Common Modelling Use Cases

• Preprocessing datasets for analysis with scvi-tools
• Model hyperparameter tuning with scVI
• Minification
• Using SHAP values and IntegratedGradients for cell type classification interpretability
• Train a scVI model using Census data
• Train a scVI model using Lamin
• Train a scVI model using Anncollection dataloader wrapper
• Train a scVI model using multiGPU

Preprocessing datasets for analysis with scvi-tools

Learn how to preprocess various types of data for use with scvi-tools models.

Common Modelling Use Cases

Model hyperparameter tuning with scVI

Automatically find optimal set of hyperparameters using autotune.

Common Modelling Use Cases

Minification

Minify a dataset by replacing count data with the model’s estimated parameters of the latent posterior distribution

Common Modelling Use Cases

Using SHAP values and IntegratedGradients for cell type classification interpretability

Use integrated gradient or SHAP values for model explainability

Common Modelling Use Cases

Train a scVI model using Census data

Learn a scalable approach using TileDBDataModule dataloader to training an scVI model on Census data.

Common Modelling Use Cases

Train a scVI model using Lamin

Use the Lamin MappedCollectionDataModule for a scalable approach to training an scVI model on multiple adata's.

Common Modelling Use Cases

Train a scVI model using Anncollection dataloader wrapper

Use the AnnCollection dataloader for a scalable approach to training an scVI model on multiple adata's.

Common Modelling Use Cases

Train a scVI model using multiGPU

Example of how to train an SCVI model using multi GPU settings

Common Modelling Use Cases