{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T06:39:35Z","timestamp":1775111975235,"version":"3.50.1"},"reference-count":15,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T00:00:00Z","timestamp":1727827200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC 2064, 390727645"],"award-info":[{"award-number":["EXC 2064, 390727645"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC 2181, 390900948"],"award-info":[{"award-number":["EXC 2181, 390900948"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003493","name":"Gemeinn\u00fctzige Hertie-Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003493","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","award":["ERC 101039115"],"award-info":[{"award-number":["ERC 101039115"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["KO6282\/2-1"],"award-info":[{"award-number":["KO6282\/2-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    A recent paper claimed that\n                    <jats:italic>t<\/jats:italic>\n                    -SNE and UMAP embeddings of single-cell datasets are \u201cspecious\u201d and fail to capture true biological structure. The authors argued that such embeddings are as arbitrary and as misleading as forcing the data into an elephant shape. Here we show that this conclusion was based on inadequate and limited metrics of embedding quality. More appropriate metrics quantifying neighborhood and class preservation reveal the elephant in the room: while\n                    <jats:italic>t<\/jats:italic>\n                    -SNE and UMAP embeddings of single-cell data do not preserve high-dimensional distances, they can nevertheless provide biologically relevant information.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1012403","type":"journal-article","created":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T13:32:25Z","timestamp":1727875945000},"page":"e1012403","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0946-412X","authenticated-orcid":true,"given":"Jan","family":"Lause","sequence":"first","affiliation":[]},{"given":"Philipp","family":"Berens","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5639-7209","authenticated-orcid":true,"given":"Dmitry","family":"Kobak","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2024,10,2]]},"reference":[{"issue":"11","key":"pcbi.1012403.ref001","article-title":"Visualizing data using t-SNE","volume":"9","author":"L Van der Maaten","year":"2008","journal-title":"Journal of Machine Learning Research"},{"issue":"1","key":"pcbi.1012403.ref002","doi-asserted-by":"crossref","first-page":"5416","DOI":"10.1038\/s41467-019-13056-x","article-title":"The art of using t-SNE for single-cell transcriptomics.","volume":"10","author":"D Kobak","year":"2019","journal-title":"Nat Commun."},{"key":"pcbi.1012403.ref003","article-title":"UMAP: Uniform manifold approximation and projection for dimension reduction.","author":"L McInnes","year":"2018","journal-title":"arXiv:180203426."},{"issue":"1","key":"pcbi.1012403.ref004","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"E Becht","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"8","key":"pcbi.1012403.ref005","doi-asserted-by":"crossref","first-page":"e1011288","DOI":"10.1371\/journal.pcbi.1011288","article-title":"The specious art of single-cell genomics","volume":"19","author":"T Chari","year":"2023","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"pcbi.1012403.ref006","doi-asserted-by":"crossref","first-page":"2650","DOI":"10.1109\/TVCG.2018.2846735","article-title":"Multidimensional projection for visual analytics: Linking techniques with distortions, tasks, and layout enrichment","volume":"25","author":"LG Nonato","year":"2018","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"9","key":"pcbi.1012403.ref007","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.cels.2023.07.002","article-title":"What cannot be seen correctly in 2D visualizations of single-cell \u2018omics data","volume":"14","author":"S Wang","year":"2023","journal-title":"Cell Systems"},{"key":"pcbi.1012403.ref008","unstructured":"Pachter L, 2021. URL https:\/\/web.archive.org\/web\/20240729115631\/https:\/\/archive.is\/2024.07.29-115414\/https:\/\/x.com\/lpachter\/status\/1431325969411821572."},{"issue":"3","key":"pcbi.1012403.ref009","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1109\/TVCG.2019.2944182","article-title":"Toward a quantitative survey of dimension reduction techniques","volume":"27","author":"M Espadoto","year":"2021","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"1","key":"pcbi.1012403.ref010","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/s42003-022-03628-x","article-title":"Towards a comprehensive evaluation of dimension reduction methods for transcriptomic data visualization","volume":"5","author":"H Huang","year":"2022","journal-title":"Communications Biology"},{"issue":"1","key":"pcbi.1012403.ref011","first-page":"2023b","article-title":"Comparative analysis of dimension reduction methods for cytometry by time-of-flight data.","volume":"14","author":"K Wang","year":"1836","journal-title":"Nat Commun"},{"issue":"7\u20139","key":"pcbi.1012403.ref012","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.neucom.2008.12.017","article-title":"Quality assessment of dimensionality reduction: Rank-based criteria.","volume":"72","author":"JA Lee","year":"2009","journal-title":"Neurocomputing."},{"key":"pcbi.1012403.ref013","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"PJ Rousseeuw","year":"1987","journal-title":"Journal of Computational and Applied Mathematics"},{"key":"pcbi.1012403.ref014","doi-asserted-by":"crossref","unstructured":"Vinh NX, Epps J, Bailey J. Information theoretic measures for clusterings comparison: is a correction for chance necessary? In Proceedings of the 26th Annual International Conference on Machine Learning, pages 1073\u20131080, 2009.","DOI":"10.1145\/1553374.1553511"},{"key":"pcbi.1012403.ref015","first-page":"201","article-title":"Robustness in the strategy of scientific model building","author":"GEP Box","year":"1979","journal-title":"Robustness in statistics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012403","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T13:32:30Z","timestamp":1727875950000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012403"}},"subtitle":[],"editor":[{"given":"Jason A.","family":"Papin","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,10,2]]},"references-count":15,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012403","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.03.26.586728","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,2]]}}}