scvi-tools biology genomics single-cell model_cls_name:SCANVI scvi_version:1.0.0 anndata_version:0.9.1 modality:rna annotated:True license:cc-by-4.0 region:us
---
license: cc-by-4.0
library_name: scvi-tools
tags:
- biology
- genomics
- single-cell
- model_cls_name:SCANVI
- scvi_version:1.0.0
- anndata_version:0.9.1
- modality:rna
- annotated:True
---

# Description

Mouse scANVI reference model

# Model properties

Many model properties are in the model tags. Some more are listed below.

**model_init_params**:
```json
{
    "n_hidden": 128,
    "n_latent": 10,
    "n_layers": 2,
    "dropout_rate": 0.1,
    "dispersion": "gene",
    "gene_likelihood": "nb",
    "linear_classifier": false,
    "latent_distribution": "normal"
}
```

**model_setup_anndata_args**:
```json
{
    "labels_key": "ct",
    "unlabeled_category": "Unknown",
    "layer": "counts",
    "batch_key": "batch",
    "size_factor_key": null,
    "categorical_covariate_keys": null,
    "continuous_covariate_keys": null
}
```

**model_summary_stats**:
|[1m [0m[1m    Summary Stat Key    [0m[1m [0m|[1m [0m[1mValue[0m[1m [0m|
|--------------------------|-------|
|[94m [0m[94m        n_batch         [0m[94m [0m|[35m [0m[35m 18  [0m[35m [0m|
|[94m [0m[94m        n_cells         [0m[94m [0m|[35m [0m[35m2004 [0m[35m [0m|
|[94m [0m[94mn_extra_categorical_covs[0m[94m [0m|[35m [0m[35m  0  [0m[35m [0m|
|[94m [0m[94mn_extra_continuous_covs [0m[94m [0m|[35m [0m[35m  0  [0m[35m [0m|
|[94m [0m[94m        n_labels        [0m[94m [0m|[35m [0m[35m 16  [0m[35m [0m|
|[94m [0m[94m         n_vars         [0m[94m [0m|[35m [0m[35m3000 [0m[35m [0m|

**model_data_registry**:
|[1m [0m[1mRegistry Key[0m[1m [0m|[1m [0m[1m   scvi-tools Location   [0m[1m [0m|
|--------------|---------------------------|
|[94m [0m[94m     X      [0m[94m [0m|[35m [0m[35m adata.layers['counts']  [0m[35m [0m|
|[94m [0m[94m   batch    [0m[94m [0m|[35m [0m[35madata.obs['_scvi_batch'] [0m[35m [0m|
|[94m [0m[94m   labels   [0m[94m [0m|[35m [0m[35madata.obs['_scvi_labels'][0m[35m [0m|

**model_parent_module**: https://zenodo.org/records/10669600/files/01_mouse_reprocessed.h5ad?download=1

**data_is_minified**: False

# Training data

This is an optional link to where the training data is stored if it is too large
to host on the huggingface Model hub.

<!-- If your model is not uploaded with any data (e.g., minified data) on the Model Hub, then make
sure to provide this field if you want users to be able to access your training data. See the scvi-tools
documentation for details. -->

Training data url: https://github.com/brickmanlab/proks-salehin-et-al

# Training code

This is an optional link to the code used to train the model.

Training code url: N/A

# References

Proks, Salehin et al., biorXiv