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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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[Dimensionality reduction] Switch t-SNE to openTSNE #275

Closed dkobak closed 1 month ago

dkobak commented 3 years ago

t-SNE is already implemented in the dimensionality reduction task, but through Scanpy. Scanpy's implementation is slow and has suboptimal parameters. I would strongly suggest to use openTSNE with default parameters. We are in the process of switching Scanpy to openTSNE, but it will take some time still: https://github.com/theislab/scanpy/issues/1233.

See https://github.com/pavlin-policar/openTSNE.

zsteve commented 3 years ago

For the time being, should openTSNE be a separate method? It might be helpful because I think a lot of people might just use the scanpy implementation params.

dkobak commented 3 years ago

I don't know if it's of interest here to benchmark different implementations of the same method, including implementations that are known to be suboptimal... Personally, I don't think so. So I'd vote to replace Scanpy.TSNE with openTSNE. But I guess it's up for discussion.

lazappi commented 3 years ago

In terms of managing PRs/merging across different people it might be cleaner to add new files now and delete the existing scanpy implementation later. Probably doesn't make a lot of difference though so whatever you decide.

github-actions[bot] commented 1 month ago

This issue has been automatically closed because it has not had recent activity.