scAlignOptions {scAlign} | R Documentation |
Defines parameters for optimizer and training procedure.
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 )
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. |
Options data.frame
options=scAlignOptions(steps=15000, log.every=5000, early.stop=FALSE, architecture="large")