scvi.module.AmortizedLDAPyroModule#

class scvi.module.AmortizedLDAPyroModule(n_input, n_topics, n_hidden, cell_topic_prior=None, topic_feature_prior=None)[source]#

Bases: PyroBaseModuleClass

An amortized implementation of Latent Dirichlet Allocation [Blei et al., 2003] implemented in Pyro.

This module uses auto encoding variational Bayes to optimize the latent variables in the model. In particular, a fully-connected neural network is used as an encoder, which takes in feature counts as input and outputs the parameters of cell topic distribution. To employ the reparametrization trick stably, the Dirichlet priors are approximated by a Logistic-Normal distribution. The input feature counts tensor is a cell by features Bag-of-Words(BoW) representation of the counts. I.e. the model treats each cell’s feature vector as ordered, not as unordered as in a Multinomial distribution.

Parameters:

  • n_input (int) – Number of input features.

  • n_topics (int) – Number of topics/topics to model.

  • n_hidden (int) – Number of nodes in the hidden layer of the encoder.

  • cell_topic_prior (Union[float, Sequence[float], None] (default: None)) – Prior of cell topic distribution. If None, defaults to 1 / n_topics.

  • topic_feature_prior (Union[float, Sequence[float], None] (default: None)) – Prior of topic feature distribution. If None, defaults to 1 / n_topics.

Attributes table#

guide

model

Methods table#

get_elbo(x, library, n_obs)

Computes ELBO.

get_topic_distribution(x, n_samples)

Converts x to its inferred topic distribution.

topic_by_feature(n_samples)

Gets a Monte-Carlo estimate of the expectation of the topic by feature matrix.

Attributes#

AmortizedLDAPyroModule.guide[source]#
AmortizedLDAPyroModule.model[source]#
AmortizedLDAPyroModule.training: bool#

Methods#

AmortizedLDAPyroModule.get_elbo(x, library, n_obs)[source]#

Computes ELBO.

Parameters:

  • x (Tensor) – Counts tensor.

  • library (Tensor) – Library sizes for each cell.

  • n_obs (int) – Size of full batch. If n_obs < x.shape[0], ELBO is scaled by (n_obs / x.shape[0]).

Return type:

float

Returns:

The positive ELBO.

AmortizedLDAPyroModule.get_topic_distribution(x, n_samples)[source]#

Converts x to its inferred topic distribution.

Parameters:

  • x (Tensor) – Counts tensor.

  • n_samples (int) – Number of samples to take for the Monte-Carlo estimate of the mean.

Return type:

Tensor

Returns:

A x.shape[0] x n_topics tensor containing the normalized topic distribution.

AmortizedLDAPyroModule.topic_by_feature(n_samples)[source]#

Gets a Monte-Carlo estimate of the expectation of the topic by feature matrix.

Assumes the module has already been trained.

Parameters:

n_samples (int) – Number of samples to take for the Monte-Carlo estimate of the mean.

Return type:

Tensor

Returns:

A n_topics x n_input tensor containing the topic by feature matrix.