/// <summary>
/// Not supported. Will throw an error.
/// </summary>
/// <param name="inputData">Not used.</param>
/// <param name="idealData">Not used.</param>
public void Add(INeuralData inputData, INeuralData idealData)
{
#if logging
UnionNeuralDataSet.logger.Error(ADD_ERROR);
#endif
throw new NeuralDataError(ADD_ERROR);
}
/// <inheritdoc/>
public void Compute(double[] input, double[] output)
{
BasicNeuralData input2 = new BasicNeuralData(input);
INeuralData output2 = this.Compute(input2);
EngineArray.ArrayCopy(output2.Data, output);
}
/// <summary>
/// Not supported. Will throw an error.
/// </summary>
/// <param name="data1">Not used.</param>
public void Add(INeuralData data1)
{
#if logging
UnionNeuralDataSet.logger.Error(ADD_ERROR);
#endif
throw new NeuralDataError(ADD_ERROR);
}
/// <summary>
/// Propagate the layer.
/// </summary>
/// <param name="synapse">The synapse for this layer.</param>
/// <param name="input">The input pattern.</param>
/// <param name="output">The output pattern.</param>
/// <returns>True if the network has become stable.</returns>
private bool PropagateLayer(ISynapse synapse, INeuralData input,
INeuralData output)
{
int i, j;
int sum, outt = 0;
bool stable;
stable = true;
for (i = 0; i < output.Count; i++)
{
sum = 0;
for (j = 0; j < input.Count; j++)
{
sum += (int)(GetWeight(synapse, input, i, j) * input[j]);
}
if (sum != 0)
{
if (sum < 0)
{
outt = -1;
}
else
{
outt = 1;
}
if (outt != (int)output[i])
{
stable = false;
output[i] = outt;
}
}
}
return(stable);
}
/// <summary>
/// Move to the next object.
/// </summary>
/// <returns>True if there is a next object.</returns>
public bool MoveNext()
{
if (!this.results.NextResult())
{
return(false);
}
INeuralData input = new BasicNeuralData(owner.inputSize);
INeuralData ideal = null;
for (int i = 1; i <= owner.inputSize; i++)
{
input[i - 1] = this.results.GetDouble(i);
}
if (owner.idealSize > 0)
{
ideal =
new BasicNeuralData(owner.idealSize);
for (int i = 1; i <= owner.idealSize; i++)
{
ideal[i - 1] =
this.results.GetDouble(i + owner.inputSize);
}
}
this.current = new BasicNeuralDataPair(input, ideal);
return(true);
}
/// <summary>
/// Compute the output for a given input to the neural network. This method
/// provides a parameter to specify an output holder to use. This holder
/// allows propagation training to track the output from each layer.
/// If you do not need this holder pass null, or use the other
/// compare method.
/// </summary>
/// <param name="input">The input provide to the neural network.</param>
/// <param name="useHolder">Allows a holder to be specified, this allows
/// propagation training to check the output of each layer.</param>
/// <returns>The results from the output neurons.</returns>
public virtual INeuralData Compute(INeuralData input,
NeuralOutputHolder useHolder)
{
NeuralOutputHolder holder;
ILayer inputLayer = this.network.GetLayer(BasicNetwork.TAG_INPUT);
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Pattern " + input.ToString()
+ " presented to neural network");
}
#endif
if (useHolder == null && this.network.Structure.Flat != null)
{
this.network.Structure.UpdateFlatNetwork();
INeuralData result = new BasicNeuralData(this.network.Structure.Flat.OutputCount);
this.network.Structure.Flat.Compute(input.Data, result.Data);
return(result);
}
if (useHolder == null)
{
holder = new NeuralOutputHolder();
}
else
{
holder = useHolder;
}
Compute(holder, inputLayer, input, null);
return(holder.Output);
}
/// <summary>
/// Perform one training iteration.
/// </summary>
public override void Iteration()
{
if (this.mustInit)
{
InitWeight();
}
ErrorCalculation error = new ErrorCalculation();
foreach (INeuralDataPair pair in this.training)
{
INeuralData output = this.parts.InstarSynapse.Compute(
pair.Input);
int j = this.parts.Winner(output);
for (int i = 0; i < this.parts.OutstarLayer.NeuronCount; i++)
{
double delta = this.learningRate
* (pair.Ideal[i] - this.parts
.OutstarSynapse.WeightMatrix[j, i]);
this.parts.OutstarSynapse.WeightMatrix.Add(j, i, delta);
}
error.UpdateError(output.Data, pair.Ideal.Data);
}
this.Error = error.Calculate();
}
/// <summary>
/// Compute the values before sending output to the next layer.
/// This function allows the activation functions to be called.
/// </summary>
/// <param name="pattern">The incoming Project.</param>
/// <returns>The output from this layer.</returns>
public override INeuralData Compute(INeuralData pattern)
{
INeuralData result = new BasicNeuralData(NeuronCount);
for (int i = 0; i < NeuronCount; i++)
{
if (this.radialBasisFunction[i] == null)
{
String str =
"Error, must define radial functions for each neuron";
#if logging
if (RadialBasisFunctionLayer.logger.IsErrorEnabled)
{
RadialBasisFunctionLayer.logger.Error(str);
}
#endif
throw new NeuralNetworkError(str);
}
IRadialBasisFunction f = this.radialBasisFunction[i];
if (pattern.Data.Length != f.Dimensions)
{
throw new Exception("Inputs must equal the number of dimensions.");
}
result[i] = f.Calculate(pattern.Data);
}
return(result);
}
/// <summary>
/// Encode the Encog dataset.
/// </summary>
/// <param name="training">The training data.</param>
/// <param name="outputIndex">The ideal element to use, this is necessary becase SVM's have
/// only a single output.</param>
/// <returns>The SVM problem.</returns>
public static svm_problem Encode(INeuralDataSet training, int outputIndex)
{
svm_problem result = new svm_problem();
result.l = (int)ObtainTrainingLength(training);
result.y = new double[result.l];
result.x = new svm_node[result.l][];
int elementIndex = 0;
foreach (INeuralDataPair pair in training)
{
INeuralData input = pair.Input;
INeuralData output = pair.Ideal;
result.x[elementIndex] = new svm_node[input.Count];
for (int i = 0; i < input.Count; i++)
{
result.x[elementIndex][i] = new svm_node();
result.x[elementIndex][i].index = i + 1;
result.x[elementIndex][i].value_Renamed = input[i];
}
result.y[elementIndex] = output[outputIndex];
elementIndex++;
}
return(result);
}
/// <summary>
/// Compute the output for a given input to the neural network. This method
/// provides a parameter to specify an output holder to use. This holder
/// allows propagation training to track the output from each layer.
/// If you do not need this holder pass null, or use the other
/// compare method.
/// </summary>
/// <param name="input">The input provide to the neural network.</param>
/// <param name="useHolder">Allows a holder to be specified, this allows
/// propagation training to check the output of each layer.</param>
/// <returns>The results from the output neurons.</returns>
public virtual INeuralData Compute(INeuralData input,
NeuralOutputHolder useHolder)
{
NeuralOutputHolder holder;
ILayer inputLayer = this.network.GetLayer(BasicNetwork.TAG_INPUT);
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Pattern " + input.ToString()
+ " presented to neural network");
}
#endif
if (useHolder == null && this.network.Structure.Flat != null)
{
this.network.Structure.UpdateFlatNetwork();
INeuralData result = new BasicNeuralData(this.network.Structure.Flat.OutputCount);
this.network.Structure.Flat.Compute(input.Data, result.Data);
return result;
}
if (useHolder == null)
{
holder = new NeuralOutputHolder();
}
else
{
holder = useHolder;
}
Compute(holder, inputLayer, input, null);
return holder.Output;
}
/// <summary>
/// Construct a context layer with the parameters specified.
/// </summary>
/// <param name="thresholdFunction">The threshold function to use.</param>
/// <param name="hasThreshold">Does this layer have thresholds?</param>
/// <param name="neuronCount">The neuron count to use.</param>
public ContextLayer(IActivationFunction thresholdFunction,
bool hasThreshold, int neuronCount)
: base(thresholdFunction, hasThreshold, neuronCount)
{
this.FlatContextIndex = -1;
this.context = new BasicNeuralData(neuronCount);
}
/// <summary>
/// Calculate the best matching unit (BMU). This is the output neuron that
/// has the lowest Euclidean distance to the input vector.
/// </summary>
/// <param name="synapse">The synapse to calculate for.</param>
/// <param name="input">The input vector.</param>
/// <returns>The output neuron number that is the BMU.</returns>
public int CalculateBMU(ISynapse synapse, INeuralData input)
{
int result = 0;
// Track the lowest distance so far.
double lowestDistance = double.MaxValue;
for (int i = 0; i < this.training.OutputNeuronCount; i++)
{
double distance = CalculateEuclideanDistance(synapse, input,
i);
// Track the lowest distance, this is the BMU.
if (distance < lowestDistance)
{
lowestDistance = distance;
result = i;
}
}
// Track the worst distance, this is the error for the entire network.
if (lowestDistance > this.worstDistance)
{
this.worstDistance = lowestDistance;
}
return(result);
}
/// <summary>
/// Calculate the best matching unit (BMU). This is the output neuron that
/// has the lowest Euclidean distance to the input vector.
/// </summary>
/// <param name="synapse">The synapse to calculate for.</param>
/// <param name="input">The input vector.</param>
/// <returns>The output neuron number that is the BMU.</returns>
public int CalculateBMU(ISynapse synapse, INeuralData input)
{
int result = 0;
// Track the lowest distance so far.
double lowestDistance = double.MaxValue;
for (int i = 0; i < this.training.OutputNeuronCount; i++)
{
double distance = CalculateEuclideanDistance(synapse, input,
i);
// Track the lowest distance, this is the BMU.
if (distance < lowestDistance)
{
lowestDistance = distance;
result = i;
}
}
// Track the worst distance, this is the error for the entire network.
if (lowestDistance > this.worstDistance)
{
this.worstDistance = lowestDistance;
}
return result;
}
/// <summary>
/// Add only input data, for an unsupervised dataset.
/// </summary>
/// <param name="data1">The data to be added.</param>
public void Add(INeuralData data1)
{
if (!this.loading)
{
throw new NeuralDataError(BufferedNeuralDataSet.ERROR_ADD);
}
egb.Write(data1.Data);
}
/// <summary>
/// Perform one Hopfield iteration.
/// </summary>
public void Run()
{
INeuralData temp = this.Compute(this.CurrentState, null);
for (int i = 0; i < temp.Count; i++)
{
this.CurrentState.SetBoolean(i, temp[i] > 0);
}
}
/// <summary>
/// Add the specified input and ideal object to the collection.
/// </summary>
/// <param name="inputData">The image to train with.</param>
/// <param name="idealData">The expected otuput form this image.</param>
public override void Add(INeuralData inputData, INeuralData idealData)
{
if (!(inputData is ImageNeuralData))
{
throw new NeuralNetworkError(ImageNeuralDataSet.MUST_USE_IMAGE);
}
base.Add(inputData, idealData);
}
/// <summary>
/// Add both the input and ideal data.
/// </summary>
/// <param name="inputData">The input data.</param>
/// <param name="idealData">The ideal data.</param>
public void Add(INeuralData inputData, INeuralData idealData)
{
if (!this.loading)
{
throw new NeuralDataError(BufferedNeuralDataSet.ERROR_ADD);
}
this.egb.Write(inputData.Data);
this.egb.Write(idealData.Data);
}
/// <summary>
/// Train for the specified synapse and BMU.
/// </summary>
/// <param name="bmu">The best matching unit for this input.</param>
/// <param name="synapse">The synapse to train.</param>
/// <param name="input">The input to train for.</param>
private void Train(int bmu, ISynapse synapse,
INeuralData input)
{
// adjust the weight for the BMU and its neighborhood
for (int outputNeuron = 0; outputNeuron < this.outputNeuronCount;
outputNeuron++)
{
TrainPattern(synapse, input, outputNeuron, bmu);
}
}
/// <summary>
/// Copy the specified input pattern to the weight matrix. This causes an
/// output neuron to learn this pattern "exactly". This is useful when a
/// winner is to be forced.
/// </summary>
/// <param name="synapse">The synapse that is the target of the copy.</param>
/// <param name="outputNeuron">The output neuron to set.</param>
/// <param name="input">The input pattern to copy.</param>
private void CopyInputPattern(ISynapse synapse,
int outputNeuron, INeuralData input)
{
for (int inputNeuron = 0; inputNeuron < this.inputNeuronCount;
inputNeuron++)
{
synapse.WeightMatrix[inputNeuron, outputNeuron] =
input[inputNeuron];
}
}
/// <summary>
/// Train the specified pattern. Find a winning neuron and adjust all
/// neurons according to the neighborhood function.
/// </summary>
/// <param name="pattern">The pattern to train.</param>
public void TrainPattern(INeuralData pattern)
{
foreach (ISynapse synapse in this.synapses)
{
INeuralData input = pattern;
int bmu = this.bmuUtil.CalculateBMU(synapse, input);
Train(bmu, synapse, input);
}
ApplyCorrection();
}
/// <summary>
/// Get the specified weight.
/// </summary>
/// <param name="synapse">The synapse to get the weight from.</param>
/// <param name="input">The input, to obtain the size from.</param>
/// <param name="x">The x matrix value. (could be row or column, depending on input)</param>
/// <param name="y">The y matrix value. (could be row or column, depending on input)</param>
/// <returns>The value from the matrix.</returns>
private double GetWeight(ISynapse synapse, INeuralData input, int x, int y)
{
if (synapse.FromNeuronCount != input.Count)
{
return(synapse.WeightMatrix[x, y]);
}
else
{
return(synapse.WeightMatrix[y, x]);
}
}
/// <summary>
/// Convert regular Encog NeuralData into the "sparse" data needed by an SVM.
/// </summary>
/// <param name="data">The data to convert.</param>
/// <returns>The SVM sparse data.</returns>
public svm_node[] MakeSparse(INeuralData data)
{
svm_node[] result = new svm_node[data.Count];
for (int i = 0; i < data.Count; i++)
{
result[i] = new svm_node();
result[i].index = i + 1;
result[i].value_Renamed = data[i];
}
return(result);
}
public void testNetwork(double[][] networkOutputs)
{
for (int i = 0; i < networkOutputs.Length; i++)
{
//INeuralData data = new BasicNeuralData(networkInput[i]);
//networkOutputs[i] = (double[])network.Compute(data).Data.Clone();
BasicNeuralData inputs = new BasicNeuralData(networkInput[i]);
INeuralData output = network.Compute(inputs);
EngineArray.ArrayCopy(output.Data, networkOutputs[i]);
}
}
/// <summary>
/// Calculate the error for this neural network. The error is calculated
/// using root-mean-square(RMS).
/// </summary>
/// <param name="data">The training set.</param>
/// <returns>The error percentage.</returns>
public double CalculateError(INeuralDataSet data)
{
ClearContext();
ErrorCalculation errorCalculation = new ErrorCalculation();
foreach (INeuralDataPair pair in data)
{
INeuralData actual = Compute(pair.Input);
errorCalculation.UpdateError(actual.Data, pair.Ideal.Data);
}
return(errorCalculation.Calculate());
}
/// <summary>
/// Evaluate the network and display (to the console) the output for every
/// value in the training set. Displays ideal and actual.
/// </summary>
/// <param name="network">The network to evaluate.</param>
/// <param name="training">The training set to evaluate.</param>
public static void Evaluate(BasicNetwork network,
INeuralDataSet training)
{
foreach (INeuralDataPair pair in training)
{
INeuralData output = network.Compute(pair.Input);
Console.WriteLine("Input="
+ EncogUtility.FormatNeuralData(pair.Input)
+ ", Actual=" + EncogUtility.FormatNeuralData(output)
+ ", Ideal="
+ EncogUtility.FormatNeuralData(pair.Ideal));
}
}
/// <summary>
/// Compute the output for the given input.
/// </summary>
/// <param name="input">The input to the SVM.</param>
/// <returns>The results from the SVM.</returns>
public override INeuralData Compute(INeuralData input)
{
INeuralData result = new BasicNeuralData(this.outputCount);
svm_node[] formattedInput = MakeSparse(input);
for (int i = 0; i < this.outputCount; i++)
{
double d = svm.svm_predict(this.models[i], formattedInput);
result[i] = d;
}
return(result);
}
/// <summary>
/// Setup the network logic, read parameters from the network.
/// NOT USED, call the run method.
/// </summary>
/// <param name="input">Not used</param>
/// <param name="useHolder">Not used</param>
/// <returns>Not used</returns>
public override INeuralData Compute(INeuralData input, NeuralOutputHolder useHolder)
{
String str = "Compute on BasicNetwork cannot be used, rather call" +
" the run method on the logic class.";
#if logging
if (logger.IsErrorEnabled)
{
logger.Error(str);
}
#endif
throw new NeuralNetworkError(str);
}
/// <summary>
/// Called to process input from the previous layer. Simply store the output
/// in the context.
/// </summary>
/// <param name="pattern">The pattern to store in the context.</param>
public override void Process(INeuralData pattern)
{
double[] target = this.context.Data;
double[] source = pattern.Data;
Array.Copy(source, target, source.Length);
#if logging
if (ContextLayer.logger.IsDebugEnabled)
{
ContextLayer.logger.Debug("Updated ContextLayer to " + pattern);
}
#endif
}
/// <summary>
/// Compute the output for a given input to the neural network. This method
/// provides a parameter to specify an output holder to use. This holder
/// allows propagation training to track the output from each layer.
/// If you do not need this holder pass null, or use the other
/// compare method.
/// </summary>
/// <param name="input">The input provide to the neural network.</param>
/// <param name="useHolder">Allows a holder to be specified, this allows
/// propagation training to check the output of each layer.</param>
/// <returns>The results from the output neurons.</returns>
public virtual INeuralData Compute(INeuralData input,
NeuralOutputHolder useHolder)
{
try
{
return(logic.Compute(input, useHolder));
}
catch (IndexOutOfRangeException ex)
{
throw new NeuralNetworkError(
"Index exception: there was likely a mismatch between layer sizes, or the size of the input presented to the network.",
ex);
}
}
/// <summary>
/// Format neural data as a list of numbers.
/// </summary>
/// <param name="data">The neural data to format.</param>
/// <returns>The formatted neural data.</returns>
private static String FormatNeuralData(INeuralData data)
{
StringBuilder result = new StringBuilder();
for (int i = 0; i < data.Count; i++)
{
if (i != 0)
{
result.Append(',');
}
result.Append(Format.FormatDouble(data[i], 4));
}
return(result.ToString());
}
/// <summary>
/// Calculate the winning neuron from the data, this is the neuron
/// that has the highest output.
/// </summary>
/// <param name="data">The data to use to determine the winning neuron.</param>
/// <returns>The winning neuron index, or -1 if no winner.</returns>
public int Winner(INeuralData data)
{
int winner = -1;
for (int i = 0; i < data.Count; i++)
{
if (winner == -1 || data[i] > data[winner])
{
winner = i;
}
}
return(winner);
}
/// <summary>
/// Internal computation method for a single layer. This is called,
/// as the neural network processes.
/// </summary>
/// <param name="holder">The output holder.</param>
/// <param name="layer">The layer to process.</param>
/// <param name="input">The input to this layer.</param>
/// <param name="source">The source synapse.</param>
private void Compute(NeuralOutputHolder holder, ILayer layer,
INeuralData input, ISynapse source)
{
try
{
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Processing layer: "
+ layer.ToString()
+ ", input= "
+ input.ToString());
}
#endif
// typically used to process any recurrent layers that feed into this
// layer.
PreprocessLayer(layer, input, source);
foreach (ISynapse synapse in layer.Next)
{
if (!holder.Result.ContainsKey(synapse))
{
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Processing synapse: " + synapse.ToString());
}
#endif
INeuralData pattern = synapse.Compute(input);
pattern = synapse.ToLayer.Compute(pattern);
synapse.ToLayer.Process(pattern);
holder.Result[synapse] = input;
Compute(holder, synapse.ToLayer, pattern, synapse);
ILayer outputLayer = this.network.GetLayer(BasicNetwork.TAG_OUTPUT);
// Is this the output from the entire network?
if (synapse.ToLayer == outputLayer)
{
holder.Output = pattern;
}
}
}
}
catch (IndexOutOfRangeException ex)
{
throw new NeuralNetworkError("Size mismatch on input of size " + input.Count + " and layer: ", ex);
}
}
/// <summary>
/// Train the neural network for the specified pattern. The neural network
/// can be trained for more than one pattern. To do this simply call the
/// train method more than once.
/// </summary>
/// <param name="pattern">The pattern to train for.</param>
public void AddPattern(INeuralData pattern)
{
// Create a row matrix from the input, convert boolean to bipolar
Matrix m2 = Matrix.CreateRowMatrix(pattern.Data);
// Transpose the matrix and multiply by the original input matrix
Matrix m1 = MatrixMath.Transpose(m2);
Matrix m3 = MatrixMath.Multiply(m1, m2);
// matrix 3 should be square by now, so create an identity
// matrix of the same size.
Matrix identity = MatrixMath.Identity(m3.Rows);
// subtract the identity matrix
Matrix m4 = MatrixMath.Subtract(m3, identity);
// now add the calculated matrix, for this pattern, to the
// existing weight matrix.
ConvertHopfieldMatrix(m4);
}
/// <summary>
/// Handle recurrent layers. See if there are any recurrent layers before
/// the specified layer that must affect the input.
/// </summary>
/// <param name="layer">The layer being processed, see if there are any recurrent
/// connections to this.</param>
/// <param name="input">The input to the layer, will be modified with the result
/// from any recurrent layers.</param>
/// <param name="source">The source synapse.</param>
public override void PreprocessLayer(ILayer layer,
INeuralData input, ISynapse source)
{
foreach (ISynapse synapse in
this.Network.Structure.GetPreviousSynapses(layer))
{
if (synapse != source)
{
#if logging
if (SimpleRecurrentLogic.logger.IsDebugEnabled)
{
SimpleRecurrentLogic.logger.Debug("Recurrent layer from: " + input.ToString());
}
#endif
INeuralData recurrentInput = synapse.FromLayer.Recur();
if (recurrentInput != null)
{
INeuralData recurrentOutput = synapse
.Compute(recurrentInput);
for (int i = 0; i < input.Count; i++)
{
input[i] = input[i]
+ recurrentOutput[i];
}
#if logging
if (SimpleRecurrentLogic.logger.IsDebugEnabled)
{
SimpleRecurrentLogic.logger.Debug("Recurrent layer to: " + input.ToString());
}
#endif
}
}
}
}
/// <summary>
/// Compute the weighted output from this synapse. Each neuron
/// in the from layer has a weighted connection to each of the
/// neurons in the next layer.
/// </summary>
/// <param name="input">The input from the synapse.</param>
/// <returns>The output from this synapse.</returns>
public override INeuralData Compute(INeuralData input)
{
INeuralData result = new BasicNeuralData(this.ToNeuronCount);
double[] inputArray = input.Data;
double[][] matrixArray = this.WeightMatrix.Data;
double[] resultArray = result.Data;
for (int i = 0; i < this.ToNeuronCount; i++) {
double sum = 0;
for(int j = 0;j<inputArray.Length;j++ )
{
sum+=inputArray[j]*matrixArray[j][i];
}
resultArray[i] = sum;
}
return result;
}
/// <summary>
/// Compute the output from this synapse.
/// </summary>
/// <param name="input">The input to this synapse.</param>
/// <returns>The output from this synapse.</returns>
public INeuralData Compute(INeuralData input)
{
INeuralData result = new BasicNeuralData(ToNeuronCount);
if (this.neurons.Count == 0)
{
throw new NeuralNetworkError("This network has not been evolved yet, it has no neurons in the NEAT synapse.");
}
int flushCount = 1;
if (snapshot)
{
flushCount = networkDepth;
}
// iterate through the network FlushCount times
for (int i = 0; i < flushCount; ++i)
{
int outputIndex = 0;
int index = 0;
result.Clear();
// populate the input neurons
while (neurons[index].NeuronType == NEATNeuronType.Input)
{
neurons[index].Output = input[index];
index++;
}
// set the bias neuron
neurons[index++].Output = 1;
while (index < neurons.Count)
{
NEATNeuron currentNeuron = neurons[index];
double sum = 0;
foreach (NEATLink link in currentNeuron.InboundLinks)
{
double weight = link.Weight;
double neuronOutput = link.FromNeuron.Output;
sum += weight * neuronOutput;
}
double[] d = new double[1];
d[0] = sum / currentNeuron.ActivationResponse;
activationFunction.ActivationFunction(d,0,1);
neurons[index].Output = d[0];
if (currentNeuron.NeuronType == NEATNeuronType.Output)
{
result.Data[outputIndex++] = currentNeuron.Output;
}
index++;
}
}
return result;
}
/// <summary>
/// Can be overridden by subclasses. Usually used to implement recurrent
/// layers.
/// </summary>
/// <param name="layer">The layer to process.</param>
/// <param name="input">The input to this layer.</param>
/// <param name="source">The source from this layer.</param>
virtual public void PreprocessLayer(ILayer layer, INeuralData input, ISynapse source)
{
// nothing to do
}
/// <summary>
/// Compute the output for the given input.
/// </summary>
/// <param name="input">The input to the SVM.</param>
/// <param name="useHolder">The output holder to use.</param>
/// <returns>The results from the SVM.</returns>
public override INeuralData Compute(INeuralData input,
NeuralOutputHolder useHolder)
{
useHolder.Output = Compute(input);
return useHolder.Output;
}
/// <summary>
/// Not supported.
/// </summary>
/// <param name="data1">Not used.</param>
public void Add(INeuralData data1)
{
throw new TrainingError(FoldedDataSet.ADD_NOT_SUPPORTED);
}
/// <summary>
/// Train for the specified synapse and BMU.
/// </summary>
/// <param name="bmu">The best matching unit for this input.</param>
/// <param name="synapse">The synapse to train.</param>
/// <param name="input">The input to train for.</param>
private void Train(int bmu, ISynapse synapse,
INeuralData input)
{
// adjust the weight for the BMU and its neighborhood
for (int outputNeuron = 0; outputNeuron < this.outputNeuronCount;
outputNeuron++)
{
TrainPattern(synapse, input, outputNeuron, bmu);
}
}
/// <summary>
/// Compute the output for a given input to the neural network. This method
/// provides a parameter to specify an output holder to use. This holder
/// allows propagation training to track the output from each layer.
/// If you do not need this holder pass null, or use the other
/// compare method.
/// </summary>
/// <param name="input">The input provide to the neural network.</param>
/// <param name="useHolder">Allows a holder to be specified, this allows
/// propagation training to check the output of each layer.</param>
/// <returns>The results from the output neurons.</returns>
public virtual INeuralData Compute(INeuralData input,
NeuralOutputHolder useHolder)
{
try
{
return logic.Compute(input, useHolder);
}
catch (IndexOutOfRangeException ex)
{
throw new NeuralNetworkError(
"Index exception: there was likely a mismatch between layer sizes, or the size of the input presented to the network.",
ex);
}
}
/// <summary>
/// Compute the output for a given input to the neural network.
/// </summary>
/// <param name="input">The input to the neural network.</param>
/// <returns>The output from the neural network.</returns>
public virtual INeuralData Compute(INeuralData input)
{
return Compute(input, null);
}
/// <summary> /// Compute the output from this synapse. /// </summary> /// <param name="input">The input to this synapse.</param> /// <returns>The output from this synapse.</returns> public abstract INeuralData Compute(INeuralData input);
/// <summary>
/// Get the specified weight.
/// </summary>
/// <param name="synapse">The synapse to get the weight from.</param>
/// <param name="input">The input, to obtain the size from.</param>
/// <param name="x">The x matrix value. (could be row or column, depending on input)</param>
/// <param name="y">The y matrix value. (could be row or column, depending on input)</param>
/// <returns>The value from the matrix.</returns>
private double GetWeight(ISynapse synapse, INeuralData input, int x, int y)
{
if (synapse.FromNeuronCount != input.Count)
return synapse.WeightMatrix[x, y];
else
return synapse.WeightMatrix[y, x];
}
/// <summary>
/// Propagate the layer.
/// </summary>
/// <param name="synapse">The synapse for this layer.</param>
/// <param name="input">The input pattern.</param>
/// <param name="output">The output pattern.</param>
/// <returns>True if the network has become stable.</returns>
private bool PropagateLayer(ISynapse synapse, INeuralData input,
INeuralData output)
{
int i, j;
int sum, outt = 0;
bool stable;
stable = true;
for (i = 0; i < output.Count; i++)
{
sum = 0;
for (j = 0; j < input.Count; j++)
{
sum += (int)(GetWeight(synapse, input, i, j) * input[j]);
}
if (sum != 0)
{
if (sum < 0)
outt = -1;
else
outt = 1;
if (outt != (int)output[i])
{
stable = false;
output[i] = outt;
}
}
}
return stable;
}
/// <summary>
/// Copy the specified input pattern to the weight matrix. This causes an
/// output neuron to learn this pattern "exactly". This is useful when a
/// winner is to be forced.
/// </summary>
/// <param name="synapse">The synapse that is the target of the copy.</param>
/// <param name="outputNeuron">The output neuron to set.</param>
/// <param name="input">The input pattern to copy.</param>
private void CopyInputPattern(ISynapse synapse,
int outputNeuron, INeuralData input)
{
for (int inputNeuron = 0; inputNeuron < this.inputNeuronCount;
inputNeuron++)
{
synapse.WeightMatrix[inputNeuron, outputNeuron] =
input[inputNeuron];
}
}
/// <summary>
/// Force any neurons that did not win to off-load patterns from overworked
/// neurons.
/// </summary>
/// <param name="synapse">An array that specifies how many times each output neuron has
/// "won".</param>
/// <param name="won">The training pattern that is the least represented by this
/// neural network.</param>
/// <param name="leastRepresented">The synapse to modify.</param>
/// <returns>True if a winner was forced.</returns>
private bool ForceWinners(ISynapse synapse, int[] won,
INeuralData leastRepresented)
{
double maxActivation = double.MinValue;
int maxActivationNeuron = -1;
INeuralData output = this.network.Compute(leastRepresented);
// Loop over all of the output neurons. Consider any neurons that were
// not the BMU (winner) for any pattern. Track which of these
// non-winning neurons had the highest activation.
for (int outputNeuron = 0; outputNeuron < won.Length; outputNeuron++)
{
// Only consider neurons that did not "win".
if (won[outputNeuron] == 0)
{
if ((maxActivationNeuron == -1)
|| (output.Data[outputNeuron] > maxActivation))
{
maxActivation = output.Data[outputNeuron];
maxActivationNeuron = outputNeuron;
}
}
}
// If a neurons was found that did not activate for any patterns, then
// force it to "win" the least represented pattern.
if (maxActivationNeuron != -1)
{
CopyInputPattern(synapse, maxActivationNeuron, leastRepresented);
return true;
}
else
{
return false;
}
}
/// <summary>
/// Train for the specified pattern.
/// </summary>
/// <param name="synapse">The synapse to train.</param>
/// <param name="input">The input pattern to train for.</param>
/// <param name="current">The current output neuron being trained.</param>
/// <param name="bmu">The best matching unit, or winning output neuron.</param>
private void TrainPattern(ISynapse synapse, INeuralData input,
int current, int bmu)
{
Matrix correction = this.correctionMatrix[synapse];
for (int inputNeuron = 0; inputNeuron < this.inputNeuronCount;
inputNeuron++)
{
double currentWeight = synapse.WeightMatrix[inputNeuron,
current];
double inputValue = input.Data[inputNeuron];
double newWeight = DetermineNewWeight(currentWeight,
inputValue, current, bmu);
correction[inputNeuron, current] = newWeight;
}
}
/// <summary>
/// Train the specified pattern. Find a winning neuron and adjust all
/// neurons according to the neighborhood function.
/// </summary>
/// <param name="pattern">The pattern to train.</param>
public void TrainPattern(INeuralData pattern)
{
foreach (ISynapse synapse in this.synapses)
{
INeuralData input = pattern;
int bmu = this.bmuUtil.CalculateBMU(synapse, input);
Train(bmu, synapse, input);
}
ApplyCorrection();
}
/// <summary>
/// Setup the network logic, read parameters from the network.
/// NOT USED, call the run method.
/// </summary>
/// <param name="input">Not used</param>
/// <param name="useHolder">Not used</param>
/// <returns>Not used</returns>
public override INeuralData Compute(INeuralData input, NeuralOutputHolder useHolder)
{
String str = "Compute on BasicNetwork cannot be used, rather call" +
" the run method on the logic class.";
#if logging
if (logger.IsErrorEnabled)
{
logger.Error(str);
}
#endif
throw new NeuralNetworkError(str);
}
/// <summary>
/// Determine which member of the output is the winning neuron.
/// </summary>
/// <param name="output">The output from the neural network.</param>
/// <returns>The winning neuron.</returns>
public static int DetermineWinner(INeuralData output)
{
int win = 0;
double biggest = double.MinValue;
for (int i = 0; i < output.Count; i++)
{
if (output[i] > biggest)
{
biggest = output[i];
win = i;
}
}
return win;
}
/// <summary>
/// Compute the output for the given input.
/// </summary>
/// <param name="input">The input to the SVM.</param>
/// <returns>The results from the SVM.</returns>
public override INeuralData Compute(INeuralData input)
{
INeuralData result = new BasicNeuralData(this.outputCount);
svm_node[] formattedInput = MakeSparse(input);
for (int i = 0; i < this.outputCount; i++)
{
double d = svm.svm_predict(this.models[i], formattedInput);
result[i] = d;
}
return result;
}
/// <summary>
/// Compute the output from this synapse.
/// </summary>
/// <param name="input">The input to this synapse.</param>
/// <returns>The output is the same as the input.</returns>
public override INeuralData Compute(INeuralData input)
{
return input;
}
/// <summary>
/// Calculate the winning neuron from the data, this is the neuron
/// that has the highest output.
/// </summary>
/// <param name="data">The data to use to determine the winning neuron.</param>
/// <returns>The winning neuron index, or -1 if no winner.</returns>
public int Winner(INeuralData data)
{
int winner = -1;
for (int i = 0; i < data.Count; i++)
{
if (winner == -1 || data[i] > data[winner])
{
winner = i;
}
}
return winner;
}
/// <summary>
/// Internal computation method for a single layer. This is called,
/// as the neural network processes.
/// </summary>
/// <param name="holder">The output holder.</param>
/// <param name="layer">The layer to process.</param>
/// <param name="input">The input to this layer.</param>
/// <param name="source">The source synapse.</param>
private void Compute(NeuralOutputHolder holder, ILayer layer,
INeuralData input, ISynapse source)
{
try
{
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Processing layer: "
+ layer.ToString()
+ ", input= "
+ input.ToString());
}
#endif
// typically used to process any recurrent layers that feed into this
// layer.
PreprocessLayer(layer, input, source);
foreach (ISynapse synapse in layer.Next)
{
if (!holder.Result.ContainsKey(synapse))
{
#if logging
if (FeedforwardLogic.logger.IsDebugEnabled)
{
FeedforwardLogic.logger.Debug("Processing synapse: " + synapse.ToString());
}
#endif
INeuralData pattern = synapse.Compute(input);
pattern = synapse.ToLayer.Compute(pattern);
synapse.ToLayer.Process(pattern);
holder.Result[synapse] = input;
Compute(holder, synapse.ToLayer, pattern, synapse);
ILayer outputLayer = this.network.GetLayer(BasicNetwork.TAG_OUTPUT);
// Is this the output from the entire network?
if (synapse.ToLayer == outputLayer)
{
holder.Output = pattern;
}
}
}
}
catch (IndexOutOfRangeException ex)
{
throw new NeuralNetworkError("Size mismatch on input of size " + input.Count + " and layer: ", ex);
}
}
/// <summary>
/// Compute the values before sending output to the next layer.
/// This function allows the activation functions to be called.
/// </summary>
/// <param name="pattern">The incoming Project.</param>
/// <returns>The output from this layer.</returns>
public override INeuralData Compute(INeuralData pattern)
{
INeuralData result = new BasicNeuralData(NeuronCount);
for (int i = 0; i < NeuronCount; i++)
{
if (this.radialBasisFunction[i] == null)
{
String str =
"Error, must define radial functions for each neuron";
#if logging
if (RadialBasisFunctionLayer.logger.IsErrorEnabled)
{
RadialBasisFunctionLayer.logger.Error(str);
}
#endif
throw new NeuralNetworkError(str);
}
IRadialBasisFunction f = this.radialBasisFunction[i];
if (pattern.Data.Length != f.Dimensions)
throw new Exception("Inputs must equal the number of dimensions.");
result[i] = f.Calculate(pattern.Data);
}
return result;
}
/// <summary>
/// Handle recurrent layers. See if there are any recurrent layers before
/// the specified layer that must affect the input.
/// </summary>
/// <param name="layer">The layer being processed, see if there are any recurrent
/// connections to this.</param>
/// <param name="input">The input to the layer, will be modified with the result
/// from any recurrent layers.</param>
/// <param name="source">The source synapse.</param>
private void HandleRecurrentInput(ILayer layer,
INeuralData input, ISynapse source)
{
foreach (ISynapse synapse
in this.structure.GetPreviousSynapses(layer))
{
if (synapse != source)
{
#if logging
if (BasicNetwork.logger.IsDebugEnabled)
{
BasicNetwork.logger.Debug("Recurrent layer from: " + input);
}
#endif
INeuralData recurrentInput = synapse.FromLayer
.Recur();
if (recurrentInput != null)
{
INeuralData recurrentOutput = synapse
.Compute(recurrentInput);
for (int i = 0; i < input.Count; i++)
{
input[i] = input[i]
+ recurrentOutput[i];
}
#if logging
if (BasicNetwork.logger.IsDebugEnabled)
{
BasicNetwork.logger.Debug("Recurrent layer to: " + input);
}
#endif
}
}
}
}
/// <summary>
/// Not supported.
/// </summary>
/// <param name="inputData">Not used.</param>
/// <param name="idealData">Not used.</param>
public void Add(INeuralData inputData, INeuralData idealData)
{
throw new TrainingError(FoldedDataSet.ADD_NOT_SUPPORTED);
}
/// <summary>
/// Convert regular Encog NeuralData into the "sparse" data needed by an SVM.
/// </summary>
/// <param name="data">The data to convert.</param>
/// <returns>The SVM sparse data.</returns>
public svm_node[] MakeSparse(INeuralData data)
{
svm_node[] result = new svm_node[data.Count];
for (int i = 0; i < data.Count; i++)
{
result[i] = new svm_node();
result[i].index = i + 1;
result[i].value_Renamed = data[i];
}
return result;
}
/// <summary>
/// Determine the winner for the specified input. This is the number of the
/// winning neuron.
/// </summary>
/// <param name="input">The input patter to present to the neural network.</param>
/// <returns>The winning neuron.</returns>
public int Winner(INeuralData input)
{
INeuralData output = Compute(input);
return DetermineWinner(output);
}
