{"id":"https://openalex.org/W2791624046","doi":"https://doi.org/10.1093/bioinformatics/bty260","title":"Random forest based similarity learning for single cell RNA sequencing data","display_name":"Random forest based similarity learning for single cell RNA sequencing data","publication_year":2018,"publication_date":"2018-04-14","ids":{"openalex":"https://openalex.org/W2791624046","doi":"https://doi.org/10.1093/bioinformatics/bty260","mag":"2791624046","pmid":"https://pubmed.ncbi.nlm.nih.gov/29950006"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty260","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i79/25098553/bty260.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i79/25098553/bty260.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005527065","display_name":"Maziyar Baran Pouyan","orcid":"https://orcid.org/0000-0003-4946-7659"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maziyar Baran Pouyan","raw_affiliation_strings":["Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010346419","display_name":"Dennis Kostka","orcid":"https://orcid.org/0000-0002-1460-5487"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dennis Kostka","raw_affiliation_strings":["Department for Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA","Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department for Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010346419"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5052,"has_fulltext":false,"cited_by_count":51,"citation_normalized_percentile":{"value":0.90080537,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"34","issue":"13","first_page":"i79","last_page":"i88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9984999895095825,"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":0.9984999895095825,"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":0.00019999999494757503,"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/T10885","display_name":"Gene expression and cancer classification","score":9.999999747378752e-05,"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/computer-science","display_name":"Computer science","score":0.7331131100654602},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6209084987640381},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5397518277168274},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5364371538162231},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.493401437997818},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46028321981430054},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.4462953209877014},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3731570243835449},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3160397410392761}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7331131100654602},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6209084987640381},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5397518277168274},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5364371538162231},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.493401437997818},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46028321981430054},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.4462953209877014},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3731570243835449},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3160397410392761},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"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":"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty260","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i79/25098553/bty260.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29950006","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29950006","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:4991065","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022547","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty260","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty260","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/i79/25098553/bty260.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G6842558296","display_name":null,"funder_award_id":"R01GM115836","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2791624046.pdf","grobid_xml":"https://content.openalex.org/works/W2791624046.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1533335653","https://openalex.org/W1754857113","https://openalex.org/W1813068103","https://openalex.org/W1825077972","https://openalex.org/W1996881001","https://openalex.org/W2010653277","https://openalex.org/W2010962306","https://openalex.org/W2021833436","https://openalex.org/W2030017878","https://openalex.org/W2033072655","https://openalex.org/W2051658465","https://openalex.org/W2068881679","https://openalex.org/W2085487226","https://openalex.org/W2085667285","https://openalex.org/W2111882541","https://openalex.org/W2125027820","https://openalex.org/W2161444669","https://openalex.org/W2162833336","https://openalex.org/W2167942713","https://openalex.org/W2186956159","https://openalex.org/W2187089797","https://openalex.org/W2193667971","https://openalex.org/W2236822143","https://openalex.org/W2306630387","https://openalex.org/W2307567449","https://openalex.org/W2337733832","https://openalex.org/W2368109179","https://openalex.org/W2567510066","https://openalex.org/W2582743722","https://openalex.org/W2591733518","https://openalex.org/W2598326928","https://openalex.org/W2612758576","https://openalex.org/W2741564801","https://openalex.org/W2752378502","https://openalex.org/W2763273291","https://openalex.org/W2911964244","https://openalex.org/W2953251392","https://openalex.org/W3037609093","https://openalex.org/W4235169531","https://openalex.org/W4285719527","https://openalex.org/W6655821685","https://openalex.org/W6672191126","https://openalex.org/W6684050148","https://openalex.org/W6743835438"],"related_works":["https://openalex.org/W3193043704","https://openalex.org/W4386259002","https://openalex.org/W1546989560","https://openalex.org/W3171520305","https://openalex.org/W2068608913","https://openalex.org/W3135126032","https://openalex.org/W1924178503","https://openalex.org/W4308716060","https://openalex.org/W4280648719","https://openalex.org/W4386937079"],"abstract_inverted_index":{"Motivation:":[0],"Genome-wide":[1],"transcriptome":[2],"sequencing":[3],"applied":[4],"to":[5,114,141,186],"single":[6],"cells":[7],"(scRNA-seq)":[8],"is":[9,47,101,133,139,226],"rapidly":[10],"becoming":[11],"an":[12],"assay":[13],"of":[14,19,32,36,63,81,90,94,178,216],"choice":[15],"across":[16,174],"many":[17,52],"fields":[18],"biological":[20],"and":[21,38,79,144,146,162,180,188,220],"biomedical":[22],"research.":[23],"Scientific":[24],"objectives":[25],"often":[26],"revolve":[27],"around":[28],"discovery":[29],"or":[30,34,93],"characterization":[31],"types":[33],"sub-types":[35],"cells,":[37],"therefore,":[39],"obtaining":[40],"accurate":[41],"cell-cell":[42,116],"similarities":[43,117,148],"from":[44,118],"scRNA-seq":[45,66,85,119,131,194,217],"data":[46,67,132,155,233],"a":[48,109,123,175,205,209],"critical":[49],"step":[50],"in":[51,60,84,193,196],"studies.":[53],"While":[54],"rapid":[55],"advances":[56],"are":[57,234],"being":[58],"made":[59],"the":[61,214],"development":[62],"tools":[64],"for":[65,97,152],"analysis,":[68],"few":[69],"approaches":[70],"exist":[71],"that":[72,88,166,181,212],"explicitly":[73],"address":[74],"this":[75],"task.":[76],"Furthermore,":[77],"abundance":[78],"type":[80],"noise":[82],"present":[83,107],"datasets":[86,195],"suggest":[87],"application":[89],"generic":[91],"methods,":[92],"methods":[95,173,200],"developed":[96],"bulk":[98],"RNA-seq":[99],"data,":[100],"likely":[102],"suboptimal.":[103],"Results:":[104],"Here,":[105],"we":[106],"RAFSIL,":[108],"random":[110],"forest":[111],"based":[112],"approach":[113,168,207],"learn":[115],"data.":[120,218],"RAFSIL":[121,147,203,223],"implements":[122,204],"two-step":[124],"procedure,":[125],"where":[126,198],"feature":[127],"construction":[128],"geared":[129],"towards":[130],"followed":[134],"by":[135],"similarity":[136],"learning.":[137],"It":[138],"designed":[140],"be":[142,150,184],"adaptable":[143],"expandable,":[145],"can":[149,183],"used":[151,185],"typical":[153],"exploratory":[154],"analysis":[156,215],"tasks":[157],"like":[158],"dimension":[159],"reduction,":[160],"visualization":[161],"clustering.":[163],"We":[164],"show":[165],"our":[167],"compares":[169],"favorably":[170],"with":[171],"current":[172],"diverse":[176],"collection":[177],"datasets,":[179],"it":[182],"detect":[187],"highlight":[189],"unwanted":[190],"technical":[191],"variation":[192],"situations":[197],"other":[199],"fail.":[201],"Overall,":[202],"flexible":[206],"yielding":[208],"useful":[210],"tool":[211],"improves":[213],"Availability":[219],"implementation:":[221],"The":[222],"R":[224],"package":[225],"available":[227,235],"at":[228,236],"www.kostkalab.net/software.html.":[229],"Supplementary":[230,232],"information:":[231],"Bioinformatics":[237],"online.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
