{"id":"https://openalex.org/W4394711143","doi":"https://doi.org/10.1093/bioinformatics/btae198","title":"scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model","display_name":"scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model","publication_year":2024,"publication_date":"2024-03-29","ids":{"openalex":"https://openalex.org/W4394711143","doi":"https://doi.org/10.1093/bioinformatics/btae198","pmid":"https://pubmed.ncbi.nlm.nih.gov/38603616"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae198/57218161/btae198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae198/57218161/btae198.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021209578","display_name":"Sijing An","orcid":"https://orcid.org/0000-0002-4488-1298"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sijing An","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":"https://orcid.org/0000-0002-4488-1298","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101334748","display_name":"Jinhui Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinhui Shi","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019848226","display_name":"Runyan Liu","orcid":"https://orcid.org/0000-0002-0113-0056"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Runyan Liu","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013486629","display_name":"Yaowen Chen","orcid":"https://orcid.org/0000-0002-7936-3861"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaowen Chen","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":"https://orcid.org/0000-0002-7936-3861","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"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/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Wang","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051351109","display_name":"Shuofeng Hu","orcid":"https://orcid.org/0000-0001-9922-5311"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuofeng Hu","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085383682","display_name":"Xinyu Xia","orcid":"https://orcid.org/0000-0001-7896-1993"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyu Xia","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101419084","display_name":"Guohua Dong","orcid":"https://orcid.org/0000-0003-1955-3804"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohua Dong","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045958734","display_name":"Xiaochen Bo","orcid":"https://orcid.org/0000-0003-1911-7922"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Xiaochen Bo","raw_affiliation_strings":["Department of Bioinformatics, Institute of Health Service and Transfusion Medicine , Beijing 100850, China"],"raw_orcid":"https://orcid.org/0000-0003-1911-7922","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100427766","display_name":"Zhen He","orcid":"https://orcid.org/0000-0003-1658-0399"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen He","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034720217","display_name":"Xiaomin Ying","orcid":"https://orcid.org/0000-0001-6126-7372"},"institutions":[{"id":"https://openalex.org/I4210139958","display_name":"Beijing Computational Science Research Center","ror":"https://ror.org/04tavf782","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210139958"]},{"id":"https://openalex.org/I4391767653","display_name":"Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences","ror":"https://ror.org/055qbch41","country_code":null,"type":"facility","lineage":["https://openalex.org/I200296433","https://openalex.org/I4391767653"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaomin Ying","raw_affiliation_strings":["Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China"],"raw_orcid":"https://orcid.org/0000-0001-6126-7372","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences , Beijing 100850, China","institution_ids":["https://openalex.org/I4210139958"]},{"raw_affiliation_string":"Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China","institution_ids":["https://openalex.org/I4391767653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5034720217","https://openalex.org/A5045958734","https://openalex.org/A5100427766"],"corresponding_institution_ids":["https://openalex.org/I4210139958","https://openalex.org/I4391767653"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1984,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52745328,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"40","issue":"4","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/T10885","display_name":"Gene expression and cancer classification","score":0.992900013923645,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.982200026512146,"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":0.8417074084281921},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.7326758503913879},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6993725299835205},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5653943419456482},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.5220884680747986},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.488159716129303},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4666340947151184},{"id":"https://openalex.org/keywords/dirichlet-process","display_name":"Dirichlet process","score":0.42413198947906494},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3820180594921112},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37484031915664673},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2055630087852478},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.13311195373535156}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8417074084281921},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7326758503913879},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6993725299835205},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5653943419456482},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.5220884680747986},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.488159716129303},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4666340947151184},{"id":"https://openalex.org/C2781280628","wikidata":"https://www.wikidata.org/wiki/Q5280766","display_name":"Dirichlet process","level":3,"score":0.42413198947906494},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3820180594921112},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37484031915664673},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2055630087852478},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.13311195373535156},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"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":"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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":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},{"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae198/57218161/btae198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38603616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38603616","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11256937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11256937","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11256937/pdf/btae198.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae198/57218161/btae198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8545628891","display_name":null,"funder_award_id":"62303488","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":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4394711143.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1967687583","https://openalex.org/W1977556410","https://openalex.org/W1987971958","https://openalex.org/W2100495367","https://openalex.org/W2131681506","https://openalex.org/W2523369352","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2560076216","https://openalex.org/W2598326928","https://openalex.org/W2601723752","https://openalex.org/W2884197618","https://openalex.org/W2886347923","https://openalex.org/W2897249806","https://openalex.org/W2902652978","https://openalex.org/W2907803516","https://openalex.org/W2936414047","https://openalex.org/W2937917790","https://openalex.org/W2952303649","https://openalex.org/W2972625781","https://openalex.org/W3000145506","https://openalex.org/W3003285681","https://openalex.org/W3024013192","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W3113251307","https://openalex.org/W3130814454","https://openalex.org/W3138479716","https://openalex.org/W3164692211","https://openalex.org/W3203176450","https://openalex.org/W3216323060","https://openalex.org/W4210840193","https://openalex.org/W4212774754","https://openalex.org/W4213136259","https://openalex.org/W4225597915","https://openalex.org/W4226296494","https://openalex.org/W4233637541","https://openalex.org/W4235169531","https://openalex.org/W4283010792","https://openalex.org/W4283171432","https://openalex.org/W4317888741","https://openalex.org/W6644682428"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W4386815338","https://openalex.org/W2145836866","https://openalex.org/W2789551765"],"abstract_inverted_index":{"MOTIVATION:":[0],"Clustering":[1,57],"analysis":[2],"for":[3],"single-cell":[4,54],"RNA":[5],"sequencing":[6],"(scRNA-seq)":[7],"data":[8,45],"is":[9,146,156,163],"an":[10],"important":[11],"step":[12],"in":[13,158],"revealing":[14],"cellular":[15],"heterogeneity.":[16],"Many":[17],"clustering":[18,33,85,116],"methods":[19,117],"have":[20],"been":[21],"proposed":[22],"to":[23,148],"discover":[24],"heterogenous":[25],"cell":[26,107,133],"types":[27,108,134],"from":[28,42],"scRNA-seq":[29,44,91,120],"data.":[30,92],"However,":[31],"adaptive":[32,84],"with":[34,86,103,112],"accurate":[35,87,130],"cluster":[36,88],"number":[37],"reflecting":[38],"intrinsic":[39],"biology":[40],"nature":[41],"large-scale":[43],"remains":[46],"quite":[47],"challenging.":[48],"RESULTS:":[49],"Here,":[50],"we":[51],"propose":[52],"a":[53],"Deep":[55],"Adaptive":[56],"(scDAC)":[58],"model":[59,76],"by":[60],"coupling":[61],"the":[62,66,75,95,142],"Autoencoder":[63],"(AE)":[64],"and":[65,80,109,137],"Dirichlet":[67],"Process":[68],"Mixture":[69],"Model":[70],"(DPMM).":[71],"By":[72],"jointly":[73],"optimizing":[74],"parameters":[77],"of":[78,97,106,132,144],"AE":[79],"DPMM,":[81],"scDAC":[82,98,126,145,155],"achieves":[83],"numbers":[89,105,131],"on":[90,99],"We":[93],"verify":[94],"performance":[96,143],"five":[100],"subsampled":[101],"datasets":[102],"different":[104],"compare":[110],"it":[111],"15":[113],"widely":[114],"used":[115],"across":[118],"nine":[119],"datasets.":[121],"Our":[122],"results":[123],"demonstrate":[124],"that":[125],"can":[127],"adaptively":[128],"find":[129],"or":[135],"subtypes":[136],"outperforms":[138],"other":[139],"methods.":[140],"Moreover,":[141],"robust":[147],"hyperparameter":[149],"changes.":[150],"AVAILABILITY":[151],"AND":[152],"IMPLEMENTATION:":[153],"The":[154,160],"implemented":[157],"Python.":[159],"source":[161],"code":[162],"available":[164],"at":[165],"https://github.com/labomics/scDAC.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-27T08:28:00.272161","created_date":"2024-04-12T00:00:00"}