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Dask Sparse PCA #3226

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ilan-gold opened this issue Sep 12, 2024 · 0 comments · May be fixed by #3263
Open

Dask Sparse PCA #3226

ilan-gold opened this issue Sep 12, 2024 · 0 comments · May be fixed by #3263

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@ilan-gold
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What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

@Intron7 and I set up a nice implementation using GPU here: https://github.com/scverse/rapids_singlecell/pull/179/files#diff-483d6f872ddf4abd63e32af66a8566e0dcb40ba853a8672771dcbffb0235b7f9

It should be straightforward (and easier) without GPU. Basic outline of computational-heavy steps:

  1. Chunked covariance matrix calculation
  2. Use already existing mean-var
  3. Eigenvalue decomp

It works well on GPU so hopefully we can get nice performance on GPU.

I suspect using numba-in-dask for the covariance matrix calculation (similar to @Intron7 's kernel) would be super helpful.

@ilan-gold ilan-gold added Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer labels Sep 12, 2024
@ilan-gold ilan-gold added this to the 1.10.3 milestone Sep 12, 2024
@flying-sheep flying-sheep modified the milestones: 1.10.3, 1.10.4 Sep 17, 2024
@flying-sheep flying-sheep removed the Triage 🩺 This issue needs to be triaged by a maintainer label Sep 26, 2024
@flying-sheep flying-sheep linked a pull request Sep 26, 2024 that will close this issue
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3 participants