{"id":"https://openalex.org/W4402335808","doi":"https://doi.org/10.1093/bib/bbae432","title":"BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation","display_name":"BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell imputation","publication_year":2024,"publication_date":"2024-07-25","ids":{"openalex":"https://openalex.org/W4402335808","doi":"https://doi.org/10.1093/bib/bbae432","pmid":"https://pubmed.ncbi.nlm.nih.gov/39242194"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae432","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae432","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100762662","display_name":"Jiaying Zhao","orcid":"https://orcid.org/0000-0002-3375-4621"},"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":"Jiaying Zhao","raw_affiliation_strings":["Department of Mathematics, The University of Hong Kong , Pokfulam Road,","Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086061723","display_name":"Wai\u2010Ki Ching","orcid":"https://orcid.org/0000-0002-5785-3210"},"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":"Wai-Ki Ching","raw_affiliation_strings":["Department of Mathematics, The University of Hong Kong , Pokfulam Road,","Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109186264","display_name":"Chi-Wing Wong","orcid":null},"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":"Chi-Wing Wong","raw_affiliation_strings":["Department of Mathematics, The University of Hong Kong , Pokfulam Road,","Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Mathematics, The University of Hong Kong , Pokfulam Road, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083624531","display_name":"Xiaoqing Cheng","orcid":"https://orcid.org/0000-0001-5321-1459"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqing Cheng","raw_affiliation_strings":["School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi'an, Shaanxi 710049,","School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi'an, Shaanxi 710049,","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi\u2019an Jiaotong University , No. 28 Xianning West Road, Xi'an, Shaanxi 710049, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.1866,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.538318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9958000183105469,"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":0.9958000183105469,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0005000000237487257,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0003000000142492354,"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/imputation","display_name":"Imputation (statistics)","score":0.7892008423805237},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6680325269699097},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.4697946310043335},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.4607670307159424},{"id":"https://openalex.org/keywords/factorization","display_name":"Factorization","score":0.4449823200702667},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39439958333969116},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3812384605407715},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.15148678421974182},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.10906457901000977},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10744431614875793}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7892008423805237},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6680325269699097},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.4697946310043335},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.4607670307159424},{"id":"https://openalex.org/C187834632","wikidata":"https://www.wikidata.org/wiki/Q188804","display_name":"Factorization","level":2,"score":0.4449823200702667},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39439958333969116},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3812384605407715},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.15148678421974182},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.10906457901000977},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10744431614875793},{"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":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"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},{"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":3,"locations":[{"id":"doi:10.1093/bib/bbae432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae432","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39242194","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39242194","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11379494","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11379494","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae432","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3155074394","display_name":null,"funder_award_id":"12090020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3237558303","display_name":null,"funder_award_id":"11801434","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G824516698","display_name":null,"funder_award_id":"12090021","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1504886279","https://openalex.org/W1580448704","https://openalex.org/W1981509058","https://openalex.org/W1984883254","https://openalex.org/W2033072655","https://openalex.org/W2069668029","https://openalex.org/W2108119513","https://openalex.org/W2114520383","https://openalex.org/W2167190345","https://openalex.org/W2178888844","https://openalex.org/W2269040222","https://openalex.org/W2316095770","https://openalex.org/W2373831850","https://openalex.org/W2465316128","https://openalex.org/W2550701680","https://openalex.org/W2564176045","https://openalex.org/W2747877289","https://openalex.org/W2751468300","https://openalex.org/W2792693509","https://openalex.org/W2805619986","https://openalex.org/W2927507212","https://openalex.org/W2951217100","https://openalex.org/W2951506174","https://openalex.org/W2977512847","https://openalex.org/W3005127469","https://openalex.org/W3009560560","https://openalex.org/W3080162757","https://openalex.org/W3107527779","https://openalex.org/W3146824751","https://openalex.org/W4205559708","https://openalex.org/W4225138617","https://openalex.org/W4388035146","https://openalex.org/W6634645511","https://openalex.org/W6676321539","https://openalex.org/W6742045897","https://openalex.org/W6749307547","https://openalex.org/W6756299674"],"related_works":["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/W2146544734","https://openalex.org/W2075222291"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single":[1],"cell":[2,29,116],"RNA":[3],"sequencing":[4],"(scRNA-seq)":[5],"technique":[6],"enables":[7],"the":[8,19,74,79,90,110,119,123,127,138,154,168],"transcriptome":[9],"profiling":[10],"of":[11,16,112,170],"hundreds":[12],"to":[13,27,57,69,88,125,136,152,181],"ten":[14],"thousands":[15],"cells":[17],"at":[18],"unprecedented":[20],"individual":[21],"level":[22],"and":[23,83,93,115,160,173,176,199],"provides":[24],"new":[25],"insights":[26],"study":[28],"heterogeneity.":[30],"However,":[31],"its":[32,177],"advantages":[33],"are":[34,192,207,219],"hampered":[35],"by":[36,78],"dropout":[37],"events.":[38],"To":[39],"address":[40],"this":[41,190],"problem,":[42],"we":[43],"propose":[44],"a":[45,65,84,97,133,149],"Blockwise":[46],"Accelerated":[47],"Non-negative":[48],"Matrix":[49],"Factorization":[50],"framework":[51],"with":[52],"Structural":[53],"network":[54,68,77,87],"constraints":[55],"(BANMF-S)":[56],"impute":[58],"those":[59],"technical":[60],"zeros.":[61],"RESULTS:":[62],"BANMF-S":[63,108,131,165],"constructs":[64],"gene-gene":[66],"similarity":[67,86],"integrate":[70],"prior":[71],"information":[72,95],"from":[73,194],"external":[75],"PPI":[76],"Triadic":[80],"Closure":[81],"Principle":[82],"cell-cell":[85],"capture":[89],"neighborhood":[91],"structure":[92],"temporal":[94],"through":[96,142],"Minimum-Spanning":[98],"Tree.":[99],"By":[100],"collaboratively":[101],"employing":[102],"these":[103],"two":[104],"networks":[105],"as":[106],"regularizations,":[107],"encourages":[109],"coherence":[111],"similar":[113],"gene":[114],"pairs":[117],"in":[118,148,189,209,222],"latent":[120],"space,":[121],"enhancing":[122],"potential":[124],"recover":[126],"underlying":[128],"features.":[129],"Besides,":[130],"adopts":[132],"blocklization":[134],"strategy":[135],"solve":[137],"traditional":[139],"NMF":[140],"problem":[141],"distributed":[143],"Stochastic":[144],"Gradient":[145],"Descent":[146],"method":[147],"parallel":[150],"way":[151],"accelerate":[153],"optimization.":[155],"Numerical":[156],"experiments":[157],"on":[158],"simulations":[159],"real":[161],"datasets":[162],"verify":[163],"that":[164],"can":[166],"improve":[167],"accuracy":[169],"downstream":[171],"clustering":[172],"pseudo-trajectory":[174],"inference,":[175],"performance":[178],"is":[179],"superior":[180],"seven":[182],"state-of-the-art":[183],"algorithms.":[184],"AVAILABILITY:":[185],"All":[186],"data":[187,197],"used":[188],"work":[191],"downloaded":[193],"publicly":[195,220],"available":[196,221],"sources,":[198],"their":[200],"corresponding":[201],"accession":[202],"numbers":[203],"or":[204],"source":[205,217],"URLs":[206],"provided":[208],"Supplementary":[210],"File":[211],"Section":[212],"5.1":[213],"Dataset":[214],"Information.":[215],"The":[216],"codes":[218],"Github":[223],"repository":[224],"https://github.com/jiayingzhao/BANMF-S.":[225]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
