{"id":"https://openalex.org/W4409349227","doi":"https://doi.org/10.1093/bib/bbaf157","title":"FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis","display_name":"FactVAE: a factorized variational autoencoder for single-cell multi-omics data integration analysis","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4409349227","doi":"https://doi.org/10.1093/bib/bbaf157","pmid":"https://pubmed.ncbi.nlm.nih.gov/40211981"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf157","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf157/62909356/bbaf157.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-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":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf157/62909356/bbaf157.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100737553","display_name":"Linjie Wang","orcid":"https://orcid.org/0009-0004-2028-7501"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Linjie Wang","raw_affiliation_strings":["School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003451352","display_name":"Huixia Zhang","orcid":"https://orcid.org/0000-0002-3319-8522"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huixia Zhang","raw_affiliation_strings":["School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087021865","display_name":"Bo Yi","orcid":"https://orcid.org/0000-0002-8073-8202"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Yi","raw_affiliation_strings":["School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083300528","display_name":"Weidong Xie","orcid":"https://orcid.org/0000-0003-1930-4509"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weidong Xie","raw_affiliation_strings":["School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108713327","display_name":"Kun Yu","orcid":"https://orcid.org/0009-0004-5623-6431"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kun Yu","raw_affiliation_strings":["College of Medicine and Bioinformation Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"College of Medicine and Bioinformation Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114608967","display_name":"Wei Li","orcid":"https://orcid.org/0009-0004-0265-9789"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Li","raw_affiliation_strings":["Key Laboratory of Intelligent Computing in Medical Image (MIIC) , Northeastern University, 110000, Shenyang,","National Frontiers Science Center for Industrial Intelligence and Systems Optimization , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Computing in Medical Image (MIIC) , Northeastern University, 110000, Shenyang,","institution_ids":["https://openalex.org/I9224756"]},{"raw_affiliation_string":"National Frontiers Science Center for Industrial Intelligence and Systems Optimization , Northeastern University, 110819, Shenyang,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087894632","display_name":"Keqin Li","orcid":"https://orcid.org/0000-0001-5224-4048"},"institutions":[{"id":"https://openalex.org/I113508548","display_name":"Albany State University","ror":"https://ror.org/01vme4277","country_code":"US","type":"education","lineage":["https://openalex.org/I113508548"]},{"id":"https://openalex.org/I392282","display_name":"University at Albany, State University of New York","ror":"https://ror.org/012zs8222","country_code":"US","type":"education","lineage":["https://openalex.org/I392282"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keqin Li","raw_affiliation_strings":["Department of Computer Science , State University of New York, Albany, NY 12561,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science , State University of New York, Albany, NY 12561,","institution_ids":["https://openalex.org/I392282","https://openalex.org/I113508548"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049764032","display_name":"Dazhe Zhao","orcid":"https://orcid.org/0000-0001-7749-4414"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dazhe Zhao","raw_affiliation_strings":["School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Northeastern University, 110819, Shenyang,","institution_ids":["https://openalex.org/I9224756"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100737553"],"corresponding_institution_ids":["https://openalex.org/I9224756"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":5.2848,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.95613042,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","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":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":0.9973999857902527,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9922000169754028,"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/autoencoder","display_name":"Autoencoder","score":0.7704530954360962},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7312190532684326},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6414157748222351},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5629068613052368},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5182583332061768},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5110934376716614},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5104578733444214},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.4769136607646942},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4660699665546417},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4517079293727875},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4136064648628235},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41351208090782166},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4129485487937927},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2075825035572052}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7704530954360962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7312190532684326},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6414157748222351},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5629068613052368},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5182583332061768},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5110934376716614},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5104578733444214},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.4769136607646942},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4660699665546417},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4517079293727875},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4136064648628235},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41351208090782166},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4129485487937927},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2075825035572052},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf157","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf157/62909356/bbaf157.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-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:40211981","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40211981","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:11986350","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11986350","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf157","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf157","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf157/62909356/bbaf157.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-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":[{"display_name":"Partnerships for the goals","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2311391187","display_name":null,"funder_award_id":"B16009","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G3624248983","display_name":null,"funder_award_id":"2023YFC2413500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409349227.pdf","grobid_xml":"https://content.openalex.org/works/W4409349227.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W2013940103","https://openalex.org/W2018838463","https://openalex.org/W2064259285","https://openalex.org/W2101234009","https://openalex.org/W2553838260","https://openalex.org/W2750049634","https://openalex.org/W2887694579","https://openalex.org/W2889236955","https://openalex.org/W2897249806","https://openalex.org/W2918127702","https://openalex.org/W2949177718","https://openalex.org/W2979911343","https://openalex.org/W2989061519","https://openalex.org/W3023456235","https://openalex.org/W3027051073","https://openalex.org/W3029148360","https://openalex.org/W3043558371","https://openalex.org/W3080500495","https://openalex.org/W3087130263","https://openalex.org/W3092493138","https://openalex.org/W3093858607","https://openalex.org/W3102434595","https://openalex.org/W3106188259","https://openalex.org/W3113863876","https://openalex.org/W3138479716","https://openalex.org/W3144696998","https://openalex.org/W3164736847","https://openalex.org/W3201518044","https://openalex.org/W3202649987","https://openalex.org/W3212601981","https://openalex.org/W4225278475","https://openalex.org/W4290659035","https://openalex.org/W4311232381","https://openalex.org/W4312182122","https://openalex.org/W4315621823","https://openalex.org/W4318189471","https://openalex.org/W4324344255","https://openalex.org/W4327683140","https://openalex.org/W4367555319","https://openalex.org/W4379521442","https://openalex.org/W4392899363","https://openalex.org/W4399801297","https://openalex.org/W4401453914","https://openalex.org/W4402072814","https://openalex.org/W4407436635","https://openalex.org/W6675354045","https://openalex.org/W6792121546","https://openalex.org/W6802049488"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3013693939","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W2566616303","https://openalex.org/W2159052453","https://openalex.org/W4312814274","https://openalex.org/W1590307681","https://openalex.org/W2536018345","https://openalex.org/W4285370786"],"abstract_inverted_index":{"Single-cell":[0],"multi-omics":[1,79,135,143,200],"technologies":[2],"have":[3],"revolutionized":[4],"the":[5,72,83,87,92,99,141,163,169,176],"study":[6],"of":[7,77,94,102,133,178],"cell":[8,46,125],"states":[9],"and":[10,34,56,74,117,128,140,180,189],"functions":[11],"by":[12,105,173],"simultaneously":[13],"profiling":[14],"multiple":[15],"molecular":[16],"layers":[17],"within":[18],"individual":[19],"cells.":[20,60],"However,":[21],"existing":[22],"methods":[23,152],"for":[24,44,71,124,198],"integrating":[25],"these":[26],"data":[27,129,160,201],"struggle":[28],"to":[29,36,53],"preserve":[30],"critical":[31],"feature":[32,95,170],"information":[33,96,104],"fail":[35],"exploit":[37],"known":[38,109],"regulatory":[39,110,183],"knowledge,":[40],"which":[41],"is":[42,112,122],"essential":[43],"understanding":[45,76],"functions.":[47],"This":[48],"limitation":[49],"hinders":[50],"their":[51],"ability":[52],"provide":[54],"comprehensive":[55],"accurate":[57,75],"insights":[58],"into":[59,86],"Here,":[61],"we":[62],"propose":[63],"FactVAE,":[64],"an":[65],"innovative":[66],"factorized":[67],"variational":[68,88],"autoencoder":[69,89],"designed":[70],"robust":[73],"single-cell":[78,134,199],"data.":[80],"FactVAE":[81,147,174],"integrates":[82],"factorization":[84],"principle":[85],"framework,":[90],"ensuring":[91],"preservation":[93],"while":[97],"leveraging":[98],"non-linear":[100],"capture":[101],"sample":[103],"neural":[106],"networks.":[107],"Additionally,":[108],"knowledge":[111,119],"incorporated":[113],"during":[114],"model":[115],"training,":[116],"a":[118,194],"transfer":[120],"strategy":[121],"employed":[123],"embedding":[126],"optimization":[127],"augmentation.":[130],"Comparative":[131],"analyses":[132],"datasets":[136],"from":[137],"different":[138],"protocols":[139],"spatial":[142],"dataset":[144],"demonstrate":[145],"that":[146,161],"not":[148],"only":[149],"outperforms":[150],"benchmark":[151],"in":[153],"clustering":[154],"performance":[155,188],"but":[156],"also":[157],"generates":[158],"augmented":[159],"reveals":[162],"clearest":[164],"cell-type-specific":[165],"motif":[166],"expression.":[167],"Moreover,":[168],"embeddings":[171],"captured":[172],"enable":[175],"inference":[177],"potential":[179],"reliable":[181],"gene":[182],"relationships.":[184],"Overall,":[185],"FactVAE's":[186],"superior":[187],"strong":[190],"scalability":[191],"make":[192],"it":[193],"promising":[195],"new":[196],"solution":[197],"analysis.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
