{"id":"https://openalex.org/W4318479578","doi":"https://doi.org/10.1093/bib/bbad021","title":"Denoising adaptive deep clustering with self-attention mechanism on single-cell sequencing data","display_name":"Denoising adaptive deep clustering with self-attention mechanism on single-cell sequencing data","publication_year":2023,"publication_date":"2023-01-28","ids":{"openalex":"https://openalex.org/W4318479578","doi":"https://doi.org/10.1093/bib/bbad021","pmid":"https://pubmed.ncbi.nlm.nih.gov/36715275"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad021","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad021","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/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":false,"raw_author_name":"Yansen Su","raw_affiliation_strings":["Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , Hefei, 230601 , China"],"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , Hefei, 230601 , China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081649203","display_name":"Rongxin Lin","orcid":null},"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":"Rongxin Lin","raw_affiliation_strings":["School of Computer Science and Technology, Anhui University , Hefei, 230601 , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Anhui University , Hefei, 230601 , China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100378443","display_name":"Jing Wang","orcid":"https://orcid.org/0000-0002-1025-5707"},"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":["School of Computer Science and Technology, Anhui University , Hefei, 230601 , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Anhui University , Hefei, 230601 , China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055373332","display_name":"Dayu Tan","orcid":"https://orcid.org/0000-0002-3960-8852"},"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":true,"raw_author_name":"Dayu Tan","raw_affiliation_strings":["Institutes of Physical Science and Information Technology, Anhui University , Hefei, 230601 , China"],"affiliations":[{"raw_affiliation_string":"Institutes of Physical Science and Information Technology, Anhui University , Hefei, 230601 , China","institution_ids":["https://openalex.org/I2802624667","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":"Chunhou Zheng","raw_affiliation_strings":["Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , Hefei, 230601 , China"],"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , Hefei, 230601 , China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5055373332","https://openalex.org/A5064185915"],"corresponding_institution_ids":["https://openalex.org/I143868143","https://openalex.org/I2802624667"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.754,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.83987327,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"2","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":0.9904000163078308,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9307000041007996,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7231870889663696},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6715776324272156},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5995350480079651},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5988220572471619},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.4998908042907715},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40917423367500305},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39860624074935913}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7231870889663696},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6715776324272156},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5995350480079651},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5988220572471619},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.4998908042907715},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40917423367500305},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39860624074935913},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"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":"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":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad021","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad021","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:36715275","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36715275","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":[{"score":0.5,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1701155033","display_name":null,"funder_award_id":"61890930-3","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2362273132","display_name":null,"funder_award_id":"62173145","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"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/G3303591644","display_name":null,"funder_award_id":"2008085QF294","funder_id":"https://openalex.org/F4320334897","funder_display_name":"Natural Science Foundation of Anhui Province"},{"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"},{"id":"https://openalex.org/G7843069097","display_name":null,"funder_award_id":"62173144","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8625284979","display_name":null,"funder_award_id":"2021YFE0102100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320334897","display_name":"Natural Science Foundation of Anhui Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1813068103","https://openalex.org/W1880262756","https://openalex.org/W1987971958","https://openalex.org/W2025768430","https://openalex.org/W2033403400","https://openalex.org/W2069089843","https://openalex.org/W2089468765","https://openalex.org/W2089497633","https://openalex.org/W2109890799","https://openalex.org/W2123649031","https://openalex.org/W2131681506","https://openalex.org/W2140405352","https://openalex.org/W2473258837","https://openalex.org/W2519794569","https://openalex.org/W2522945402","https://openalex.org/W2526262591","https://openalex.org/W2551194178","https://openalex.org/W2598326928","https://openalex.org/W2779692282","https://openalex.org/W2783644856","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2885673883","https://openalex.org/W2902652978","https://openalex.org/W2919115771","https://openalex.org/W2937917790","https://openalex.org/W2949177718","https://openalex.org/W2951381561","https://openalex.org/W2953251392","https://openalex.org/W2955621471","https://openalex.org/W2964015378","https://openalex.org/W2972625781","https://openalex.org/W2977618190","https://openalex.org/W3003444384","https://openalex.org/W3005127469","https://openalex.org/W3008563687","https://openalex.org/W3009302866","https://openalex.org/W3099768174","https://openalex.org/W3113251307","https://openalex.org/W3127011314","https://openalex.org/W3173371682","https://openalex.org/W3202332579","https://openalex.org/W4213270761","https://openalex.org/W4385245566","https://openalex.org/W6639619044","https://openalex.org/W6726873649","https://openalex.org/W6739901393","https://openalex.org/W6747233776","https://openalex.org/W6782783850"],"related_works":["https://openalex.org/W2382997850","https://openalex.org/W2390968135","https://openalex.org/W2382213751","https://openalex.org/W2351750670","https://openalex.org/W1597848696","https://openalex.org/W2354715126","https://openalex.org/W4298130764","https://openalex.org/W2388563748","https://openalex.org/W2375179084","https://openalex.org/W2366646518"],"abstract_inverted_index":{"A":[0],"large":[1],"number":[2],"of":[3,19,36,49,60,110,170],"works":[4],"have":[5,52],"presented":[6],"the":[7,14,22,40,57,74,81,85,94,106,132,138,150,154],"single-cell":[8,23],"RNA":[9],"sequencing":[10],"(scRNA-seq)":[11],"to":[12,56,88,104,130,148],"study":[13],"diversity":[15],"and":[16,45,77,97,174],"biological":[17],"functions":[18],"cells":[20],"at":[21,197],"level.":[24],"Clustering":[25],"identifies":[26],"unknown":[27],"cell":[28,90,139],"types,":[29],"which":[30],"is":[31,126,178],"essential":[32],"for":[33,114,123,186],"downstream":[34],"analysis":[35,59],"scRNA-seq":[37,50,61,161,187],"samples.":[38,62],"However,":[39],"high":[41,43],"dimensionality,":[42],"noise":[44],"pervasive":[46],"dropout":[47],"rate":[48],"samples":[51,188],"a":[53,66,99,111,143],"significant":[54],"challenge":[55],"cluster":[58],"Herein,":[63],"we":[64,141],"propose":[65],"new":[67,144],"adaptive":[68,119,145],"fuzzy":[69],"clustering":[70,95,120,125,155,171,181],"model":[71,182,192],"based":[72],"on":[73,158],"denoising":[75,101,116,151],"autoencoder":[76],"self-attention":[78,112],"mechanism":[79,113,147],"called":[80],"scDASFK.":[82],"It":[83],"implements":[84],"comparative":[86],"learning":[87],"integrate":[89],"similar":[91],"information":[92],"into":[93],"method":[96],"uses":[98],"deep":[100],"network":[102],"module":[103],"denoise":[105],"data.":[107],"scDASFK":[108,165,177,191],"consists":[109],"further":[115],"where":[117],"an":[118,179],"optimization":[121],"function":[122],"iterative":[124],"implemented.":[127],"In":[128],"order":[129],"make":[131],"denoised":[133],"latent":[134],"features":[135],"better":[136],"reflect":[137],"structure,":[140],"introduce":[142],"feedback":[146],"supervise":[149],"process":[152],"through":[153],"results.":[156],"Experiments":[157],"16":[159],"real":[160],"datasets":[162],"show":[163],"that":[164],"performs":[166],"well":[167],"in":[168],"terms":[169],"accuracy,":[172],"scalability":[173],"stability.":[175],"Overall,":[176],"effective":[180],"with":[183],"great":[184],"potential":[185],"analysis.":[189],"Our":[190],"codes":[193],"are":[194],"freely":[195],"available":[196],"https://github.com/LRX2022/scDASFK.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
