[212],"cancer-specific":[215],"(COSMIC),":[217],"evidencing":[218],"its":[219],"potential":[220],"disclose":[222],"massive":[223],"unknown":[224],"biology.":[225],"example,":[228],"discovered":[230,263],"five":[231],"sitting":[234],"center":[237],"Lysine":[239],"degradation":[240],"(hsa00310)":[241],"pathway,":[242],"displaying":[243],"distinct":[244],"interaction":[245],"patterns":[246],"tumor":[248],"normal":[250],"tissues.":[251],"conclusion,":[253],"facilitates":[255],"explainable":[256,265],"empowers":[267],"study":[269],"interactions.":[272]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
