--- library_name: scvi-tools license: cc-by-4.0 tags: - biology - genomics - single-cell - model_cls_name:CondSCVI - scvi_version:1.2.0 - anndata_version:0.11.1 - modality:rna - tissue:various - annotated:True --- CondSCVI is a variational inference model for single-cell RNA-seq data that can learn an underlying latent space. The predictions of the model are meant to be afterward used for deconvolution of a second spatial transcriptomics dataset in DestVI. DestVI predicts the cell-type proportions as well as cell type-specific activation state in the spatial data. CondSCVI takes as input a scRNA-seq gene expression matrix with cells and genes as well as a cell-type annotation for all cells. We provide an extensive [user guide](https://docs.scvi-tools.org/en/1.2.0/user_guide/models/destvi.html) for DestVI including a description of CondSCVI. - See our original manuscript for further details of the model: [DestVI manuscript](https://www.nature.com/articles/s41587-022-01272-8). - See our manuscript on [scvi-hub](https://www.biorxiv.org/content/10.1101/2024.03.01.582887v2) how to leverage pre-trained models. # 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. # Metrics We provide here key performance metrics for the uploaded model, if provided by the data uploader.
Coefficient of variation 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 | 3.28 | 3.51 | | Pearson Correlation | 0.31 | 0.32 | | Spearman Correlation | 0.45 | 0.45 | | R² (R-Squared) | -6.24 | -6.81 | 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 | 20.71 | | Pearson Correlation | 0.11 | | Spearman Correlation | 0.32 | | R² (R-Squared) | -2584.71 |
Differential expression metric 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 | | --- | --- | --- | --- | --- | --- | --- | --- | | fibroblast | 0.55 | 2.86 | 0.15 | 0.14 | 0.52 | 0.90 | 1239.00 | | neutrophil | 0.09 | 6.02 | 0.06 | 0.06 | 0.41 | 0.93 | 758.00 | | macrophage | 0.15 | 3.95 | 0.04 | 0.01 | 0.53 | 0.88 | 528.00 | | CD8-positive, alpha-beta T cell | 0.22 | 5.78 | 0.09 | 0.07 | 0.44 | 0.82 | 464.00 | | B cell | 0.24 | 5.10 | 0.04 | 0.01 | 0.49 | 0.86 | 462.00 | | basal cell | 0.30 | 3.85 | 0.04 | 0.09 | 0.53 | 0.81 | 291.00 | | ciliated cell | 0.29 | 4.62 | 0.09 | 0.22 | 0.55 | 0.88 | 278.00 | | endothelial cell | 0.35 | 5.09 | 0.05 | 0.07 | 0.52 | 0.84 | 224.00 | | secretory cell | 0.36 | 4.14 | 0.04 | 0.09 | 0.53 | 0.80 | 179.00 | | plasma cell | 0.03 | 6.73 | 0.00 | 0.01 | 0.65 | 0.95 | 133.00 | | T cell | 0.22 | 7.19 | 0.04 | 0.03 | 0.50 | 0.74 | 131.00 | | smooth muscle cell | 0.18 | 7.49 | 0.05 | 0.06 | 0.52 | 0.77 | 96.00 | | tracheal goblet cell | 0.29 | 5.07 | 0.04 | 0.11 | 0.52 | 0.74 | 77.00 | | mast cell | 0.13 | 10.09 | 0.06 | 0.05 | 0.51 | 0.78 | 69.00 | | CD4-positive, alpha-beta T cell | 0.23 | 10.04 | 0.10 | 0.03 | 0.49 | 0.75 | 65.00 | | mucus secreting cell | 0.28 | 6.76 | 0.03 | 0.07 | 0.54 | 0.76 | 64.00 | | serous cell of epithelium of trachea | 0.19 | 9.60 | 0.05 | 0.05 | 0.48 | 0.72 | 41.00 | | ionocyte | 0.21 | 14.39 | 0.07 | 0.03 | 0.47 | 0.72 | 13.00 |
# Model Properties We provide here key parameters used to setup and train the model.
Model Parameters These provide the settings to setup the original model: ```json { "n_hidden": 128, "n_latent": 5, "n_layers": 2, "weight_obs": false, "dropout_rate": 0.05 } ```
Setup Data Arguments Arguments passed to setup_anndata of the original model: ```json { "labels_key": "cell_ontology_class", "layer": null, "batch_key": null } ```
Data Registry Registry elements for AnnData manager: | Registry Key | scvi-tools Location | |--------------|---------------------------| | X | adata.X | | labels | adata.obs['_scvi_labels'] | - **Data is Minified**: False
Summary Statistics | Summary Stat Key | Value | |------------------|-------| | n_cells | 5112 | | n_labels | 18 | | n_vars | 3000 |
Training **Training data url**: Not provided by uploader 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 URL**: https://github.com/YosefLab/scvi-hub-models/blob/main/src/scvi_hub_models/TS_train_all_tissues.ipynb
# 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