darch: Fit a deep neural network
In darch: Package for Deep Architectures and Restricted Boltzmann Machines

Description Usage Arguments Details Value Author(s) References See Also Examples

Fit a deep neural network with optional pre-training and one of various fine-tuning algorithms.

darch(x, ...)

## Default S3 method:
darch(x, y, layers = 10, ..., autosave = F,
  autosave.epochs = round(darch.numEpochs/20),
  autosave.dir = "./darch.autosave", autosave.trim = F, bp.learnRate = 1,
  bp.learnRateScale = 1, bootstrap = F, bootstrap.unique = T,
  bootstrap.num = 0, cg.length = 2, cg.switchLayers = 1, darch = NULL,
  darch.batchSize = 1, darch.dither = F, darch.dropout = 0,
  darch.dropout.dropConnect = F, darch.dropout.momentMatching = 0,
  darch.dropout.oneMaskPerEpoch = F, darch.elu.alpha = 1,
  darch.errorFunction = if (darch.isClass) crossEntropyError else mseError,
  darch.finalMomentum = 0.9, darch.fineTuneFunction = backpropagation,
  darch.initialMomentum = 0.5, darch.isClass = T,
  darch.maxout.poolSize = 2, darch.maxout.unitFunction = linearUnit,
  darch.momentumRampLength = 1, darch.nesterovMomentum = T,
  darch.numEpochs = 100, darch.returnBestModel = T,
  darch.returnBestModel.validationErrorFactor = 1 - exp(-1),
  darch.stopClassErr = -Inf, darch.stopErr = -Inf,
  darch.stopValidClassErr = -Inf, darch.stopValidErr = -Inf,
  darch.trainLayers = T, darch.unitFunction = sigmoidUnit,
  darch.weightDecay = 0,
  darch.weightUpdateFunction = weightDecayWeightUpdate, dataSet = NULL,
  dataSetValid = NULL,
  generateWeightsFunction = generateWeightsGlorotUniform, gputools = F,
  gputools.deviceId = 0, logLevel = NULL, normalizeWeights = F,
  normalizeWeightsBound = 15, paramsList = list(),
  preProc.factorToNumeric = F, preProc.factorToNumeric.targets = F,
  preProc.fullRank = T, preProc.fullRank.targets = F,
  preProc.orderedToFactor.targets = T, preProc.params = F,
  preProc.targets = F, rbm.allData = F, rbm.batchSize = 1,
  rbm.consecutive = T, rbm.errorFunction = mseError,
  rbm.finalMomentum = 0.9, rbm.initialMomentum = 0.5, rbm.lastLayer = 0,
  rbm.learnRate = 1, rbm.learnRateScale = 1, rbm.momentumRampLength = 1,
  rbm.numCD = 1, rbm.numEpochs = 0, rbm.unitFunction = sigmoidUnitRbm,
  rbm.updateFunction = rbmUpdate, rbm.weightDecay = 2e-04, retainData = F,
  rprop.decFact = 0.5, rprop.incFact = 1.2, rprop.initDelta = 1/80,
  rprop.maxDelta = 50, rprop.method = "iRprop+", rprop.minDelta = 1e-06,
  seed = NULL, shuffleTrainData = T, weights.max = 0.1,
  weights.mean = 0, weights.min = -0.1, weights.sd = 0.01,
  xValid = NULL, yValid = NULL)

## S3 method for class 'formula'
darch(x, data, layers, ..., xValid = NULL, dataSet = NULL,
  dataSetValid = NULL, logLevel = NULL, paramsList = list(),
  darch = NULL)

## S3 method for class 'DataSet'
darch(x, ...)

`x`	Input data matrix or `data.frame` (`darch.default`) or `formula` (`darch.formula`) or `DataSet` (`darch.DataSet`).
`...`	Additional parameters.
`y`	Target data matrix or `data.frame`, if `x` is an input data matrix or `data.frame`.
`layers`	Vector containing one integer for the number of neurons of each layer. Defaults to c(`a`, 10, `b`), where `a` is the number of columns in the training data and `b` the number of columns in the targets. If this has length 1, it is used as the number of neurons in the hidden layer, not as the number of layers!
`autosave`	Logical indicating whether to activate automatically saving the `DArch` instance to a file during fine-tuning.
`autosave.epochs`	After how many epochs should auto-saving happen, by default after every 5 1, the network will only be saved once when thee fine-tuning is done.
`autosave.dir`	Directory for the autosave files, the file names will be e.g. autosave_010.net for the DArch instance after 10 epochs
`autosave.trim`	Whether to trim the network before saving it. This will remove the dataset and the layer weights, resulting in a network that is no longer usable for predictions or training. Useful when only statistics and settings need to be stored.
`bp.learnRate`	Learning rates for backpropagation, length is either one or the same as the number of weight matrices when using different learning rates for each layer.
`bp.learnRateScale`	The learn rate is multiplied by this value after each epoch.
`bootstrap`	Logical indicating whether to use bootstrapping to create a training and validation data set from the given training data.
`bootstrap.unique`	Logical indicating whether to take only unique samples for the training (`TRUE`, default) or take all drawn samples (`FALSE`), which will results in a bigger training set with duplicates. Note: This is ignored if `bootstrap.num` is greater than 0.
`bootstrap.num`	If this is greater than 0, bootstrapping will draw this number of training samples without replacement.
`cg.length`	Numbers of line search
`cg.switchLayers`	Indicates when to train the full network instead of only the upper two layers
`darch`	Existing `DArch` instance for which training is to be resumed. Note: When enabling pre-training, previous training results we be lost, see explanation for parameter `rbm.numEpochs`.
`darch.batchSize`	Batch size, i.e. the number of training samples that are presented to the network before weight updates are performed, for fine-tuning.
`darch.dither`	Whether to apply dither to numeric columns in the training input data.
`darch.dropout`	Dropout rates. If this is a vector it will be treated as the dropout rates for each individual layer. If one element is missing, the input dropout will be set to 0. When enabling `darch.dropout.dropConnect`, this vector needs an additional element (one element per weight matrix between two layers as opposed to one element per layer excluding the last layer).
`darch.dropout.dropConnect`	Whether to use DropConnect instead of dropout for the hidden layers. Will use `darch.dropout` as the dropout rates.
`darch.dropout.momentMatching`	How many iterations to perform during moment matching for dropout inference, 0 to disable moment matching.
`darch.dropout.oneMaskPerEpoch`	Whether to generate a new mask for each batch (`FALSE`, default) or for each epoch (`TRUE`).
`darch.elu.alpha`	Alpha parameter for the exponential linear unit function. See `exponentialLinearUnit`.
`darch.errorFunction`	Error function during fine-tuning. Possible error functions include `mseError`,`rmseError`, and `crossEntropyError`.
`darch.finalMomentum`	Final momentum during fine-tuning.
`darch.fineTuneFunction`	Fine-tuning function. Possible values include `backpropagation` (default), `rpropagation`, `minimizeClassifier` and `minimizeAutoencoder` (unsupervised).
`darch.initialMomentum`	Initial momentum during fine-tuning.
`darch.isClass`	Whether output should be treated as class labels during fine-tuning and classification rates should be printed.
`darch.maxout.poolSize`	Pool size for maxout units, when using the maxout acitvation function. See `maxoutUnit`.
`darch.maxout.unitFunction`	Inner unit function used by maxout. See `darch.unitFunction` for possible unit functions.
`darch.momentumRampLength`	After how many epochs, relative to the overall number of epochs trained, should the momentum reach `darch.finalMomentum`? A value of 1 indicates that the `darch.finalMomentum` should be reached in the final epoch, a value of 0.5 indicates that `darch.finalMomentum` should be reached after half of the training is complete. Note that this will lead to bumps in the momentum ramp if training is resumed with the same parameters for `darch.initialMomentum` and `darch.finalMomentum`. Set `darch.momentumRampLength` to 0 to avoid this problem when resuming training.
`darch.nesterovMomentum`	Whether to use Nesterov Accelerated Momentum. (NAG) for gradient descent based fine-tuning algorithms.
`darch.numEpochs`	Number of epochs of fine-tuning.
`darch.returnBestModel`	Logical indicating whether to return the best model at the end of training, instead of the last.
`darch.returnBestModel.validationErrorFactor`	When evaluating models with validation data, how high should the validation error be valued, compared to the training error? This is a value between 0 and 1. By default, this value is `1 - exp(-1)`. The training error factor and the validation error factor will always add to 1, so if you pass 1 here, the training error will be ignored, and if you pass 0 here, the validation error will be ignored.
`darch.stopClassErr`	When the classification error is lower than or equal to this value, training is stopped (0..100).
`darch.stopErr`	When the value of the error function is lower than or equal to this value, training is stopped.
`darch.stopValidClassErr`	When the classification error on the validation data is lower than or equal to this value, training is stopped (0..100).
`darch.stopValidErr`	When the value of the error function on the validation data is lower than or equal to this value, training is stopped.
`darch.trainLayers`	Either TRUE to train all layers or a mask containing TRUE for all layers which should be trained and FALSE for all layers that should not be trained (no entry for the input layer).
`darch.unitFunction`	Layer function or vector of layer functions of length `number of layers` - 1. Note that the first entry signifies the layer function between layers 1 and 2, i.e. the output of layer 2. Layer 1 does not have a layer function, since the input values are used directly. Possible unit functions include `linearUnit`, `sigmoidUnit`, `tanhUnit`, `rectifiedLinearUnit`, `softplusUnit`, `softmaxUnit`, and `maxoutUnit`.
`darch.weightDecay`	Weight decay factor, defaults to `0`. All weights will be multiplied by (1 - `darch.weightDecay`) prior to each weight update.
`darch.weightUpdateFunction`	Weight update function or vector of weight update functions, very similar to `darch.unitFunction`. Possible weight update functions include `weightDecayWeightUpdate` and `maxoutWeightUpdate` Note that `maxoutWeightUpdate` must be used on the layer after the maxout activation function!
`dataSet`	`DataSet` instance, passed from darch.DataSet(), may be specified manually.
`dataSetValid`	`DataSet` instance containing validation data.
`generateWeightsFunction`	Weight generation function or vector of layer generation functions of length `number of layers` - 1. Possible weight generation functions include `generateWeightsUniform` (default), `generateWeightsNormal`, `generateWeightsGlorotNormal`, `generateWeightsGlorotUniform`, `generateWeightsHeNormal`, and `generateWeightsHeUniform`.
`gputools`	Logical indicating whether to use gputools for matrix multiplication, if available.
`gputools.deviceId`	Integer specifying the device to use for GPU matrix multiplication. See `chooseGpu`.
`logLevel`	`futile.logger` log level. Uses the currently set log level by default, which is `futile.logger::flog.info` if it was not changed. Other available levels include, from least to most verbose: `FATAL`, `ERROR`, `WARN`, `DEBUG`, and `TRACE`.
`normalizeWeights`	Logical indicating whether to normalize weights (L2 norm = `normalizeWeightsBound`).
`normalizeWeightsBound`	Upper bound on the L2 norm of incoming weight vectors. Used only if `normalizeWeights` is `TRUE`.
`paramsList`	List of parameters, can include and does overwrite specified parameters listed above. Primary for convenience or for use in scripts.
`preProc.factorToNumeric`	Whether all factors should be converted to numeric.
`preProc.factorToNumeric.targets`	Whether all factors should be converted to numeric in the target data.
`preProc.fullRank`	Whether to use full rank encoding. See preProcess for details.
`preProc.fullRank.targets`	Whether to use full rank encoding for target data. See preProcess for details.
`preProc.orderedToFactor.targets`	Whether ordered factors in the target data should be converted to unordered factors. Note: Ordered factors are converted to numeric by `dummyVars` and no longer usable for classification tasks.
`preProc.params`	List of parameters to pass to the `preProcess` function for the input data or `FALSE` to disable input data pre-processing.
`preProc.targets`	Whether target data is to be centered and scaled. Unlike `preProc.params`, this is just a logical turning pre-processing for target data on or off, since this pre-processing has to be reverted when predicting new data. Most useful for regression tasks. Note: This will skew the raw network error.
`rbm.allData`	Logical indicating whether to use training and validation data for pre-training. Note: This also applies when using bootstrapping.
`rbm.batchSize`	Pre-training batch size.
`rbm.consecutive`	Logical indicating whether to train the RBMs one at a time for `rbm.numEpochs` epochs (`TRUE`, default) or alternatingly training each RBM for one epoch at a time (`FALSE`).
`rbm.errorFunction`	Error function during pre-training. This is only used to estimate the RBM error and does not affect the training itself. Possible error functions include `mseError` and `rmseError`.
`rbm.finalMomentum`	Final momentum during pre-training.
`rbm.initialMomentum`	Initial momentum during pre-training.
`rbm.lastLayer`	`Numeric` indicating at which layer to stop the pre-training. Possible values include `0`, meaning that all layers are trained; positive integers, meaning to stop training after the RBM where `rbm.lastLayer` forms the visible layer; negative integers, meaning to stop the training at `rbm.lastLayer` RBMs from the top RBM.
`rbm.learnRate`	Learning rate during pre-training.
`rbm.learnRateScale`	The learn rates will be multiplied with this value after each epoch.
`rbm.momentumRampLength`	After how many epochs, relative to `rbm.numEpochs`, should the momentum reach `rbm.finalMomentum`? A value of 1 indicates that the `rbm.finalMomentum` should be reached in the final epoch, a value of 0.5 indicates that `rbm.finalMomentum` should be reached after half of the training is complete.
`rbm.numCD`	Number of full steps for which contrastive divergence is performed. Increasing this will slow training down considerably.
`rbm.numEpochs`	Number of pre-training epochs. Note: When passing a value other than `0` here and also passing an existing `DArch` instance via the `darch` parameter, the weights of the network will be completely reset! Pre-training is essentially a form of advanced weight initialization and it makes no sense to perform pre-training on a previously trained network.
`rbm.unitFunction`	Unit function during pre-training. Possible functions include `sigmoidUnitRbm` (default), `tanhUnitRbm`, and `linearUnitRbm`.
`rbm.updateFunction`	Update function during pre-training. Currently, `darch` only provides `rbmUpdate`.
`rbm.weightDecay`	Pre-training weight decay. Weights will be multiplied by (1 - `rbm.weightDecay`) prior to each weight update.
`retainData`	Logical indicating whether to store the training data in the `DArch` instance after training or when saving it to disk.
`rprop.decFact`	Decreasing factor for the training. Default is `0.6`.
`rprop.incFact`	Increasing factor for the training Default is `1.2`.
`rprop.initDelta`	Initialisation value for the update. Default is `0.0125`.
`rprop.maxDelta`	Upper bound for step size. Default is `50`
`rprop.method`	The method for the training. Default is "iRprop+"
`rprop.minDelta`	Lower bound for step size. Default is `0.000001`
`seed`	Allows the specification of a seed which will be set via `set.seed`. Used in the context of `darchBench`.
`shuffleTrainData`	Logical indicating whether to shuffle training data before each epoch.
`weights.max`	`max` parameter to the runif function.
`weights.mean`	`mean` parameter to the rnorm function.
`weights.min`	`min` parameter to the runif function.
`weights.sd`	`sd` parameter to the rnorm function.
`xValid`	Validation input data matrix or `data.frame`.
`yValid`	Validation target data matrix or `data.frame`, if `x` is a data matrix or `data.frame`.
`data`	`data.frame` containing the dataset, if `x` is a `formula`.

The darch package implements Deep Architecture Networks and restricted Boltzmann machines.

The creation of this package is motivated by the papers from G. Hinton et. al. from 2006 (see references for details) and from the MATLAB source code developed in this context. This package provides the possibility to generate deep architecture networks (darch) like the deep belief networks from Hinton et. al.. The deep architectures can then be trained with the contrastive divergence method. After this pre-training it can be fine tuned with several learning methods like backpropagation, resilient backpropagation and conjugate gradients as well as more recent techniques like dropout and maxout.

See https://github.com/maddin79/darch for further information, documentation, and releases.

Package:	darch
Type:	Package
Version:	0.10.0
Date:	2015-11-12
License:	GPL-2 or later
LazyLoad:	yes

Fitted DArch instance

Martin Drees mdrees@stud.fh-dortmund.de and contributors.

Hinton, G. E., S. Osindero, Y. W. Teh, A fast learning algorithm for deep belief nets, Neural Computation 18(7), S. 1527-1554, DOI: 10.1162/neco.2006.18.7.1527 2006.

Hinton, G. E., R. R. Salakhutdinov, Reducing the dimensionality of data with neural networks, Science 313(5786), S. 504-507, DOI: 10.1126/science.1127647, 2006.

Hinton, Geoffrey E. et al. (2012). "Improving neural networks by preventing coadaptation of feature detectors". In: Clinical Orthopaedics and Related Research abs/1207.0580. URL : http://arxiv.org/abs/1207.0580.

Goodfellow, Ian J. et al. (2013). "Maxout Networks". In: Proceedings of the 30th International Conference on Machine Learning, ICML 2013, Atlanta, GA, USA, 16-21 June 2013, pp. 1319-1327. URL: http://jmlr.org/proceedings/papers/v28/goodfellow13.html.

Drees, Martin (2013). "Implementierung und Analyse von tiefen Architekturen in R". German. Master's thesis. Fachhochschule Dortmund.

Rueckert, Johannes (2015). "Extending the Darch library for deep architectures". Project thesis. Fachhochschule Dortmund. URL: http://static.saviola.de/publications/rueckert_2015.pdf.

Other darch interface functions: darchBench, darchTest, plot.DArch, predict.DArch, print.DArch

## Not run: 
data(iris)
model <- darch(Species ~ ., iris)
print(model)
predictions <- predict(model, newdata = iris, type = "class")
cat(paste("Incorrect classifications:", sum(predictions != iris[,5])))

trainData <- matrix(c(0,0,0,1,1,0,1,1), ncol = 2, byrow = TRUE)
trainTargets <- matrix(c(0,1,1,0), nrow = 4)
model2 <- darch(trainData, trainTargets, layers = c(2, 10, 1),
  darch.numEpochs = 500, darch.stopClassErr = 0, retainData = T)
e <- darchTest(model2)
cat(paste0("Incorrect classifications on all examples: ", e[3], " (",
  e[2], "%)\n"))

plot(model2)

## End(Not run)

#
# More examples can be found at
# https://github.com/maddin79/darch/tree/v0.12.0/examples