get_default_stochastic_options {MOFA2} | R Documentation

## Get default stochastic options

### Description

Function to obtain the default options for stochastic variational inference.

### Usage

    get_default_stochastic_options(object)

### Arguments

`object` | an untrained `MOFA`

### Details

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

### Value

Returns a list with default options

### Examples

    # 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
    )

[Package MOFA2 version 1.0.1 Index]