Hello:
I recently got the following problem while analyzing CITE-Seq data with TOTALVI: RuntimeWarning: The lr scheduler dict contains the key(s) ['monitor'], but the keys will be ignored. you need to call
lr_scheduler.step() manually in manual optimization.
I’m not sure what’s wrong, has anyone had a similar problem? Can you provide any help?
My code is as follows:
adata = mdata["rna"].copy()
adata.obsm["protein_expression"] = mdata["protein"].layers["counts"].A.copy()
scvi.model.TOTALVI.setup_anndata(
adata,
layer="counts",
batch_key="Batch",
protein_expression_obsm_key="protein_expression",
)
arches_params = dict(
use_layer_norm="Both",
use_batch_norm="none",
n_layers_decoder=2,
n_layers_encoder=2,
)
vae = scvi.model.TOTALVI(adata, **arches_params)
vae.train()
By the way, the versions of scvi and torch are 1.0.2 and 2.0.1+cu117 respectively.