You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
currently pp.scale with a mask_obs with a sparse matrix and with zero_center== False takes a really long time to update the sparse matrix. This also takes up a lot of memory because of the parity calculations. I would suggest a numba kernel that just swaps out the data. This works really well for rapids-singlecell and greatly improves performance and reduces the memory overhead.
I would open a PR with this kernel.
Performance for 90k cells and 25k genes:
without mask:
CPU 645 ms | GPU 37 ms | 20x
with mask:
CPU 22 s | GPU 50 ms | 460x
The text was updated successfully, but these errors were encountered:
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
currently
pp.scale
with amask_obs
with a sparse matrix and withzero_center== False
takes a really long time to update the sparse matrix. This also takes up a lot of memory because of the parity calculations. I would suggest a numba kernel that just swaps out the data. This works really well for rapids-singlecell and greatly improves performance and reduces the memory overhead.I would open a PR with this kernel.
Performance for 90k cells and 25k genes:
without mask:
CPU 645 ms | GPU 37 ms | 20x
with mask:
CPU 22 s | GPU 50 ms | 460x
The text was updated successfully, but these errors were encountered: