scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
Hi, I am unable to import the name 'MRVI' from 'scvi.external'. I am currently using scvi version 1.1.2. I found that the mrVI tutorial (https://docs.scvi-tools.org/en/latest/tutorials/notebooks/scrna/MrVI_tutorial.html) uses scvi version 1.1.3. However,...
There is currently a problem when using the scvi model with `gene_likelihood='poisson'` and trying to get the normalized expression: ``` vae = scvi.model.SCVI( adata, gene_likelihood='poisson' ) vae.get_normalized_expression( adata=adata, library_size="latent", )...
I'm trying to follow installation requirements and recommendations for scvi-tools, and I'm installing packages within Anaconda Prompt on a Windows system. The readout as as follows when trying to run...
autotune fails with an error message _no attribute 'autotune'_. I created a fresh conda environment with the latest scvi-tools on python 3.11. Please advise, Itamar ```python tuner = scvi.autotune.ModelTuner(model_cls) tuner...
Could scVI models support weighed loss and weighing individual cells or batch_key groups? **Some potential uses** - Downweighing over-represented atlases with low interesting variation. - Improving ELBO on poorly represented...
Should be easy to reimplement VAEMixin for JAX models. Will require a whole new class since the forward pass call is completely different. Example implementation of `get_reconstruction_error`: ```python def get_reconstruction_error(...
