UMAP

Topological data analysis

https://www.youtube.com/watch?v=YPJQydzTLwQ

Related to t SNE? https://openreview.net/forum?id=B8a1FcY0vi

Tutorials and usage tips

Libraries

Drawbacks and criticisms

Lior Pachter has been a vocal critic. For instance, see this thread and Chari2021specious.

Tips

By Filipi:

If you see such a weird umap, it may be creating disconnected components in the knn network, which will be expelled from the center of the viz. Recommendations are: (1) increase the number of neighbors if you have a lot of data. (2) sample your data! check if a sample of ~100k points results in something meaningful. (3) If you see a blob without much structure, you may need to increase epochs. (4) If you are using a older version of cuml, use random initialization as spectral initialization was broken.If nothing works, it could be another cuml bug. (5) Try umap-learn with a smaller sample to double check.