mypackage.MyPyroModel¶
-
class
mypackage.
MyPyroModel
(adata, n_hidden=128, n_latent=10, n_layers=1, **model_kwargs)[source]¶ Skeleton for a pyro version of a scvi-tools model.
Please use this skeleton to create new models.
- Parameters
- adata :
AnnData
AnnData
AnnData object that has been registered via
setup_anndata()
.- n_hidden :
int
int
(default:128
) Number of nodes per hidden layer.
- n_latent :
int
int
(default:10
) Dimensionality of the latent space.
- n_layers :
int
int
(default:1
) Number of hidden layers used for encoder and decoder NNs.
- **model_kwargs
Keyword args for
MyModule
- adata :
Examples
>>> adata = anndata.read_h5ad(path_to_anndata) >>> scvi.data.setup_anndata(adata, batch_key="batch") >>> vae = mypackage.MyModel(adata) >>> vae.train() >>> adata.obsm["X_mymodel"] = vae.get_latent_representation()
Attributes
Returns computed metrics during training.
Methods
get_latent
([adata, indices, batch_size])Return the latent representation for each cell.
load
(dir_path[, adata, use_gpu])Instantiate a model from the saved output.
save
(dir_path[, overwrite, save_anndata])Save the state of the model.
to_device
(device)Move model to device.
train
([max_epochs, use_gpu, train_size, …])Train the model.