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Java example source code file (TestGraph.java)
This example Java source code file (TestGraph.java) is included in the alvinalexander.com
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Learn more about this Java project at its project page.
The TestGraph.java Java example source code
package org.deeplearning4j.graph.graph;
import org.apache.commons.lang3.ArrayUtils;
import org.deeplearning4j.graph.api.*;
import org.deeplearning4j.graph.data.GraphLoader;
import org.deeplearning4j.graph.iterator.RandomWalkIterator;
import org.deeplearning4j.graph.iterator.WeightedRandomWalkIterator;
import org.deeplearning4j.graph.vertexfactory.VertexFactory;
import org.junit.Test;
import org.nd4j.linalg.io.ClassPathResource;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static junit.framework.TestCase.assertTrue;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
public class TestGraph {
@Test
public void testSimpleGraph() {
Graph<String, String> graph = new Graph<>(10, false, new VFactory());
assertEquals(10, graph.numVertices());
for (int i = 0; i < 10; i++) {
//Add some undirected edges
String str = i + "--" + (i + 1) % 10;
Edge<String> edge = new Edge<>(i, (i + 1) % 10, str, false);
graph.addEdge(edge);
}
for (int i = 0; i < 10; i++) {
List<Edge edges = graph.getEdgesOut(i);
assertEquals(2, edges.size());
//expect for example 0->1 and 9->0
Edge<String> first = edges.get(0);
if (first.getFrom() == i) {
//undirected edge: i -> i+1 (or 9 -> 0)
assertEquals(i, first.getFrom());
assertEquals((i + 1) % 10, first.getTo());
} else {
//undirected edge: i-1 -> i (or 9 -> 0)
assertEquals((i + 10 - 1) % 10, first.getFrom());
assertEquals(i, first.getTo());
}
Edge<String> second = edges.get(1);
assertNotEquals(first.getFrom(), second.getFrom());
if (second.getFrom() == i) {
//undirected edge: i -> i+1 (or 9 -> 0)
assertEquals(i, second.getFrom());
assertEquals((i + 1) % 10, second.getTo());
} else {
//undirected edge: i-1 -> i (or 9 -> 0)
assertEquals((i + 10 - 1) % 10, second.getFrom());
assertEquals(i, second.getTo());
}
}
}
private static class VFactory implements VertexFactory<String> {
@Override
public Vertex<String> create(int vertexIdx) {
return new Vertex<>(vertexIdx, String.valueOf(vertexIdx));
}
}
@Test
public void testRandomWalkIterator() {
Graph<String, String> graph = new Graph<>(10, false, new VFactory());
assertEquals(10, graph.numVertices());
for (int i = 0; i < 10; i++) {
//Add some undirected edges
String str = i + "--" + (i + 1) % 10;
Edge<String> edge = new Edge<>(i, (i + 1) % 10, str, false);
graph.addEdge(edge);
}
int walkLength = 4;
RandomWalkIterator<String> iter = new RandomWalkIterator(graph, walkLength, 1235, NoEdgeHandling.EXCEPTION_ON_DISCONNECTED);
int count = 0;
Set<Integer> startIdxSet = new HashSet<>();
while (iter.hasNext()) {
count++;
IVertexSequence<String> sequence = iter.next();
int seqCount = 1;
int first = sequence.next().vertexID();
int previous = first;
while (sequence.hasNext()) {
//Possible next vertices for this particular graph: (previous+1)%10 or (previous-1+10)%10
int left = (previous - 1 + 10) % 10;
int right = (previous + 1) % 10;
int current = sequence.next().vertexID();
assertTrue("expected: " + left + " or " + right + ", got " + current, current == left || current == right);
seqCount++;
previous = current;
}
assertEquals(seqCount, walkLength + 1); //walk of 0 -> 1 element, walk of 2 -> 3 elements etc
assertFalse(startIdxSet.contains(first)); //Expect to see each node exactly once
startIdxSet.add(first);
}
assertEquals(10, count); //Expect exactly 10 starting nodes
assertEquals(10, startIdxSet.size());
}
@Test
public void testWeightedRandomWalkIterator() throws Exception {
//Load a directed, weighted graph from file
String path = new ClassPathResource("WeightedGraph.txt").getFile().getAbsolutePath();
int numVertices = 9;
String delim = ",";
String[] ignoreLinesStartingWith = new String[]{"//"}; //Comment lines start with "//"
IGraph<String, Double> graph = GraphLoader.loadWeightedEdgeListFile(path, numVertices, delim, true, ignoreLinesStartingWith);
assertEquals(numVertices, graph.numVertices());
int[] vertexOutDegrees = {2, 2, 1, 2, 2, 1, 1, 1, 1};
for (int i = 0; i < numVertices; i++) assertEquals(vertexOutDegrees[i], graph.getVertexDegree(i));
int[][] edges = new int[][]{
{1, 3}, //0->1 and 1->3
{2, 4}, //1->2 and 1->4
{5}, //etc
{4, 6},
{5, 7},
{8},
{7},
{8},
{0}
};
double[][] edgeWeights = new double[][]{
{1, 3},
{12, 14},
{25},
{34, 36},
{45, 47},
{58},
{67},
{78},
{80}
};
double[][] edgeWeightsNormalized = new double[edgeWeights.length][0];
for( int i=0; i<edgeWeights.length; i++ ){
double sum = 0.0;
for( int j=0; j<edgeWeights[i].length; j++ ) sum += edgeWeights[i][j];
edgeWeightsNormalized[i] = new double[edgeWeights[i].length];
for( int j=0; j<edgeWeights[i].length; j++ ) edgeWeightsNormalized[i][j] = edgeWeights[i][j] / sum;
}
int walkLength = 5;
WeightedRandomWalkIterator<String> iterator = new WeightedRandomWalkIterator(graph, walkLength, 12345);
int walkCount = 0;
Set<Integer> set = new HashSet<>();
while (iterator.hasNext()) {
IVertexSequence<String> walk = iterator.next();
assertEquals(walkLength + 1, walk.sequenceLength()); //Walk length of 5 -> 6 vertices (inc starting point)
int thisWalkCount = 0;
boolean first = true;
int lastVertex = -1;
while (walk.hasNext()) {
Vertex<String> vertex = walk.next();
if (first) {
assertFalse(set.contains(vertex.vertexID()));
set.add(vertex.vertexID());
lastVertex = vertex.vertexID();
first = false;
} else {
//Ensure that a directed edge exists from lastVertex -> vertex
int currVertex = vertex.vertexID();
assertTrue(ArrayUtils.contains(edges[lastVertex], currVertex));
lastVertex = currVertex;
}
thisWalkCount++;
}
assertEquals(walkLength + 1, thisWalkCount); //Walk length of 5 -> 6 vertices (inc starting point)
walkCount++;
}
double[][] transitionProb = new double[numVertices][numVertices];
int nWalks = 2000;
for( int i=0; i<nWalks; i++ ) {
iterator.reset();
while (iterator.hasNext()) {
IVertexSequence<String> seq = iterator.next();
int last = -1;
while (seq.hasNext()) {
int curr = seq.next().vertexID();
if(last != -1) {
transitionProb[last][curr] += 1.0;
}
last = curr;
}
}
}
for(int i=0; i<transitionProb.length; i++ ){
double sum = 0.0;
for( int j=0; j<transitionProb[i].length; j++ ) sum += transitionProb[i][j];
for( int j=0; j<transitionProb[i].length; j++ ) transitionProb[i][j] /= sum;
System.out.println(Arrays.toString(transitionProb[i]));
}
//Check that transition probs are essentially correct (within bounds of random variation)
for( int i=0; i<numVertices; i++ ){
for( int j=0; j<numVertices; j++ ){
if(!ArrayUtils.contains(edges[i],j)){
assertEquals(0.0,transitionProb[i][j],0.0);
} else {
int idx = ArrayUtils.indexOf(edges[i],j);
assertEquals(edgeWeightsNormalized[i][idx],transitionProb[i][j],0.01);
}
}
}
for (int i = 0; i < numVertices; i++) assertTrue(set.contains(i));
assertEquals(numVertices, walkCount);
}
}
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