{"id":"https://openalex.org/W4412902560","doi":"https://doi.org/10.1093/gpbjnl/qzaf062","title":"ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration","display_name":"ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4412902560","doi":"https://doi.org/10.1093/gpbjnl/qzaf062","pmid":"https://pubmed.ncbi.nlm.nih.gov/40757914"},"language":"en","primary_location":{"id":"doi:10.1093/gpbjnl/qzaf062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf062","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf062/63927927/qzaf062.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; 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/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf062/63927927/qzaf062.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011286905","display_name":"Xuhua Yan","orcid":"https://orcid.org/0000-0002-3183-3342"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuhua Yan","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and Engineering, Central South University, Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-3183-3342","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102766473","display_name":"Jinmiao Chen","orcid":"https://orcid.org/0000-0001-7547-6423"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210126319","display_name":"Duke-NUS Medical School","ror":"https://ror.org/02j1m6098","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596","https://openalex.org/I170897317","https://openalex.org/I4210126319"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Jinmiao Chen","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Singapore 138671,","Center for Computational Biology and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School , Singapore 169857,","Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS) , Singapore 117545,","Center for Computational Biology and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore","Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore","Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117545, Singapore"],"raw_orcid":"https://orcid.org/0000-0001-7547-6423","affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , Singapore 138671,","institution_ids":["https://openalex.org/I115228651"]},{"raw_affiliation_string":"Center for Computational Biology and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School , Singapore 169857,","institution_ids":["https://openalex.org/I4210126319"]},{"raw_affiliation_string":"Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS) , Singapore 117545,","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Center for Computational Biology and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore","institution_ids":["https://openalex.org/I4210126319"]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117545, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044328870","display_name":"Ruiqing Zheng","orcid":"https://orcid.org/0000-0001-6372-6798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruiqing Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and Engineering, Central South University, Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0001-6372-6798","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083,","School of Computer Science and Engineering, Central South University, Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-0188-1394","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3650},"apc_paid":{"value":3500,"currency":"USD","value_usd":3650},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11790134,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","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":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9984999895095825,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9926999807357788,"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/spec#","display_name":"Spec#","score":0.7427578568458557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.721868634223938},{"id":"https://openalex.org/keywords/modality","display_name":"Modality (human\u2013computer interaction)","score":0.67971271276474},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.5737131834030151},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4360140860080719},{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.4348711669445038},{"id":"https://openalex.org/keywords/mosaic","display_name":"Mosaic","score":0.41633331775665283},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35522907972335815},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23387956619262695},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.21327555179595947}],"concepts":[{"id":"https://openalex.org/C2778565505","wikidata":"https://www.wikidata.org/wiki/Q2207566","display_name":"Spec#","level":2,"score":0.7427578568458557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.721868634223938},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.67971271276474},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.5737131834030151},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4360140860080719},{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.4348711669445038},{"id":"https://openalex.org/C110739175","wikidata":"https://www.wikidata.org/wiki/Q133067","display_name":"Mosaic","level":2,"score":0.41633331775665283},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35522907972335815},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23387956619262695},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21327555179595947},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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/gpbjnl/qzaf062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf062","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf062/63927927/qzaf062.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40757914","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40757914","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11391423","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12582371","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/gpbjnl/qzaf062","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf062","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf062/63927927/qzaf062.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8663586063","display_name":null,"funder_award_id":"62225209","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412902560.pdf","grobid_xml":"https://content.openalex.org/works/W4412902560.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W2035618305","https://openalex.org/W2510746232","https://openalex.org/W2616922646","https://openalex.org/W2617955321","https://openalex.org/W2739492614","https://openalex.org/W2750049634","https://openalex.org/W2784311950","https://openalex.org/W2800392236","https://openalex.org/W2895456557","https://openalex.org/W2897249806","https://openalex.org/W2943883990","https://openalex.org/W2949177718","https://openalex.org/W2984472267","https://openalex.org/W3093858607","https://openalex.org/W3112300343","https://openalex.org/W3129866267","https://openalex.org/W3138860023","https://openalex.org/W3159800610","https://openalex.org/W3164692211","https://openalex.org/W3164839005","https://openalex.org/W4200581587","https://openalex.org/W4210829655","https://openalex.org/W4220939068","https://openalex.org/W4225598893","https://openalex.org/W4303201711","https://openalex.org/W4311183657","https://openalex.org/W4317884487","https://openalex.org/W4321611764","https://openalex.org/W4367555319","https://openalex.org/W4378212544","https://openalex.org/W4378212624","https://openalex.org/W4382632237","https://openalex.org/W4391168615"],"related_works":["https://openalex.org/W73545470","https://openalex.org/W4224266612","https://openalex.org/W2383394264","https://openalex.org/W4320153225","https://openalex.org/W4293261942","https://openalex.org/W3125968744","https://openalex.org/W203959209","https://openalex.org/W2004831463","https://openalex.org/W2110287964","https://openalex.org/W2167701463"],"abstract_inverted_index":{"The":[0,138],"integration":[1,17,39,100,119],"of":[2,45,105,113,130,141],"single-cell":[3],"multi-omics":[4,90],"datasets":[5,134],"is":[6,124],"critical":[7],"for":[8,66,92,133],"deciphering":[9],"cellular":[10,131],"heterogeneities.":[11],"Mosaic":[12],"integration,":[13],"the":[14,72,80,103,128],"most":[15],"general":[16],"task,":[18],"poses":[19],"a":[20,37,61],"greater":[21],"challenge":[22],"regarding":[23],"disparity":[24],"in":[25],"modality":[26,51,68,81],"abundance":[27],"across":[28,97],"datasets.":[29,94],"Here,":[30],"we":[31],"present":[32],"Align":[33],"and":[34,55,84,117],"CompletE":[35],"(ACE),":[36],"mosaic":[38,99],"framework":[40],"that":[41,122],"assembles":[42],"two":[43,107],"types":[44],"strategies":[46,108],"to":[47,70,87,115,126],"handle":[48],"this":[49],"problem:":[50],"alignment-based":[52],"strategy":[53,57],"(ACE-align)":[54],"regression-based":[56],"(ACE-spec).":[58],"ACE-align":[59],"utilizes":[60],"novel":[62],"contrastive":[63],"learning":[64],"objective":[65],"explicit":[67],"alignment":[69,82],"uncover":[71],"shared":[73],"latent":[74],"representations":[75,86,91],"behind":[76],"modalities.":[77,137],"ACE-spec":[78,114,123],"combines":[79],"results":[83],"modality-specific":[85],"construct":[88],"complete":[89],"all":[93],"Extensive":[95],"experiments":[96],"various":[98],"scenarios":[101,120],"demonstrate":[102],"superiority":[104],"ACE's":[106],"over":[109],"existing":[110],"methods.":[111],"Application":[112],"bi-modal":[116],"tri-modal":[118],"showcases":[121],"able":[125],"enhance":[127],"representation":[129],"heterogeneities":[132],"with":[135],"incomplete":[136],"source":[139],"code":[140],"ACE":[142],"can":[143],"be":[144],"accessed":[145],"at":[146],"https://github.com/CSUBioGroup/ACE-main.":[147]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
