{"id":"https://openalex.org/W7117992623","doi":"https://doi.org/10.1371/journal.pcbi.1013824","title":"CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning","display_name":"CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning","publication_year":2026,"publication_date":"2026-01-02","ids":{"openalex":"https://openalex.org/W7117992623","doi":"https://doi.org/10.1371/journal.pcbi.1013824","pmid":"https://pubmed.ncbi.nlm.nih.gov/41481570"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013824","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013824","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5121777711","display_name":"Yan Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I78978612","display_name":"Yangzhou University","ror":"https://ror.org/03tqb8s11","country_code":"CN","type":"education","lineage":["https://openalex.org/I78978612"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Liu","raw_affiliation_strings":["Department of Computer Science, Yangzhou University, Yangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yangzhou University, Yangzhou, China","institution_ids":["https://openalex.org/I78978612"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121796284","display_name":"Yu Xia","orcid":null},"institutions":[{"id":"https://openalex.org/I78978612","display_name":"Yangzhou University","ror":"https://ror.org/03tqb8s11","country_code":"CN","type":"education","lineage":["https://openalex.org/I78978612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Xia","raw_affiliation_strings":["Department of Computer Science, Yangzhou University, Yangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yangzhou University, Yangzhou, China","institution_ids":["https://openalex.org/I78978612"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121384010","display_name":"He Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I167027274","display_name":"Nanjing Forestry University","ror":"https://ror.org/03m96p165","country_code":"CN","type":"education","lineage":["https://openalex.org/I167027274"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"He Yan","raw_affiliation_strings":["College of Information Science and Technology & Artificial Intelligence, Nanjing Forestry University, Nanjing, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology & Artificial Intelligence, Nanjing Forestry University, Nanjing, P. R. China","institution_ids":["https://openalex.org/I167027274"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024036815","display_name":"Long-Chen Shen","orcid":"https://orcid.org/0000-0002-0045-4745"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long-Chen Shen","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121813959","display_name":"Yiheng Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I119454577","display_name":"Nanjing Agricultural University","ror":"https://ror.org/05td3s095","country_code":"CN","type":"education","lineage":["https://openalex.org/I119454577"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiheng Zhu","raw_affiliation_strings":["College of Artificial Inteligence, Nanjing Agricultural University, Nanjing, Jiangsu Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Artificial Inteligence, Nanjing Agricultural University, Nanjing, Jiangsu Province, China","institution_ids":["https://openalex.org/I119454577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121396693","display_name":"Ji-Peng Qiang","orcid":null},"institutions":[{"id":"https://openalex.org/I78978612","display_name":"Yangzhou University","ror":"https://ror.org/03tqb8s11","country_code":"CN","type":"education","lineage":["https://openalex.org/I78978612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ji-Peng Qiang","raw_affiliation_strings":["Department of Computer Science, Yangzhou University, Yangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yangzhou University, Yangzhou, China","institution_ids":["https://openalex.org/I78978612"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121751136","display_name":"Guo Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guo Wei","raw_affiliation_strings":["School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China"],"raw_orcid":"https://orcid.org/0000-0002-2525-1776","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China","institution_ids":["https://openalex.org/I881766915"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5121777711"],"corresponding_institution_ids":["https://openalex.org/I78978612"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01011858,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"e1013824","last_page":"e1013824"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.994700014591217,"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":0.994700014591217,"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":0.003100000089034438,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.800000011920929},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6675999760627747},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.5884000062942505},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.555400013923645},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5281000137329102},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5123999714851379},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5092999935150146},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.492000013589859},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.4300000071525574}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.800000011920929},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7609999775886536},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6675999760627747},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6190000176429749},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.5884000062942505},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.555400013923645},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5357999801635742},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5281000137329102},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5123999714851379},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5092999935150146},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.492000013589859},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4300000071525574},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4108999967575073},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.39899998903274536},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.38989999890327454},{"id":"https://openalex.org/C2776434776","wikidata":"https://www.wikidata.org/wiki/Q19246213","display_name":"Domain adaptation","level":3,"score":0.36469998955726624},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.32249999046325684},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.3125999867916107},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3102000057697296},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.3095000088214874},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3021000027656555},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.2831000089645386},{"id":"https://openalex.org/C63085389","wikidata":"https://www.wikidata.org/wiki/Q4287912","display_name":"Medoid","level":3,"score":0.27639999985694885},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.2736000120639801},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.27070000767707825},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.2599000036716461}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1013824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013824","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41481570","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41481570","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12758788","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12758788/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013824","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013824","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.7578046917915344,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G669005089","display_name":null,"funder_award_id":"No.62306142","funder_id":"https://openalex.org/F4320315254","funder_display_name":"Innovative Research Group Project of the National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320315254","display_name":"Innovative Research Group Project of the National Natural Science Foundation of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1991026693","https://openalex.org/W2115403315","https://openalex.org/W2520774990","https://openalex.org/W2907514116","https://openalex.org/W2946232537","https://openalex.org/W2966569571","https://openalex.org/W2979509742","https://openalex.org/W3004607725","https://openalex.org/W3092295864","https://openalex.org/W3095467524","https://openalex.org/W3099179344","https://openalex.org/W3164839005","https://openalex.org/W3196650609","https://openalex.org/W3210860076","https://openalex.org/W4205514149","https://openalex.org/W4211255280","https://openalex.org/W4221065117","https://openalex.org/W4225278475","https://openalex.org/W4225598893","https://openalex.org/W4281958589","https://openalex.org/W4287180559","https://openalex.org/W4297243391","https://openalex.org/W4312067472","https://openalex.org/W4316096017","https://openalex.org/W4360999291","https://openalex.org/W4362523594","https://openalex.org/W4378212544","https://openalex.org/W4382022265","https://openalex.org/W4387639594","https://openalex.org/W4391512208","https://openalex.org/W4392251648"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"cell":[1,200,216],"type":[2,217],"annotation":[3,179,218],"is":[4],"fundamental":[5],"to":[6,30,94,117,131,165,168,172],"single-cell":[7,220],"analysis,":[8],"yet":[9],"remains":[10],"challenging":[11],"across":[12,72,163],"heterogeneous":[13,119],"datasets":[14],"and":[15,23,35,52,75,84,113,121,154,170,184,211],"modalities.":[16],"In":[17],"particular,":[18],"transferring":[19],"labels":[20],"between":[21,104],"scRNA-seq":[22],"scATAC-seq":[24],"data":[25],"poses":[26],"unique":[27],"difficulties":[28],"due":[29],"discrepancies":[31],"in":[32,181,219],"sequencing":[33],"protocols":[34],"feature":[36,155],"spaces.":[37],"Existing":[38],"methods":[39,180],"typically":[40],"handle":[41],"only":[42],"a":[43,60,80,123],"subset":[44],"of":[45,91,100],"these":[46,203],"challenges,":[47],"often":[48],"requiring":[49],"scenario-specific":[50],"adjustments":[51],"offering":[53],"limited":[54],"interpretability.":[55],"Here,":[56],"we":[57],"present":[58],"CellPredX,":[59],"structurally":[61],"unified":[62,81],"but":[63],"adaptively":[64],"parameterized,":[65],"semi-supervised":[66],"cross-modality":[67,215],"framework":[68],"for":[69,96,214],"label":[70],"transfer":[71],"scRNA-seq,":[73],"scATAC-seq,":[74],"cross-protocol":[76],"datasets.":[77],"While":[78],"maintaining":[79],"model":[82,158],"architecture":[83],"optimization":[85],"strategy,":[86],"CellPredX":[87,109,175,207],"allows":[88],"adaptive":[89],"tuning":[90],"loss-weight":[92],"hyperparameters":[93],"account":[95],"the":[97],"varying":[98],"degree":[99],"similarity":[101],"or":[102],"discrepancy":[103],"different":[105],"reference-query":[106],"dataset":[107],"pairs.":[108],"integrates":[110],"domain":[111],"adaptation":[112],"deep":[114],"metric":[115],"learning":[116],"align":[118],"embeddings,":[120],"introduces":[122],"sparse":[124],"center":[125],"loss":[126],"with":[127,198],"an":[128,139,209],"attention":[129],"mechanism":[130],"enhance":[132],"discriminative":[133],"representations":[134],"while":[135],"suppressing":[136],"noise.":[137],"Moreover,":[138],"integrated":[140],"interpreter":[141,187],"module":[142,188],"based":[143],"on":[144],"gradient":[145],"attribution":[146],"enables":[147],"biological":[148],"interpretability":[149],"by":[150],"identifying":[151],"key":[152],"markers":[153],"dimensions":[156],"driving":[157],"predictions.":[159],"Through":[160],"extensive":[161],"benchmarking":[162],"scRNA":[164,171,173],"scATAC,":[166,169],"scATAC":[167],"transfers,":[174],"consistently":[176],"outperforms":[177],"state-of-the-art":[178],"both":[182],"accuracy":[183],"robustness.":[185],"The":[186],"further":[189],"reveals":[190],"biologically":[191],"meaningful":[192],"marker":[193],"patterns":[194],"that":[195,206],"are":[196],"consistent":[197],"known":[199],"hierarchies.":[201],"Together,":[202],"results":[204],"demonstrate":[205],"provides":[208],"interpretable":[210],"scalable":[212],"solution":[213],"multi-omic":[221],"integration.":[222]},"counts_by_year":[],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2026-01-02T00:00:00"}
