sergiocamarap/Functional-cart-atlas-model

Description

Pretrained scVI integration model for the Functional CAR-T Cell Atlas

Model properties

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

model_init_params:

{
    "n_hidden": 128,
    "n_latent": 30,
    "n_layers": 2,
    "dropout_rate": 0.1,
    "dispersion": "gene",
    "gene_likelihood": "nb",
    "latent_distribution": "normal"
}

model_setup_anndata_args:

{
    "layer": "counts",
    "batch_key": "Product_norm",
    "labels_key": null,
    "size_factor_key": null,
    "categorical_covariate_keys": [
        "orig_ident"
    ],
    "continuous_covariate_keys": null
}

model_summary_stats:

Summary Stat Key	Value
n_batch	182
n_cells	414619
n_extra_categorical_covs	1
n_extra_continuous_covs	0
n_labels	1
n_vars	2000

model_data_registry:

Registry Key	scvi-tools Location
X	adata.layers['counts']
batch	adata.obs['_scvi_batch']
extra_categorical_covs	adata.obsm['_scvi_extra_categorical_covs']
labels	adata.obs['_scvi_labels']

model_parent_module: scvi.model

data_is_minified: True

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.

Training data url: https://doi.org/10.5281/zenodo.17213452

Training code

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

Training code url: https://github.com/ML4BM-Lab/Functional-cart-atlas

References

Reference pending - manuscript in preparation.