Java tutorial
/* * Copyright (C) 2009 Istvan Fehervari, Wilfried Elmenreich * Original project page: http://www.frevotool.tk * * This program is free software; you can redistribute it and/or modify it * under the terms of the GNU General Public License Version 3 as published * by the Free Software Foundation http://www.gnu.org/licenses/gpl-3.0.txt * * There is no warranty for this free software. The GPL requires that * modified versions be marked as changed, so that their problems will * not be attributed erroneously to authors of previous versions. */ package threeLayerNetwork; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.util.ArrayList; import java.util.Hashtable; import net.jodk.lang.FastMath; import org.dom4j.Element; import org.dom4j.Node; import core.FileType; import core.AbstractRepresentation; import core.XMLFieldEntry; import utils.NESRandom; /** * A not recursive layered neural network * * @author Wil */ public class ThreeLayerNetwork extends AbstractRepresentation { protected NESRandom generator; protected float[][] weight; protected float[] bias; protected float[] output; protected float[] activation; protected int rank; protected int nodes; protected int input_nodes; protected int output_nodes; protected int hidden_nodes; protected float weight_range; protected float bias_range; protected int stepnumber; protected ArrayList<FileType> exportList = new ArrayList<FileType>(); public ThreeLayerNetwork(int inputnumber, int outputnumber, NESRandom random, Hashtable<String, XMLFieldEntry> properties) { super(inputnumber, outputnumber, random, properties); this.setProperties(properties); generator = random; input_nodes = inputnumber; output_nodes = outputnumber; // load properties XMLFieldEntry snumber = getProperties().get("stepNumber"); stepnumber = Integer.parseInt(snumber.getValue()); XMLFieldEntry wr = getProperties().get("weight_range"); this.weight_range = Float.parseFloat(wr.getValue()); XMLFieldEntry br = getProperties().get("bias_range"); this.bias_range = Float.parseFloat(br.getValue()); XMLFieldEntry hn = getProperties().get("hiddenNodes"); hidden_nodes = Integer.parseInt(hn.getValue()); nodes = input_nodes + output_nodes + hidden_nodes; // generate structure this.weight = new float[this.nodes][this.nodes]; this.bias = new float[this.nodes]; this.output = new float[this.nodes]; this.activation = new float[this.nodes]; if (random != null) randomizeWB(); // this step is not needed for cloning, otherwise // random is not null } public String getHash() { double sum = 0; // add bias for (int i = 0; i < bias.length; i++) { sum += bias[i]; } // add weights for (int i = input_nodes; i < nodes; i++) { for (int j = 0; j < nodes; j++) { sum += this.weight[j][i]; } } String res = Double.toString(sum); int resint = res.hashCode(); return Integer.toHexString(resint & 0xFFFFF); } private void randomizeWB() { // randomize connections between hidden nodes and input nodes for (int i = input_nodes; i < nodes - output_nodes; i++) // all hidden nodes { for (int j = 0; j < input_nodes; j++) // all input nodes { this.weight[j][i] = rand_range(weight_range); } this.bias[i] = rand_range(bias_range); } // randomize connections between hidden nodes and output nodes for (int i = nodes - output_nodes; i < nodes; i++) // all output nodes { for (int j = input_nodes; j < nodes - output_nodes; j++) // all hidden nodes { this.weight[j][i] = rand_range(weight_range); } this.bias[i] = rand_range(bias_range); } // no bias for input nodes } // *f private float rand_range(float border) { double val; val = generator.nextDouble() * 2 * border - border; // *f return (float) val; } @Override public int getNumberofMutationFunctions() { return 2; } @Override public int getNumberOfRecombinationFunctions() { return 1; } @Override protected void mutationFunction(float severity, float probability, int method) { this.mutateBias(severity, probability, method); this.mutateWeight(severity, probability, method); } public void mutateBias(float severity, float p, int method) { float rate = severity * bias_range; for (int i = input_nodes; i < bias.length; i++) { if (generator.nextFloat() < p) { switch (method) { case 1: this.bias[i] += rand_range(rate); break; case 2: // smart method, facilitates the mutation to fine-tune // small parameters this.bias[i] += rand_range((int) Math.max(this.bias[i] / 5.0, 10)); // 20% mutation break; default: this.bias[i] += rand_range(rate); break; } } } } public void mutateWeight(float severity, float p, int method) { float rate = severity * weight_range; for (int i = 0; i < bias.length; i++) { for (int j = input_nodes; j < weight.length; j++) { if (generator.nextFloat() < p) switch (method) { case 1: this.weight[i][j] += rand_range(rate); break; case 2: // smart method, facilitates the mutation to // fine-tune small parameters this.weight[i][j] += rand_range((int) Math.max(this.weight[i][j] / 5.0, 10)); // 20% mutation break; default: this.weight[i][j] += rand_range(rate); break; } } } } private int rndIndex(int range) { if (range < 1) return 0; return generator.nextInt(Integer.MAX_VALUE) % range; } @Override public void recombinationFunction(AbstractRepresentation other, int method) { if (!(other instanceof ThreeLayerNetwork)) throw new IllegalArgumentException("Xover between different network classes not possible!"); int noninodes = nodes - input_nodes; int count = rndIndex(noninodes - 1) + 1; // minimum 1, maximum all // but 1 int start = input_nodes + rndIndex(noninodes); ThreeLayerNetwork offspring = this; ThreeLayerNetwork father = (ThreeLayerNetwork) other; for (int i = start; i < start + count; i++) { if (i >= nodes) break; for (int j = 0; j < nodes; j++) offspring.weight[j][i] = father.weight[j][i]; offspring.bias[i] = father.bias[i]; } } public float activate(float x) { if (x >= 1) return 1; else if (x <= 0) return 0; else return (short) x; } public static float sigmoidActivate(float x) { return (float) (1.0f / (1.0f + FastMath.exp(-x))); } public void reset() { for (int i = 0; i < nodes; i++) this.output[i] = 0; } /** Provides the networks output for the given input */ public ArrayList<Float> getOutput(ArrayList<Float> input) { for (int i = 0; i < stepnumber - 1; i++) { getStep(input); } return getStep(input); } /** * Calculate an output vector for the given input vector * @param input given input vector * @return calculated output vector */ public ArrayList<Float> getStep(ArrayList<Float> input) { if (input.size() != this.input_nodes) throw new IllegalArgumentException("Input vector size inappropriate!"); for (int i = 0; i < input.size(); i++) { this.output[i] = input.get(i); } // propagate input to hidden layer for (int i = input_nodes; i < nodes - output_nodes; i++) // all hidden // nodes { float sum = 0; for (int j = 0; j < input_nodes; j++) // all input nodes { sum += this.weight[j][i] * this.output[j]; } this.activation[i] = this.bias[i] + sum; this.output[i] = sigmoidActivate(this.activation[i]); } // propagate information to output layer for (int i = nodes - output_nodes; i < nodes; i++) // all output nodes { float sum = 0; for (int j = input_nodes; j < nodes - output_nodes; j++) // all // hidden // nodes { sum += this.weight[j][i] * this.output[j]; } this.activation[i] = this.bias[i] + sum; this.output[i] = sigmoidActivate(this.activation[i]); } ArrayList<Float> outputVector = new ArrayList<Float>(); for (int i = nodes - output_nodes; i < nodes; i++) { outputVector.add(this.output[i]); } return outputVector; } @Override public double diffTo(AbstractRepresentation o) { double diff = 0; int n = 0; if (!(o instanceof ThreeLayerNetwork)) throw new IllegalArgumentException("diffTo between different network classes not possible!"); ThreeLayerNetwork network = (ThreeLayerNetwork) o; // add differences from input to hidden layer for (int i = input_nodes; i < nodes - output_nodes; i++) // all hidden // nodes { for (int j = 0; j < input_nodes; j++) // all input nodes { diff += Math.abs(network.weight[j][i] - this.weight[j][i]) / weight_range; } } n += (nodes - output_nodes - input_nodes) * input_nodes; // add differences from hidden to output layer for (int i = nodes - output_nodes; i < nodes; i++) // all output nodes { for (int j = input_nodes; j < nodes - output_nodes; j++) // all hidden { diff += Math.abs(network.weight[j][i] - this.weight[j][i]) / weight_range; } } n += output_nodes * (nodes - output_nodes - input_nodes); // bias of all hidden and output nodes for (int i = input_nodes; i < this.bias.length; i++) diff += Math.abs(network.bias[i] - this.bias[i]) / bias_range; n += this.bias.length - input_nodes; return diff / n; } public AbstractRepresentation cloneFunction() { ThreeLayerNetwork res = new ThreeLayerNetwork(input_nodes, output_nodes, generator, getProperties()); for (int i = 0; i < weight.length; i++) { System.arraycopy(weight[i], 0, res.weight[i], 0, weight[i].length); } res.bias = this.bias.clone(); res.output = this.output.clone(); res.activation = this.activation.clone(); res.rank = this.rank; return res; } public float getWeight(int nr, int from) { if (nr >= nodes) throw new IllegalArgumentException("Id " + nr + " is not a node!"); { if (from >= nodes) throw new IllegalArgumentException("Id " + from + " is not a node!"); return this.weight[from][nr]; } } /** Method used for saving the properties of this component */ public void exportToXmlElement(Element element) { Element nn = element.addElement("ThreeLayerNetwork"); nn.addAttribute("input_nodes", String.valueOf(this.input_nodes)); nn.addAttribute("output_nodes", String.valueOf(this.output_nodes)); nn.addAttribute("nodes", String.valueOf(this.nodes)); nn.addAttribute("weight_range", String.valueOf(this.weight_range)); nn.addAttribute("bias_range", String.valueOf(this.bias_range)); if (this.isEvaluated()) { nn.addAttribute("fitness", String.valueOf(this.getFitness())); } Element dnodes = nn.addElement("nodes"); for (int i = 0; i < this.nodes; i++) { Element node; if (i < input_nodes) { node = dnodes.addElement("node"); node.addAttribute("nr", String.valueOf(i)); node.addAttribute("type", "inputNode"); } else { node = dnodes.addElement("node"); node.addAttribute("nr", String.valueOf(i)); node.addAttribute("type", "node"); Element bias = node.addElement("bias"); bias.addText(String.valueOf(this.bias[i])); Element weights = node.addElement("weights"); for (int j = 0; j < this.nodes; j++) { Element weight = weights.addElement("weight"); weight.addAttribute("from", String.valueOf(j)); weight.addText(String.valueOf(this.getWeight(i, j))); } } } } /** * Sets the generator of random numbers for the current representation. */ @Override public void setGenerator(NESRandom generator) { this.generator = generator; } @Override public AbstractRepresentation loadFromXML(Node nd) { try { String fitnessString = nd.valueOf("./@fitness"); if (!fitnessString.isEmpty()) { this.setFitness(Double.parseDouble(fitnessString)); } this.input_nodes = Integer.parseInt(nd.valueOf("./@input_nodes")); this.output_nodes = Integer.parseInt(nd.valueOf("./@output_nodes")); this.nodes = Integer.parseInt(nd.valueOf("./@nodes")); this.weight_range = Float.parseFloat(nd.valueOf("./@weight_range")); this.bias_range = Float.parseFloat(nd.valueOf("./@bias_range")); // this.iteration = // Integer.parseInt(nd.valueOf("./simulation/@iteration")); // this.score = Integer.parseInt(nd.valueOf("./simulation/@score")); this.activation = new float[this.nodes]; this.output = new float[this.nodes]; this.bias = new float[this.nodes]; this.weight = new float[this.nodes][this.nodes]; Node dnodes = nd.selectSingleNode("./nodes"); for (int nr = this.input_nodes; nr < this.nodes; nr++) { Node curnode = dnodes.selectSingleNode("./node[@nr='" + nr + "']"); if (curnode == null) throw new IllegalArgumentException("ThreeLayerNetwork: node tags inconsistent!" + "\ncheck 'nr' attributes and nodes count in nnetwork!"); this.bias[nr] = Float.parseFloat(curnode.valueOf("./bias")); Node dweights = curnode.selectSingleNode("./weights"); for (int from = 0; from < this.nodes; from++) { String ws = dweights.valueOf("./weight[@from='" + from + "']"); if (ws.length() == 0) throw new IllegalArgumentException("ThreeLayerNetwork: weight tags inconsistent!" + "\ncheck 'from' attributes and nodes count in nnetwork!"); float val = Float.parseFloat(ws); this.weight[from][nr] = val; } } // this.gahist = new GAHistory(this.config, nd); } catch (NumberFormatException e) { throw new IllegalArgumentException("ThreeLayerNetwork: NumberFormatException! Check XML File"); } return this; } @Override public Hashtable<String, String> getDetails() { Hashtable<String, String> result = new Hashtable<String, String>(); result.put("input neurons", Integer.toString(this.input_nodes)); result.put("output neurons", Integer.toString(this.output_nodes)); result.put("hidden neurons", Integer.toString(nodes - input_nodes - output_nodes)); result.put("weight range", Float.toString(this.weight_range)); result.put("bias range", Float.toString(this.bias_range)); for (int n = 0; n < nodes; n++) { result.put("bias node " + n, Float.toString(this.bias[n])); for (int from = 0; from < this.nodes; from++) { result.put("weight from " + from + " to " + n, Float.toString(this.weight[from][n])); } } return result; } @Override public void exportToFile(File saveFile) { System.out.println("Exporting Pajek network file to " + saveFile.getName()); try { // Create file FileWriter fstream = new FileWriter(saveFile); BufferedWriter out = new BufferedWriter(fstream); out.write("*Vertices " + this.nodes); out.newLine(); // use newline instead of \n to avoid system // dependency // input neurons for (int i = 1; i < input_nodes + 1; i++) { out.write(i + " \"I" + i + "\""); out.newLine(); } for (int h = input_nodes + 1; h < nodes - output_nodes + 1; h++) { out.write(h + " \"H" + (h - input_nodes) + "\""); out.newLine(); } int a = 1; for (int o = nodes - output_nodes + 1; o < nodes + 1; o++) { out.write(o + " \"O" + a + "\""); out.newLine(); a++; } // Edges out.write("*Edges"); out.newLine(); // add edges from hidden neurons to input neurons for (int n = input_nodes; n < (nodes - output_nodes); n++) { // take // all // hidden // neurons for (int from = 0; from < input_nodes; from++) { // take all // input // neurons out.write((n + 1) + " " + (from + 1) + " " + weight[from][n]); out.newLine(); } } // add edges from output neurons to hidden neurons for (int n = (nodes - output_nodes); n < nodes; n++) { // take all // output // neurons for (int from = input_nodes; from < (nodes - output_nodes); from++) { // take // all // hidden // neurons out.write((n + 1) + " " + (from + 1) + " " + weight[from][n]); out.newLine(); } } // Close the output stream out.close(); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); } } }