Romain Lopez

icon indicating a website link https://romain-lopez.github.io/ icon indicating an email [email protected]

icon company @Genentech & @Stanford icon location I am a joint postdoctoral scholar at Stanford University and Genentech Research and Early Development, hosted by Jonathan Pritchard and Aviv Regev

Results 10 comments of Romain Lopez

Error during make

Ran into a similar error a few years later, it'd be great to have a more precise install procedure :) this thread helped a lot!

GPU memory overflow (leak?) for large datasets

Hi @sjfleming, thanks for posting this issue. I agree with Adam, indeed I think it's surprising the early stopping did not converge after much less than 50 iterations. We are...

GPU memory overflow (leak?) for large datasets

Remark to self, it would be great to manually check if we can reproduce this bug, as scalability is an important feature of the codebase.

GPU memory overflow (leak?) for large datasets

should we create a random anndata matrix of large size (1M per 20k) and try to run scvi overnight?

GPU memory overflow (leak?) for large datasets

@khalilouardini would you like to work on this issue? it should be a quick one! Please try to run scVI with either a simulated AnnData or with the 1.3M cells...

[TOTALVI] NaN values during training when `empirical_protein_background_prior=True`

yes that sounds like a good advice, it'd be great to put this in the tutorial maybe?

Error in eval(parse(text = genome)): object 'BSgenome.Mmusculus.UCSC.mm10' not found

Ran into this today :) it's not fun when analyzing a large data set! Although, agreed that it's a easy fix

Interaction with AnnData

I did not get any answers, so I reimplemented stereoscope on another codebase. It takes now a couples of lines of code to run stereoscope from AnnData, and it works...

Interaction with AnnData

Also, I found that the number of epochs per default can be a bit conservative. The model can run for many less, and therefore much quicker.

Interaction with AnnData

Thanks! You should be able to checkout this branch and install scvi-tools in editable mode; and then you can directly run the notebook (data is not on the branch, but...