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
New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
Please describe your wishes
I've thought for a while that we should have NMF in scanpy (#941).
But it's always been pretty trivial to implement, so not that much work for someone to cover. But now that we're increasing the amount of out of core support in scanpy I think we can offer a lot more value here with out-of-core NMF support.
For out of core implementations, it'll be a bit more work. Some thoughts:
sklearn offers MiniBatchNMF which allows updating by batch. While this is out of core, it's effectively serial and may not scale well with increasing compute
What kind of feature would you like to request?
New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools
?Please describe your wishes
I've thought for a while that we should have NMF in scanpy (#941).
But it's always been pretty trivial to implement, so not that much work for someone to cover. But now that we're increasing the amount of out of core support in scanpy I think we can offer a lot more value here with out-of-core NMF support.
I would suggest we start with a simple
sklearn.decompositions.NMF
wrapper for in memory datasets.For out of core implementations, it'll be a bit more work. Some thoughts:
sklearn
offersMiniBatchNMF
which allows updating by batch. While this is out of core, it's effectively serial and may not scale well with increasing computeThe text was updated successfully, but these errors were encountered: