/**
* Determine the class using part of an array.
*
* @param pos The position to begin.
* @param data The array to check.
* @return The class item.
*/
public final ClassItem determineClass(final int pos, final double[] data) {
int resultIndex = 0;
final double[] d = new double[getColumnsNeeded()];
EngineArray.arrayCopy(data, pos, d, 0, d.length);
switch (this.action) {
case Equilateral:
resultIndex = this.eq.decode(d);
break;
case OneOf:
resultIndex = EngineArray.indexOfLargest(d);
break;
case SingleField:
resultIndex = (int) d[0];
break;
default:
throw new AnalystError("Invalid action: " + this.action);
}
if (resultIndex < 0) {
return null;
}
return this.classes.get(resultIndex);
}
/** {@inheritDoc} */
@Override
public void decodeFromArray(double[] encoded) {
EngineArray.arrayCopy(encoded, 0, getFlat().getWeights(), 0, getFlat().getWeights().length);
int index = getFlat().getWeights().length;
for (RadialBasisFunction rbf : flat.getRBF()) {
rbf.setWidth(encoded[index++]);
EngineArray.arrayCopy(encoded, index, rbf.getCenters(), 0, rbf.getCenters().length);
index += rbf.getCenters().length;
}
}
public static ObjectPair<double[][], double[][]> trainingToArray(MLDataSet training) {
int length = (int) training.getRecordCount();
double[][] a = new double[length][training.getInputSize()];
double[][] b = new double[length][training.getIdealSize()];
int index = 0;
for (MLDataPair pair : training) {
EngineArray.arrayCopy(pair.getInputArray(), a[index]);
EngineArray.arrayCopy(pair.getIdealArray(), b[index]);
index++;
}
return new ObjectPair<double[][], double[][]>(a, b);
}
/**
* Calculate the output for the given input.
*
* @param input The input.
* @param output Output will be placed here.
*/
public void compute(final double[] input, final double[] output) {
final int sourceIndex = this.layerOutput.length - this.layerCounts[this.layerCounts.length - 1];
EngineArray.arrayCopy(input, 0, this.layerOutput, sourceIndex, this.inputCount);
for (int i = this.layerIndex.length - 1; i > 0; i--) {
computeLayer(i);
}
// update context values
final int offset = this.contextTargetOffset[0];
EngineArray.arrayCopy(this.layerOutput, 0, layerOutput, offset, this.contextTargetSize[0]);
EngineArray.arrayCopy(this.layerOutput, 0, output, 0, this.outputCount);
}
/**
* Construct a 2d neighborhood function based on the sizes for the x and y dimensions.
*
* @param type The RBF type to use.
* @param x The size of the x-dimension.
* @param y The size of the y-dimension.
*/
public NeighborhoodRBF(final RBFEnum type, final int x, final int y) {
final int[] size = new int[2];
size[0] = x;
size[1] = y;
final double[] centerArray = new double[2];
centerArray[0] = 0;
centerArray[1] = 0;
final double[] widthArray = new double[2];
widthArray[0] = 1;
widthArray[1] = 1;
switch (type) {
case Gaussian:
this.rbf = new GaussianFunction(2);
break;
case InverseMultiquadric:
this.rbf = new InverseMultiquadricFunction(2);
break;
case Multiquadric:
this.rbf = new MultiquadricFunction(2);
break;
case MexicanHat:
this.rbf = new MexicanHatFunction(2);
break;
}
this.rbf.setWidth(1);
EngineArray.arrayCopy(centerArray, this.rbf.getCenters());
this.size = size;
calculateDisplacement();
}
/**
* Classify the input.
*
* @param input The input to classify.
*/
@Override
public int classify(MLData input) {
if (this.classificationTarget < 0 || this.classificationTarget >= this.events.size()) {
throw new BayesianError(
"Must specify classification target by calling setClassificationTarget.");
}
int[] d = this.determineClasses(input);
// properly tag all of the events
for (int i = 0; i < this.events.size(); i++) {
BayesianEvent event = this.events.get(i);
if (i == this.classificationTarget) {
this.query.defineEventType(event, EventType.Outcome);
} else if (this.inputPresent[i]) {
this.query.defineEventType(event, EventType.Evidence);
this.query.setEventValue(event, d[i]);
} else {
this.query.defineEventType(event, EventType.Hidden);
this.query.setEventValue(event, d[i]);
}
}
// loop over and try each outcome choice
BayesianEvent outcomeEvent = this.events.get(this.classificationTarget);
this.classificationProbabilities = new double[outcomeEvent.getChoices().size()];
for (int i = 0; i < outcomeEvent.getChoices().size(); i++) {
this.query.setEventValue(outcomeEvent, i);
this.query.execute();
classificationProbabilities[i] = this.query.getProbability();
}
return EngineArray.maxIndex(this.classificationProbabilities);
}
/**
* Construct a network analyze class. Analyze the specified network.
*
* @param network The network to analyze.
*/
public AnalyzeNetwork(final BasicNetwork network) {
final int assignDisabled = 0;
final int assignedTotal = 0;
final List<Double> biasList = new ArrayList<Double>();
final List<Double> weightList = new ArrayList<Double>();
final List<Double> allList = new ArrayList<Double>();
for (int layerNumber = 0; layerNumber < network.getLayerCount() - 1; layerNumber++) {
final int fromCount = network.getLayerNeuronCount(layerNumber);
final int fromBiasCount = network.getLayerTotalNeuronCount(layerNumber);
final int toCount = network.getLayerNeuronCount(layerNumber + 1);
// weights
for (int fromNeuron = 0; fromNeuron < fromCount; fromNeuron++) {
for (int toNeuron = 0; toNeuron < toCount; toNeuron++) {
final double v = network.getWeight(layerNumber, fromNeuron, toNeuron);
weightList.add(v);
allList.add(v);
}
}
// bias
if (fromCount != fromBiasCount) {
final int biasNeuron = fromCount;
for (int toNeuron = 0; toNeuron < toCount; toNeuron++) {
final double v = network.getWeight(layerNumber, biasNeuron, toNeuron);
biasList.add(v);
allList.add(v);
}
}
}
for (final Layer layer : network.getStructure().getLayers()) {
if (layer.hasBias()) {
for (int i = 0; i < layer.getNeuronCount(); i++) {}
}
}
this.disabledConnections = assignDisabled;
this.totalConnections = assignedTotal;
this.weights = new NumericRange(weightList);
this.bias = new NumericRange(biasList);
this.weightsAndBias = new NumericRange(allList);
this.weightValues = EngineArray.listToDouble(weightList);
this.allValues = EngineArray.listToDouble(allList);
this.biasValues = EngineArray.listToDouble(biasList);
}
/**
* Decode the specified data into the weights of the neural network. This method performs the
* opposite of encodeNetwork.
*
* @param data The data to be decoded.
*/
public void decodeNetwork(final double[] data) {
if (data.length != this.weights.length) {
throw new EncogError(
"Incompatible weight sizes, can't assign length="
+ data.length
+ " to length="
+ this.weights.length);
}
this.weights = EngineArray.arrayCopy(data);
}
public void testAnalyze() {
BasicNetwork network = EncogUtility.simpleFeedForward(2, 2, 0, 1, false);
double[] weights = new double[network.encodedArrayLength()];
EngineArray.fill(weights, 1.0);
network.decodeFromArray(weights);
AnalyzeNetwork analyze = new AnalyzeNetwork(network);
Assert.assertEquals(weights.length, analyze.getWeightsAndBias().getSamples());
Assert.assertEquals(3, analyze.getBias().getSamples());
Assert.assertEquals(6, analyze.getWeights().getSamples());
}
/** Finalize the structure of this Bayesian network. */
public void finalizeStructure() {
for (BayesianEvent e : this.eventMap.values()) {
e.finalizeStructure();
}
if (this.query != null) {
this.query.finalizeStructure();
}
this.inputPresent = new boolean[this.events.size()];
EngineArray.fill(this.inputPresent, true);
this.classificationTarget = -1;
}
/**
* Clone into the flat network passed in.
*
* @param result The network to copy into.
*/
public void cloneFlatNetwork(final FlatNetwork result) {
result.inputCount = this.inputCount;
result.layerCounts = EngineArray.arrayCopy(this.layerCounts);
result.layerIndex = EngineArray.arrayCopy(this.layerIndex);
result.layerOutput = EngineArray.arrayCopy(this.layerOutput);
result.layerSums = EngineArray.arrayCopy(this.layerSums);
result.layerFeedCounts = EngineArray.arrayCopy(this.layerFeedCounts);
result.contextTargetOffset = EngineArray.arrayCopy(this.contextTargetOffset);
result.contextTargetSize = EngineArray.arrayCopy(this.contextTargetSize);
result.layerContextCount = EngineArray.arrayCopy(this.layerContextCount);
result.biasActivation = EngineArray.arrayCopy(this.biasActivation);
result.outputCount = this.outputCount;
result.weightIndex = this.weightIndex;
result.weights = this.weights;
result.layerDropoutRates = EngineArray.arrayCopy(this.layerDropoutRates);
result.activationFunctions = new ActivationFunction[this.activationFunctions.length];
for (int i = 0; i < result.activationFunctions.length; i++) {
result.activationFunctions[i] = this.activationFunctions[i].clone();
}
result.beginTraining = this.beginTraining;
result.endTraining = this.endTraining;
}
/**
* Determine what class the specified data belongs to.
*
* @param data The data to analyze.
* @return The class the data belongs to.
*/
public final ClassItem determineClass(final double[] data) {
int resultIndex = 0;
switch (this.action) {
case Equilateral:
resultIndex = this.eq.decode(data);
break;
case OneOf:
resultIndex = EngineArray.indexOfLargest(data);
break;
case SingleField:
resultIndex = (int) data[0];
break;
default:
throw new AnalystError("Unknown action: " + this.action);
}
return this.classes.get(resultIndex);
}
/** {@inheritDoc} */
@Override
public final void iteration() {
if (this.mustInit) {
initWeights();
}
double worstDistance = Double.NEGATIVE_INFINITY;
for (final MLDataPair pair : this.training) {
final MLData out = this.network.computeInstar(pair.getInput());
// determine winner
final int winner = EngineArray.indexOfLargest(out.getData());
// calculate the distance
double distance = 0;
for (int i = 0; i < pair.getInput().size(); i++) {
final double diff =
pair.getInput().getData(i) - this.network.getWeightsInputToInstar().get(i, winner);
distance += diff * diff;
}
distance = BoundMath.sqrt(distance);
if (distance > worstDistance) {
worstDistance = distance;
}
// train
for (int j = 0; j < this.network.getInputCount(); j++) {
final double delta =
this.learningRate
* (pair.getInput().getData(j)
- this.network.getWeightsInputToInstar().get(j, winner));
this.network.getWeightsInputToInstar().add(j, winner, delta);
}
}
setError(worstDistance);
}
/**
* Calculate a layer.
*
* @param currentLayer The layer to calculate.
*/
protected void computeLayer(final int currentLayer) {
final int inputIndex = this.layerIndex[currentLayer];
final int outputIndex = this.layerIndex[currentLayer - 1];
final int inputSize = this.layerCounts[currentLayer];
final int outputSize = this.layerFeedCounts[currentLayer - 1];
final double dropoutRate;
if (this.layerDropoutRates.length > currentLayer - 1) {
dropoutRate = this.layerDropoutRates[currentLayer - 1];
} else {
dropoutRate = 0;
}
int index = this.weightIndex[currentLayer - 1];
final int limitX = outputIndex + outputSize;
final int limitY = inputIndex + inputSize;
// weight values
for (int x = outputIndex; x < limitX; x++) {
double sum = 0;
for (int y = inputIndex; y < limitY; y++) {
sum += this.weights[index++] * this.layerOutput[y] * (1 - dropoutRate);
}
this.layerSums[x] = sum;
this.layerOutput[x] = sum;
}
this.activationFunctions[currentLayer - 1].activationFunction(
this.layerOutput, outputIndex, outputSize);
// update context values
final int offset = this.contextTargetOffset[currentLayer];
EngineArray.arrayCopy(
this.layerOutput,
outputIndex,
this.layerOutput,
offset,
this.contextTargetSize[currentLayer]);
}
/**
* Copy an int array.
*
* @param input The array to copy.
* @return The result of the copy.
*/
public static int[] arrayCopy(final int[] input) {
final int[] result = new int[input.length];
EngineArray.arrayCopy(input, result);
return result;
}
/**
* Construct a fold from the specified flat network.
*
* @param flat THe flat network.
*/
public NetworkFold(final FlatNetwork flat) {
this.weights = EngineArray.arrayCopy(flat.getWeights());
this.output = EngineArray.arrayCopy(flat.getLayerOutput());
}
public int winner(MLData output) {
return EngineArray.maxIndex(output.getData());
}
/**
* Set the layer sums.
*
* @param d The layer sums.
*/
public void setLayerSums(double[] d) {
this.layerSums = EngineArray.arrayCopy(d);
}
/**
* Copy weights and output to the network.
*
* @param target The network to copy to.
*/
public final void copyToNetwork(final FlatNetwork target) {
EngineArray.arrayCopy(this.weights, target.getWeights());
EngineArray.arrayCopy(this.output, target.getLayerOutput());
}
/**
* Set the weight index.
*
* @param weightIndex The weight index.
*/
public void setWeightIndex(final int[] weightIndex) {
this.weightIndex = EngineArray.arrayCopy(weightIndex);
}
/**
* Set the weights.
*
* @param weights The weights.
*/
public void setWeights(final double[] weights) {
this.weights = EngineArray.arrayCopy(weights);
}
/**
* Set the layer index.
*
* @param i The layer index.
*/
public void setLayerIndex(final int[] i) {
this.layerIndex = EngineArray.arrayCopy(i);
}
/**
* Set the layer output.
*
* @param layerOutput The layer output.
*/
public void setLayerOutput(final double[] layerOutput) {
this.layerOutput = EngineArray.arrayCopy(layerOutput);
}
/**
* Set the layer context count.
*
* @param layerContextCount The layer context count.
*/
public void setLayerContextCount(final int[] layerContextCount) {
this.layerContextCount = EngineArray.arrayCopy(layerContextCount);
}
public void setLayerFeedCounts(final int[] layerFeedCounts) {
this.layerFeedCounts = EngineArray.arrayCopy(layerFeedCounts);
}
/**
* Set the context target size.
*
* @param contextTargetSize The context target size.
*/
public void setContextTargetSize(final int[] contextTargetSize) {
this.contextTargetSize = EngineArray.arrayCopy(contextTargetSize);
}
/**
* Set the context target offset.
*
* @param contextTargetOffset The context target offset.
*/
public void setContextTargetOffset(final int[] contextTargetOffset) {
this.contextTargetOffset = EngineArray.arrayCopy(contextTargetOffset);
}
/**
* Copy the weights and output from the network.
*
* @param source The network to copy from.
*/
public final void copyFromNetwork(final FlatNetwork source) {
EngineArray.arrayCopy(source.getWeights(), this.weights);
EngineArray.arrayCopy(source.getLayerOutput(), this.output);
}
/**
* Copy a byte array.
*
* @param input The array to copy.
* @return The result of the copy.
*/
public static byte[] arrayCopy(final byte[] input) {
final byte[] result = new byte[input.length];
EngineArray.arrayCopy(input, result);
return result;
}
/** Clear the weight matrix. */
public void clearMatrix() {
EngineArray.fill(this.hopfield.getWeights(), 0);
}
