scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
Fixes #1068 Here is the code we discussed for lvm-DE, an importance-sampling-based procedure for calibrated DE gene predictions. A parallel PR will be opened asap for the associated notebook introducing...
Uses proportions computed in other deconvolution method to infer cell activation state of those cells. Application activation for e.g. Cell2Location results. L1 loss changed. Still in discussion. Optional obsm field.
The documentation differentiating batch_key and categorical_covariate_keys currently does not clarify the difference between them well. From chat with Allon: 1. is there a difference if I add a discrete batch...
- "zinb" vs "nb". Negative binomial seems more sensible of a default. Stipulation of changing will be rerunning all tutorials. - encode_covariates=True/False. Typically we set this to True to improve...
In models/_condscvi.py line 139, we don't check for log_variational (default is true in CondSCVI). The input for the decoder at inference is therefore different from the training input. Effect is...
Error when using Flax LayerNorm in the Decoder in place of BatchNorm for JaxPEAKVI ## Code ```python class FlaxDecoder(nn.Module): n_input: int dropout_rate: float n_hidden: int def setup(self): self.dense1 = Dense(self.n_hidden)...
1. Write a custom [`DistributedSampler`](https://pytorch.org/docs/stable/data.html#torch.utils.data.distributed.DistributedSampler) that also takes as input the overall set of indices to pull data from (i.e., train set or test set or val set indices). Probably...
As mentioned in https://github.com/scverse/scvi-tools/issues/1564, if we find a way to default `training` without explicitly passing it in, this should be enough to move the necessary logic from `JaxModuleWrapper` to `JaxBaseModuleClass`...
I'm using linux but have this problem! I followed this issue but it couldn't help me solve this. https://github.com/scverse/scvi-tools/issues?q=H5Pset_fapl_ros3#issue-1235458517 ``` import scvi --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Input...
