metadata

license: cc-by-4.0
library_name: scvi-tools
tags:
  - biology
  - genomics
  - single-cell
  - model_cls_name:SCVI
  - scvi_version:1.1.0
  - anndata_version:0.10.3
  - modality:rna
  - tissue:Pancreas
  - annotated:True

Description

To be added...

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",
    "latent_distribution": "normal",
    "use_batch_norm": "none",
    "use_layer_norm": "both",
    "encode_covariates": true
}

model_setup_anndata_args:

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

model_summary_stats:

Summary Stat Key	Value
n_batch	4
n_cells	13488
n_extra_categorical_covs	0
n_extra_continuous_covs	0
n_labels	14
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['_scvi_latent_qzm']
latent_qzv	adata.obsm['_scvi_latent_qzv']
minify_type	adata.uns['_scvi_adata_minify_type']
observed_lib_size	adata.obs['_scvi_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: N/A

Training code

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

Training code url: N/A

References

To be added...