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--- |
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license: cc-by-4.0 |
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library_name: scvi-tools |
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tags: |
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- biology |
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- genomics |
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- single-cell |
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- model_cls_name:SCANVI |
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- scvi_version:1.1.0 |
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- anndata_version:0.10.3 |
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- modality:rna |
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- tissue:Thymus |
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- annotated:True |
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--- |
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# Description |
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Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. |
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# Model properties |
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Many model properties are in the model tags. Some more are listed below. |
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**model_init_params**: |
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```json |
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{ |
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"n_hidden": 128, |
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"n_latent": 20, |
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"n_layers": 3, |
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"dropout_rate": 0.05, |
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"dispersion": "gene", |
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"gene_likelihood": "nb", |
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"linear_classifier": false, |
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"latent_distribution": "normal", |
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"use_batch_norm": "none", |
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"use_layer_norm": "both", |
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"encode_covariates": true |
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} |
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``` |
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**model_setup_anndata_args**: |
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```json |
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{ |
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"labels_key": "cell_ontology_class", |
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"unlabeled_category": "unknown", |
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"layer": null, |
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"batch_key": "donor_assay", |
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"size_factor_key": null, |
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"categorical_covariate_keys": null, |
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"continuous_covariate_keys": null |
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} |
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``` |
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**model_summary_stats**: |
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| Summary Stat Key | Value | |
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|--------------------------|-------| |
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| n_batch | 2 | |
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| n_cells | 21575 | |
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| n_extra_categorical_covs | 0 | |
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| n_extra_continuous_covs | 0 | |
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| n_labels | 22 | |
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| n_latent_qzm | 20 | |
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| n_latent_qzv | 20 | |
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| n_vars | 4000 | |
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**model_data_registry**: |
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| Registry Key | scvi-tools Location | |
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|-------------------|----------------------------------------| |
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| X | adata.X | |
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| batch | adata.obs['_scvi_batch'] | |
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| labels | adata.obs['_scvi_labels'] | |
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| latent_qzm | adata.obsm['_scanvi_latent_qzm'] | |
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| latent_qzv | adata.obsm['_scanvi_latent_qzv'] | |
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| minify_type | adata.uns['_scvi_adata_minify_type'] | |
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| observed_lib_size | adata.obs['_scanvi_observed_lib_size'] | |
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**model_parent_module**: scvi.model |
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**data_is_minified**: True |
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# Training data |
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This is an optional link to where the training data is stored if it is too large |
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to host on the huggingface Model hub. |
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<!-- If your model is not uploaded with any data (e.g., minified data) on the Model Hub, then make |
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sure to provide this field if you want users to be able to access your training data. See the scvi-tools |
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documentation for details. --> |
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Training data url: https://zenodo.org/records/7608635/files/Thymus_training_data.h5ad |
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# Training code |
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This is an optional link to the code used to train the model. |
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Training code url: N/A |
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# References |
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The Tabula Sapiens Consortium. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, May 2022. doi:10.1126/science.abl4896 |
