scAlignOptions {scAlign} | R Documentation

## Set training options

### Description

Defines parameters for optimizer and training procedure.

### Usage

    scAlignOptions(
      steps = 15000,
      steps.decoder = 10000,
      batch.size = 150,
      learning.rate = 1e-04,
      log.every = 5000,
      architecture = "large",
      batch.norm.layer = FALSE,
      dropout.layer = TRUE,
      num.dim = 32,
      perplexity = 30,
      betas = 0,
      norm = TRUE,
      full.norm = FALSE,
      early.stop = FALSE,
      walker.loss = TRUE,
      reconc.loss = FALSE,
      walker.weight = 1,
      classifier.weight = 1,
      classifier.delay = NA,
      gpu.device = "0",
      seed = 1234
    )

### Arguments

`steps` | (default: 15000) Number of training iterations for neural networks.
`steps.decoder` | Number of training iterations for neural networks.
`batch.size` | (default: 150) Number of input samples per training batch.
`learning.rate` | (default: 1e-4) Initial learning rate for ADAM.
`log.every` | (default: 5000) Number of steps before saving results.
`architecture` | (default: "small") Network function name for scAlign.
`batch.norm.layer` | (default: FALSE) Include batch normalization in the network structure.
`dropout.layer` | (default: TRUE) Include dropout in the network.
`num.dim` | (default: 32) Number of dimensions for joint embedding space.
`perplexity` | (default: 30) Determines the neighborhood size for each sample.
`betas` | (default: 0) Sets the bandwidth of the gaussians to be the same if > 0. Otherwise per cell beta is computed.
`norm` | (default: TRUE) Normalize the data mini batches while training scAlign (repeated).
`full.norm` | (default: FALSE) Normalize the data matrix prior to scAlign (done once).
`early.stop` | (default: TRUE) Early stopping during network training.
`walker.loss` | (default: TRUE) Add walker loss to model.
`reconc.loss` | (default: FALSE) Add reconstruction loss to model during alignment.
`walker.weight` | (default: 1.0) Weight on walker loss component
`classifier.weight` | (default: 1.0) Weight on classifier loss component
`classifier.delay` | (default: NULL) Delay classifier component of loss function until specific training step. Defaults to (2/3)*steps.
`gpu.device` | (default: '0') Which gpu to use.
`seed` | (default: 1245) Sets graph level random seed in tensorflow.

### Value

Options data.frame

### Examples

    options=scAlignOptions(steps=15000,
                           log.every=5000,
                           early.stop=FALSE,
                           architecture="large")

[Package scAlign version 1.8.0 Index]