Pre-defined validation data

Help scvi-tools
1

I am training multiple models and have pre-existing h5ad files corresponding to train/test/validation datasets that are fixed across the models. Is there a way to manually set the train and validation anndata objects when training an scvi.model.SCVI model? I see that there is a setter for validation_indices, is the best way to just concatenate the two anndata objects and then manually set validation_indices?

My idea solution would look something like this:

model = scvi.model.SCVI(train_adata, val_adata, n_layers=n_layers, n_latent=n_latent, n_hidden=n_hidden, gene_likelihood="nb")

but I’m not sure that this would be a broadly applicable change for other users.

2

Hi, yes concatenating and setting validation indices is the correct way (only works in the current main branch and will be released for 1.2). ScVI-tools requires a single AnnData object. We are working with other group to lift this restrictions.