Implement sparse covariance_eigh PCA using Dask
#3263
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flying-sheep
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Sep 26, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3263 +/- ##
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+ Coverage 77.01% 77.18% +0.16%
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Files 110 111 +1
Lines 12492 12582 +90
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+ Hits 9621 9711 +90
Misses 2871 2871
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flying-sheep
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Sep 30, 2024
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| if isinstance(adata.X, DaskArray) and issparse(adata.X._meta): | ||
| reason = "TruncatedSVD is not supported for sparse Dask yet" | ||
| request.applymarker(pytest.mark.xfail(reason=reason)) |
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@Intron7 you said it would be possible to adapt the code to do TruncatedSVD as well?
I think this PR is pretty clean, so maybe we can extend it in another PR?
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Agree, PR into this PR if we start pre-merge
ilan-gold
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Oct 18, 2024
Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
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covariance_eigh PCA using Dask
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Oct 18, 2024
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Can we add a test here to find out (or to at least know) how far our implementation here is from #3296 for sparse? |
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Done! |
ilan-gold
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Oct 18, 2024
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If everything passes CI, good to go from me
ilan-gold
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Oct 18, 2024
ilan-gold
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Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
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An alternative would be to subclass
PCA, but that would involve erroring out or reimplementing all of its options.Ideally #3267 would be merged first and this one integrated into its improved decision tree.