How to pass .dat file using JAVA HUgin API for EM learning.

[Ajay Tiwari]

Can anybody please tell me how to pass a .dat file for EM learning using JAVA HUGIN API.

[Martin]

Can anybody please tell me how to pass a .dat file for EM learning using JAVA HUGIN API.

This is the procedure for using EM-learning:
1. Create instance of Domain (either by Loading a NET-file or by manually construct the network from the code)

2. Load data (Domain.parseCases)

3. Compile domain (Domain.compile)

4. Run EM-algorithm (Domain.learnTables)

Here is example code for loading a random network with discrete chance nodes, parsing a random data file and running EM-algorithm for computing new maximal likelihoods for the CPTs. After learning, the new CPTs are printed.

Code: [Select]

import java.util.*;

import COM.hugin.HAPI.*;

class EMLearning {
    public static void main(String[] args) {
if (args.length < 2) {
    System.err.println("use arguments: <network.net> <data.dat>");
    return;
}
String netFile = args[0];
String dataFile = args[1];
try {
    //load domain
    Domain dom = new Domain(netFile, new DefaultClassParseListener());
   
    //compile using defaults
    dom.compile();

    NodeList nodes = dom.getNodes();
    ListIterator li = nodes.listIterator();
    while (li.hasNext()) {
Node n = (Node)li.next();
if (n instanceof DiscreteChanceNode) {
    //make sure that all discrete chance nodes have experience tables with entries set to 0
    //to compute maximal likelihood estimates of CPTs
    DiscreteChanceNode dcc = (DiscreteChanceNode)n;
    Table experience = dcc.getExperienceTable();
    int size = experience.getSize();
    for (int i = 0; i < size; i++) {
experience.setDataItem(i, 0.0);
    }
}
    }
   
    //load data file
    dom.parseCases(dataFile, new DefaultClassParseListener());

    /* use these for configuring when EM should terminate
    dom.setMaxNumberOfEMIterations(0);
    dom.setLogLikelihoodTolerance(0.0001);
    */
   
    dom.learnTables();

    //print CPTs after EM-learning
    System.out.println("New tables after EM-learning:");
    li = nodes.listIterator();
    while (li.hasNext()) {
Node n = (Node)li.next();
if (n instanceof DiscreteChanceNode) {
    DiscreteChanceNode dcc = (DiscreteChanceNode)n;
    Table CPT = dcc.getTable();
    printTable(CPT);
}
    }

} catch (ExceptionHugin eh) {
    System.err.println(eh);
}
    }

    //print tables for all discrete chance nodes
    public static void printTable (Table CPT) throws ExceptionHugin {
NodeList nodes = CPT.getNodes();
int[] configuration = new int[nodes.size()];
int tableSize = CPT.getSize();
for (int i = 0; i < tableSize; i++) {
    CPT.getConfiguration(configuration, i);
    for (int j = 0; j < nodes.size(); j++) {
Node n = (Node)nodes.get(j);
System.out.print(n.getName() + "=" + configuration[j] + " ");
    }
    System.out.println(":= " + CPT.getDataItem(i));
}
    }
}

Compile code with javac:
javac -classpath <path to hapiXX.jar> -d <dir to place compiled class files> <path to source files *.java>

And run with java:
java -classpath <path to hapiXX.jar>;<dir with compiled class files> -Djava.library.path=<path to dir with hapiXX.dll> EMLearning (arguments)

(where (arguments) are the netfile to load and the datafile to use for EM-learning, e.g. asia.dat datafile.dat)

For more specific details of the EM-learning functionally in Hugin check out the API-Manual section 11.6 Learning conditional probability tables.

For details on compiling with the Hugin Java API (and APIs for other languages) refer to the API-manual section 1.3 Using the HUGIN API on Windows platforms.

[kari]

Hi,
I tried to compile this with the instructions given but got three errors:

kari@kant:~$ javac -classpath /usr/local/hugin/lib64/hapi71-64.jar -d EMclassfiles EMlearning.java
EMlearning.java:29: possible loss of precision
found   : long
required: int
          int size = experience.getSize();
                                       ^
EMlearning.java:67: possible loss of precision
found   : long
required: int
   int tableSize = CPT.getSize();
                              ^
EMlearning.java:69: getConfiguration(long[],long) in COM.hugin.HAPI.Table cannot be applied to (int[],int)
       CPT.getConfiguration(configuration, i);
          ^
3 errors

Any suggestions how to get rid of them? I am running Hugin Developer 7.1

[Anders L Madsen]

Hi Kari,

You are trying to compile the example with the 64-bit version of the HUGIN Java API. To compile the example successfully you can either 1) use the 32-bit version of the HUGIN Java API or 2) change int to long in the following declarations

Code: [Select]

int size = experience.getSize();

Code: [Select]

int[] configuration = new int[nodes.size()];

Code: [Select]

int tableSize = CPT.getSize();

Code: [Select]

int i = 0;

[Lyceum]

Hi martin,

      do we parseCases before domain compile or after domain compile? based on your description parseCases should be called before compiling the domain, but the coding seem to be another way round.


     thanks

     In edit mode, there is a EM Learning Wizard button which allow me to select .dat file , set iteration and tolerance.
     In run mode, i will need to load the Data via "File->Load Case".

     so the domain.parseCases actually simulate the Load case in run mode? or the EM Learning in edit mode?

From
Thomas

[Martin]

The order of Domain.parseCases and Domain.compile does not matter.

When a set of cases has been loaded with Domain.parseCases the entire set can be used for doing EM Domain.learnTables(), and/or a single case can be entered as evidence in a compiled domain using Domain.enterCase(casenum).