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:nose
- tissue:respiratory airway
- tissue:lung parenchyma
- annotated:True
Description
The first integrated, universal transcriptomic reference of the human lung on the single-cell level. For more details, see https: //github.com/LungCellAtlas/HLCA.
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",
"encode_covariates": true,
"deeply_inject_covariates": false,
"use_layer_norm": "both",
"use_batch_norm": "none"
}
model_setup_anndata_args:
{
"labels_key": "scanvi_label",
"unlabeled_category": "unlabeled",
"layer": null,
"batch_key": "dataset",
"size_factor_key": null,
"categorical_covariate_keys": null,
"continuous_covariate_keys": null
}
model_summary_stats:
| Summary Stat Key | Value |
|---|---|
| n_batch | 14 |
| n_cells | 584884 |
| n_extra_categorical_covs | 0 |
| n_extra_continuous_covs | 0 |
| n_labels | 29 |
| n_latent_qzm | 30 |
| n_latent_qzv | 30 |
| n_vars | 2000 |
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://cellxgene.cziscience.com/e/066943a2-fdac-4b29-b348-40cede398e4e.cxg/
Training code
This is an optional link to the code used to train the model.
Training code url: https://github.com/LungCellAtlas/HLCA_reproducibility
References
An integrated cell atlas of the human lung in health and disease. L Sikkema, D Strobl, L Zappia, E Madissoon, NS Markov, L Zaragosi, M Ansari, M Arguel, L Apperloo, C Bécavin, M Berg, E Chichelnitskiy, M Chung, A Collin, ACA Gay, B Hooshiar Kashani, M Jain, T Kapellos, TM Kole, C Mayr, M von Papen, L Peter, C Ramírez-Suástegui, J Schniering, C Taylor, T Walzthoeni, C Xu, LT Bui, C de Donno, L Dony, M Guo, AJ Gutierrez, L Heumos, N Huang, I Ibarra, N Jackson, P Kadur Lakshminarasimha Murthy, M Lotfollahi, T Tabib, C Talavera-Lopez, K Travaglini, A Wilbrey-Clark, KB Worlock, M Yoshida, Lung Biological Network Consortium, T Desai, O Eickelberg, C Falk, N Kaminski, M Krasnow, R Lafyatis, M Nikolíc, J Powell, J Rajagopal, O Rozenblatt-Rosen, MA Seibold, D Sheppard, D Shepherd, SA Teichmann, A Tsankov, J Whitsett, Y Xu, NE Banovich, P Barbry, TE Duong, KB Meyer, JA Kropski, D Pe’er, HB Schiller, PR Tata, JL Schultze, AV Misharin, MC Nawijn, MD Luecken, F Theis. bioRxiv 2022.03.10.483747; doi: https: //doi.org/10.1101/2022.03.10.483747