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README.md

@@ -1,27 +1,135 @@
 ---
-license: cc-by-4.0
 library_name: scvi-tools
+license: cc-by-4.0
 tags:
 - biology
 - genomics
 - single-cell
 - model_cls_name:SCVI
-- scvi_version:1.1.0
-- anndata_version:0.10.3
+- scvi_version:1.2.0
+- anndata_version:0.11.1
 - modality:rna
-- tissue:Lung
+- tissue:various
 - annotated:True
 ---
 
-# Description
 
-Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects.
+ScVI is a variational inference model for single-cell RNA-seq data that can learn an underlying
+latent space, integrate technical batches and impute dropouts.
+The learned low-dimensional latent representation of the data can be used for visualization and
+clustering.
+
+scVI takes as input a scRNA-seq gene expression matrix with cells and genes.
+We provide an extensive [user guide](https://docs.scvi-tools.org/en/1.2.0/user_guide/models/scvi.html).
 
-# Model properties
+- See our original manuscript for further details of the model:
+[scVI manuscript](https://www.nature.com/articles/s41592-018-0229-2).
+- See our manuscript on [scvi-hub](https://www.biorxiv.org/content/10.1101/2024.03.01.582887v2) how
+to leverage pre-trained models.
 
-Many model properties are in the model tags. Some more are listed below.
+This model can be used for fine tuning on new data using our Arches framework:
+[Arches tutorial](https://docs.scvi-tools.org/en/1.0.0/tutorials/notebooks/scarches_scvi_tools.html).
+
+
+# Model 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_init_params**:
+# Metrics
+
+We provide here key performance metrics for the uploaded model, if provided by the data uploader.
+
+<details>
+<summary><strong>Coefficient of variation</strong></summary>
+
+The cell-wise coefficient of variation summarizes how well variation between different cells is
+preserved by the generated model expression. Below a squared Pearson correlation coefficient of 0.4
+, we would recommend not to use generated data for downstream analysis, while the generated latent
+space might still be useful for analysis.
+
+**Cell-wise Coefficient of Variation**:
+
+| Metric                  | Training Value | Validation Value |
+|-------------------------|----------------|------------------|
+| Mean Absolute Error | 1.86  | 1.96           |
+| Pearson Correlation | 0.82  | 0.80  |
+| Spearman Correlation | 0.77 | 0.76  |
+| R² (R-Squared) | 0.58  | 0.51      |
+
+The gene-wise coefficient of variation summarizes how well variation between different genes is
+preserved by the generated model expression. This value is usually quite high.
+
+**Gene-wise Coefficient of Variation**:
+
+| Metric                  | Training Value |
+|-------------------------|----------------|
+| Mean Absolute Error | 17.35   |
+| Pearson Correlation | 0.73  |
+| Spearman Correlation | 0.82 |
+| R² (R-Squared) | 0.26  |
+
+</details>
+
+<details>
+<summary><strong>Differential expression metric</strong></summary>
+
+The differential expression metric provides a summary of the differential expression analysis
+between cell types or input clusters. We provide here the F1-score, Pearson Correlation
+Coefficient of Log-Foldchanges, Spearman Correlation Coefficient, and Area Under the Precision
+Recall Curve (AUPRC) for the differential expression analysis using Wilcoxon Rank Sum test for each
+cell-type.
+
+**Differential expression**:
+
+| Index | gene_f1 | lfc_mae | lfc_pearson | lfc_spearman | roc_auc | pr_auc | n_cells |
+| --- | --- | --- | --- | --- | --- | --- | --- |
+| macrophage | 0.94 | 1.19 | 0.79 | 0.94 | 0.24 | 0.92 | 12160.00 |
+| type II pneumocyte | 0.95 | 0.78 | 0.83 | 0.95 | 0.32 | 0.87 | 9146.00 |
+| basal cell | 0.90 | 1.49 | 0.69 | 0.85 | 0.43 | 0.82 | 2188.00 |
+| capillary endothelial cell | 0.95 | 2.72 | 0.65 | 0.80 | 0.27 | 0.79 | 1534.00 |
+| classical monocyte | 0.91 | 3.16 | 0.62 | 0.76 | 0.21 | 0.81 | 1487.00 |
+| club cell | 0.93 | 2.87 | 0.64 | 0.73 | 0.29 | 0.78 | 1038.00 |
+| non-classical monocyte | 0.89 | 2.92 | 0.69 | 0.76 | 0.28 | 0.83 | 1005.00 |
+| respiratory goblet cell | 0.91 | 2.29 | 0.70 | 0.78 | 0.33 | 0.81 | 762.00 |
+| basophil | 0.93 | 3.55 | 0.64 | 0.69 | 0.25 | 0.84 | 686.00 |
+| lung ciliated cell | 0.62 | 2.41 | 0.75 | 0.84 | 0.41 | 0.84 | 602.00 |
+| CD8-positive, alpha-beta T cell | 0.89 | 3.65 | 0.64 | 0.70 | 0.27 | 0.82 | 552.00 |
+| CD4-positive, alpha-beta T cell | 0.90 | 3.88 | 0.62 | 0.65 | 0.26 | 0.82 | 543.00 |
+| vein endothelial cell | 0.92 | 3.70 | 0.60 | 0.70 | 0.34 | 0.77 | 508.00 |
+| lung microvascular endothelial cell | 0.90 | 3.83 | 0.63 | 0.68 | 0.31 | 0.85 | 485.00 |
+| adventitial cell | 0.76 | 2.90 | 0.75 | 0.90 | 0.34 | 0.80 | 373.00 |
+| fibroblast | 0.86 | 4.30 | 0.56 | 0.70 | 0.33 | 0.76 | 336.00 |
+| dendritic cell | 0.87 | 4.03 | 0.65 | 0.74 | 0.30 | 0.81 | 316.00 |
+| intermediate monocyte | 0.91 | 3.95 | 0.64 | 0.64 | 0.31 | 0.83 | 252.00 |
+| pericyte | 0.87 | 4.51 | 0.59 | 0.60 | 0.33 | 0.77 | 213.00 |
+| type I pneumocyte | 0.89 | 3.83 | 0.64 | 0.68 | 0.32 | 0.77 | 211.00 |
+| endothelial cell of artery | 0.86 | 5.03 | 0.57 | 0.64 | 0.33 | 0.77 | 187.00 |
+| neutrophil | 0.87 | 4.44 | 0.60 | 0.58 | 0.28 | 0.88 | 174.00 |
+| plasma cell | 0.78 | 4.28 | 0.61 | 0.58 | 0.27 | 0.85 | 134.00 |
+| effector CD4-positive, alpha-beta T cell | 0.89 | 3.91 | 0.65 | 0.63 | 0.32 | 0.80 | 132.00 |
+| mature NK T cell | 0.84 | 4.93 | 0.56 | 0.55 | 0.37 | 0.79 | 132.00 |
+| B cell | 0.76 | 4.84 | 0.57 | 0.52 | 0.34 | 0.75 | 87.00 |
+| bronchial smooth muscle cell | 0.71 | 5.09 | 0.59 | 0.59 | 0.33 | 0.77 | 81.00 |
+| effector CD8-positive, alpha-beta T cell | 0.81 | 4.19 | 0.63 | 0.60 | 0.35 | 0.82 | 80.00 |
+| vascular associated smooth muscle cell | 0.79 | 4.85 | 0.59 | 0.58 | 0.36 | 0.78 | 80.00 |
+| endothelial cell of lymphatic vessel | 0.47 | 6.03 | 0.52 | 0.49 | 0.34 | 0.74 | 47.00 |
+| blood vessel endothelial cell | 0.70 | 4.01 | 0.67 | 0.66 | 0.35 | 0.80 | 47.00 |
+| smooth muscle cell | 0.66 | 4.11 | 0.64 | 0.61 | 0.35 | 0.79 | 25.00 |
+| pulmonary ionocyte | 0.42 | 6.28 | 0.46 | 0.32 | 0.34 | 0.72 | 19.00 |
+| plasmacytoid dendritic cell | 0.58 | 5.38 | 0.48 | 0.48 | 0.35 | 0.83 | 18.00 |
+| mesothelial cell | 0.54 | 5.63 | 0.54 | 0.48 | 0.37 | 0.73 | 17.00 |
+| serous cell of epithelium of bronchus | 0.60 | 5.07 | 0.54 | 0.47 | 0.37 | 0.79 | 15.00 |
+
+</details>
+
+# Model Properties
+
+We provide here key parameters used to setup and train the model.
+
+<details>
+<summary><strong>Model Parameters</strong></summary>
+
+These provide the settings to setup the original model:
 ```json
 {
     "n_hidden": 128,
@@ -37,7 +145,12 @@ Many model properties are in the model tags. Some more are listed below.
 }
 ```
 
-**model_setup_anndata_args**:
+</details>
+
+<details>
+<summary><strong>Setup Data Arguments</strong></summary>
+
+Arguments passed to setup_anndata of the original model:
 ```json
 {
     "layer": null,
@@ -49,7 +162,29 @@ Many model properties are in the model tags. Some more are listed below.
 }
 ```
 
-**model_summary_stats**:
+</details>
+
+<details>
+<summary><strong>Data Registry</strong></summary>
+
+Registry elements for AnnData manager:
+|   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['observed_lib_size']    |
+
+- **Data is Minified**: False
+
+</details>
+
+<details>
+<summary><strong>Summary Statistics</strong></summary>
+
 |     Summary Stat Key     | Value |
 |--------------------------|-------|
 |         n_batch          |   5   |
@@ -59,40 +194,27 @@ Many model properties are in the model tags. Some more are listed below.
 |         n_labels         |  36   |
 |       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
+|          n_vars          | 3000  |
 
-**data_is_minified**: True
+</details>
 
-# 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.
+<details>
+<summary><strong>Training</strong></summary>
 
 <!-- If your model is not uploaded with any data (e.g., minified data) on the Model Hub, then make
-sure to provide this field if you want users to be able to access your training data. See the scvi-tools
-documentation for details. -->
+sure to provide this field if you want users to be able to access your training data. See the
+scvi-tools documentation for details. -->
+**Training data url**: Not provided by uploader
 
-Training data url: https://zenodo.org/records/7608635/files/Lung_training_data.h5ad
+If provided by the original uploader, for those interested in understanding or replicating the
+training process, the code is available at the link below.
 
-# Training code
+**Training Code URL**: Not provided by uploader
 
-This is an optional link to the code used to train the model.
+</details>
 
-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
+The Tabula Sapiens Consortium. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, May 2022. doi:10.1126/science.abl4896