license: cc-by-4.0
library_name: scvi-tools
tags:
- biology
- genomics
- single-cell
- model_cls_name:SCANVI
- scvi_version:0.20.3
- anndata_version:0.8.0
- modality:rna
- tissue:lung
- annotated:True
Description
The single cell lung cancer atlas is a resource integrating more than 1.2 million cells from 309 patients across 29 datasets.
Model properties
Many model properties are in the model tags. Some more are listed below.
model_init_params:
{
"n_hidden": 128,
"n_latent": 10,
"n_layers": 2,
"dropout_rate": 0.2,
"dispersion": "gene",
"gene_likelihood": "zinb",
"latent_distribution": "normal",
"use_layer_norm": "both",
"use_batch_norm": "none",
"encode_covariates": true
}
model_setup_anndata_args:
{
"labels_key": "cell_type",
"unlabeled_category": "unknown",
"layer": null,
"batch_key": "sample",
"size_factor_key": null,
"categorical_covariate_keys": null,
"continuous_covariate_keys": null
}
model_summary_stats:
| Summary Stat Key | Value |
|---|---|
| n_batch | 505 |
| n_cells | 892296 |
| n_extra_categorical_covs | 0 |
| n_extra_continuous_covs | 0 |
| n_labels | 45 |
| n_latent_qzm | 10 |
| n_latent_qzv | 10 |
| n_vars | 6000 |
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/record/7227571/files/core_atlas_scanvi_model.tar.gz
Training code
This is an optional link to the code used to train the model.
Training code url: https://github.com/icbi-lab/luca
References
High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. S Salcher, G Sturm, L Horvath, G Untergasser, C Kuempers, G Fotakis, E Panizzolo, A Martowicz, M Trebo, G Pall, G Gamerith, M Sykora, F Augustin, K Schmitz, F Finotello, D Rieder, S Perner, S Sopper, D Wolf, A Pircher, Z Trajanoski. Cancer Cell. 2022; 40 (12): 1503-1520.e8. https: //doi.org/10.1016/j.ccell.2022.10.008