Hello everyone,
I need some suggestions about debuging the Affinity Appropogation
algorithm for gelly.
In my implementation, there is a problem with the MessagingFunction in
Vertex Centric Iteration
The test graph is a completed directed graph (25 vertices in total),
i.e. there are two opposite directed edges between every two vertices.
The value of each vertex is a hashmap, in which contians information of
all of the vertex's neigbor vertices.
My MessagingFunction is implemented as follow,
if (getSuperstepNumber() % 2 == 1){
/*Odd step: Propagate availability*/
int msgCnt = 0; //Debug variable, count out going
edge number
for (Edge<Long, Double> e: getOutgoingEdges()){
Long dest = e.getTarget();
sendMessageTo(dest, new Tuple2<Long,
Double>(vertexKey, vertexValue.get(dest).f2));
msgCnt++;
}
System.err.format("Step %d: Vertex %d send %d\n",
getSuperstepNumber(), vertexKey, msgCnt);
}else{
/*Even step: propagate responsibility*/
for (Edge<Long, Double> e: getOutgoingEdges()){
Long dest = e.getTarget();
sendMessageTo(dest, new Tuple2<Long,
Double>(vertexKey, vertexValue.get(dest).f1));
}
}
I use a msgCnt for conuting the neigbor edges in the odd step. During
the 1st super step , every vertex should send message to 24 neighbor
vertices. However, the real result is quite strange. For some
vertices, they appropogate messages to all the adjacent vertices.
however, for serveral other vertices, they send nothing or only part of
their neighbors. i.e the getOutgoingEdges() returns none.
Step 1: Vertex 3 send 0
Step 1: Vertex 1 send 0
Step 1: Vertex 5 send 0
Step 1: Vertex 8 send 0
Step 1: Vertex 14 send 0
Step 1: Vertex 16 send 0
Step 1: Vertex 2 send 24
Step 1: Vertex 7 send 18
Step 1: Vertex 9 send 24
Step 1: Vertex 6 send 24
Step 1: Vertex 11 send 0
Step 1: Vertex 15 send 0
Step 1: Vertex 12 send 0
Step 1: Vertex 21 send 0
Step 1: Vertex 13 send 0
Step 1: Vertex 25 send 0
Step 1: Vertex 22 send 24
Step 1: Vertex 18 send 0
Step 1: Vertex 23 send 24
Step 1: Vertex 19 send 0
Step 1: Vertex 20 send 0
Step 1: Vertex 24 send 24
I do not know how to detect the problem, can anyone give me some
suggestions?
I attached the code and data also. The iteration is loaded in line 118
in AffinityPropogation.java
Thank you
Best regards.
ZHOU Yi
package org.ua.ap;
import java.util.HashMap;
import java.util.Map.Entry;
import org.apache.flink.api.common.functions.FilterFunction;
import org.apache.flink.api.common.functions.MapFunction;
import org.apache.flink.api.java.DataSet;
import org.apache.flink.api.java.ExecutionEnvironment;
import org.apache.flink.api.java.tuple.Tuple2;
import org.apache.flink.api.java.tuple.Tuple3;
import org.apache.flink.graph.Edge;
import org.apache.flink.graph.EdgeDirection;
import org.apache.flink.graph.Graph;
import org.apache.flink.graph.GraphAlgorithm;
import org.apache.flink.graph.NeighborsFunctionWithVertexValue;
import org.apache.flink.graph.Vertex;
import org.apache.flink.graph.spargel.MessageIterator;
import org.apache.flink.graph.spargel.MessagingFunction;
import org.apache.flink.graph.spargel.VertexCentricIteration;
import org.apache.flink.graph.spargel.VertexUpdateFunction;
@SuppressWarnings({ "serial", "hiding" })
public class AffinityPropogation implements GraphAlgorithm<Long, Long, Double> {
private int maxIterations;
private Double lambda;
public AffinityPropogation(int maxIterations, double lambda){
this.maxIterations = maxIterations;
this.lambda = lambda;
}
/**
* For each vertex v, the value is a hashmap including [k': s(v,k'), r(v, k'), a(k',v)]
* @param originalGraph
* @return
*/
private Graph<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Double> transferGraph(Graph<Long, Long, Double> originalGraph){
/*Reconstruct a graph*/
DataSet<Vertex<Long, Long>> vertices = originalGraph.getVertices();
DataSet<Edge<Long, Double>> edges = originalGraph.getEdges();
/*Transfer the vertex value to a hash map, which stores the <Similarity, Responsibility, Availability> to the neigbor vertices */
DataSet<Vertex<Long,HashMap<Long, Tuple3<Double, Double,Double>>>> newVertices = vertices.map(
new MapFunction<Vertex<Long, Long>,Vertex<Long,HashMap<Long, Tuple3<Double, Double,Double>>>>(){
@Override
public Vertex<Long, HashMap<Long, Tuple3<Double, Double, Double>>> map(
Vertex<Long, Long> v) throws Exception {
// TODO Auto-generated method stub
HashMap<Long, Tuple3<Double, Double, Double>> hashmap =
new HashMap<Long, Tuple3<Double, Double,Double>>();
hashmap.put(v.getId(),new Tuple3<Double, Double, Double>(0.0, 0.0, 0.0));
return new Vertex<Long, HashMap<Long, Tuple3<Double, Double, Double>>>(v.getId(),
hashmap);
}
});
/*Construct a new graph with HashMap<key, <Similarity, Responsibility, Availability>> value for each vertex*/
Graph<Long, HashMap<Long, Tuple3<Double, Double, Double>>, Double> newGraph =
Graph.fromDataSet(newVertices, edges, ExecutionEnvironment.getExecutionEnvironment());
/*Create a vertex centric iteration to construct the hash map for each vertex*/
// VertexCentricIteration<Long, HashMap<Long, Tuple3<Double, Double, Double>>, Tuple2<Long, Double>, Double> iteration =
// newGraph.createVertexCentricIteration(new InitialVertexUpdater(), new InitialMessenger(), 1);
/*run iteration*/
Graph<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Double> hashMappedGraph =
newGraph.runVertexCentricIteration(new InitialVertexUpdater(), new InitialMessenger(), 1);
/*Eliminate the self edges*/
Graph<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Double> finalGraph =
hashMappedGraph.filterOnEdges(new FilterFunction<Edge<Long,Double>>(){
@Override
public boolean filter(Edge<Long, Double> edge)
throws Exception {
return edge.f0 != edge.f1;
}
});
return finalGraph;
}
public static final class InitialVertexUpdater
extends VertexUpdateFunction<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Tuple2<Long, Double>>{
@Override
public void updateVertex(Long vertexKey, HashMap<Long, Tuple3<Double, Double,Double>> vertexValue,
MessageIterator<Tuple2<Long, Double>> inMessages)
throws Exception {
for (Tuple2<Long, Double> message: inMessages){
if (!vertexValue.containsValue(message.f0)){
vertexValue.put(message.f0, new Tuple3<Double, Double,Double>(message.f1, 0.0, 0.0));
}else{
vertexValue.get(message.f0).f0 = message.f1;
}
}
setNewVertexValue(vertexValue);
}
}
public static final class InitialMessenger
extends MessagingFunction<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Tuple2<Long, Double>, Double>{
@Override
public void sendMessages(Long vertexKey, HashMap<Long, Tuple3<Double, Double,Double>> vertexValue)
throws Exception {
for (Edge<Long, Double> e: getOutgoingEdges()){
sendMessageTo(e.getTarget(), new Tuple2<Long, Double>(vertexKey, e.getValue()));
}
}
}
@Override
public Graph<Long, Long, Double> run(Graph<Long, Long, Double> input) throws Exception {
/*Transfer the vertex value to HashMap<Long, Tuple3<Double, Double,Double>>*/
Graph<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Double> graph = transferGraph(input);
// create the vertex-centric iteration
// VertexCentricIteration<Long, HashMap<Long, Tuple3<Double, Double, Double>>, Tuple2<Long, Double>, Double> iteration =
// graph.createVertexCentricIteration(new VertexUpdater(lambda), new InformationMessenger(), 2*maxIterations);
//Run the vertex centric iteration
Graph<Long, HashMap<Long, Tuple3<Double, Double, Double>>, Double> stableGraph = graph.runVertexCentricIteration(
new VertexUpdater(lambda), new InformationMessenger(), maxIterations*1);
DataSet<Vertex<Long, Long>> resultSet = stableGraph.reduceOnNeighbors(new NeighborSelection(), EdgeDirection.OUT);
//
Graph<Long, Long, Double> resultGraph = Graph.fromDataSet(resultSet,
input.getEdges(), ExecutionEnvironment.getExecutionEnvironment());
return resultGraph;
}
public static final class NeighborSelection
implements NeighborsFunctionWithVertexValue<Long, HashMap<Long, Tuple3<Double, Double, Double>>, Double, Vertex<Long, Long>>{
@Override
public Vertex<Long, Long> iterateNeighbors(
Vertex<Long, HashMap<Long, Tuple3<Double, Double, Double>>> vertex,
Iterable<Tuple2<Edge<Long, Double>, Vertex<Long, HashMap<Long, Tuple3<Double, Double, Double>>>>> neighbors)
throws Exception {
// TODO Auto-generated method stub
/*Get Evidence*/
HashMap<Long, Tuple3<Double, Double, Double>> hmap = vertex.getValue();
Double selfEvidence = hmap.get(vertex.getId()).f1 + hmap.get(vertex.getId()).f2;
if (selfEvidence>0){
return new Vertex<Long, Long>(vertex.getId(), vertex.getId());
}else{
Double maxSimilarity = Double.NEGATIVE_INFINITY;
Long belongExemplar = vertex.getId();
for (Tuple2<Edge<Long, Double>, Vertex<Long, HashMap<Long, Tuple3<Double, Double, Double>>>> neigbor: neighbors){
Long neigborId = neigbor.f1.getId();
HashMap<Long, Tuple3<Double, Double, Double>> neigborMap = neigbor.f1.getValue();
Double neigborEvidence = neigborMap.get(neigborId).f1 + neigborMap.get(neigborId).f2;
if (neigborEvidence > 0 ){
Double neigborSimilarity = vertex.getValue().get(neigborId).f1;
if (neigborSimilarity > maxSimilarity){
belongExemplar = neigborId;
maxSimilarity = neigborEvidence;
}
}
}
return new Vertex<Long, Long>(vertex.getId(), belongExemplar);
}
}
}
/***************************************************************************************************/
/*Update r(i,k) for each vertex*/
public static final class VertexUpdater
extends VertexUpdateFunction<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Tuple2<Long, Double>>{
private Double lambda;
public VertexUpdater(Double lambda){
this.lambda = lambda;
}
@Override
public void updateVertex(Long vertexKey,
HashMap<Long, Tuple3<Double, Double, Double>> vertexValue,
MessageIterator<Tuple2<Long, Double>> inMessages)
throws Exception {
int step = getSuperstepNumber();
if (step % 2 == 1){
/*Start from odd step: receive neighbor responsibility and update the responsibility*/
Double selfSum = vertexValue.get(vertexKey).f0 + vertexValue.get(vertexKey).f2;
/*Find the max a(v, k) + s(v, k)*/
Double maxSum = selfSum;
Long maxKey = vertexKey;
Double secondMaxSum = Double.NEGATIVE_INFINITY;
int msgCnt = 0;
for (Tuple2<Long, Double> msg: inMessages){
Long adjacentVertex = msg.f0;
Double sum = msg.f1 + vertexValue.get(adjacentVertex).f0;
if (sum > maxSum ){
secondMaxSum = maxSum;
maxSum = sum;
maxKey = adjacentVertex;
}else if(sum > secondMaxSum){
secondMaxSum = sum;
}
msgCnt++;
// System.out.format("Evaluate %d-%d %f\n",msg.f0,vertexKey, sum);
}
//DEBUG
System.err.format("Super %d, msg count %d\n", step, msgCnt);
if (maxKey != vertexKey && selfSum> secondMaxSum){
secondMaxSum = selfSum;
}
/*Find the second max*/
if (maxKey != vertexKey)
secondMaxSum = vertexValue.get(vertexKey).f0 + vertexValue.get(vertexKey).f2;
/*Update responsibility*/
for (Entry<Long, Tuple3<Double, Double, Double>> entry: vertexValue.entrySet()){
Double newRespons = 0.0;
if (entry.getKey() != maxKey){
newRespons = entry.getValue().f0 - maxSum;
}else{
newRespons = entry.getValue().f0 - secondMaxSum;
}
entry.getValue().f1 = (1 - lambda) * newRespons + lambda * entry.getValue().f1;
// System.out.format("Super step%d "
// + "Update response %d: %d(%f)\n", getSuperstepNumber(),
// vertexKey, entry.getKey(), entry.getValue().f1);
}
/*reset the hashmap of the vertex*/
setNewVertexValue(vertexValue);
}else{
/*Odd step: receive responsibility and update availability */
double sum = 0.0;
for (Tuple2<Long, Double> msg: inMessages){
sum += (msg.f1 > 0? msg.f1: 0);
}
Double selfRespons = vertexValue.get(vertexKey).f1;
Double newAvailability = 0.0;
for (Tuple2<Long, Double> msg: inMessages){
Double a = selfRespons + sum - msg.f1;
newAvailability = a < 0? a: 0;
vertexValue.get(msg.f0).f2 = (1 - lambda) * newAvailability + lambda * vertexValue.get(msg.f0).f2;
}
/*update self-availability*/
vertexValue.get(vertexKey).f2 = (1 - lambda) * sum + lambda *vertexValue.get(vertexKey).f2;
/*reset the hash map*/
setNewVertexValue(vertexValue);
}
}
}
/*Send a(k',i) to k'*/
public static final class InformationMessenger
extends MessagingFunction<Long, HashMap<Long, Tuple3<Double, Double,Double>>, Tuple2<Long, Double>, Double>{
@Override
public void sendMessages(Long vertexKey,
HashMap<Long, Tuple3<Double, Double, Double>> vertexValue)
throws Exception {
if (getSuperstepNumber() % 2 == 1){
/*Odd step: Propagate availability*/
int msgCnt = 0;
for (Edge<Long, Double> e: getOutgoingEdges()){
Long dest = e.getTarget();
sendMessageTo(dest, new Tuple2<Long, Double>(vertexKey, vertexValue.get(dest).f2));
msgCnt++;
}
System.err.format("Step %d: Vertex %d send %d\n", getSuperstepNumber(), vertexKey, msgCnt);
}else{
/*Even step: propagate responsibility*/
for (Edge<Long, Double> e: getOutgoingEdges()){
Long dest = e.getTarget();
sendMessageTo(dest, new Tuple2<Long, Double>(vertexKey, vertexValue.get(dest).f1));
}
}
}
}
}
package org.ua.ap;
import org.apache.flink.api.common.ProgramDescription;
import org.apache.flink.api.common.functions.MapFunction;
import org.apache.flink.api.java.DataSet;
import org.apache.flink.api.java.ExecutionEnvironment;
import org.apache.flink.api.java.tuple.Tuple2;
import org.apache.flink.api.java.tuple.Tuple3;
import org.apache.flink.graph.Edge;
import org.apache.flink.graph.Graph;
import org.apache.flink.graph.Vertex;
import org.apache.flink.util.Collector;
public class AffinityPropogationExample implements ProgramDescription{
public static final String vertexPreferenceInputPath = "ToyProblemPreferences.txt";
public static final String similarGraphInputPath = "ToyProblemSimilarities.txt";
public static final int maxIterations = 100;
@Override
public String getDescription() {
// TODO Auto-generated method stub
return "This is an example of Affinity Propogation";
}
public static void main(String[] args) throws Exception{
/*set up environment*/
ExecutionEnvironment env = ExecutionEnvironment.getExecutionEnvironment();
/*Set up graph*/
DataSet<Vertex<Long, Long>> vertices = getVertexDataSet(env);
DataSet<Edge<Long, Double>> distanceEdges = getEdgeDataSet(env);
DataSet<Edge<Long, Double>> selfEdges = getPreferenceSet(env);
DataSet<Edge<Long, Double>> allEdges = distanceEdges.union(selfEdges);
Graph<Long, Long, Double> graph = Graph.fromDataSet(vertices, allEdges, env);
/*Run affinity propagation algorithm*/
Graph<Long, Long, Double> result = graph.run(new AffinityPropogation(100, 0.5));
result.getVertices().print();
// result.getVertices().writeAsCsv("result.txt","\n", " ");
/*Test*/
env.execute("Affinity Propogation Example");
}
@SuppressWarnings("serial")
public static DataSet<Vertex<Long, Long>> getVertexDataSet(ExecutionEnvironment env){
return env.readCsvFile(vertexPreferenceInputPath).
fieldDelimiter(' ').lineDelimiter("\n").
types(Long.class, Double.class).
map(new MapFunction<Tuple2<Long, Double>, Vertex<Long, Long>>() {
@Override
public Vertex<Long, Long> map(Tuple2<Long, Double> tuple2) throws Exception {
return new Vertex<Long, Long>(tuple2.f0, tuple2.f0);
}
});
}
@SuppressWarnings("serial")
public static DataSet<Edge<Long, Double>> getEdgeDataSet(ExecutionEnvironment env){
return env.readCsvFile(similarGraphInputPath)
.fieldDelimiter(' ').lineDelimiter("\n")
.types(Long.class, Long.class, Double.class)
.map(new MapFunction<Tuple3<Long, Long, Double>, Edge<Long, Double>>(){
@Override
public Edge<Long, Double> map(
Tuple3<Long, Long, Double> tuple3) throws Exception {
// TODO Auto-generated method stub
return new Edge<Long, Double>(tuple3.f0, tuple3.f1,tuple3.f2);
}
});
}
@SuppressWarnings("serial")
public static DataSet<Edge<Long, Double>> getPreferenceSet(ExecutionEnvironment env){
return env.readCsvFile(vertexPreferenceInputPath)
.fieldDelimiter(' ').lineDelimiter("\n")
.types(Long.class, Double.class)
.map(new MapFunction<Tuple2<Long, Double>, Edge<Long, Double>>(){
@Override
public Edge<Long, Double> map(Tuple2<Long, Double> value)
throws Exception {
return new Edge<Long, Double>(value.f0, value.f0, value.f1);
}
});
}
}
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