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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 "Java Source Code Warehouse" project. The intent of this project is to help you "Learn Java by Example" TM.

Learn more about this Java project at its project page.

Java - Java tags/keywords

edge, expect, graph, hashset, ivertexsequence, list, randomwalkiterator, set, string, test, testgraph, util, vfactory, walk, weightedrandomwalkiterator

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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