scvi-tools/tabula-sapiens-lymph_node-scanvi

Description

Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects.

Model properties

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

model_init_params:

{
    "n_hidden": 128,
    "n_latent": 20,
    "n_layers": 3,
    "dropout_rate": 0.05,
    "dispersion": "gene",
    "gene_likelihood": "nb",
    "linear_classifier": false,
    "latent_distribution": "normal",
    "use_batch_norm": "none",
    "use_layer_norm": "both",
    "encode_covariates": true
}

model_setup_anndata_args:

{
    "labels_key": "cell_ontology_class",
    "unlabeled_category": "unknown",
    "layer": null,
    "batch_key": "donor_assay",
    "size_factor_key": null,
    "categorical_covariate_keys": null,
    "continuous_covariate_keys": null
}

model_summary_stats:

Summary Stat Key	Value
n_batch	4
n_cells	43502
n_extra_categorical_covs	0
n_extra_continuous_covs	0
n_labels	23
n_latent_qzm	20
n_latent_qzv	20
n_vars	4000

model_data_registry:

Registry Key	scvi-tools Location
X	adata.X
batch	adata.obs['_scvi_batch']
labels	adata.obs['_scvi_labels']
latent_qzm	adata.obsm['_scanvi_latent_qzm']
latent_qzv	adata.obsm['_scanvi_latent_qzv']
minify_type	adata.uns['_scvi_adata_minify_type']
observed_lib_size	adata.obs['_scanvi_observed_lib_size']

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://zenodo.org/records/7608635/files/Lymph_Node_training_data.h5ad

Training code

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

Training code url: N/A

References

The Tabula Sapiens Consortium. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, May 2022. doi:10.1126/science.abl4896