{"id":"https://openalex.org/W3192272070","doi":"https://doi.org/10.3390/sym13081467","title":"A Multiple Comprehensive Analysis of scATAC-seq Based on Auto-Encoder and Matrix Decomposition","display_name":"A Multiple Comprehensive Analysis of scATAC-seq Based on Auto-Encoder and Matrix Decomposition","publication_year":2021,"publication_date":"2021-08-11","ids":{"openalex":"https://openalex.org/W3192272070","doi":"https://doi.org/10.3390/sym13081467","mag":"3192272070"},"language":"en","primary_location":{"id":"doi:10.3390/sym13081467","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13081467","pdf_url":"https://www.mdpi.com/2073-8994/13/8/1467/pdf?version=1628651718","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2073-8994/13/8/1467/pdf?version=1628651718","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001148624","display_name":"Yu\u2010Yao Huang","orcid":"https://orcid.org/0000-0002-4501-6140"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuyao Huang","raw_affiliation_strings":["College of Chemistry, Sichuan University, Chengdu 610064, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Chemistry, Sichuan University, Chengdu 610064, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719729","display_name":"Yizhou Li","orcid":"https://orcid.org/0000-0002-0351-1792"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yizhou Li","raw_affiliation_strings":["School of Cyber Science and Engineering, Sichuan University, Chengdu 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Cyber Science and Engineering, Sichuan University, Chengdu 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390946","display_name":"Yuan Liu","orcid":"https://orcid.org/0000-0003-3892-480X"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Liu","raw_affiliation_strings":["College of Chemistry, Sichuan University, Chengdu 610064, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Chemistry, Sichuan University, Chengdu 610064, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063197812","display_name":"Runyu Jing","orcid":"https://orcid.org/0000-0003-3375-1014"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Runyu Jing","raw_affiliation_strings":["School of Cyber Science and Engineering, Sichuan University, Chengdu 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Cyber Science and Engineering, Sichuan University, Chengdu 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100703866","display_name":"Menglong Li","orcid":"https://orcid.org/0000-0001-7365-0344"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Menglong Li","raw_affiliation_strings":["College of Chemistry, Sichuan University, Chengdu 610064, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Chemistry, Sichuan University, Chengdu 610064, China","institution_ids":["https://openalex.org/I24185976"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5063197812","https://openalex.org/A5100703866"],"corresponding_institution_ids":["https://openalex.org/I24185976"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2227},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2227},"fwci":0.2221,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.48756263,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"13","issue":"8","first_page":"1467","last_page":"1467"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983999729156494,"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":0.991100013256073,"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/autoencoder","display_name":"Autoencoder","score":0.7342711687088013},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6815388202667236},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5863178968429565},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.5492284297943115},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45884832739830017},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41051048040390015},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36227554082870483},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3526170551776886}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7342711687088013},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6815388202667236},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5863178968429565},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.5492284297943115},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45884832739830017},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41051048040390015},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36227554082870483},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3526170551776886},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/sym13081467","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13081467","pdf_url":"https://www.mdpi.com/2073-8994/13/8/1467/pdf?version=1628651718","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:1dd8998636094f46bfb661a007927c87","is_oa":true,"landing_page_url":"https://doaj.org/article/1dd8998636094f46bfb661a007927c87","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":"Symmetry, Vol 13, Iss 8, p 1467 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2073-8994/13/8/1467/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/sym13081467","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Symmetry","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/sym13081467","is_oa":true,"landing_page_url":"https://doi.org/10.3390/sym13081467","pdf_url":"https://www.mdpi.com/2073-8994/13/8/1467/pdf?version=1628651718","source":{"id":"https://openalex.org/S190787756","display_name":"Symmetry","issn_l":"2073-8994","issn":["2073-8994"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Symmetry","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1395312755","display_name":"\u57fa\u4e8e\u591a\u8c03\u63a7\u56e0\u5b50\u7684\u7ec6\u80de/\u7ec4\u7ec7\u7279\u5f02\u6027\u57fa\u56e0\u8c03\u63a7\u673a\u7406\u7814\u7a76","funder_award_id":"21775107","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W2966661","https://openalex.org/W1492083415","https://openalex.org/W1526741802","https://openalex.org/W1538685017","https://openalex.org/W1602702667","https://openalex.org/W1823022514","https://openalex.org/W1902027874","https://openalex.org/W1984883254","https://openalex.org/W2053757129","https://openalex.org/W2054141820","https://openalex.org/W2097310219","https://openalex.org/W2110096996","https://openalex.org/W2117757143","https://openalex.org/W2118718620","https://openalex.org/W2122538988","https://openalex.org/W2522945402","https://openalex.org/W2790768464","https://openalex.org/W2800392236","https://openalex.org/W2884689635","https://openalex.org/W2889326414","https://openalex.org/W2892648189","https://openalex.org/W2901677030","https://openalex.org/W2934716754","https://openalex.org/W2949177718","https://openalex.org/W2953322088","https://openalex.org/W2979464975","https://openalex.org/W3014641307","https://openalex.org/W3017348419","https://openalex.org/W3024013192","https://openalex.org/W3126363652","https://openalex.org/W3131634425","https://openalex.org/W3175242715","https://openalex.org/W4235169531","https://openalex.org/W4295312788","https://openalex.org/W4298289240","https://openalex.org/W6637568146","https://openalex.org/W6638577820","https://openalex.org/W6677759377","https://openalex.org/W6753302441","https://openalex.org/W6766978945","https://openalex.org/W6991377603"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W34555840"],"abstract_inverted_index":{"Single-cell":[0],"ATAC-seq":[1],"(scATAC-seq),":[2],"as":[3,86],"the":[4,24,30,34,41,58,63,107,123,126,129,142,154,159,165],"updating":[5],"of":[6,19,26,33,43,65,83,94,100,131],"ATAC-seq,":[7],"provides":[8],"a":[9,46,73,87,116,135,152],"novel":[10],"method":[11,155],"for":[12,76,111,148,157],"probing":[13],"open":[14],"chromatin":[15],"sites.":[16],"Currently,":[17],"research":[18],"scATAC-seq":[20,78,149],"is":[21],"faced":[22],"with":[23],"problem":[25],"high":[27],"dimensionality":[28],"and":[29,51,91,110,128,145],"inherent":[31],"sparsity":[32,160],"generated":[35,166],"data.":[36,60],"Recently,":[37],"several":[38],"works":[39],"proposed":[40],"use":[42],"an":[44],"autoencoder\u2013decoder,":[45],"symmetry":[47,88],"neural":[48,89],"network":[49],"architecture,":[50],"non-negative":[52],"matrix":[53,95],"factorization":[54,96],"methods":[55,127],"to":[56,105],"characterize":[57],"high-dimensional":[59],"To":[61],"evaluate":[62],"performance":[64,124],"multiple":[66,74],"methods,":[67],"in":[68,134,164],"this":[69],"work,":[70],"we":[71,120,139],"performed":[72],"comparison":[75],"characterizing":[77],"based":[79],"on":[80],"four":[81],"kinds":[82,93],"auto-encoders":[84],"known":[85],"network,":[90],"two":[92],"methods.":[97],"Different":[98],"sizes":[99],"latent":[101,132],"features":[102,133],"were":[103],"used":[104],"generate":[106],"UMAP":[108],"plots":[109],"further":[112],"K-means":[113],"clustering.":[114],"Using":[115],"gold-standard":[117],"data":[118],"set,":[119],"practically":[121],"explored":[122],"among":[125],"number":[130],"comprehensive":[136],"way.":[137],"Finally,":[138],"briefly":[140],"discuss":[141],"underlying":[143],"difficulties":[144],"future":[146],"directions":[147],"characterizing.":[150],"As":[151],"result,":[153],"designed":[156],"handling":[158],"outperforms":[161],"other":[162],"tools":[163],"dataset.":[167]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
