{"id":"https://openalex.org/W4408565368","doi":"https://doi.org/10.1109/tcbbio.2025.3553068","title":"scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering","display_name":"scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering","publication_year":2025,"publication_date":"2025-03-18","ids":{"openalex":"https://openalex.org/W4408565368","doi":"https://doi.org/10.1109/tcbbio.2025.3553068","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811359"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3553068","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3553068","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pubmed.ncbi.nlm.nih.gov/40811359/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057660606","display_name":"Xiang Lin","orcid":"https://orcid.org/0000-0002-7634-5780"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiang Lin","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","Department of Computer Science, New Jersey Institute of Technology, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101154561","display_name":"Jianlan Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianlan Ren","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","Department of Computer Science, New Jersey Institute of Technology, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047289560","display_name":"Le Gao","orcid":"https://orcid.org/0000-0003-2625-8774"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Le Gao","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","Department of Computer Science, New Jersey Institute of Technology, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100704437","display_name":"Junwen Wang","orcid":"https://orcid.org/0000-0003-2426-8944"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Junwen Wang","raw_affiliation_strings":["Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001916237","display_name":"Zhi Wei","orcid":"https://orcid.org/0000-0001-6059-4267"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhi Wei","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","Department of Computer Science, New Jersey Institute of Technology, NJ, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5057660606"],"corresponding_institution_ids":["https://openalex.org/I118118575"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03804455,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"3","first_page":"1086","last_page":"1094"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.8179000020027161,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.8179000020027161,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7835000157356262,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.6947000026702881,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6669394969940186},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6595869660377502},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5194392204284668},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.42799198627471924},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39815688133239746},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3558417856693268}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6669394969940186},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6595869660377502},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5194392204284668},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.42799198627471924},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39815688133239746},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3558417856693268}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbbio.2025.3553068","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3553068","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811359","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811359","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 transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:hub.hku.hk:10722/357969","is_oa":false,"landing_page_url":"https://hub.hku.hk/handle/10722/357969","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12421913","is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811359/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12421913","is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811359/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1988391018","https://openalex.org/W2000517438","https://openalex.org/W2025768430","https://openalex.org/W2063974591","https://openalex.org/W2092131698","https://openalex.org/W2100495367","https://openalex.org/W2124678205","https://openalex.org/W2158175056","https://openalex.org/W2338756998","https://openalex.org/W2513922839","https://openalex.org/W2794521141","https://openalex.org/W2794891507","https://openalex.org/W2908782956","https://openalex.org/W2937917790","https://openalex.org/W2948469692","https://openalex.org/W2949177718","https://openalex.org/W2962073995","https://openalex.org/W2967177832","https://openalex.org/W2984472267","https://openalex.org/W3005127469","https://openalex.org/W3021272327","https://openalex.org/W3124814274","https://openalex.org/W3129866267","https://openalex.org/W3137285774","https://openalex.org/W3164852867","https://openalex.org/W3176693948","https://openalex.org/W6685380521","https://openalex.org/W6685562342","https://openalex.org/W6756040250"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"The":[0,11],"scRNA-seq":[1,66],"technology":[2,19],"enables":[3],"high-resolution":[4],"profiling":[5],"and":[6,16,100,170],"analysis":[7],"of":[8,14,45,74,161],"individual":[9],"cells.":[10],"increasing":[12],"availability":[13],"datasets":[15,27,31,47,137,205],"advancements":[17],"in":[18,55,84,123,134,143,159],"have":[20,62,88,148,175],"prompted":[21],"researchers":[22],"to":[23,40,104,117,131,138,152,183],"integrate":[24,184],"existing":[25],"annotated":[26,140],"with":[28],"newly":[29],"sequenced":[30],"for":[32,65,202],"a":[33,72,90,97,200],"more":[34],"comprehensive":[35],"analysis.":[36],"It":[37],"is":[38,70],"important":[39],"ensure":[41],"that":[42,76,154,177,194],"the":[43,51,56,80,119,124,135,139,144],"integration":[44],"new":[46,136],"does":[48],"not":[49],"alter":[50],"cell":[52,141],"clusters":[53,142],"defined":[54],"old/reference":[57],"datasets.":[58,111,146,172,187],"Although":[59],"several":[60],"methods":[61,158],"been":[63],"developed":[64],"data":[67,162],"integration,":[68,163],"there":[69],"currently":[71],"lack":[73],"tools":[75],"can":[77,179],"simultaneously":[78],"achieve":[79],"aforementioned":[81],"objectives.":[82],"Therefore,":[83],"this":[85],"study,":[86],"we":[87,174,192],"introduced":[89],"novel":[91],"tool":[92,201],"called":[93],"scDILT,":[94],"which":[95],"leverages":[96],"conditional":[98],"autoencoder":[99],"deep":[101],"embedding":[102],"clustering":[103],"effectively":[105],"remove":[106],"batch":[107],"effects":[108],"among":[109],"different":[110,208],"Moreover,":[112],"scDILT":[113,155,178,195],"utilizes":[114],"homogeneous":[115],"constraints":[116,130],"preserve":[118],"cell-type/clustering":[120],"patterns":[121],"observed":[122],"reference":[125,145],"datasets,":[126],"while":[127],"employing":[128],"heterogeneous":[129],"map":[132],"cells":[133],"We":[147],"conducted":[149],"extensive":[150],"experiments":[151],"demonstrate":[153],"outperforms":[156],"other":[157],"terms":[160],"as":[164,199],"confirmed":[165],"by":[166],"evaluations":[167],"on":[168,189],"simulated":[169],"real":[171],"Furthermore,":[173],"shown":[176],"be":[180],"successfully":[181],"applied":[182],"multi-omics":[185],"single-cell":[186,204],"Based":[188],"these":[190],"findings,":[191],"conclude":[193],"holds":[196],"great":[197],"promise":[198],"integrating":[203],"derived":[206],"from":[207],"batches,":[209],"experiments,":[210],"times,":[211],"or":[212],"interventions.":[213]},"counts_by_year":[],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}
