scvi.module.LDVAE

class scvi.module.LDVAE(n_input, n_batch=0, n_labels=0, n_hidden=128, n_latent=10, n_layers_encoder=1, dropout_rate=0.1, dispersion='gene', log_variational=True, gene_likelihood='nb', use_batch_norm=True, bias=False, latent_distribution='normal')[source]

Bases: scvi.module._vae.VAE

Linear-decoded Variational auto-encoder model.

Implementation of [Svensson20].

This model uses a linear decoder, directly mapping the latent representation to gene expression levels. It still uses a deep neural network to encode the latent representation.

Compared to standard VAE, this model is less powerful, but can be used to inspect which genes contribute to variation in the dataset. It may also be used for all scVI tasks, like differential expression, batch correction, imputation, etc. However, batch correction may be less powerful as it assumes a linear model.

Parameters
n_input : intint

Number of input genes

n_batch : intint (default: 0)

Number of batches

n_labels : intint (default: 0)

Number of labels

n_hidden : intint (default: 128)

Number of nodes per hidden layer (for encoder)

n_latent : intint (default: 10)

Dimensionality of the latent space

n_layers_encoder : intint (default: 1)

Number of hidden layers used for encoder NNs

dropout_rate : floatfloat (default: 0.1)

Dropout rate for neural networks

dispersion : strstr (default: 'gene')

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 : boolbool (default: True)

Log(data+1) prior to encoding for numerical stability. Not normalization.

gene_likelihood : strstr (default: 'nb')

One of

  • 'nb' - Negative binomial distribution

  • 'zinb' - Zero-inflated negative binomial distribution

use_batch_norm : boolbool (default: True)

Bool whether to use batch norm in decoder

bias : boolbool (default: False)

Bool whether to have bias term in linear decoder

use_observed_lib_size

Use observed library size for RNA as scaling factor in mean of conditional distribution

Methods

get_loadings()

Extract per-gene weights (for each Z, shape is genes by dim(Z)) in the linear decoder.