{"id":"https://openalex.org/W4390206253","doi":"https://doi.org/10.1093/bib/bbad475","title":"CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification","display_name":"CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4390206253","doi":"https://doi.org/10.1093/bib/bbad475","pmid":"https://pubmed.ncbi.nlm.nih.gov/38145950"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad475","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad475/54827420/bbad475.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad475/54827420/bbad475.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100642610","display_name":"Jin Liu","orcid":"https://orcid.org/0000-0002-4961-7074"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Liu","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108888951","display_name":"Weixing Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weixing Zeng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025341442","display_name":"Shichao Kan","orcid":"https://orcid.org/0000-0003-0097-6196"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shichao Kan","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044328870","display_name":"Ruiqing Zheng","orcid":"https://orcid.org/0000-0001-6372-6798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ruiqing Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044328870"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.068,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.87948359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9830999970436096,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9695000052452087,"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/cluster-analysis","display_name":"Cluster analysis","score":0.8387833833694458},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.748550295829773},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6828484535217285},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6595270037651062},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5290383696556091},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4673709273338318},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4408608675003052},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.43958455324172974},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4053153991699219},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10065868496894836}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8387833833694458},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.748550295829773},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6828484535217285},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6595270037651062},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5290383696556091},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4673709273338318},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4408608675003052},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43958455324172974},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4053153991699219},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10065868496894836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad475","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad475/54827420/bbad475.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38145950","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38145950","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10749894","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10749894","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10749894/pdf/bbad475.pdf","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,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad475","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad475","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad475/54827420/bbad475.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4000000059604645,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G7748339813","display_name":null,"funder_award_id":"2023JJ40780","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G827679422","display_name":null,"funder_award_id":"62202503","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8663586063","display_name":null,"funder_award_id":"62225209","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"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390206253.pdf"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1821462560","https://openalex.org/W2047860205","https://openalex.org/W2088252378","https://openalex.org/W2102212449","https://openalex.org/W2131681506","https://openalex.org/W2135978691","https://openalex.org/W2345356016","https://openalex.org/W2473258837","https://openalex.org/W2510746232","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2741943936","https://openalex.org/W2772052731","https://openalex.org/W2800392236","https://openalex.org/W2805410771","https://openalex.org/W2842511635","https://openalex.org/W2889326414","https://openalex.org/W2894687190","https://openalex.org/W2897249806","https://openalex.org/W2900387735","https://openalex.org/W2902647266","https://openalex.org/W2907783748","https://openalex.org/W2917551568","https://openalex.org/W2918882492","https://openalex.org/W2931036699","https://openalex.org/W2937917790","https://openalex.org/W2951381561","https://openalex.org/W2953251392","https://openalex.org/W2963469388","https://openalex.org/W3005680577","https://openalex.org/W3009302866","https://openalex.org/W3017924613","https://openalex.org/W3027758526","https://openalex.org/W3029148360","https://openalex.org/W3088401235","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W3121633709","https://openalex.org/W3138479716","https://openalex.org/W3156636935","https://openalex.org/W3157192658","https://openalex.org/W3163972593","https://openalex.org/W3164692211","https://openalex.org/W3165190053","https://openalex.org/W3216323060","https://openalex.org/W4205916264","https://openalex.org/W4225501139","https://openalex.org/W4229335045","https://openalex.org/W4236965008","https://openalex.org/W4288384188","https://openalex.org/W4295717668","https://openalex.org/W4307092192","https://openalex.org/W4311125341","https://openalex.org/W4386387831","https://openalex.org/W4386796019","https://openalex.org/W6742649196","https://openalex.org/W6750782655","https://openalex.org/W6770717842"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W2389214306","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W4235240664","https://openalex.org/W2965083567","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W1838576100","https://openalex.org/W2383687187"],"abstract_inverted_index":{"Single":[0],"cell":[1,11,21,81,102,132,136,169],"sequencing":[2,145],"technology":[3],"has":[4],"provided":[5],"unprecedented":[6],"opportunities":[7],"for":[8,80,89],"comprehensively":[9],"deciphering":[10],"heterogeneity.":[12],"Nevertheless,":[13],"the":[14,47,90,106,121,148,166],"high":[15],"dimensionality":[16],"and":[17,63,84,100,104,113,134,154,160],"intricate":[18],"nature":[19],"of":[20,43,70,92,111,150,168],"heterogeneity":[22,170],"have":[23,34],"presented":[24],"substantial":[25],"challenges":[26],"to":[27,37,118],"computational":[28],"methods.":[29],"Numerous":[30],"novel":[31,62],"clustering":[32,66,93,107,155],"methods":[33,45],"been":[35],"proposed":[36],"address":[38],"this":[39,56],"issue.":[40],"However,":[41],"none":[42],"these":[44],"achieve":[46],"consistently":[48],"better":[49],"performance":[50,108],"under":[51],"different":[52],"biological":[53],"scenarios.":[54],"In":[55],"study,":[57],"we":[58],"developed":[59],"CAKE,":[60],"a":[61,71,76,85],"scalable":[64],"self-supervised":[65],"method,":[67],"which":[68],"consists":[69],"contrastive":[72],"learning":[73],"model":[74,88],"with":[75],"mixture":[77],"neighborhood":[78],"augmentation":[79],"representation":[82],"learning,":[83],"self-Knowledge":[86],"Distiller":[87],"refinement":[91],"results.":[94],"These":[95],"designs":[96],"provide":[97],"more":[98,129],"condensed":[99],"cluster-friendly":[101],"representations":[103],"improve":[105],"in":[109,116,152,165],"term":[110],"accuracy":[112],"robustness.":[114],"Furthermore,":[115],"addition":[117],"accurately":[119],"identifying":[120],"major":[122],"type":[123],"cells,":[124],"CAKE":[125,151],"could":[126],"also":[127],"find":[128],"biologically":[130],"meaningful":[131],"subgroups":[133],"rare":[135],"types.":[137],"The":[138],"comprehensive":[139],"experiments":[140],"on":[141],"real":[142],"single-cell":[143],"RNA":[144],"datasets":[146],"demonstrated":[147],"superiority":[149],"visualization":[153],"over":[156],"other":[157],"comparison":[158],"methods,":[159],"indicated":[161],"its":[162],"extensive":[163],"application":[164],"field":[167],"analysis.":[171],"Contact:":[172],"Ruiqing":[173],"Zheng.":[174],"(rqzheng@csu.edu.cn).":[175]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
