I've heard a lot of people discussing UMAP recently as though it has essentially superseded t-SNE for visualizing scRNA-seq data. UMAP is certainly impressive, but it seems to me that there are a lot of things one can do to pretty dramatically improve the output of t-SNE - for example, perplexity annealing, or PCA initialization followed by merging two perplexities (all of which are described here https://www.biorxiv.org/content/10.1101/453449v2, for example). All of the comparisons that I have seen between UMAP and t-SNE compare UMAP to t-SNE alone (e.g. https://www.nature.com/articles/nbt.4314.pdf), without these "tricks" that can improve the t-SNE plots. This feels a little like a strawman to me; has anyone done any work or seen any studies comparing UMAP to t-SNE for scRNA-seq data visualization with these improvements?
Question: UMAP vs "rigorous" t-SNE
16 months ago by
rtrende • 20
rtrende • 20 wrote:
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