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Java example source code file (ml.xml)

This example Java source code file (ml.xml) 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.

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Java - Java tags/keywords

apache, asf, clusterable, dbscan, kmeans/kmeans, kmeansplusplusclusterer, learning, license, list, locationwrapper, machine, see, the, you

The ml.xml Java example source code

<?xml version="1.0"?>

<!--
   Licensed to the Apache Software Foundation (ASF) under one or more
  contributor license agreements.  See the NOTICE file distributed with
  this work for additional information regarding copyright ownership.
  The ASF licenses this file to You under the Apache License, Version 2.0
  (the "License"); you may not use this file except in compliance with
  the License.  You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.
  -->
  
<?xml-stylesheet type="text/xsl" href="./xdoc.xsl"?>
<document url="ml.html">

  <properties>
    <title>The Commons Math User Guide - Machine Learning
  </properties>

  <body>
    <section name="16 Machine Learning">
      <subsection name="16.1 Overview" href="overview">
        <p>
           Machine learning support in commons-math currently provides operations to cluster
           data sets based on a distance measure.
        </p>
      </subsection>
      <subsection name="16.2 Clustering algorithms and distance measures" href="clustering">
        <p>
          The <a href="../apidocs/org/apache/commons/math3/ml/clustering/Clusterer.html">
          Clusterer</a> class represents a clustering algorithm.
          The following algorithms are available:
          <ul>
          <li>KMeans++:
          It is based on the well-known kMeans algorithm, but uses a different method for 
          choosing the initial values (or "seeds") and thus avoids cases where KMeans sometimes 
          results in poor clusterings. KMeans/KMeans++ clustering aims to partition n observations 
          into k clusters in such that each point belongs to the cluster with the nearest center. 
          </li>
          <li>Fuzzy-KMeans:
          A variation of the classical K-Means algorithm, with the major difference that a single
          data point is not uniquely assigned to a single cluster. Instead, each point i has a set
          of weights u<sub>ij which indicate the degree of membership to the cluster j. The fuzzy
          variant does not require initial values for the cluster centers and is thus more robust, although
          slower than the original kMeans algorithm.
          </li>
          <li>DBSCAN:
          Density-based spatial clustering of applications with noise (DBSCAN) finds a number of 
          clusters starting from the estimated density distribution of corresponding nodes. The
          main advantages over KMeans/KMeans++ are that DBSCAN does not require the specification
          of an initial number of clusters and can find arbitrarily shaped clusters.
          </li>
          <li>Multi-KMeans++:
          Multi-KMeans++ is a meta algorithm that basically performs n runs using KMeans++ and then
          chooses the best clustering (i.e., the one with the lowest distance variance over all clusters)
          from those runs.
          </li>
          </ul>
        </p>
        <p>
          An comparison of the available clustering algorithms:<br/>
          <img src="../images/userguide/cluster_comparison.png" alt="Comparison of clustering algorithms"/>
        </p>
      </subsection>
      <subsection name="16.3 Distance measures" href="distance">
        <p>
          Each clustering algorithm requires a distance measure to determine the distance
          between two points (either data points or cluster centers).
          The following distance measures are available:
          <ul>
          <li>Canberra distance
          <li>ChebyshevDistance distance
          <li>EuclideanDistance distance
          <li>ManhattanDistance distance
          <li>Earth Mover's distance
          </ul>
        </p>
      </subsection>
      <subsection name="16.3 Example" href="example">
        <p>
        Here is an example of a clustering execution. Let us assume we have a set of locations from our domain model,
        where each location has a method <code>double getX() and double getY()
        representing their current coordinates in a 2-dimensional space. We want to cluster the locations into
        10 different clusters based on their euclidean distance.
        </p>
        <p>
        The cluster algorithms expect a list of <a href="../apidocs/org/apache/commons/math3/ml/cluster/Clusterable.html">Clusterable
        as input. Typically, we don't want to pollute our domain objects with interfaces from helper APIs.
        Hence, we first create a wrapper object:
        <source>
// wrapper class
public static class LocationWrapper implements Clusterable {
    private double[] points;
    private Location location;

    public LocationWrapper(Location location) {
        this.location = location;
        this.points = new double[] { location.getX(), location.getY() }
    }

    public Location getLocation() {
        return location;
    }

    public double[] getPoint() {
        return points;
    }
}
        </source>
        Now we will create a list of these wrapper objects (one for each location), 
        which serves as input to our clustering algorithm. 
        <source>
// we have a list of our locations we want to cluster. create a      
List<Location> locations = ...;
List<LocationWrapper> clusterInput = new ArrayList<LocationWrapper>(locations.size());
for (Location location : locations)
    clusterInput.add(new LocationWrapper(location));
        </source>
        Finally, we can apply our clustering algorithm and output the found clusters.
        <source>       
// initialize a new clustering algorithm. 
// we use KMeans++ with 10 clusters and 10000 iterations maximum.
// we did not specify a distance measure; the default (euclidean distance) is used.
KMeansPlusPlusClusterer<LocationWrapper> clusterer = new KMeansPlusPlusClusterer<LocationWrapper>(10, 10000);
List<CentroidCluster<LocationWrapper>> clusterResults = clusterer.cluster(clusterInput);

// output the clusters
for (int i=0; i<clusterResults.size(); i++) {
    System.out.println("Cluster " + i);
    for (LocationWrapper locationWrapper : clusterResults.get(i).getPoints())
        System.out.println(locationWrapper.getLocation());
    System.out.println();
}
        </source>
        </p>
      </subsection>
  </section>
  </body>
</document>

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