{"id":"https://openalex.org/W4414739338","doi":"https://doi.org/10.1101/2025.09.27.678942","title":"scPhoenix: A Contrastive Learning-based Framework with Aux\u2013Core Feature Disentanglement Enhances Sparse Cellular Multi-omics Translation","display_name":"scPhoenix: A Contrastive Learning-based Framework with Aux\u2013Core Feature Disentanglement Enhances Sparse Cellular Multi-omics Translation","publication_year":2025,"publication_date":"2025-09-29","ids":{"openalex":"https://openalex.org/W4414739338","doi":"https://doi.org/10.1101/2025.09.27.678942"},"language":"en","primary_location":{"id":"doi:10.1101/2025.09.27.678942","doi":"https://doi.org/10.1101/2025.09.27.678942","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.27.678942","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/2025.09.27.678942","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100302747","display_name":"Chaoyu Yan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4400600959","display_name":"Nanfang College Guangzhou","ror":"https://ror.org/04vrxqg89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4400600959"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chaoyu Yan","raw_affiliation_strings":["School of Electrical and Computer Engineering, Nanfang College, Guangzhou, China","Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","Sun Yat-sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Nanfang College, Guangzhou, China","institution_ids":["https://openalex.org/I4400600959"]},{"raw_affiliation_string":"Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108752809","display_name":"Zijian He","orcid":"https://orcid.org/0009-0003-8731-6090","observed_orcids":["https://orcid.org/0009-0003-8731-6090","https://orcid.org/0009-0003-1845-2195"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zijian He","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086760551","display_name":"Lihang Ye","orcid":"https://orcid.org/0000-0003-3942-0283","observed_orcids":["https://orcid.org/0000-0003-3942-0283"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihang Ye","raw_affiliation_strings":["Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101323660","display_name":"Shikang Zheng","orcid":"https://orcid.org/0009-0003-9578-1937","observed_orcids":["https://orcid.org/0009-0003-9578-1937","https://orcid.org/0009-0009-1999-4619"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shikang Zheng","raw_affiliation_strings":["School of Medicine, Sun Yat-sen University, Shenzhen, China","Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine, Sun Yat-sen University, Shenzhen, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Nan Lin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4400600959","display_name":"Nanfang College Guangzhou","ror":"https://ror.org/04vrxqg89","country_code":"CN","type":"education","lineage":["https://openalex.org/I4400600959"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nan Lin","raw_affiliation_strings":["School of Electrical and Computer Engineering, Nanfang College, Guangzhou, China","Nanfang College, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical and Computer Engineering, Nanfang College, Guangzhou, China","institution_ids":["https://openalex.org/I4400600959"]},{"raw_affiliation_string":"Nanfang College, China","institution_ids":["https://openalex.org/I4400600959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042965510","display_name":"Guanbin Li","orcid":"https://orcid.org/0000-0002-4805-0926","observed_orcids":["https://orcid.org/0000-0002-4805-0926","https://orcid.org/0000-0002-2486-2890"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guanbin Li","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","Sun Yat-Sen University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101583301","display_name":"Weizhong Li","orcid":"https://orcid.org/0000-0002-9003-7733","observed_orcids":["https://orcid.org/0000-0002-9003-7733","https://orcid.org/0009-0002-7047-7640"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weizhong Li","raw_affiliation_strings":["School of Medicine, Sun Yat-sen University, Shenzhen, China","Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","Sun Yat-Sen University"],"raw_orcid":"https://orcid.org/0000-0002-9003-7733","affiliations":[{"raw_affiliation_string":"School of Medicine, Sun Yat-sen University, Shenzhen, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101583301"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9990000128746033,"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":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/contrastive-learning","display_name":"contrastive learning","score":0.9789999723434448},{"id":"https://openalex.org/keywords/feature-disentanglement","display_name":"feature disentanglement","score":0.8859999775886536},{"id":"https://openalex.org/keywords/sparsity","display_name":"sparsity","score":0.6620000004768372},{"id":"https://openalex.org/keywords/spatial-heterogeneity","display_name":"spatial heterogeneity","score":0.9480000138282776},{"id":"https://openalex.org/keywords/data-augmentation","display_name":"data augmentation","score":0.7620000243186951},{"id":"https://openalex.org/keywords/spatial-multi-omics","display_name":"spatial multi-omics","score":0.6890000104904175},{"id":"https://openalex.org/keywords/cell-heterogeneity","display_name":"cellular heterogeneity","score":0.8169999718666077}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7799999713897705},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6804999709129333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6230000257492065},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6140000224113464},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.49889999628067017},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.39570000767707825},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.39079999923706055},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3846000134944916},{"id":"https://openalex.org/C2779757391","wikidata":"https://www.wikidata.org/wiki/Q6002292","display_name":"Image translation","level":3,"score":0.3172000050544739},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.296099990606308},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.29260000586509705},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28999999165534973},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.2597000002861023},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2025.09.27.678942","doi":"https://doi.org/10.1101/2025.09.27.678942","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.27.678942","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2025.09.27.678942","doi":"https://doi.org/10.1101/2025.09.27.678942","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.09.27.678942","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1963633","display_name":null,"funder_award_id":"2021YFF1200903","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6090290359","display_name":null,"funder_award_id":"92474107","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"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W2194775991","https://openalex.org/W2743416243","https://openalex.org/W2766437506","https://openalex.org/W2889236955","https://openalex.org/W2897249806","https://openalex.org/W2949177718","https://openalex.org/W2951343553","https://openalex.org/W2951381561","https://openalex.org/W2979911343","https://openalex.org/W2989061519","https://openalex.org/W3006800618","https://openalex.org/W3093858607","https://openalex.org/W3120224790","https://openalex.org/W3129866267","https://openalex.org/W3144696998","https://openalex.org/W3153110198","https://openalex.org/W3159800610","https://openalex.org/W3164692211","https://openalex.org/W3182503854","https://openalex.org/W4206337866","https://openalex.org/W4211255280","https://openalex.org/W4225598893","https://openalex.org/W4281778744","https://openalex.org/W4282579661","https://openalex.org/W4289835859","https://openalex.org/W4305013698","https://openalex.org/W4306648087","https://openalex.org/W4307407679","https://openalex.org/W4312210661","https://openalex.org/W4321611267","https://openalex.org/W4324046169","https://openalex.org/W4324344255","https://openalex.org/W4368361703","https://openalex.org/W4375947188","https://openalex.org/W4378649427","https://openalex.org/W4379521442","https://openalex.org/W4382632237","https://openalex.org/W4383737426","https://openalex.org/W4386923465","https://openalex.org/W4394011009","https://openalex.org/W4399892951","https://openalex.org/W4401995829","https://openalex.org/W4403098994","https://openalex.org/W4407436635","https://openalex.org/W4407611158","https://openalex.org/W4409412744"],"related_works":["https://openalex.org/W4413105168","https://openalex.org/W7203618894","https://openalex.org/W4394011009","https://openalex.org/W7152653171","https://openalex.org/W4412987760","https://openalex.org/W7163597315","https://openalex.org/W4403577864","https://openalex.org/W4405178918","https://openalex.org/W4408079479","https://openalex.org/W4414738222"],"abstract_inverted_index":{"Abstract":[0],"Recent":[1],"advances":[2],"in":[3,36,121],"single-cell":[4,50,103],"multi-omics":[5,39,116],"co-assays":[6],"and":[7,23,31,77,114],"spatiotemporal":[8],"sequencing":[9],"technologies":[10],"have":[11],"provided":[12],"unprecedented":[13],"opportunities":[14],"for":[15,49,81],"systematically":[16],"characterizing":[17],"cellular":[18,38,73],"heterogeneity.":[19,126],"However,":[20],"severe":[21],"sparsity":[22],"pronounced":[24],"spatial":[25,115,125],"heterogeneity\u2014hallmark":[26],"features":[27],"of":[28],"complex":[29],"diseases":[30],"tumor":[32],"microenvironment\u2014remain":[33],"major":[34],"obstacles":[35],"deciphering":[37],"data.":[40,104],"Here,":[41],"we":[42],"present":[43],"scPhoenix,":[44],"a":[45,55,91],"contrastive":[46,92],"learning\u2013based":[47],"framework":[48,89,94],"cross-modality":[51,65],"translation.":[52],"scPhoenix":[53,127],"adopts":[54],"two-stage":[56],"Aux\u2013Core":[57],"strategy":[58],"to":[59,102,110],"disentangle":[60],"modality-specific":[61],"feature":[62,66],"extraction":[63],"from":[64],"interaction.":[67],"Across":[68],"diverse":[69],"datasets,":[70],"it":[71],"preserves":[72],"heterogeneity":[74],"during":[75],"translation":[76],"demonstrates":[78],"significant":[79],"advantages":[80],"data":[82,98,112],"with":[83,95,123],"high":[84,124],"sparsity.":[85],"In":[86],"addition,":[87],"the":[88],"integrates":[90],"learning":[93],"five":[96],"effective":[97],"augmentation":[99],"methods":[100],"tailored":[101],"Moreover,":[105],"scPhoenix\u2019s":[106],"design":[107],"supports":[108],"extensions":[109],"unpaired":[111],"training":[113],"translation,":[117],"enabling":[118],"robust":[119],"performance":[120],"scenarios":[122],"is":[128],"freely":[129],"available":[130],"at":[131],"https://github.com/liwz-lab/scPhoenix":[132],".":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2025-10-10T00:00:00"}