autoencoder: Train an Autoencoding Neural Network
In ANN2: Artificial Neural Networks for Anomaly Detection

Description Usage Arguments Details Value Examples

Construct and train an Autoencoder by setting the target variables equal to the input variables. The number of nodes in the middle layer should be smaller than the number of input variables in X in order to create a bottleneck layer.

autoencoder(
  X,
  hidden.layers,
  standardize = TRUE,
  loss.type = "squared",
  huber.delta = 1,
  activ.functions = "tanh",
  step.H = 5,
  step.k = 100,
  optim.type = "sgd",
  learn.rates = 1e-04,
  L1 = 0,
  L2 = 0,
  sgd.momentum = 0.9,
  rmsprop.decay = 0.9,
  adam.beta1 = 0.9,
  adam.beta2 = 0.999,
  n.epochs = 100,
  batch.size = 32,
  drop.last = TRUE,
  val.prop = 0.1,
  verbose = TRUE,
  random.seed = NULL
)

`X`	matrix with explanatory variables
`hidden.layers`	vector specifying the number of nodes in each layer. The number of hidden layers in the network is implicitly defined by the length of this vector. Set `hidden.layers` to `NA` for a network with no hidden layers
`standardize`	logical indicating if X and Y should be standardized before training the network. Recommended to leave at `TRUE` for faster convergence.
`loss.type`	which loss function should be used. Options are "squared", "absolute", "huber" and "pseudo-huber"
`huber.delta`	used only in case of loss functions "huber" and "pseudo-huber". This parameter controls the cut-off point between quadratic and absolute loss.
`activ.functions`	character vector of activation functions to be used in each hidden layer. Possible options are 'tanh', 'sigmoid', 'relu', 'linear', 'ramp' and 'step'. Should be either the size of the number of hidden layers or equal to one. If a single activation type is specified, this type will be broadcasted across the hidden layers.
`step.H`	number of steps of the step activation function. Only applicable if activ.functions includes 'step'
`step.k`	parameter controlling the smoothness of the step activation function. Larger values lead to a less smooth step function. Only applicable if activ.functions includes 'step'.
`optim.type`	type of optimizer to use for updating the parameters. Options are 'sgd', 'rmsprop' and 'adam'. SGD is implemented with momentum.
`learn.rates`	the size of the steps to make in gradient descent. If set too large, the optimization might not converge to optimal values. If set too small, convergence will be slow. Should be either the size of the number of hidden layers plus one or equal to one. If a single learn rate is specified, this learn rate will be broadcasted across the layers.
`L1`	L1 regularization. Non-negative number. Set to zero for no regularization.
`L2`	L2 regularization. Non-negative number. Set to zero for no regularization.
`sgd.momentum`	numeric value specifying how much momentum should be used. Set to zero for no momentum, otherwise a value between zero and one.
`rmsprop.decay`	level of decay in the rms term. Controls the strength of the exponential decay of the squared gradients in the term that scales the gradient before the parameter update. Common values are 0.9, 0.99 and 0.999
`adam.beta1`	level of decay in the first moment estimate (the mean). The recommended value is 0.9
`adam.beta2`	level of decay in the second moment estimate (the uncentered variance). The recommended value is 0.999
`n.epochs`	the number of epochs to train. One epoch is a single iteration through the training data.
`batch.size`	the number of observations to use in each batch. Batch learning is computationally faster than stochastic gradient descent. However, large batches might not result in optimal learning, see Efficient Backprop by LeCun for details.
`drop.last`	logical. Only applicable if the size of the training set is not perfectly devisible by the batch size. Determines if the last chosen observations should be discarded (in the current epoch) or should constitute a smaller batch. Note that a smaller batch leads to a noisier approximation of the gradient.
`val.prop`	proportion of training data to use for tracking the loss on a validation set during training. Useful for assessing the training process and identifying possible overfitting. Set to zero for only tracking the loss on the training data.
`verbose`	logical indicating if additional information should be printed
`random.seed`	optional seed for the random number generator

A function for training Autoencoders. During training, the network will learn a generalised representation of the data (generalised since the middle layer acts as a bottleneck, resulting in reproduction of only the most important features of the data). As such, the network models the normal state of the data and therefore has a denoising property. This property can be exploited to detect anomalies by comparing input to reconstruction. If the difference (the reconstruction error) is large, the observation is a possible anomaly.

An ANN object. Use function plot(<object>) to assess loss on training and optionally validation data during training process. Use function predict(<object>, <newdata>) for prediction.

# Autoencoder example
X <- USArrests
AE <- autoencoder(X, c(10,2,10), loss.type = 'pseudo-huber',
                  activ.functions = c('tanh','linear','tanh'),
                  batch.size = 8, optim.type = 'adam',
                  n.epochs = 1000, val.prop = 0)

# Plot loss during training
plot(AE)

# Make reconstruction and compression plots
reconstruction_plot(AE, X)
compression_plot(AE, X)

# Reconstruct data and show states with highest anomaly scores
recX <- reconstruct(AE, X)
sort(recX$anomaly_scores, decreasing = TRUE)[1:5]