{"id":"https://openalex.org/W4315621823","doi":"https://doi.org/10.1093/bib/bbac625","title":"scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network","display_name":"scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4315621823","doi":"https://doi.org/10.1093/bib/bbac625","pmid":"https://pubmed.ncbi.nlm.nih.gov/36631401"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac625","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac625","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084369069","display_name":"Jing Wang","orcid":"https://orcid.org/0000-0002-1345-1092"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Wang","raw_affiliation_strings":["Anhui University Anhui Provincial Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, , Hefei, China"],"affiliations":[{"raw_affiliation_string":"Anhui University Anhui Provincial Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, , Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I2802624667","display_name":"Hefei Institutes of Physical Science","ror":"https://ror.org/046n57345","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802624667"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Anhui University Institutes of Physical Science and Information Technology, , Hefei, China"],"affiliations":[{"raw_affiliation_string":"Anhui University Institutes of Physical Science and Information Technology, , Hefei, China","institution_ids":["https://openalex.org/I2802624667","https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100601478","display_name":"Haiyun Wang","orcid":"https://orcid.org/0000-0002-4726-7349"},"institutions":[{"id":"https://openalex.org/I96908189","display_name":"Xinjiang University","ror":"https://ror.org/059gw8r13","country_code":"CN","type":"education","lineage":["https://openalex.org/I96908189"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haiyun Wang","raw_affiliation_strings":["School of Mathematics and Systems Science , Xinjiang University, Urumqi, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Systems Science , Xinjiang University, Urumqi, China","institution_ids":["https://openalex.org/I96908189"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071754273","display_name":"Yansen Su","orcid":"https://orcid.org/0000-0002-3855-7133"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yansen Su","raw_affiliation_strings":["Anhui University School of Artificial Intelligence, , Hefei, China"],"affiliations":[{"raw_affiliation_string":"Anhui University School of Artificial Intelligence, , Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064185915","display_name":"Chun-Hou Zheng","orcid":"https://orcid.org/0000-0002-2695-1926"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["Anhui University School of Artificial Intelligence, , Hefei, China"],"affiliations":[{"raw_affiliation_string":"Anhui University School of Artificial Intelligence, , Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5064185915","https://openalex.org/A5071754273"],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":9.186,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.98483871,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9921000003814697,"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":0.9850999712944031,"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":0.8062028884887695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7670844793319702},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6500866413116455},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6089815497398376},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5444504022598267},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5358039140701294},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.5140093564987183},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4643891751766205},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42796140909194946},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4154955744743347},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4123968183994293},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.384723424911499}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8062028884887695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7670844793319702},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6500866413116455},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6089815497398376},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5444504022598267},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5358039140701294},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.5140093564987183},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4643891751766205},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42796140909194946},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4154955744743347},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4123968183994293},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.384723424911499},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac625","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac625","pdf_url":null,"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:36631401","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36631401","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":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.7300000190734863,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G247010507","display_name":null,"funder_award_id":"61873001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3925882961","display_name":null,"funder_award_id":"62072003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5006237592","display_name":null,"funder_award_id":"U19A2064","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":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W6908809","https://openalex.org/W1552434751","https://openalex.org/W1580018887","https://openalex.org/W1979283544","https://openalex.org/W1981641790","https://openalex.org/W2025768430","https://openalex.org/W2066617774","https://openalex.org/W2069089843","https://openalex.org/W2101234009","https://openalex.org/W2135937351","https://openalex.org/W2306630387","https://openalex.org/W2520619240","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2601723752","https://openalex.org/W2605810679","https://openalex.org/W2626990934","https://openalex.org/W2736547131","https://openalex.org/W2743416243","https://openalex.org/W2761069142","https://openalex.org/W2766959028","https://openalex.org/W2769933977","https://openalex.org/W2788348358","https://openalex.org/W2794858133","https://openalex.org/W2800392236","https://openalex.org/W2807884764","https://openalex.org/W2887886950","https://openalex.org/W2894687190","https://openalex.org/W2902652978","https://openalex.org/W2908510526","https://openalex.org/W2936414047","https://openalex.org/W2937917790","https://openalex.org/W2949787092","https://openalex.org/W2951381561","https://openalex.org/W2953251392","https://openalex.org/W2963074118","https://openalex.org/W3003444384","https://openalex.org/W3029148360","https://openalex.org/W3087124270","https://openalex.org/W3113251307","https://openalex.org/W3127011314","https://openalex.org/W3130814454","https://openalex.org/W3138479716","https://openalex.org/W3163972593","https://openalex.org/W3216323060","https://openalex.org/W4205281625","https://openalex.org/W4206023053","https://openalex.org/W4206581595","https://openalex.org/W4226097900","https://openalex.org/W4235169531","https://openalex.org/W4249346235","https://openalex.org/W4309098239","https://openalex.org/W6600284362","https://openalex.org/W6675354045","https://openalex.org/W6682250724","https://openalex.org/W6769832198","https://openalex.org/W6782959951","https://openalex.org/W6792121546"],"related_works":["https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4310873165","https://openalex.org/W4392946183","https://openalex.org/W2355395139","https://openalex.org/W3088732000","https://openalex.org/W4285596704","https://openalex.org/W2983142544","https://openalex.org/W2891059443","https://openalex.org/W4281663961"],"abstract_inverted_index":{"The":[0,243],"advances":[1],"in":[2,25,200,217],"single-cell":[3],"ribonucleic":[4],"acid":[5],"sequencing":[6],"(scRNA-seq)":[7],"allow":[8],"researchers":[9],"to":[10,59,106,115,132,144],"explore":[11,61],"cellular":[12],"heterogeneity":[13],"and":[14,39,67,95,110,118,158,170,181,197,223,227,236],"human":[15],"diseases":[16],"at":[17,166,247],"cell":[18,32,112,184,198],"resolution.":[19],"Cell":[20,225],"clustering":[21,77,86,104,199,235],"is":[22,245],"a":[23,48,82,92,96,102,125,139],"prerequisite":[24],"scRNA-seq":[26,43,241],"analysis":[27,229,239],"since":[28],"it":[29,47],"can":[30],"recognize":[31],"identities.":[33],"However,":[34],"the":[35,62,68,75,146,153,159,164,168,171,175],"high":[36],"dimensionality,":[37],"noises":[38],"significant":[40],"sparsity":[41],"of":[42,65,149,206,219],"data":[44,120],"have":[45,54],"made":[46],"big":[49],"challenge.":[50],"Although":[51],"many":[52],"methods":[53,216],"emerged,":[55],"they":[56],"still":[57],"fail":[58],"fully":[60],"intrinsic":[63],"properties":[64],"cells":[66],"relationship":[69],"among":[70],"cells,":[71],"which":[72,193],"seriously":[73],"affects":[74],"downstream":[76,238],"performance.":[78],"Here,":[79],"we":[80],"propose":[81],"new":[83],"deep":[84,103],"contrastive":[85,98,141],"algorithm":[87],"called":[88],"scDCCA.":[89],"It":[90],"integrates":[91],"denoising":[93,126],"auto-encoder":[94,131],"dual":[97,140],"learning":[99,142,190,196],"module":[100,143],"into":[101],"framework":[105],"extract":[107,133],"valuable":[108],"features":[109,180],"realize":[111],"clustering.":[113],"Specifically,":[114],"better":[116,183],"characterize":[117],"learn":[119,177],"representations":[121],"robustly,":[122],"scDCCA":[123,137,187,212,232],"utilizes":[124],"Zero-Inflated":[127],"Negative":[128],"Binomial":[129],"model-based":[130],"low-dimensional":[134],"features.":[135],"Meanwhile,":[136],"incorporates":[138],"capture":[145],"pairwise":[147],"proximity":[148],"cells.":[150],"By":[151],"increasing":[152],"similarities":[154],"between":[155,161],"positive":[156],"pairs":[157],"differences":[160],"negative":[162],"ones,":[163],"contrasts":[165],"both":[167],"instance":[169],"cluster":[172],"level":[173],"help":[174],"model":[176],"more":[178],"discriminative":[179],"achieve":[182],"segregation.":[185],"Furthermore,":[186],"joins":[188],"feature":[189],"with":[191],"clustering,":[192],"realizes":[194],"representation":[195],"an":[201],"end-to-end":[202],"manner.":[203],"Experimental":[204],"results":[205],"14":[207],"real":[208],"datasets":[209],"validate":[210],"that":[211,231],"outperforms":[213],"eight":[214],"state-of-the-art":[215],"terms":[218],"accuracy,":[220],"generalizability,":[221],"scalability":[222],"efficiency.":[224],"visualization":[226],"biological":[228],"demonstrate":[230],"significantly":[233],"improves":[234],"facilitates":[237],"for":[240],"data.":[242],"code":[244],"available":[246],"https://github.com/WJ319/scDCCA.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":26},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":9}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}