{"id":"https://openalex.org/W4409148523","doi":"https://doi.org/10.1093/bib/bbaf126","title":"CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data","display_name":"CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4409148523","doi":"https://doi.org/10.1093/bib/bbaf126","pmid":"https://pubmed.ncbi.nlm.nih.gov/40178283"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf126","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":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://doi.org/10.1093/bib/bbaf126","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067587169","display_name":"Yahao Wu","orcid":"https://orcid.org/0009-0006-4264-317X"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yahao Wu","raw_affiliation_strings":["School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115595012","display_name":"Jing Liu","orcid":"https://orcid.org/0009-0008-2772-0418"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Liu","raw_affiliation_strings":["School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022540617","display_name":"Yanni Xiao","orcid":"https://orcid.org/0000-0003-0432-7628"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanni Xiao","raw_affiliation_strings":["School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024866341","display_name":"Shuqin Zhang","orcid":"https://orcid.org/0000-0001-8223-844X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuqin Zhang","raw_affiliation_strings":["Fudan University , Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, , 220 Handan Road, 200433 Shanghai ,","School of Mathematical Sciences , Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, , 220 Handan Road, 200433 Shanghai ,","School of Mathematical Sciences, Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, Fudan University, 220 Handan Road, 200433 Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-8223-844X","affiliations":[{"raw_affiliation_string":"Fudan University , Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, , 220 Handan Road, 200433 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"School of Mathematical Sciences , Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, , 220 Handan Road, 200433 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"School of Mathematical Sciences, Center for Applied Mathematics, Research Institute of Intelligent Complex Systems, and Shanghai Key Laboratory for Contemporary Applied Mathematics, Fudan University, 220 Handan Road, 200433 Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100388546","display_name":"Limin Li","orcid":"https://orcid.org/0000-0003-3572-6832"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Limin Li","raw_affiliation_strings":["School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China"],"raw_orcid":"https://orcid.org/0000-0003-3572-6832","affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi\u2019an, Shaanxi 710049 ,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi'an Jiaotong University, No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.9472,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.8499055,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"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":0.9905999898910522,"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":0.9905999898910522,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9294999837875366,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/computer-science","display_name":"Computer science","score":0.5603041052818298},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47440314292907715},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4145314693450928},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3217119574546814},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18659144639968872}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5603041052818298},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47440314292907715},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4145314693450928},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3217119574546814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18659144639968872}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":false},{"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":false},{"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":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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf126","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":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:40178283","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40178283","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:11966612","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11966612","pdf_url":null,"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":"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/bbaf126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf126","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":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":[{"id":"https://openalex.org/G4688883714","display_name":null,"funder_award_id":"12471350","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5626646322","display_name":null,"funder_award_id":"12222115","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6395729102","display_name":null,"funder_award_id":"92470106","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8578675226","display_name":"\u5f02\u8d28\u6027\u6570\u636e\u6574\u5408\u7684\u6570\u5b66\u65b9\u6cd5\u53ca\u5728\u751f\u7269\u6570\u636e\u4e2d\u7684\u5e94 \u7528","funder_award_id":"23JC1401000","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W2561754210","https://openalex.org/W2562947047","https://openalex.org/W2577994754","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2897748644","https://openalex.org/W2901677030","https://openalex.org/W2902000707","https://openalex.org/W2951381561","https://openalex.org/W2965552103","https://openalex.org/W2985979440","https://openalex.org/W2993905360","https://openalex.org/W3021575042","https://openalex.org/W3024643080","https://openalex.org/W3034168389","https://openalex.org/W3042427971","https://openalex.org/W3047168254","https://openalex.org/W3047402958","https://openalex.org/W3093149076","https://openalex.org/W3117464799","https://openalex.org/W3160682313","https://openalex.org/W3170265427","https://openalex.org/W3196650609","https://openalex.org/W4200119326","https://openalex.org/W4210826564","https://openalex.org/W4220905914","https://openalex.org/W4281777185","https://openalex.org/W4293023608","https://openalex.org/W4294032363","https://openalex.org/W4296139725","https://openalex.org/W4297241634","https://openalex.org/W4378640029","https://openalex.org/W4385223880","https://openalex.org/W4385760593","https://openalex.org/W4389166577","https://openalex.org/W4392251634","https://openalex.org/W4394853345","https://openalex.org/W4403931101","https://openalex.org/W6631190155","https://openalex.org/W6640963894","https://openalex.org/W6687045409","https://openalex.org/W6720208624","https://openalex.org/W6748816842","https://openalex.org/W6752497557","https://openalex.org/W6785155162","https://openalex.org/W6804857273","https://openalex.org/W6810601423","https://openalex.org/W6839242349"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"With":[0],"the":[1,22,37,45,58,67,90,124,147,163,181],"rapid":[2],"advances":[3],"in":[4,17,27,66,120,167,185],"single-cell":[5,59,92,188],"sequencing":[6],"technology,":[7],"it":[8],"is":[9,31,54,96],"now":[10],"feasible":[11],"to":[12,29,88,145],"conduct":[13],"in-depth":[14],"genetic":[15],"analysis":[16],"individual":[18],"cells.":[19],"Study":[20],"on":[21,171],"dynamics":[23],"of":[24,32,41,47,69,98,159],"single":[25,160],"cells":[26,114,161],"response":[28],"perturbations":[30],"great":[33],"significance":[34],"for":[35,110,191],"understanding":[36],"functions":[38],"and":[39,112,134,138,149,174],"behaviors":[40],"living":[42],"organisms.":[43],"However,":[44],"acquisition":[46],"post-perturbation":[48],"cellular":[49],"states":[50],"via":[51,115,131],"biological":[52],"experiments":[53],"frequently":[55],"cost-prohibitive.":[56],"Predicting":[57],"perturbation":[60],"responses":[61],"poses":[62],"a":[63,77,104,132,154],"critical":[64],"challenge":[65],"field":[68],"computational":[70],"biology.":[71],"In":[72],"this":[73],"work,":[74],"we":[75],"propose":[76],"novel":[78],"deep":[79],"learning":[80],"method":[81],"called":[82],"coupled":[83,100],"variational":[84],"autoencoders":[85],"(CoupleVAE),":[86],"devised":[87],"predict":[89],"postperturbation":[91],"RNA-Seq":[93],"data.":[94],"CoupleVAE":[95,152,179],"composed":[97],"two":[99,116,128,142],"VAEs":[101],"connected":[102],"by":[103,141],"coupler,":[105,133],"initially":[106],"extracting":[107],"latent":[108,125,164],"features":[109],"controlled":[111,137],"perturbed":[113,139,192],"encoders,":[117],"subsequently":[118],"engaging":[119],"mutual":[121],"translation":[122],"within":[123,162],"space":[126],"through":[127],"nonlinear":[129],"mappings":[130],"ultimately":[135],"generating":[136],"data":[140,190],"separate":[143],"decoders":[144],"process":[146],"encoded":[148],"translated":[150],"features.":[151],"facilitates":[153],"more":[155],"intricate":[156],"state":[157],"transformation":[158],"space.":[165],"Experiments":[166],"three":[168],"real":[169],"datasets":[170],"infection,":[172],"stimulation":[173],"cross-species":[175],"prediction":[176],"show":[177],"that":[178],"surpasses":[180],"existing":[182],"comparative":[183],"models":[184],"effectively":[186],"predicting":[187],"RNA-seq":[189],"cells,":[193],"achieving":[194],"superior":[195],"accuracy.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
