---
license: cc-by-4.0
library_name: scvi-tools
tags:
- biology
- genomics
- single-cell
- model_cls_name:SCANVI
- modality:rna
- annotated:True
---

# Description

Mouse preimplantation development model spanning early stages of development. The
model was trained utilizing single‐cell ANnotation using Variational Inference
(scANVI, [Xu et al., 2021]) implemented in [scvi-tools]. In short, scANVI raw
single-cell RNA sequencing (scRNA-seq) count matrix - cell by gene, where values
represent gene expression measured by counting number of transcribed RNA.

# Model Training

- [raw dataset](https://zenodo.org/records/13749348/files/01_mouse_reprocessed.h5ad)
- [notebook analysis](https://github.com/brickmanlab/proks-salehin-et-al/blob/master/notebooks/15_mouse_scANVI_fix.ipynb)

# Metrics

Cell type (`ct`) prediction

| Metric            |  Score              |
|-------------------|---------------------|
| Accuracy score    |  0.9126746506986028 |
| Balanced accuracy |  0.9572872718187365 |
| F1 (micro)        |  0.9126746506986028 |
| F1 (macro)        |  0.9201654923575322 |

# Model parameters

Below we provide settings for scANVI setup

`lvae.init_params_["non_kwargs"]`

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

`lvae.adata_manager.registry['setup_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
}
```

# References

Proks, M., Salehin, N. & Brickman, J.M. Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing. Nat Methods 22, 207–216 (2025). [https://doi.org/10.1038/s41592-024-02511-3](https://doi.org/10.1038/s41592-024-02511-3)

[Xu et al., 2021]: https://www.embopress.org/doi/full/10.15252/msb.20209620
[scvi-tools]: http://scvi-tools.org