scvi-tools
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Deep probabilistic analysis of single-cell and spatial omics data
There is a fair amount of things we can do with a loaded model without needing access to the full adata, using only the latent representation and cell metadata (obs/obsm)....
I followed the api_overview.ipynb step by step and trained a successful model. When I want to run PCA then generate UMAP plots under guiding, the error happens. I tested the...
(Addresses #2393) While certain multimodal models (e.g. totalVI) can be used with either `AnnData` or `MuData` objects, currently the `ArchesMixin` class only supports `AnnData`-based models and so reference mapping cannot...
In the current (1.0.4) version of scvi-tools, multimodal models (e.g. totalVI) can be set up and trained with either AnnData or MuData objects. Thus, it would be nice to be...
- [ ] Closes #xxxx (Replace xxxx with the GitHub issue number) - [X] Tests added and passed if fixing a bug or adding a new feature - [X] All...
Error occurs when a model is saved with Pandas =2 ``` scvi/model/base/_base_model.py:691: in load ) = _load_saved_files( scvi/model/base/_utils.py:68: in _load_saved_files model = torch.load(model_path, map_location=map_location) ../../.../python3.11/site-packages/torch/serialization.py:1014: in load return _load(opened_zipfile, ../../.../python3.11/site-packages/torch/serialization.py:1422:...
Reproducible script: ``` vae = SCANVAE(n_input=100, n_labels=1) x = torch.randint(0, 100, (10, 100), dtype=torch.float32) batch = torch.zeros(10, dtype=torch.long) labels = torch.zeros(10, dtype=torch.long) tensors = { REGISTRY_KEYS.X_KEY: x, REGISTRY_KEYS.BATCH_KEY: batch, REGISTRY_KEYS.LABELS_KEY:...