scvi.module.VAE#
- class scvi.module.VAE(n_input, n_batch=0, n_labels=0, n_hidden=128, n_latent=10, n_layers=1, n_continuous_cov=0, n_cats_per_cov=None, dropout_rate=0.1, dispersion='gene', log_variational=True, gene_likelihood='zinb', latent_distribution='normal', encode_covariates=False, deeply_inject_covariates=True, use_batch_norm='both', use_layer_norm='none', use_size_factor_key=False, use_observed_lib_size=True, library_log_means=None, library_log_vars=None, var_activation=None)[source]#
Bases:
BaseMinifiedModeModuleClass
Variational auto-encoder model.
This is an implementation of the scVI model described in [Lopez et al., 2018].
- Parameters:
n_input (int) – Number of input genes
n_batch (int) – Number of batches, if 0, no batch correction is performed.
n_labels (int) – Number of labels
n_hidden (Tunable_[int]) – Number of nodes per hidden layer
n_latent (Tunable_[int]) – Dimensionality of the latent space
n_layers (Tunable_[int]) – Number of hidden layers used for encoder and decoder NNs
n_continuous_cov (int) – Number of continuous covarites
n_cats_per_cov (Optional[Iterable[int]]) – Number of categories for each extra categorical covariate
dropout_rate (Tunable_[float]) – Dropout rate for neural networks
dispersion (Tunable_[Literal['gene', 'gene-batch', 'gene-label', 'gene-cell']]) –
One of the following
'gene'
- dispersion parameter of NB is constant per gene across cells'gene-batch'
- dispersion can differ between different batches'gene-label'
- dispersion can differ between different labels'gene-cell'
- dispersion can differ for every gene in every cell
log_variational (bool) – Log(data+1) prior to encoding for numerical stability. Not normalization.
gene_likelihood (Tunable_[Literal['zinb', 'nb', 'poisson']]) –
One of
'nb'
- Negative binomial distribution'zinb'
- Zero-inflated negative binomial distribution'poisson'
- Poisson distribution
latent_distribution (Tunable_[Literal['normal', 'ln']]) –
One of
'normal'
- Isotropic normal'ln'
- Logistic normal with normal params N(0, 1)
encode_covariates (Tunable_[bool]) – Whether to concatenate covariates to expression in encoder
deeply_inject_covariates (Tunable_[bool]) – Whether to concatenate covariates into output of hidden layers in encoder/decoder. This option only applies when
n_layers
> 1. The covariates are concatenated to the input of subsequent hidden layers.use_batch_norm (Tunable_[Literal['encoder', 'decoder', 'none', 'both']]) – Whether to use batch norm in layers.
use_layer_norm (Tunable_[Literal['encoder', 'decoder', 'none', 'both']]) – Whether to use layer norm in layers.
use_size_factor_key (bool) – Use size_factor AnnDataField defined by the user as scaling factor in mean of conditional distribution. Takes priority over
use_observed_lib_size
.use_observed_lib_size (bool) – Use observed library size for RNA as scaling factor in mean of conditional distribution
library_log_means (Optional[ndarray]) – 1 x n_batch array of means of the log library sizes. Parameterizes prior on library size if not using observed library size.
library_log_vars (Optional[ndarray]) – 1 x n_batch array of variances of the log library sizes. Parameterizes prior on library size if not using observed library size.
var_activation (Optional[Callable]) – Callable used to ensure positivity of the variational distributions’ variance. When
None
, defaults totorch.exp
.
Attributes table#
Methods table#
|
Runs the generative model. |
|
Computes the loss function for the model. |
|
Computes the marginal log likelihood of the model. |
|
Generate observation samples from the posterior predictive distribution. |
Attributes#
training
Methods#
generative
- VAE.generative(z, library, batch_index, cont_covs=None, cat_covs=None, size_factor=None, y=None, transform_batch=None)[source]#
Runs the generative model.
loss
- VAE.loss(tensors, inference_outputs, generative_outputs, kl_weight=1.0)[source]#
Computes the loss function for the model.
- Parameters:
kl_weight (float) –
marginal_ll
sample
- VAE.sample(tensors, n_samples=1, library_size=1)[source]#
Generate observation samples from the posterior predictive distribution.
The posterior predictive distribution is written as \(p(\hat{x} \mid x)\).
- Parameters:
tensors – Tensors dict
n_samples – Number of required samples for each cell
library_size – Library size to scale samples to
- Returns:
x_new :
torch.Tensor
tensor with shape (n_cells, n_genes, n_samples)- Return type: