{"id":"https://openalex.org/W3123671946","doi":"https://doi.org/10.1109/access.2021.3052923","title":"Cell Subtype Classification via Representation Learning Based on a Denoising Autoencoder for Single-Cell RNA Sequencing","display_name":"Cell Subtype Classification via Representation Learning Based on a Denoising Autoencoder for Single-Cell RNA Sequencing","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3123671946","doi":"https://doi.org/10.1109/access.2021.3052923","mag":"3123671946"},"language":"en","primary_location":{"id":"doi:10.1109/access.2021.3052923","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3052923","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09328422.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09328422.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080551816","display_name":"Joung Min Choi","orcid":"https://orcid.org/0000-0003-2090-3330"},"institutions":[{"id":"https://openalex.org/I31766871","display_name":"Sookmyung Women's University","ror":"https://ror.org/00vvvt117","country_code":"KR","type":"education","lineage":["https://openalex.org/I31766871"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Joungmin Choi","raw_affiliation_strings":["Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0003-2090-3330","affiliations":[{"raw_affiliation_string":"Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I31766871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012207088","display_name":"Je\u2010Keun Rhee","orcid":"https://orcid.org/0000-0003-4811-8895"},"institutions":[{"id":"https://openalex.org/I141371507","display_name":"Soongsil University","ror":"https://ror.org/017xnm587","country_code":"KR","type":"education","lineage":["https://openalex.org/I141371507"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Je-Keun Rhee","raw_affiliation_strings":["School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I141371507"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101608081","display_name":"Heejoon Chae","orcid":"https://orcid.org/0000-0002-0960-5829"},"institutions":[{"id":"https://openalex.org/I31766871","display_name":"Sookmyung Women's University","ror":"https://ror.org/00vvvt117","country_code":"KR","type":"education","lineage":["https://openalex.org/I31766871"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Heejoon Chae","raw_affiliation_strings":["Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-0960-5829","affiliations":[{"raw_affiliation_string":"Division of Computer Science, Sookmyung Women's University, Seoul, Republic of Korea","institution_ids":["https://openalex.org/I31766871"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.4071,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.57875716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"9","issue":null,"first_page":"14540","last_page":"14548"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9980999827384949,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9884999990463257,"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/softmax-function","display_name":"Softmax function","score":0.7391155958175659},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7325021028518677},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6707645654678345},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6682809591293335},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5962405204772949},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5743157267570496},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5466778874397278},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5221907496452332},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5103215575218201},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.44199028611183167},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.4312775135040283},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.42109888792037964},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3875158131122589},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34603869915008545},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15872102975845337},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07645851373672485}],"concepts":[{"id":"https://openalex.org/C188441871","wikidata":"https://www.wikidata.org/wiki/Q7554146","display_name":"Softmax function","level":3,"score":0.7391155958175659},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7325021028518677},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6707645654678345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6682809591293335},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5962405204772949},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5743157267570496},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5466778874397278},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5221907496452332},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5103215575218201},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.44199028611183167},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.4312775135040283},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.42109888792037964},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3875158131122589},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34603869915008545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15872102975845337},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07645851373672485},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2021.3052923","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3052923","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09328422.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:c06a647e432a4c4888cfcf3d9f07d828","is_oa":true,"landing_page_url":"https://doaj.org/article/c06a647e432a4c4888cfcf3d9f07d828","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":"IEEE Access, Vol 9, Pp 14540-14548 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2021.3052923","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2021.3052923","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9312710/09328422.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3030330391","display_name":null,"funder_award_id":"2019M3E5D3073365","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G647744068","display_name":null,"funder_award_id":"NRF-2018R1C1B6005304","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G7152094987","display_name":null,"funder_award_id":"2019M3E5D3073365","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G7161383449","display_name":null,"funder_award_id":"2019M3E5D3073365","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G8319804727","display_name":null,"funder_award_id":"PJ0143072019","funder_id":"https://openalex.org/F4320322035","funder_display_name":"Rural Development Administration"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322035","display_name":"Rural Development Administration","ror":"https://ror.org/03xs9yg50"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3123671946.pdf","grobid_xml":"https://content.openalex.org/works/W3123671946.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W1522301498","https://openalex.org/W1596717185","https://openalex.org/W1813068103","https://openalex.org/W1967327758","https://openalex.org/W1985987855","https://openalex.org/W2020541351","https://openalex.org/W2030017878","https://openalex.org/W2036109700","https://openalex.org/W2095705004","https://openalex.org/W2100002341","https://openalex.org/W2100471807","https://openalex.org/W2109890799","https://openalex.org/W2111547563","https://openalex.org/W2140258573","https://openalex.org/W2176412452","https://openalex.org/W2179438025","https://openalex.org/W2187089797","https://openalex.org/W2259632819","https://openalex.org/W2273468961","https://openalex.org/W2342423616","https://openalex.org/W2507880739","https://openalex.org/W2523246573","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2610332124","https://openalex.org/W2610509384","https://openalex.org/W2612502013","https://openalex.org/W2735897797","https://openalex.org/W2741564801","https://openalex.org/W2760692740","https://openalex.org/W2763051133","https://openalex.org/W2768772838","https://openalex.org/W2778345128","https://openalex.org/W2788348358","https://openalex.org/W2789949350","https://openalex.org/W2791624046","https://openalex.org/W2793258150","https://openalex.org/W2795687816","https://openalex.org/W2796170779","https://openalex.org/W2801820889","https://openalex.org/W2886347923","https://openalex.org/W2897346235","https://openalex.org/W2901677030","https://openalex.org/W2918882492","https://openalex.org/W2937917790","https://openalex.org/W2951029718","https://openalex.org/W2951914955","https://openalex.org/W2952001873","https://openalex.org/W2963285578","https://openalex.org/W2963735582","https://openalex.org/W2964121744","https://openalex.org/W2964643116","https://openalex.org/W2971398276","https://openalex.org/W2973034691","https://openalex.org/W2984629040","https://openalex.org/W2995410603","https://openalex.org/W3105657793","https://openalex.org/W4245863050","https://openalex.org/W4253759977","https://openalex.org/W6610017368","https://openalex.org/W6631190155","https://openalex.org/W6674330103","https://openalex.org/W6674813771","https://openalex.org/W6685562342","https://openalex.org/W6727249380","https://openalex.org/W6745935776","https://openalex.org/W6751647823"],"related_works":["https://openalex.org/W2769441402","https://openalex.org/W2594436708","https://openalex.org/W4360994128","https://openalex.org/W3086240734","https://openalex.org/W2789476480","https://openalex.org/W4310873165","https://openalex.org/W2355395139","https://openalex.org/W4285596704","https://openalex.org/W3120400911","https://openalex.org/W4321789545"],"abstract_inverted_index":{"Identification":[0],"of":[1,6,17,57,186,207,225],"single-cell":[2,22,119,219],"subtypes":[3,188,220],"is":[4,215,230],"one":[5],"the":[7,58,87,139,195,208],"fundamental":[8],"processes":[9],"required":[10],"to":[11,52,203],"understand":[12],"a":[13,96,113,128,150,183],"heterogeneous":[14],"population":[15],"composed":[16],"multiple":[18,171],"cells,":[19],"based":[20],"on":[21,179],"RNA":[23],"sequencing":[24],"data.":[25],"Previously,":[26],"cell":[27,160,187,192,227],"subtype":[28,59,120,161],"identification":[29,121,162],"was":[30,155],"mainly":[31],"carried":[32],"out":[33],"by":[34,138,145],"dimension":[35],"reduction":[36],"and":[37,54,93,141,164,189,221],"clustering":[38],"approaches":[39,65],"that":[40,211],"grouped":[41],"cells":[42],"with":[43,123,201],"similar":[44],"expressed":[45],"profiles":[46],"together.":[47],"However,":[48],"for":[49,118],"high":[50],"robustness":[51],"noises":[53],"systematic":[55],"annotation":[56],"in":[60,80,103,217],"each":[61,226],"cell,":[62],"supervised":[63],"classification":[64],"have":[66,76],"been":[67,77],"widely":[68,78],"used.":[69],"Recently,":[70],"deep":[71],"neural":[72],"network":[73],"(DNN)":[74],"models":[75],"presented":[79],"various":[81],"fields,":[82],"including":[83],"biology.":[84],"By":[85],"capturing":[86],"composite":[88],"relationship":[89],"between":[90],"sample":[91],"features":[92,193],"target":[94],"outcomes,":[95],"DNN":[97,114],"model":[98,154,197,214],"enables":[99],"significant":[100],"performance":[101],"improvements":[102],"biological":[104],"data":[105,180],"mining":[106],"analyses.":[107],"In":[108],"this":[109],"paper,":[110],"we":[111],"constructed":[112],"model,":[115],"called":[116],"scDAE":[117,173,229],"combined":[122],"representative":[124,224],"feature":[125,134],"extraction":[126],"using":[127,149],"multilayer":[129],"denoising":[130],"autoencoder":[131],"(DAE).":[132],"The":[133,153,205],"sets":[135,181],"were":[136,142,198],"learned":[137],"DAE":[140],"further":[143],"tuned":[144],"fully":[146],"connected":[147],"layers":[148],"softmax":[151],"classifier.":[152],"compared":[156],"against":[157],"four":[158],"state-of-the-art":[159],"methods":[163,177],"two":[165],"conventional":[166],"machine":[167],"learning":[168],"algorithms.":[169],"From":[170],"tests,":[172],"significantly":[174],"outperformed":[175],"competing":[176],"especially":[178],"having":[182],"large":[184],"number":[185],"noises.":[190],"Extracted":[191],"from":[194],"proposed":[196,213],"clearly":[199],"clustered":[200],"respect":[202],"subtype.":[204,228],"results":[206],"experiments":[209],"indicated":[210],"our":[212],"effective":[216],"identifying":[218],"molecular":[222],"signatures":[223],"publicly":[231],"available":[232],"at":[233],"https://github.com/cbi-bioinfo/scDAE.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
