get_default_stochastic_options {MOFA2} | R Documentation |
Function to obtain the default options for stochastic variational inference.
get_default_stochastic_options(object)
object |
an untrained |
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) load(file) # 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 )