get_default_stochastic_options: Get default stochastic options

View source: R/prepare_mofa.R

get_default_stochastic_optionsR Documentation

Get default stochastic options


Function to obtain the default options for stochastic variational inference.





an untrained MOFA


This function provides a default set of stochastic inference options that can be modified and passed to the MOFA object in the prepare_mofa step), i.e. after creating a MOFA object (using create_mofa) and before starting the training (using run_mofa) These options are only relevant when activating stochastic inference in training_options (see example). The stochastic inference options are the following:

  • batch_size: numeric value indicating the batch size (as a fraction). Default is 0.5 (half of the data set).

  • learning_rate: numeric value indicating the learning rate. Default is 1.0

  • forgetting_rate: numeric indicating the forgetting rate. Default is 0.5

  • start_stochastic: integer indicating the first iteration to start stochastic inference Default is 1


Returns a list with default options


# Using an existing simulated data with two groups and two views
file <- system.file("extdata", "test_data.RData", package = "MOFA2")

# Load data dt (in data.frame format)

# Create the MOFA object
MOFAmodel <- create_mofa(dt)

# activate stochastic inference in training options
train_opts <- get_default_training_options(MOFAmodel)
train_opts$stochastic <- TRUE

# Load default stochastic options
stochastic_opts <- get_default_stochastic_options(MOFAmodel)

# Edit some of the stochastic options
stochastic_opts$learning_rate <- 0.75
stochastic_opts$batch_size <- 0.25

# Prepare the MOFA object
MOFAmodel <- prepare_mofa(MOFAmodel, 
  training_options = train_opts,
  stochastic_options = stochastic_opts

bioFAM/MOFA2 documentation built on March 21, 2023, 5:27 p.m.