{"id":"https://openalex.org/W4403703547","doi":"https://doi.org/10.1093/bib/bbae540","title":"Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism","display_name":"Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4403703547","doi":"https://doi.org/10.1093/bib/bbae540","pmid":"https://pubmed.ncbi.nlm.nih.gov/39438079"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae540","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae540/59963457/bbae540.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/25/6/bbae540/59963457/bbae540.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030404516","display_name":"Zhiwei Rong","orcid":"https://orcid.org/0000-0002-0970-8545"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhiwei Rong","raw_affiliation_strings":["Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102023999","display_name":"Jiali Song","orcid":"https://orcid.org/0009-0009-1286-0108"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiali Song","raw_affiliation_strings":["Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023987738","display_name":"Yipei Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yipei Yu","raw_affiliation_strings":["Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101934544","display_name":"Lan Mi","orcid":"https://orcid.org/0000-0001-5513-4901"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210093964","display_name":"Peking University Cancer Hospital","ror":"https://ror.org/00nyxxr91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093964"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lan Mi","raw_affiliation_strings":["Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China"],"affiliations":[{"raw_affiliation_string":"Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]},{"raw_affiliation_string":"Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073873341","display_name":"M. Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210124809","display_name":"Peking University People's Hospital","ror":"https://ror.org/035adwg89","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210124809"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"ManTang Qiu","raw_affiliation_strings":["Department of Thoracic Surgery, Peking University People\u2019s Hospital , No. 11 Xizhimen South Street, Xicheng District, Beijing 100044 ,","Department of Thoracic Surgery, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China"],"affiliations":[{"raw_affiliation_string":"Department of Thoracic Surgery, Peking University People\u2019s Hospital , No. 11 Xizhimen South Street, Xicheng District, Beijing 100044 ,","institution_ids":["https://openalex.org/I4210124809","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Thoracic Surgery, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing 100044, China","institution_ids":["https://openalex.org/I4210124809","https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066795023","display_name":"Yuqin Song","orcid":"https://orcid.org/0000-0003-3067-5554"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210093964","display_name":"Peking University Cancer Hospital","ror":"https://ror.org/00nyxxr91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093964"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuqin Song","raw_affiliation_strings":["Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China"],"affiliations":[{"raw_affiliation_string":"Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]},{"raw_affiliation_string":"Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064587024","display_name":"Yan Hou","orcid":"https://orcid.org/0000-0002-3658-8147"},"institutions":[{"id":"https://openalex.org/I111483173","display_name":"King University","ror":"https://ror.org/01evb6z23","country_code":"US","type":"education","lineage":["https://openalex.org/I111483173"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210093964","display_name":"Peking University Cancer Hospital","ror":"https://ror.org/00nyxxr91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093964"]},{"id":"https://openalex.org/I4210161752","display_name":"Beijing Haidian Hospital","ror":"https://ror.org/058x5eq06","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161752"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yan Hou","raw_affiliation_strings":["Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","Peking University Clinical Research Center, Peking University , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China","Peking University Clinical Research Center, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Peking University , School of Public Health, , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210161752"]},{"raw_affiliation_string":"Peking University Cancer Hospital , 52 Fucheng Rd., Haidian District, Beijing 100142 ,","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]},{"raw_affiliation_string":"Peking University Clinical Research Center, Peking University , 38 Xueyuan Rd., Haidian District, Beijing 100191 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I111483173"]},{"raw_affiliation_string":"Peking University Cancer Hospital, 52 Fucheng Rd., Haidian District, Beijing 100142, China","institution_ids":["https://openalex.org/I4210161752","https://openalex.org/I20231570","https://openalex.org/I4210093964"]},{"raw_affiliation_string":"Peking University Clinical Research Center, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biostatistics, School of Public Health, Peking University, 38 Xueyuan Rd., Haidian District, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5030404516"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210161752"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.7074,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.8163075,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9941999912261963,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9941999912261963,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9631999731063843,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.7665833234786987},{"id":"https://openalex.org/keywords/mosaic","display_name":"Mosaic","score":0.648470938205719},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5837162733078003},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5610466599464417},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4384012520313263},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08911222219467163},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.07451805472373962},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07375147938728333},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.06959745287895203}],"concepts":[{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.7665833234786987},{"id":"https://openalex.org/C110739175","wikidata":"https://www.wikidata.org/wiki/Q133067","display_name":"Mosaic","level":2,"score":0.648470938205719},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5837162733078003},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5610466599464417},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4384012520313263},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08911222219467163},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.07451805472373962},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07375147938728333},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.06959745287895203},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae540","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae540/59963457/bbae540.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:39438079","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39438079","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:11495875","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11495875","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11495875/pdf/bbae540.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae540","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae540/59963457/bbae540.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403703547.pdf","grobid_xml":"https://content.openalex.org/works/W4403703547.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W2117757143","https://openalex.org/W2135937351","https://openalex.org/W2555502666","https://openalex.org/W2739492614","https://openalex.org/W2744040456","https://openalex.org/W2793965282","https://openalex.org/W2885927965","https://openalex.org/W2901677030","https://openalex.org/W2935703330","https://openalex.org/W3039317077","https://openalex.org/W3041129226","https://openalex.org/W3092295864","https://openalex.org/W3093858607","https://openalex.org/W3121168830","https://openalex.org/W3129125493","https://openalex.org/W3129866267","https://openalex.org/W3155656876","https://openalex.org/W3159800610","https://openalex.org/W3209455776","https://openalex.org/W4200581587","https://openalex.org/W4210829655","https://openalex.org/W4225278475","https://openalex.org/W4225535314","https://openalex.org/W4225598893","https://openalex.org/W4311415873","https://openalex.org/W4317884487","https://openalex.org/W4378212624","https://openalex.org/W4379521442","https://openalex.org/W4385405823","https://openalex.org/W4391168615","https://openalex.org/W6637618735","https://openalex.org/W6675944832"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2493552207","https://openalex.org/W2397874377","https://openalex.org/W4249026204","https://openalex.org/W2027673787","https://openalex.org/W2327982655","https://openalex.org/W428377179","https://openalex.org/W1483215156"],"abstract_inverted_index":{"The":[0,161],"integration":[1],"of":[2,39,79,106,146],"data":[3,24,32],"from":[4],"multiple":[5],"modalities":[6,33],"generated":[7],"by":[8],"single-cell":[9,67],"omics":[10,80,123],"technologies":[11],"is":[12,164],"crucial":[13],"for":[14,66,138],"accurately":[15],"identifying":[16],"cell":[17,89,121,139],"states.":[18],"One":[19],"challenge":[20],"in":[21,26,29,36,120],"comprehending":[22],"multi-omics":[23],"resides":[25],"mosaic":[27,68],"integration,":[28],"which":[30,118],"different":[31,37,159],"are":[34],"profiled":[35],"subsets":[38],"cells,":[40],"as":[41],"it":[42],"requires":[43],"simultaneous":[44],"batch":[45],"effect":[46],"removal":[47],"and":[48,108,125,148],"modality":[49],"alignment.":[50],"Here,":[51],"we":[52],"develop":[53],"Multi-omics":[54],"Mosaic":[55],"Auto-scaling":[56],"Attention":[57],"Variational":[58],"Inference":[59],"(mmAAVI),":[60],"a":[61],"scalable":[62],"deep":[63],"generative":[64],"model":[65,92],"integration.":[69],"Leveraging":[70],"auto-scaling":[71],"self-attention":[72],"mechanisms,":[73],"mmAAVI":[74,107,128],"can":[75,93],"map":[76],"arbitrary":[77],"combinations":[78],"to":[81,97],"the":[82,91,104],"common":[83],"embedding":[84],"space.":[85],"If":[86],"existing":[87,99],"well-annotated":[88],"states,":[90],"perform":[94],"semisupervised":[95],"learning":[96],"utilize":[98],"these":[100],"annotations.":[101],"We":[102,133],"validated":[103,135],"performance":[105],"five":[109],"other":[110],"commonly":[111],"used":[112],"methods":[113],"on":[114],"four":[115],"benchmark":[116],"datasets,":[117],"vary":[119],"numbers,":[122],"types,":[124],"missing":[126],"patterns.":[127],"consistently":[129],"demonstrated":[130],"its":[131],"superiority.":[132],"also":[134],"mmAAVI's":[136],"ability":[137],"state":[140],"knowledge":[141],"transfer,":[142],"achieving":[143],"balanced":[144],"accuracies":[145],"0.82":[147],"0.97":[149],"with":[150,157],"less":[151],"1%":[152],"labeled":[153],"cells":[154],"between":[155],"batches":[156],"completely":[158],"omics.":[160],"full":[162],"package":[163],"available":[165],"at":[166],"https://github.com/luyiyun/mmAAVI.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-07T13:37:22.277990","created_date":"2025-10-10T00:00:00"}
