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jlmelville / uwot

An R package implementing the UMAP dimensionality reduction method.
https://jlmelville.github.io/uwot/
GNU General Public License v3.0
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Support binary metric #92

Open frederikziebell opened 2 years ago

frederikziebell commented 2 years ago

For binary data, it would be helpful to support the binary metric as implemented in dist(metric="binary"). Currently, the only way is to pass the dist object directly, which is very memory inefficient.

jlmelville commented 2 years ago

The description in the doc for ?dist seems to be indicate that method = "binary" is the Jaccard/Tanimoto distance. Supporting this will require an alternative to Annoy, so it won't be happening any time soon, unfortunately.

jlmelville commented 8 months ago

Although not as convenient as full integration with uwot, rnndescent supports the Jaccard/Tanimoto coefficient with binary data. See the rnndescent article for details on using it with uwot.