Question: UMAP vs "rigorous" t-SNE
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gravatar for rtrende
16 months ago by
rtrende20
Purdue University
rtrende20 wrote:

I've heard a lot of people discussing UMAP recently as though it has essentially superseded t-SNE for visualizing scRNA-seq data.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?

ADD COMMENTlink modified 16 months ago • written 16 months ago by rtrende20
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Part of the issue with t-SNE is that you get different results each run, it doesn't scale well, and the "rigorous" improvements you mention require extra setup or aren't supported in most packages. If it's shown to be a real improvement, it will likely be adopted in time as people become more aware of it (as was/is the case for UMAP). Convenience often reigns supreme.

ADD REPLYlink written 16 months ago by jared.andrews077.9k

Hi rtrende, what package do you use to run UMAP?

thanks

ADD REPLYlink written 16 months ago by Morris_Chair220
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I've been running UMAP using Seurat, which uses the python umap-learn package

ADD REPLYlink written 16 months ago by rtrende20
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There is also the umap package in R (on CRAN).

ADD REPLYlink written 15 months ago by Kevin Blighe67k
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The Bioconductor package scater offers convenience functions for both t-SNE and UMAP.

ADD REPLYlink written 6 months ago by ATpoint42k
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