scvelo.tl.VELOVI.get_reconstruction_error

VELOVI.get_reconstruction_error(adata=None, indices=None, batch_size=None)

Return the reconstruction error for the data.

This is typically written as \(p(x \mid z)\), the likelihood term given one posterior sample. Note, this is not the negative likelihood, higher is better.

Parameters

adata : AnnData, None

AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.

indices : Sequence[int], None

Indices of cells in adata to use. If None, all cells are used.

batch_size : int, None

Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.

Return type

float