{"id":"https://openalex.org/W4406259913","doi":"https://doi.org/10.1109/bibm62325.2024.10822866","title":"scMonica: Single-cell Mosaic Omics Nonlinear Integration and Clustering Analysis","display_name":"scMonica: Single-cell Mosaic Omics Nonlinear Integration and Clustering Analysis","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259913","doi":"https://doi.org/10.1109/bibm62325.2024.10822866"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822866","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5100418684","display_name":"Xiaoli Li","orcid":"https://orcid.org/0000-0002-0762-6562"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoli Li","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100421963","display_name":"Rui Zhang","orcid":"https://orcid.org/0000-0001-8258-3585"},"institutions":[{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Zhang","raw_affiliation_strings":["Chinese Academy of Sciences,Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology,Shenzhen,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology,Shenzhen,China","institution_ids":["https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052697587","display_name":"Saba Aslam","orcid":"https://orcid.org/0000-0001-7681-4324"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Saba Aslam","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100346092","display_name":"Huijun Li","orcid":"https://orcid.org/0000-0002-2896-3867"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huijun Li","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100764264","display_name":"Yuxi Chen","orcid":"https://orcid.org/0000-0001-9450-8793"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxi Chen","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101810352","display_name":"Zequn Zhang","orcid":"https://orcid.org/0000-0002-2138-845X"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zequn Zhang","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090067435","display_name":"R. Stephanie Huang","orcid":"https://orcid.org/0000-0002-9862-0368"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Ruey-Song Huang","raw_affiliation_strings":["University of Macau,Centre for Cognitive and Brain Sciences,Macau SAR,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Macau,Centre for Cognitive and Brain Sciences,Macau SAR,China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102437907","display_name":"Hongyan Wu","orcid":"https://orcid.org/0000-0002-8670-4978"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongyan Wu","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.9124,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.88825983,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1579","last_page":"1583"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9932000041007996,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9932000041007996,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9785000085830688,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9746999740600586,"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/mosaic","display_name":"Mosaic","score":0.7761425971984863},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5981432199478149},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5874816179275513},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45625975728034973},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.4255322813987732},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3927375376224518},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33440667390823364},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3226383328437805},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26257675886154175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25016480684280396},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.1478322446346283},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07429766654968262}],"concepts":[{"id":"https://openalex.org/C110739175","wikidata":"https://www.wikidata.org/wiki/Q133067","display_name":"Mosaic","level":2,"score":0.7761425971984863},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5981432199478149},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5874816179275513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45625975728034973},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.4255322813987732},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3927375376224518},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33440667390823364},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3226383328437805},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26257675886154175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25016480684280396},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.1478322446346283},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07429766654968262},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"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":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822866","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W2739492614","https://openalex.org/W2886347923","https://openalex.org/W2896457183","https://openalex.org/W2944851425","https://openalex.org/W2991023348","https://openalex.org/W3152371839","https://openalex.org/W3153732845","https://openalex.org/W3164692211","https://openalex.org/W3164839005","https://openalex.org/W4220939068","https://openalex.org/W4225278475","https://openalex.org/W4225598893","https://openalex.org/W4281758439","https://openalex.org/W4297243391","https://openalex.org/W4311183657","https://openalex.org/W4317884487","https://openalex.org/W4378212624","https://openalex.org/W4378838672","https://openalex.org/W4385245566","https://openalex.org/W4391168615","https://openalex.org/W4392168151","https://openalex.org/W4392807611","https://openalex.org/W4396912918","https://openalex.org/W4399387478","https://openalex.org/W6739901393","https://openalex.org/W6755207826","https://openalex.org/W6866635673"],"related_works":["https://openalex.org/W2493552207","https://openalex.org/W2397874377","https://openalex.org/W4249026204","https://openalex.org/W2027673787","https://openalex.org/W4404777802","https://openalex.org/W2327982655","https://openalex.org/W428377179","https://openalex.org/W1483215156","https://openalex.org/W4252212339","https://openalex.org/W2796222479"],"abstract_inverted_index":{"Single-cell":[0,107],"mosaic":[1,41,186],"integration":[2,39,172],"has":[3],"revolutionized":[4],"our":[5,168,196],"understanding":[6],"of":[7,29,40,60,129,160,179,185,195,241],"cellular":[8,14],"heterogeneity,":[9],"offering":[10,198],"unprecedented":[11],"resolution":[12],"into":[13],"states":[15],"and":[16,63,71,93,112,183,193,201,221,231,244],"contexts.":[17],"While":[18],"large":[19],"language":[20],"models":[21,80],"(LLMs)":[22],"have":[23],"achieved":[24],"success":[25],"in":[26,51,203,216],"the":[27,38,69,106,127,155,171,180,191,225,239],"analysis":[28],"single-cell":[30,217],"omics":[31],"data,":[32],"their":[33,150,229],"application":[34],"specifically":[35],"focused":[36],"on":[37,58],"data":[42,61,98,205],"remains":[43],"limited.":[44],"Current":[45],"computational":[46],"approaches":[47],"often":[48],"fall":[49],"short":[50],"addressing":[52],"these":[53,79,102,165],"challenges.":[54],"They":[55],"frequently":[56],"depend":[57],"assumptions":[59],"completeness":[62],"uniform":[64],"quality,":[65],"failing":[66],"to":[67,212,237],"manage":[68],"variability":[70],"noise":[72],"effectively":[73],"introduced":[74],"by":[75],"missing":[76],"data.":[77],"Moreover,":[78],"might":[81],"not":[82],"efficiently":[83],"process":[84,173],"large,":[85],"diverse":[86],"datasets":[87],"or":[88],"account":[89],"for":[90,149,176],"biological":[91],"heterogeneity":[92,182],"long-ranging":[94],"dependencies":[95,140],"across":[96],"various":[97],"types.":[99],"To":[100],"address":[101],"shortcomings,":[103],"we":[104],"introduce":[105],"Mosaic":[108],"Omics":[109],"Nonlinear":[110],"Integration":[111],"Clustering":[113],"Analysis":[114],"(scMonica)":[115],"framework,":[116],"which":[117,135],"employs":[118],"a":[119],"LSTM-transformer":[120],"hybrid":[121],"architecture.":[122],"This":[123],"innovative":[124],"model":[125],"combines":[126],"strengths":[128],"Long":[130],"Short-Term":[131],"Memory":[132],"(LSTM)":[133],"networks,":[134],"excel":[136],"at":[137],"capturing":[138],"long-range":[139],"within":[141],"sequential":[142],"gene":[143],"expression":[144],"patterns,":[145],"with":[146],"transformers,":[147],"renowned":[148],"attention":[151],"mechanisms":[152],"that":[153,235],"handle":[154],"complex,":[156],"non-linear":[157],"interactions":[158],"characteristic":[159],"multi-layered":[161],"datasets.":[162,187],"By":[163],"leveraging":[164],"complementary":[166],"strengths,":[167],"approach":[169],"enhances":[170],"significantly,":[174],"allowing":[175],"nuanced":[177],"management":[178],"intrinsic":[181],"sparsity":[184],"Comprehensive":[188],"evaluations":[189],"demonstrate":[190],"robustness":[192],"effectiveness":[194],"approach,":[197],"unparalleled":[199],"versatility":[200],"accuracy":[202],"multi-omics":[204],"analysis.":[206],"These":[207],"advancements":[208],"underscore":[209],"scMonica\u2019s":[210],"potential":[211],"drive":[213],"significant":[214],"insights":[215],"developmental":[218],"biology,":[219],"oncology,":[220],"beyond.":[222],"We":[223],"discuss":[224],"underlying":[226],"technologies,":[227],"analyze":[228],"applications,":[230],"contemplate":[232],"future":[233],"directions":[234],"promise":[236],"extend":[238],"boundaries":[240],"both":[242],"research":[243],"clinical":[245],"domains.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
