public EM_Cluster(String tf, String[] options) throws Exception {
this.model = new EM();
this.training_f = tf;
this.options = options;
BufferedReader r = new BufferedReader(new FileReader(tf));
Instances data = new Instances(r);
model.setOptions(options);
model.buildClusterer(data);
}
@operator(
value = {"clustering_em"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by EM Algorithm based on the given attributes. Some paremeters can be defined: "
+ "max_iterations: the maximum number of iterations to perform;"
+ "num_clusters: the number of clusters; minStdDev: minimum allowable standard deviation",
examples = {
@example(
value =
"clustering_em([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"max_iterations\"::10, \"num_clusters\"::3])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_simple_kmeans",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringEM(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
EM em = new EM();
em.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("max_iterations")) {
em.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
}
if (parameters.containsKey("num_clusters")) {
em.setNumClusters(Cast.asInt(scope, parameters.get("num_clusters")));
}
if (parameters.containsKey("minStdDev")) {
em.setMinStdDev(Cast.asFloat(scope, parameters.get("minStdDev")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, em, attributes, agents);
return groupes;
}
public JSONArray Cluster(String wekaFilePath, int clusterNum) throws Exception {
File inputFile = new File(wekaFilePath);
ArffLoader arf = new ArffLoader();
arf.setFile(inputFile);
Instances originIns = arf.getDataSet();
Instances insTest = new Instances(originIns);
insTest.deleteStringAttributes();
int totalNum = insTest.numInstances();
// SimpleKMeans sm = new SimpleKMeans();
EM em = new EM();
em.setNumClusters(clusterNum);
MakeDensityBasedClusterer sm = new MakeDensityBasedClusterer();
sm.setClusterer(em);
sm.buildClusterer(insTest);
System.out.println("totalNum:" + insTest.numInstances());
System.out.println("============================");
System.out.println(sm.toString());
Map<Integer, ArrayList<String>> result = new HashMap<Integer, ArrayList<String>>();
for (int i = 0; i < clusterNum; i++) {
result.put(i, new ArrayList<String>());
}
for (int i = 0; i < totalNum; i++) {
Instance ins = originIns.instance(i);
String word = ins.stringValue(0);
Instance tempIns = new Instance(ins);
tempIns.deleteAttributeAt(0);
int cluster = sm.clusterInstance(tempIns);
result.get(cluster).add(word);
}
// print the result
ArrayList<String> words = new ArrayList<String>();
JSONArray keyWords = new JSONArray();
for (int k : result.keySet()) {
words = result.get(k);
PriorityQueue<MyTerm> clusterQueue = new PriorityQueue<MyTerm>(1, MyTermCompare);
for (int i = 0; i < words.size(); i++) {
String s = words.get(i);
assert linkMap.containsKey(s);
int freq = linkMap.get(s).totalFreq;
clusterQueue.add(linkMap.get(s));
words.set(i, "(" + s + ":" + freq + ")");
}
JSONArray clusterArray = new JSONArray();
int num = clusterQueue.size() / 10 + 1; // 5%
int totalFreq = 0;
int totalLength = 0;
for (int i = 0; i < num && !clusterQueue.isEmpty(); ) {
JSONObject mem = new JSONObject();
MyTerm myTerm = clusterQueue.poll();
String word = myTerm.originTrem.text();
if (word.length() == 1) {
continue;
}
mem.put("text", word);
mem.put("freq", myTerm.totalFreq);
clusterArray.put(mem);
i++;
totalFreq += myTerm.totalFreq;
totalLength += word.length();
}
double averFreq = totalFreq * 1.0 / num;
double averLength = totalLength * 1.0 / num;
int count = 0;
while (!clusterQueue.isEmpty() && count < num) {
MyTerm myTerm = clusterQueue.poll();
String word = myTerm.originTrem.text();
int freq = myTerm.totalFreq;
int times = (int) (word.length() / averFreq) + 1;
if (freq > averFreq / times) {
JSONObject mem = new JSONObject();
mem.put("text", word);
mem.put("freq", freq);
mem.put("extra", true);
clusterArray.put(mem);
}
}
keyWords.put(clusterArray);
System.out.println(
"cluster" + k + ":" + words.size() + ":\t" + (int) (words.size() * 1.0 / totalNum * 100));
if (result.get(k).size() < 100) {
System.out.println(result.get(k));
}
}
// System.out.println("errorNum:"+errorNum);
return keyWords;
}