Will Townes

Note to self- this will probably depend on first addressing #1 , since the CSR (row-oriented sparsity) format is more standard in the python world, whereas CSC is more standard...

Yes, I agree this is a big problem and I am becoming increasingly convinced that the diagonal Fisher scoring approach in the current implementation is not a good optimizer. I...

Great idea! I'll try to put something together. In the meantime, you can convert any of the .ipy files into .ipynb using [jupytext](https://jupytext.readthedocs.io/en/latest/). For example, here is where we fit...

Thanks @Alea4jacta6est ! For what it's worth, I was running everything in python 3.8.10 when I created the code originally. You can see all the detailed dependencies in the [methods...

Copying over from a slack thread to hopefully boost visibility. I understand the way to do this is through the `entry_point.predict_factor` method. When I tried this it throws the following...

Try using the NSFH model instead, it is more numerically stable than NSF.

I don't really have a proper tutorial but you can follow along with some of these notebooks: https://github.com/willtownes/nsf-paper/tree/main/scrna/visium_brain_sagittal