{"id":"https://openalex.org/W4380729781","doi":"https://doi.org/10.1093/bioinformatics/btad382","title":"Ensemble deep learning of embeddings for clustering multimodal single-cell omics data","display_name":"Ensemble deep learning of embeddings for clustering multimodal single-cell omics data","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4380729781","doi":"https://doi.org/10.1093/bioinformatics/btad382","pmid":"https://pubmed.ncbi.nlm.nih.gov/37314966"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad382","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad382","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad382/50603727/btad382.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad382/50603727/btad382.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101451530","display_name":"Lijia Yu","orcid":"https://orcid.org/0000-0001-6735-9569"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Lijia Yu","raw_affiliation_strings":["Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","institution_ids":["https://openalex.org/I146584863","https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719418","display_name":"Chunlei Liu","orcid":"https://orcid.org/0000-0002-1138-7488"},"institutions":[{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]},{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Chunlei Liu","raw_affiliation_strings":["Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","institution_ids":["https://openalex.org/I146584863","https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028524705","display_name":"Jean Yang","orcid":"https://orcid.org/0000-0002-5271-2603"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jean Yee Hwa Yang","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia","Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park , Hong Kong SAR, China","School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia"],"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park , Hong Kong SAR, China","institution_ids":[]},{"raw_affiliation_string":"School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114375167","display_name":"Pengyi Yang","orcid":"https://orcid.org/0000-0003-1098-3138"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Pengyi Yang","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia","Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park , Hong Kong SAR, China","School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia"],"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Computational Systems Biology Group, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , Westmead, NSW 2145, Australia","institution_ids":["https://openalex.org/I146584863","https://openalex.org/I129604602"]},{"raw_affiliation_string":"Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park , Hong Kong SAR, China","institution_ids":[]},{"raw_affiliation_string":"School of Mathematics and Statistics, Faculty of Science, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, University of Sydney , NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia","institution_ids":["https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101451530"],"corresponding_institution_ids":["https://openalex.org/I129604602","https://openalex.org/I146584863"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.1633,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.87482659,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9945999979972839,"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":0.9782000184059143,"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/cluster-analysis","display_name":"Cluster analysis","score":0.806503415107727},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7698525190353394},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5251973867416382},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5151256918907166},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5093954205513},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4428237974643707},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.44171109795570374},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.41829565167427063}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.806503415107727},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7698525190353394},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5251973867416382},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5151256918907166},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5093954205513},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4428237974643707},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.44171109795570374},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.41829565167427063},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"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":"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":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad382","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad382","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad382/50603727/btad382.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37314966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37314966","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt3c77k765","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/3c77k765","pdf_url":"https://escholarship.org/content/qt3c77k765/qt3c77k765.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 39, iss 6","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10287920","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10287920","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10287920/pdf/btad382.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad382","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad382","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad382/50603727/btad382.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3100051334","display_name":null,"funder_award_id":"1173469","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320320966","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12"},{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4380729781.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W2124044975","https://openalex.org/W2739492614","https://openalex.org/W2888562574","https://openalex.org/W2953251392","https://openalex.org/W2971653850","https://openalex.org/W2979464975","https://openalex.org/W2979911343","https://openalex.org/W2995268793","https://openalex.org/W2997207862","https://openalex.org/W3023456235","https://openalex.org/W3027051073","https://openalex.org/W3036137852","https://openalex.org/W3049002444","https://openalex.org/W3093858607","https://openalex.org/W3120427588","https://openalex.org/W3129866267","https://openalex.org/W3152371839","https://openalex.org/W3153732845","https://openalex.org/W3154836057","https://openalex.org/W3159101980","https://openalex.org/W3159702793","https://openalex.org/W3164692211","https://openalex.org/W3195317458","https://openalex.org/W3215916291","https://openalex.org/W4205421285","https://openalex.org/W4210840193","https://openalex.org/W4311232381","https://openalex.org/W4324018599","https://openalex.org/W4382632237"],"related_works":["https://openalex.org/W4376643315","https://openalex.org/W4324137541","https://openalex.org/W2900445707","https://openalex.org/W4285741730","https://openalex.org/W1191482210","https://openalex.org/W4285046548","https://openalex.org/W4210302090","https://openalex.org/W3092276832","https://openalex.org/W3111529524","https://openalex.org/W4375951447"],"abstract_inverted_index":{"SnapCCESS":[0],"is":[1,8],"implemented":[2],"as":[3],"a":[4],"Python":[5],"package":[6],"and":[7],"freely":[9],"available":[10,27],"from":[11],"https://github.com/PYangLab/SnapCCESS":[12],"under":[13],"the":[14],"open-source":[15],"license":[16],"of":[17],"GPL-3.":[18],"The":[19],"data":[20],"used":[21],"in":[22],"this":[23],"study":[24],"are":[25],"publicly":[26],"(see":[28],"section":[29],"'Data":[30],"availability').":[31]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
