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brickmanlab
/
human-scanvi

scvi-tools
biology
genomics
single-cell
model_cls_name:SCANVI
scvi_version:1.0.0
anndata_version:0.9.1
modality:rna
annotated:True
Model card Files Community
human-scanvi
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---
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

Human 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_fine",
    "unlabeled_category": "Unknown",
    "layer": "counts",
    "batch_key": "batch",
    "size_factor_key": null,
    "categorical_covariate_keys": null,
    "continuous_covariate_keys": null
}
```

**model_summary_stats**:
|     Summary Stat Key     | Value |
|--------------------------|-------|
|         n_batch          |   6   |
|         n_cells          | 2323  |
| n_extra_categorical_covs |   0   |
| n_extra_continuous_covs  |   0   |
|         n_labels         |  15   |
|          n_vars          | 3000  |

**model_data_registry**:
| Registry Key |    scvi-tools Location    |
|--------------|---------------------------|
|      X       |  adata.layers['counts']   |
|    batch     | adata.obs['_scvi_batch']  |
|    labels    | adata.obs['_scvi_labels'] |

**model_parent_module**: https://zenodo.org/records/10669600/files/32_human_adata.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