{"id":"https://openalex.org/W4392449793","doi":"https://doi.org/10.1109/tcbb.2024.3372970","title":"Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data","display_name":"Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data","publication_year":2024,"publication_date":"2024-03-05","ids":{"openalex":"https://openalex.org/W4392449793","doi":"https://doi.org/10.1109/tcbb.2024.3372970","pmid":"https://pubmed.ncbi.nlm.nih.gov/38442065"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3372970","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3372970","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061270485","display_name":"Yuhang Jia","orcid":"https://orcid.org/0000-0002-0412-3812"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuhang Jia","raw_affiliation_strings":["School of Statistics and Data Science, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-0412-3812","affiliations":[{"raw_affiliation_string":"School of Statistics and Data Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104652195","display_name":"Siyu Li","orcid":"https://orcid.org/0000-0001-7233-7903"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siyu Li","raw_affiliation_strings":["School of Statistics and Data Science, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0001-7233-7903","affiliations":[{"raw_affiliation_string":"School of Statistics and Data Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100623015","display_name":"Rui Jiang","orcid":"https://orcid.org/0000-0002-7533-3753"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Jiang","raw_affiliation_strings":["BNRIST/Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-7533-3753","affiliations":[{"raw_affiliation_string":"BNRIST/Department of Automation, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046058016","display_name":"Shengquan Chen","orcid":"https://orcid.org/0000-0002-3503-9306"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]},{"id":"https://openalex.org/I4401200345","display_name":"Laboratoire de physique de la mati\u00e8re condens\u00e9e","ror":"https://ror.org/05brss208","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4401200345","https://openalex.org/I4647051"]}],"countries":["CN","FR"],"is_corresponding":false,"raw_author_name":"Shengquan Chen","raw_affiliation_strings":["School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-3503-9306","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279","https://openalex.org/I4401200345"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061270485"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":0.8907,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.71768393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"21","issue":"3","first_page":"461","last_page":"471"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"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":0.9997000098228455,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9991000294685364,"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"}},{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","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"}}],"keywords":[{"id":"https://openalex.org/keywords/cascade","display_name":"Cascade","score":0.8267508745193481},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7622549533843994},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6756216287612915},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4778454005718231},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4476704001426697},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40931418538093567},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3236328661441803},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3208900988101959},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12719941139221191}],"concepts":[{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.8267508745193481},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7622549533843994},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6756216287612915},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4778454005718231},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4476704001426697},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40931418538093567},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3236328661441803},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3208900988101959},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12719941139221191},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3372970","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3372970","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38442065","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38442065","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1037446360","display_name":null,"funder_award_id":"63231137","funder_id":"https://openalex.org/F4320323021","funder_display_name":"Nankai University"},{"id":"https://openalex.org/G4168565681","display_name":null,"funder_award_id":"62273194","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5364641554","display_name":null,"funder_award_id":"62203236","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/F4320323021","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W2008056655","https://openalex.org/W2122111042","https://openalex.org/W2790768464","https://openalex.org/W2796170779","https://openalex.org/W2801527818","https://openalex.org/W2887910040","https://openalex.org/W2894687190","https://openalex.org/W2911555896","https://openalex.org/W2911964244","https://openalex.org/W2916020270","https://openalex.org/W2934716754","https://openalex.org/W2953322088","https://openalex.org/W2962862931","https://openalex.org/W2971653850","https://openalex.org/W2979464975","https://openalex.org/W2989061519","https://openalex.org/W2995896027","https://openalex.org/W3002417351","https://openalex.org/W3135165543","https://openalex.org/W3153110198","https://openalex.org/W3161070260","https://openalex.org/W3161076052","https://openalex.org/W3182503854","https://openalex.org/W3198123874","https://openalex.org/W3198658154","https://openalex.org/W4205428105","https://openalex.org/W4211255280","https://openalex.org/W4312210661","https://openalex.org/W4313156423","https://openalex.org/W6737947904","https://openalex.org/W6769472948"],"related_works":["https://openalex.org/W2153719181","https://openalex.org/W1971748923","https://openalex.org/W1566155057","https://openalex.org/W2060986072","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2052574922","https://openalex.org/W2218034408","https://openalex.org/W64588465"],"abstract_inverted_index":{"Rapid":[0],"advances":[1],"in":[2,37,121,157,172],"single-cell":[3],"chromatin":[4],"accessibility":[5],"sequencing":[6],"(scCAS)":[7],"technologies":[8],"have":[9],"enabled":[10],"the":[11,18,41,82,90,117,129,154],"characterization":[12],"of":[13,23,72,84,92,119,131,142],"epigenomic":[14],"heterogeneity":[15,171],"and":[16,40,48,63,88,96,105,123,140],"increased":[17],"demand":[19],"for":[20,33,46,103,151],"automatic":[21],"annotation":[22,36,58,101],"cell":[24,34,50,86,107,143,155,170],"types.":[25,51,108,144],"However,":[26],"there":[27],"are":[28],"few":[29],"computational":[30],"methods":[31,43,150],"tailored":[32],"type":[35],"scCAS":[38,73,173],"data":[39,138,174],"existing":[42],"perform":[44],"poorly":[45],"differentiating":[47,104],"imbalanced":[49,106],"Here,":[52],"we":[53,75,110],"propose":[54],"CASCADE,":[55],"a":[56,70],"novel":[57],"method":[59],"based":[60],"on":[61,69],"simulation-":[62],"denoising-based":[64],"strategies.":[65],"With":[66],"comprehensive":[67],"experiments":[68,114,126],"number":[71,141],"datasets,":[74],"showed":[76],"that":[77,163],"CASCADE":[78,122,132,146,164],"can":[79],"effectively":[80],"distinguish":[81],"patterns":[83],"different":[85],"types":[87,156],"mitigate":[89],"effect":[91],"high":[93],"noise":[94],"levels,":[95],"thus":[97],"achieve":[98],"significantly":[99,147],"better":[100],"performance":[102],"Besides,":[109],"performed":[111],"model":[112],"ablation":[113],"to":[115,127,133],"show":[116],"contribution":[118],"modules":[120],"conducted":[124],"extensive":[125],"demonstrate":[128],"robustness":[130],"batch":[134],"effect,":[135],"imbalance":[136],"degree,":[137],"sparsity,":[139],"Moreover,":[145],"outperformed":[148],"baseline":[149],"accurately":[152],"annotating":[153],"newly":[158],"sequenced":[159],"data.":[160],"We":[161],"anticipate":[162],"will":[165],"greatly":[166],"assist":[167],"with":[168],"characterizing":[169],"analysis.":[175]},"counts_by_year":[{"year":2025,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}