{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T09:36:35Z","timestamp":1774690595524,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,7,14]],"date-time":"2020-07-14T00:00:00Z","timestamp":1594684800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["667403"],"award-info":[{"award-number":["667403"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["292402"],"award-info":[{"award-number":["292402"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["325956"],"award-info":[{"award-number":["325956"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["314395"],"award-info":[{"award-number":["314395"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sigrid Jus\u00e9lius Foundation; and the Finnish Cancer Association"},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["322927"],"award-info":[{"award-number":["322927"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer. Our results show that these improvements make qSNE significantly faster than regular t-SNE packages and enables full analysis of large datasets, such as mass cytometry data, without downsampling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and documentation are openly available at https:\/\/bitbucket.org\/anthakki\/qsne\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa637","type":"journal-article","created":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T11:11:49Z","timestamp":1594206709000},"page":"5086-5092","source":"Crossref","is-referenced-by-count":7,"title":["qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets"],"prefix":"10.1093","volume":"36","author":[{"given":"Antti","family":"H\u00e4kkinen","sequence":"first","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , 00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juha","family":"Koiranen","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , 00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Casado","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , 00014 Helsinki, 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University Hospital , Turku 20521, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sakari","family":"Hietanen","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital , Turku 20521, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olli","family":"Carp\u00e9n","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , 00014 Helsinki, Finland"},{"name":"Research Center for Cancer, Infections and Immunity, Institute of Biomedicine, University of Turku , Turku 20014, Finland"},{"name":"Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital , Helsinki 00014, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luca","family":"Pasquini","sequence":"additional","affiliation":[{"name":"Major Equipments and Core 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