{"id":"https://openalex.org/W3120463602","doi":"https://doi.org/10.1371/journal.pcbi.1008569","title":"Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data","display_name":"Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data","publication_year":2021,"publication_date":"2021-01-07","ids":{"openalex":"https://openalex.org/W3120463602","doi":"https://doi.org/10.1371/journal.pcbi.1008569","mag":"3120463602","pmid":"https://pubmed.ncbi.nlm.nih.gov/33411784"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008569","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008569","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.1008569","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083934419","display_name":"Andreas Tj\u00e4rnberg","orcid":"https://orcid.org/0000-0003-0064-1791"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andreas Tj\u00e4rnberg","raw_affiliation_strings":["Center For Genomics and Systems Biology, NYU, New York, New York, USA","Center for Developmental Genetics, New York University, New York, New York, USA","Department of Biology, NYU, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0003-0064-1791","affiliations":[{"raw_affiliation_string":"Center For Genomics and Systems Biology, NYU, New York, New York, USA","institution_ids":[]},{"raw_affiliation_string":"Center for Developmental Genetics, New York University, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Biology, NYU, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069024112","display_name":"Omar Mahmood","orcid":"https://orcid.org/0000-0002-4437-5416"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Omar Mahmood","raw_affiliation_strings":["Center For Data Science, NYU, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0002-4437-5416","affiliations":[{"raw_affiliation_string":"Center For Data Science, NYU, New York, New York, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047772808","display_name":"Christopher A. Jackson","orcid":"https://orcid.org/0000-0002-8769-2710"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher A. Jackson","raw_affiliation_strings":["Center For Genomics and Systems Biology, NYU, New York, New York, USA","Department of Biology, NYU, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0002-8769-2710","affiliations":[{"raw_affiliation_string":"Center For Genomics and Systems Biology, NYU, New York, New York, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Biology, NYU, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088855943","display_name":"Giuseppe-Antonio Saldi","orcid":"https://orcid.org/0000-0002-9994-7354"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Giuseppe-Antonio Saldi","raw_affiliation_strings":["Center For Genomics and Systems Biology, NYU, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0002-9994-7354","affiliations":[{"raw_affiliation_string":"Center For Genomics and Systems Biology, NYU, New York, New York, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091175785","display_name":"Kyunghyun Cho","orcid":"https://orcid.org/0000-0003-1669-3211"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I4210107338","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyunghyun Cho","raw_affiliation_strings":["Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, USA","Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0003-1669-3211","affiliations":[{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York, USA","institution_ids":["https://openalex.org/I4210107338"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080705309","display_name":"Lionel Christiaen","orcid":"https://orcid.org/0000-0001-5930-5667"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lionel A. Christiaen","raw_affiliation_strings":["Center for Developmental Genetics, New York University, New York, New York, USA","Department of Biology, NYU, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0001-5930-5667","affiliations":[{"raw_affiliation_string":"Center for Developmental Genetics, New York University, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Biology, NYU, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I4210107338","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard A. Bonneau","raw_affiliation_strings":["Center For Data Science, NYU, New York, New York, USA","Center For Genomics and Systems Biology, NYU, New York, New York, USA","Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, USA","Department of Biology, NYU, New York, New York, USA","Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York, USA"],"raw_orcid":"https://orcid.org/0000-0003-4354-7906","affiliations":[{"raw_affiliation_string":"Center For Data Science, NYU, New York, New York, USA","institution_ids":[]},{"raw_affiliation_string":"Center For Genomics and Systems Biology, NYU, New York, New York, USA","institution_ids":[]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, Computer Science Department, New York University, New York, New York, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Department of Biology, NYU, New York, New York, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York, USA","institution_ids":["https://openalex.org/I4210107338"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5055203249","https://openalex.org/A5083934419"],"corresponding_institution_ids":["https://openalex.org/I36672615","https://openalex.org/I4210107338","https://openalex.org/I57206974"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.3615,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.89407095,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"e1008569","last_page":"e1008569"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9900000095367432,"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":0.9879999756813049,"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/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.6382392048835754},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6280782222747803},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5225838422775269},{"id":"https://openalex.org/keywords/noise-reduction","display_name":"Noise reduction","score":0.516669750213623},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4812181293964386},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.4798271656036377},{"id":"https://openalex.org/keywords/skewness","display_name":"Skewness","score":0.4190516471862793},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.3816866874694824},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3709942102432251},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2695576548576355},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26397836208343506},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2262319028377533}],"concepts":[{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.6382392048835754},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6280782222747803},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5225838422775269},{"id":"https://openalex.org/C163294075","wikidata":"https://www.wikidata.org/wiki/Q581861","display_name":"Noise reduction","level":2,"score":0.516669750213623},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4812181293964386},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.4798271656036377},{"id":"https://openalex.org/C122342681","wikidata":"https://www.wikidata.org/wiki/Q330828","display_name":"Skewness","level":2,"score":0.4190516471862793},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.3816866874694824},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3709942102432251},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2695576548576355},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26397836208343506},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2262319028377533}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":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":"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":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1008569","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008569","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:33411784","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33411784","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:RePEc:plo:pcbi00:1008569","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008569","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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:doaj.org/article:a8a4056d539749db956875c60e591791","is_oa":true,"landing_page_url":"https://doaj.org/article/a8a4056d539749db956875c60e591791","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 1, p e1008569 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:6748256","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7817019","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7817019","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7817019","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.1008569","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008569","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":[],"awards":[{"id":"https://openalex.org/G2456854700","display_name":null,"funder_award_id":"1546218","funder_id":"https://openalex.org/F4320337399","funder_display_name":"Division of Integrative Organismal Systems"},{"id":"https://openalex.org/G2726022791","display_name":null,"funder_award_id":"IOS-1546218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3703319430","display_name":"DMREF: Computationally Driven-Genetically Engineered Materials (CD-GEM)","funder_award_id":"1728858","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4004435369","display_name":null,"funder_award_id":"R01HD096770","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7133022921","display_name":"RESEARCH-PGR: Systems Genomics of Rice Stress Adaptation","funder_award_id":"1546218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8288036582","display_name":null,"funder_award_id":"NIH R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"},{"id":"https://openalex.org/F4320337399","display_name":"Division of Integrative Organismal Systems","ror":"https://ror.org/01rvays47"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1994267372","https://openalex.org/W2092923243","https://openalex.org/W2128120736","https://openalex.org/W2131681506","https://openalex.org/W2146292423","https://openalex.org/W2177432730","https://openalex.org/W2338756998","https://openalex.org/W2342688693","https://openalex.org/W2509957998","https://openalex.org/W2526262591","https://openalex.org/W2751468300","https://openalex.org/W2766437506","https://openalex.org/W2773035279","https://openalex.org/W2774761491","https://openalex.org/W2786672974","https://openalex.org/W2792693509","https://openalex.org/W2800392236","https://openalex.org/W2800912249","https://openalex.org/W2805619986","https://openalex.org/W2889326414","https://openalex.org/W2898821675","https://openalex.org/W2900510132","https://openalex.org/W2901677030","https://openalex.org/W2907783748","https://openalex.org/W2922102242","https://openalex.org/W2923101443","https://openalex.org/W2924067995","https://openalex.org/W2947275143","https://openalex.org/W2947877009","https://openalex.org/W2949177718","https://openalex.org/W2949725501","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2951890476","https://openalex.org/W2953852587","https://openalex.org/W2976333423","https://openalex.org/W2980495984","https://openalex.org/W2989807288","https://openalex.org/W2989879898","https://openalex.org/W3000145506","https://openalex.org/W3003223963","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W6755861362","https://openalex.org/W6759001153","https://openalex.org/W6761048162","https://openalex.org/W6768183699"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549","https://openalex.org/W3123177881"],"abstract_inverted_index":{"The":[0,65,94,179],"analysis":[1,21],"of":[2,22,40,86,116,136,158,273],"single-cell":[3,177],"genomics":[4],"data":[5,24,61,183,219,249,282],"presents":[6],"several":[7,238],"statistical":[8],"challenges,":[9],"and":[10,32,34,51,62,78,82,91,108,143,160,189,227,251,275,280],"extensive":[11],"efforts":[12],"have":[13],"been":[14,49,98],"made":[15],"to":[16,73,113,128,140,196,215,247],"produce":[17],"methods":[18,103,126,163,217,244],"for":[19,36,101,122,169,264,283],"the":[20,59,75,84,99,114,144,156],"this":[23,152],"that":[25,202,245],"impute":[26],"missing":[27],"values,":[28],"address":[29],"sampling":[30],"issues":[31],"quantify":[33],"correct":[35],"noise.":[37],"In":[38,151],"spite":[39],"such":[41],"efforts,":[42],"no":[43],"consensus":[44],"on":[45,58],"best":[46],"practices":[47],"has":[48,96],"established":[50,221],"all":[52],"current":[53],"approaches":[54],"vary":[55],"substantially":[56],"based":[57],"available":[60,286],"empirical":[63],"tests.":[64],"k-Nearest":[66],"Neighbor":[67],"Graph":[68],"(kNN-G)":[69],"is":[70,83,213,285],"often":[71],"used":[72,89],"infer":[74],"identities":[76],"of,":[77],"relationships":[79],"between,":[80],"cells":[81],"basis":[85,100],"many":[87],"widely":[88],"dimensionality-reduction":[90],"projection":[92],"methods.":[93,278],"kNN-G":[95],"also":[97],"imputation":[102],"using,":[104],"e.g.,":[105],"neighbor":[106],"averaging":[107],"graph":[109,263],"diffusion.":[110],"However,":[111],"due":[112],"lack":[115],"an":[117],"agreed-upon":[118],"optimal":[119,205],"objective":[120,210],"function":[121,211],"choosing":[123],"hyperparameters,":[124],"these":[125,267],"tend":[127,246],"oversmooth":[129,248],"data,":[130],"thereby":[131],"resulting":[132],"in":[133,176],"a":[134,165,185,193,259,270],"loss":[135],"information":[137],"with":[138,164,184,204],"regard":[139],"cell":[141],"identity":[142,226],"specific":[145],"gene-to-gene":[146],"patterns":[147],"underlying":[148],"regulatory":[149],"mechanisms.":[150],"paper,":[153],"we":[154],"investigate":[155],"tuning":[157],"kNN-":[159,274],"diffusion-based":[161,276],"denoising":[162,203,277],"novel":[166],"non-stochastic":[167],"method":[168],"optimally":[170],"preserving":[171],"biologically":[172],"relevant":[173],"informative":[174],"variance":[175,236],"data.":[178],"framework,":[180],"Denoising":[181],"Expression":[182],"Weighted":[186],"Affinity":[187],"Kernel":[188],"Self-Supervision":[190],"(DEW\u00c4KSS),":[191],"uses":[192,258],"self-supervised":[194],"technique":[195],"tune":[197],"its":[198],"parameters.":[199],"We":[200],"demonstrate":[201],"parameters":[206],"selected":[207],"by":[208],"our":[209],"(i)":[212],"robust":[214,229],"preprocessing":[216],"using":[218],"from":[220],"benchmarks,":[222],"(ii)":[223],"disentangles":[224],"cellular":[225],"maintains":[228,235],"clusters":[230],"over":[231],"dimension-reduction":[232],"methods,":[233],"(iii)":[234],"along":[237],"expression":[239],"dimensions,":[240],"unlike":[241],"previous":[242],"heuristic-based":[243],"variance,":[250],"(iv)":[252],"rarely":[253],"involves":[254],"diffusion":[255],"but":[256],"rather":[257],"fixed":[260],"weighted":[261],"kNN":[262],"denoising.":[265],"Together,":[266],"findings":[268],"provide":[269],"new":[271],"understanding":[272],"Code":[279],"example":[281],"DEW\u00c4KSS":[284],"at":[287],"https://gitlab.com/Xparx/dewakss/-/tree/Tjarnberg2020branch.":[288]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":7}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
