{"id":"https://openalex.org/W4377287490","doi":"https://doi.org/10.1088/2632-2153/acd7c3","title":"scGMM-VGAE: a Gaussian mixture model-based variational graph autoencoder algorithm for clustering single-cell RNA-seq data","display_name":"scGMM-VGAE: a Gaussian mixture model-based variational graph autoencoder algorithm for clustering single-cell RNA-seq data","publication_year":2023,"publication_date":"2023-05-22","ids":{"openalex":"https://openalex.org/W4377287490","doi":"https://doi.org/10.1088/2632-2153/acd7c3"},"language":"en","primary_location":{"id":"doi:10.1088/2632-2153/acd7c3","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/acd7c3","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/acd7c3/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://iopscience.iop.org/article/10.1088/2632-2153/acd7c3/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012158443","display_name":"Eric Lin","orcid":"https://orcid.org/0000-0002-0905-7105"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eric Lin","raw_affiliation_strings":["University of Toronto, Division of Biostatistics, Toronto, Ontario, M5S 1A1, CANADA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Toronto, Division of Biostatistics, Toronto, Ontario, M5S 1A1, CANADA","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101545201","display_name":"Boyuan Liu","orcid":"https://orcid.org/0009-0007-4163-6557"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Boyuan Liu","raw_affiliation_strings":["University of Toronto, Division of Biostatistics, Toronto, Ontario, M5S 1A1, CANADA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Toronto, Division of Biostatistics, Toronto, Ontario, M5S 1A1, CANADA","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035261993","display_name":"Leann Lac","orcid":null},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Leann Lac","raw_affiliation_strings":["University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057863026","display_name":"Daryl L. X. Fung","orcid":null},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Daryl L X Fung","raw_affiliation_strings":["University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016113718","display_name":"Carson K. Leung","orcid":"https://orcid.org/0000-0002-7541-9127"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Carson K Leung","raw_affiliation_strings":["University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA"],"raw_orcid":"https://orcid.org/0000-0002-7541-9127","affiliations":[{"raw_affiliation_string":"University of Manitoba, Department of Computer Science, Winnipeg, Manitoba, R3T 2N2, CANADA","institution_ids":["https://openalex.org/I46247651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035024838","display_name":"Pingzhao Hu","orcid":"https://orcid.org/0000-0002-9546-2245"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Pingzhao Hu","raw_affiliation_strings":["Computer Science, Western University, Medical Sciences Building Rm. 362, London, Ontario, N6A 3K7, CANADA"],"raw_orcid":"https://orcid.org/0000-0002-9546-2245","affiliations":[{"raw_affiliation_string":"Computer Science, Western University, Medical Sciences Building Rm. 362, London, Ontario, N6A 3K7, CANADA","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035024838"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":1600,"currency":"GBP","value_usd":1962},"apc_paid":{"value":1600,"currency":"GBP","value_usd":1962},"fwci":1.7444,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84410186,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"4","issue":"3","first_page":"035013","last_page":"035013"},"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":0.987500011920929,"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9187999963760376,"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/autoencoder","display_name":"Autoencoder","score":0.9123362898826599},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.829329252243042},{"id":"https://openalex.org/keywords/mixture-model","display_name":"Mixture model","score":0.7733820676803589},{"id":"https://openalex.org/keywords/adjacency-matrix","display_name":"Adjacency matrix","score":0.6182693839073181},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5834200978279114},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4584604501724243},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4578799605369568},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45591744780540466},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.45214611291885376},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45174527168273926},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39040184020996094},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.19483405351638794},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.11083528399467468}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.9123362898826599},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.829329252243042},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.7733820676803589},{"id":"https://openalex.org/C180356752","wikidata":"https://www.wikidata.org/wiki/Q727035","display_name":"Adjacency matrix","level":3,"score":0.6182693839073181},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5834200978279114},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4584604501724243},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4578799605369568},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45591744780540466},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.45214611291885376},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45174527168273926},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39040184020996094},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.19483405351638794},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.11083528399467468},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1088/2632-2153/acd7c3","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/acd7c3","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/acd7c3/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:2ad3fa2850704c3a942a46b003492d03","is_oa":true,"landing_page_url":"https://doaj.org/article/2ad3fa2850704c3a942a46b003492d03","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Machine Learning: Science and Technology, Vol 4, Iss 3, p 035013 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1088/2632-2153/acd7c3","is_oa":true,"landing_page_url":"https://doi.org/10.1088/2632-2153/acd7c3","pdf_url":"https://iopscience.iop.org/article/10.1088/2632-2153/acd7c3/pdf","source":{"id":"https://openalex.org/S4210200687","display_name":"Machine Learning Science and Technology","issn_l":"2632-2153","issn":["2632-2153"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320083","host_organization_name":"IOP Publishing","host_organization_lineage":["https://openalex.org/P4310320083","https://openalex.org/P4310311669"],"host_organization_lineage_names":["IOP Publishing","Institute of Physics"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning: Science and Technology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.46000000834465027}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310811","display_name":"Manitoba Medical Service Foundation","ror":"https://ror.org/00mfkwp51"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4377287490.pdf"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W21730848","https://openalex.org/W1552434751","https://openalex.org/W1558051366","https://openalex.org/W1771769277","https://openalex.org/W1959608418","https://openalex.org/W2125310307","https://openalex.org/W2154986869","https://openalex.org/W2399891531","https://openalex.org/W2523620612","https://openalex.org/W2727913218","https://openalex.org/W2730106296","https://openalex.org/W2746479894","https://openalex.org/W2770487168","https://openalex.org/W2794480084","https://openalex.org/W2796190345","https://openalex.org/W2889326414","https://openalex.org/W2901677030","https://openalex.org/W2926010705","https://openalex.org/W2949177718","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2964015378","https://openalex.org/W2979464975","https://openalex.org/W2979835214","https://openalex.org/W2989716250","https://openalex.org/W2991174006","https://openalex.org/W2996009698","https://openalex.org/W2997909961","https://openalex.org/W3009854800","https://openalex.org/W3019913914","https://openalex.org/W3049679592","https://openalex.org/W3113251307","https://openalex.org/W3129725981","https://openalex.org/W3133678705","https://openalex.org/W3134779741","https://openalex.org/W3164692211","https://openalex.org/W3173371682","https://openalex.org/W3197108411","https://openalex.org/W3198138654","https://openalex.org/W3212718277","https://openalex.org/W4214889288","https://openalex.org/W4221133638","https://openalex.org/W4226296494","https://openalex.org/W4322614756","https://openalex.org/W6632813477","https://openalex.org/W6634685263","https://openalex.org/W6638112188","https://openalex.org/W6640963894","https://openalex.org/W6726873649","https://openalex.org/W6730084236"],"related_works":["https://openalex.org/W4287995534","https://openalex.org/W2998168123","https://openalex.org/W2897995864","https://openalex.org/W2292254049","https://openalex.org/W2592385986","https://openalex.org/W2610906757","https://openalex.org/W4281924768","https://openalex.org/W3099179464","https://openalex.org/W2772780115","https://openalex.org/W4309838615"],"abstract_inverted_index":{"Abstract":[0],"Cell":[1,18],"type":[2],"identification":[3],"using":[4],"single-cell":[5],"RNA":[6],"sequencing":[7],"data":[8,47,91],"is":[9,113],"critical":[10],"for":[11,28,95],"understanding":[12],"disease":[13],"mechanisms":[14],"and":[15,75,122,133,141],"drug":[16],"discovery.":[17],"clustering":[19,53,65,97,177],"analysis":[20],"has":[21,183],"been":[22],"widely":[23],"studied":[24],"in":[25,155,175,192,199],"health":[26,193],"research":[27],"rare":[29,189],"tumor":[30],"cell":[31,64,96,156,176,190],"detection.":[32],"In":[33],"this":[34,200],"study,":[35],"we":[36],"propose":[37],"a":[38,51,56,70,76,81,109,184],"Gaussian":[39,100],"mixture":[40,101],"model-based":[41],"variational":[42,83],"graph":[43,72,82],"autoencoder":[44,84],"on":[45,129,151,166,178,187],"scRNA-seq":[46,167,179],"(scGMM-VGAE)":[48],"that":[49],"integrates":[50],"statistical":[52],"model":[54,68,102],"to":[55,60,86],"deep":[57,163],"learning":[58,164],"algorithm":[59],"significantly":[61],"improve":[62],"the":[63,99,107,120,126,169],"performance.":[66],"This":[67,181],"feeds":[69],"cell-cell":[71],"adjacency":[73],"matrix":[74,79],"gene":[77],"feature":[78],"into":[80,162],"(VGAE)":[85],"generate":[87],"latent":[88],"data.":[89,180],"These":[90],"are":[92],"then":[93],"used":[94,198],"by":[98,115],"(GMM)":[103],"module.":[104],"To":[105],"optimize":[106],"algorithm,":[108],"designed":[110],"loss":[111],"function":[112],"derived":[114],"combining":[116],"parameter":[117],"estimates":[118],"from":[119],"GMM":[121,161],"VGAE.":[123],"We":[124],"test":[125],"proposed":[127,170],"method":[128,171],"four":[130,147],"publicly":[131],"available":[132],"three":[134,152],"simulated":[135],"datasets":[136],"which":[137],"contain":[138],"many":[139],"biological":[140],"technical":[142],"zeros.":[143],"The":[144],"scGMM-VGAE":[145],"outperforms":[146],"selected":[148],"baseline":[149],"methods":[150],"evaluation":[153],"metrics":[154],"clustering.":[157],"By":[158],"successfully":[159],"incorporating":[160],"VGAE":[165],"data,":[168],"shows":[172],"higher":[173],"accuracy":[174],"improvement":[182],"significant":[185],"impact":[186],"detecting":[188],"types":[191],"research.":[194],"All":[195],"source":[196],"codes":[197],"study":[201],"can":[202],"be":[203],"found":[204],"at":[205],"https://github.com/ericlin1230/scGMM-VGAE":[206],".":[207]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}