{"id":"https://openalex.org/W2982605893","doi":"https://doi.org/10.1007/s10994-021-06043-1","title":"Embedding to reference t-SNE space addresses batch effects in single-cell classification","display_name":"Embedding to reference t-SNE space addresses batch effects in single-cell classification","publication_year":2021,"publication_date":"2021-08-24","ids":{"openalex":"https://openalex.org/W2982605893","doi":"https://doi.org/10.1007/s10994-021-06043-1","mag":"2982605893"},"language":"en","primary_location":{"id":"doi:10.1007/s10994-021-06043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-021-06043-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-021-06043-1.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10994-021-06043-1.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054118774","display_name":"Pavlin G. Poli\u010dar","orcid":"https://orcid.org/0000-0002-6462-9372"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Pavlin G. Poli\u010dar","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0002-6462-9372","affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054448749","display_name":"Martin Stra\u017ear","orcid":"https://orcid.org/0000-0003-3064-1055"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Martin Stra\u017ear","raw_affiliation_strings":["Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073792028","display_name":"Bla\u017e Zupan","orcid":"https://orcid.org/0000-0002-5864-7056"},"institutions":[{"id":"https://openalex.org/I153976015","display_name":"University of Ljubljana","ror":"https://ror.org/05njb9z20","country_code":"SI","type":"education","lineage":["https://openalex.org/I153976015"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["SI","US"],"is_corresponding":false,"raw_author_name":"Bla\u017e Zupan","raw_affiliation_strings":["Baylor College of Medicine, Houston, TX, 77030, USA","Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Faculty of Computer and Information Science, University of Ljubljana, Ve\u010dna pot 113, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I153976015"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054118774"],"corresponding_institution_ids":["https://openalex.org/I153976015"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.6289,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.83601285,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"112","issue":"2","first_page":"721","last_page":"740"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.991599977016449,"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":0.9868000149726868,"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/embedding","display_name":"Embedding","score":0.8292131423950195},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7528325915336609},{"id":"https://openalex.org/keywords/compendium","display_name":"Compendium","score":0.6009814739227295},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5861844420433044},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.568914532661438},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5546907186508179},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5444104075431824},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5201275944709778},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.518513560295105},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4871063232421875},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3462124764919281},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32838958501815796}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.8292131423950195},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7528325915336609},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.6009814739227295},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5861844420433044},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.568914532661438},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5546907186508179},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5444104075431824},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5201275944709778},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.518513560295105},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4871063232421875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3462124764919281},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32838958501815796},{"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/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s10994-021-06043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-021-06043-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-021-06043-1.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s10994-021-06043-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-021-06043-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-021-06043-1.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5769677123","display_name":"Artificial Intelligence and Intelligent Systems","funder_award_id":"P2-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G7323532721","display_name":null,"funder_award_id":"Program Grant P2-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"},{"id":"https://openalex.org/F4320323569","display_name":"Ministrstvo za Izobra\u017eevanje, Znanost in \u0160port","ror":"https://ror.org/05tahaz79"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2982605893.pdf","grobid_xml":"https://content.openalex.org/works/W2982605893.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1593532658","https://openalex.org/W1757909678","https://openalex.org/W1875842236","https://openalex.org/W1888008453","https://openalex.org/W2057491655","https://openalex.org/W2084942072","https://openalex.org/W2089468765","https://openalex.org/W2102212449","https://openalex.org/W2128053425","https://openalex.org/W2160208155","https://openalex.org/W2161336914","https://openalex.org/W2162651021","https://openalex.org/W2170612786","https://openalex.org/W2187089797","https://openalex.org/W2233301138","https://openalex.org/W2395579298","https://openalex.org/W2510746232","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2542768043","https://openalex.org/W2586421092","https://openalex.org/W2601723752","https://openalex.org/W2766959028","https://openalex.org/W2773035279","https://openalex.org/W2777699329","https://openalex.org/W2786672974","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2794891507","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2889326414","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2922445328","https://openalex.org/W2942880491","https://openalex.org/W2946379049","https://openalex.org/W2949177718","https://openalex.org/W2950976066","https://openalex.org/W2951638683","https://openalex.org/W2967177832","https://openalex.org/W2968378480","https://openalex.org/W2978997241","https://openalex.org/W2984472267","https://openalex.org/W2989747508","https://openalex.org/W2990200213","https://openalex.org/W2998840182","https://openalex.org/W3021272327","https://openalex.org/W3105146463","https://openalex.org/W3117504517","https://openalex.org/W3127452014","https://openalex.org/W4254491045","https://openalex.org/W6684642658"],"related_works":["https://openalex.org/W2384167225","https://openalex.org/W2113182373","https://openalex.org/W2119005669","https://openalex.org/W2088998312","https://openalex.org/W4255195499","https://openalex.org/W2481793228","https://openalex.org/W2403214044","https://openalex.org/W2379604225","https://openalex.org/W2994280181","https://openalex.org/W4281258283"],"abstract_inverted_index":{"Abstract":[0],"Dimensionality":[1],"reduction":[2],"techniques,":[3],"such":[4],"as":[5,60,140],"t-SNE,":[6],"can":[7],"construct":[8],"informative":[9],"visualizations":[10,35,152],"of":[11,23,29,106,123,125,129,160,174,188,200,210],"high-dimensional":[12],"data.":[13,181],"When":[14],"jointly":[15],"visualising":[16],"multiple":[17],"data":[18,58,66,69,76,96,117,142,168],"sets,":[19],"a":[20,51,56,61,72],"straightforward":[21],"application":[22],"these":[24,41],"methods":[25],"often":[26],"fails;":[27],"instead":[28],"revealing":[30],"underlying":[31],"classes,":[32],"the":[33,84,94,104,141,164,175,179,185,198,207],"resulting":[34],"expose":[36],"dataset-specific":[37],"clusters.":[38],"To":[39],"circumvent":[40],"batch":[42,100,132,161],"effects,":[43,162],"we":[44],"propose":[45],"an":[46],"embedding":[47,64],"procedure":[48],"that":[49,205,212],"uses":[50],"t-SNE":[52,195],"visualization":[53],"constructed":[54,153],"on":[55],"reference":[57,85],"set":[59],"scaffold":[62],"for":[63],"new":[65],"points.":[67],"Each":[68],"instance":[70],"from":[71,144,166,178],"new,":[73],"unseen,":[74],"secondary":[75,95,167],"is":[77],"embedded":[78],"independently":[79],"and":[80,97,127,163],"does":[81],"not":[82],"change":[83],"embedding.":[86],"This":[87],"prevents":[88],"any":[89],"interactions":[90],"between":[91],"instances":[92],"in":[93,134,194],"implicitly":[98],"mitigates":[99],"effects.":[101],"We":[102,182],"demonstrate":[103],"utility":[105],"this":[107],"approach":[108,157,193],"by":[109,154],"analyzing":[110],"six":[111],"recently":[112],"published":[113],"single-cell":[114],"gene":[115],"expression":[116],"sets":[118,169],"with":[119,172],"up":[120],"to":[121],"tens":[122],"thousands":[124,128],"cells":[126,165,173],"genes.":[130],"The":[131,151],"effects":[133],"our":[135,155,189],"studies":[136],"are":[137,158],"particularly":[138],"strong":[139],"comes":[143],"different":[145,148],"institutions":[146],"using":[147],"experimental":[149],"protocols.":[150],"proposed":[156],"clear":[159],"correctly":[170],"co-cluster":[171],"same":[176],"type":[177],"primary":[180],"also":[183],"show":[184],"predictive":[186],"power":[187],"simple,":[190],"visual":[191],"classification":[192],"space":[196],"matches":[197],"accuracy":[199],"specialized":[201],"machine":[202],"learning":[203],"techniques":[204],"consider":[206],"entire":[208],"compendium":[209],"features":[211],"profile":[213],"single":[214],"cells.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}