org.carrot2.clustering.kmeans.BisectingKMeansClusteringAlgorithm Maven / Gradle / Ivy
/*
* Carrot2 project.
*
* Copyright (C) 2002-2016, Dawid Weiss, Stanisław Osiński.
* All rights reserved.
*
* Refer to the full license file "carrot2.LICENSE"
* in the root folder of the repository checkout or at:
* http://www.carrot2.org/carrot2.LICENSE
*/
package org.carrot2.clustering.kmeans;
import java.util.Collections;
import java.util.Comparator;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.lang.ObjectUtils;
import org.carrot2.core.Cluster;
import org.carrot2.core.Document;
import org.carrot2.core.IClusteringAlgorithm;
import org.carrot2.core.LanguageCode;
import org.carrot2.core.ProcessingComponentBase;
import org.carrot2.core.ProcessingException;
import org.carrot2.core.attribute.AttributeNames;
import org.carrot2.core.attribute.CommonAttributes;
import org.carrot2.core.attribute.Init;
import org.carrot2.core.attribute.Internal;
import org.carrot2.core.attribute.Processing;
import org.carrot2.text.analysis.ITokenizer;
import org.carrot2.text.clustering.IMonolingualClusteringAlgorithm;
import org.carrot2.text.clustering.MultilingualClustering;
import org.carrot2.text.preprocessing.LabelFormatter;
import org.carrot2.text.preprocessing.PreprocessingContext;
import org.carrot2.text.preprocessing.pipeline.BasicPreprocessingPipeline;
import org.carrot2.text.preprocessing.pipeline.IPreprocessingPipeline;
import org.carrot2.text.vsm.ReducedVectorSpaceModelContext;
import org.carrot2.text.vsm.TermDocumentMatrixBuilder;
import org.carrot2.text.vsm.TermDocumentMatrixReducer;
import org.carrot2.text.vsm.VectorSpaceModelContext;
import org.carrot2.util.attribute.Attribute;
import org.carrot2.util.attribute.AttributeLevel;
import org.carrot2.util.attribute.Bindable;
import org.carrot2.util.attribute.DefaultGroups;
import org.carrot2.util.attribute.Group;
import org.carrot2.util.attribute.Input;
import org.carrot2.util.attribute.Label;
import org.carrot2.util.attribute.Level;
import org.carrot2.util.attribute.Output;
import org.carrot2.util.attribute.Required;
import org.carrot2.util.attribute.constraint.ImplementingClasses;
import org.carrot2.util.attribute.constraint.IntRange;
import com.carrotsearch.hppc.IntArrayList;
import com.carrotsearch.hppc.IntIntHashMap;
import com.carrotsearch.hppc.IntIntMap;
import com.carrotsearch.hppc.cursors.IntCursor;
import com.carrotsearch.hppc.cursors.IntIntCursor;
import com.carrotsearch.hppc.sorting.IndirectComparator;
import com.carrotsearch.hppc.sorting.IndirectSort;
import org.carrot2.mahout.math.function.Functions;
import org.carrot2.mahout.math.matrix.DoubleMatrix1D;
import org.carrot2.mahout.math.matrix.DoubleMatrix2D;
import org.carrot2.mahout.math.matrix.impl.DenseDoubleMatrix1D;
import org.carrot2.mahout.math.matrix.impl.DenseDoubleMatrix2D;
import org.carrot2.shaded.guava.common.collect.Lists;
/**
* A very simple implementation of bisecting k-means clustering. Unlike other algorithms
* in Carrot2, this one creates hard clusterings (one document belongs only to one
* cluster). On the other hand, the clusters are labeled only with individual words that
* may not always fully correspond to all documents in the cluster.
*/
@Bindable(prefix = "BisectingKMeansClusteringAlgorithm", inherit = CommonAttributes.class)
public class BisectingKMeansClusteringAlgorithm extends ProcessingComponentBase implements
IClusteringAlgorithm
{
/** {@link Group} name. */
private final static String GROUP_KMEANS = "K-means";
@Processing
@Input
@Required
@Internal
@Attribute(key = AttributeNames.DOCUMENTS, inherit = true)
public List documents;
@Processing
@Output
@Internal
@Attribute(key = AttributeNames.CLUSTERS, inherit = true)
public List clusters = null;
/**
* The number of clusters to create. The algorithm will create at most the specified
* number of clusters.
*/
@Processing
@Input
@Attribute
@IntRange(min = 2)
@Group(DefaultGroups.CLUSTERS)
@Level(AttributeLevel.BASIC)
@Label("Cluster count")
public int clusterCount = 25;
/**
* The maximum number of k-means iterations to perform.
*/
@Processing
@Input
@Attribute
@IntRange(min = 1)
@Group(GROUP_KMEANS)
@Level(AttributeLevel.BASIC)
@Label("Maximum iterations")
public int maxIterations = 15;
/**
* Use dimensionality reduction. If true, k-means will be applied on the
* dimensionality-reduced term-document matrix with the number of dimensions being
* equal to twice the number of requested clusters. If the number of dimensions is
* lower than the number of input documents, reduction will not be performed.
* If false, the k-means will
* be performed directly on the original term-document matrix.
*/
@Processing
@Input
@Attribute
@Group(GROUP_KMEANS)
@Level(AttributeLevel.BASIC)
@Label("Use dimensionality reduction")
public boolean useDimensionalityReduction = true;
/**
* Partition count. The number of partitions to create at each k-means clustering
* iteration.
*/
@Processing
@Input
@Attribute
@IntRange(min = 2, max = 10)
@Group(GROUP_KMEANS)
@Level(AttributeLevel.BASIC)
@Label("Partition count")
public int partitionCount = 2;
/**
* Label count. The minimum number of labels to return for each cluster.
*/
@Processing
@Input
@Attribute
@IntRange(min = 1, max = 10)
@Group(DefaultGroups.CLUSTERS)
@Level(AttributeLevel.BASIC)
@Label("Label count")
public int labelCount = 3;
/**
* Common preprocessing tasks handler.
*/
@Init
@Input
@Attribute
@Internal
@ImplementingClasses(classes = {}, strict = false)
@Level(AttributeLevel.ADVANCED)
public IPreprocessingPipeline preprocessingPipeline = new BasicPreprocessingPipeline();
/**
* Term-document matrix builder for the algorithm, contains bindable attributes.
*/
public final TermDocumentMatrixBuilder matrixBuilder = new TermDocumentMatrixBuilder();
/**
* Term-document matrix reducer for the algorithm, contains bindable attributes.
*/
public final TermDocumentMatrixReducer matrixReducer = new TermDocumentMatrixReducer();
/**
* Cluster label formatter, contains bindable attributes.
*/
public final LabelFormatter labelFormatter = new LabelFormatter();
/**
* A helper for performing multilingual clustering.
*/
public final MultilingualClustering multilingualClustering = new MultilingualClustering();
@Override
public void process() throws ProcessingException
{
// There is a tiny trick here to support multilingual clustering without
// refactoring the whole component: we remember the original list of documents
// and invoke clustering for each language separately within the
// IMonolingualClusteringAlgorithm implementation below. This is safe because
// processing components are not thread-safe by definition and
// IMonolingualClusteringAlgorithm forbids concurrent execution by contract.
final List originalDocuments = documents;
clusters = multilingualClustering.process(documents,
new IMonolingualClusteringAlgorithm()
{
public List process(List documents, LanguageCode language)
{
BisectingKMeansClusteringAlgorithm.this.documents = documents;
BisectingKMeansClusteringAlgorithm.this.cluster(language);
return BisectingKMeansClusteringAlgorithm.this.clusters;
}
});
documents = originalDocuments;
}
/**
* Perform clustering for a given language.
*/
protected void cluster(LanguageCode language)
{
// Preprocessing of documents
final PreprocessingContext preprocessingContext =
preprocessingPipeline.preprocess(documents, null, language);
// Add trivial AllLabels so that we can reuse the common TD matrix builder
final int [] stemsMfow = preprocessingContext.allStems.mostFrequentOriginalWordIndex;
final short [] wordsType = preprocessingContext.allWords.type;
final IntArrayList featureIndices = new IntArrayList(stemsMfow.length);
for (int i = 0; i < stemsMfow.length; i++)
{
final short flag = wordsType[stemsMfow[i]];
if ((flag & (ITokenizer.TF_COMMON_WORD | ITokenizer.TF_QUERY_WORD | ITokenizer.TT_NUMERIC)) == 0)
{
featureIndices.add(stemsMfow[i]);
}
}
preprocessingContext.allLabels.featureIndex = featureIndices.toArray();
preprocessingContext.allLabels.firstPhraseIndex = -1;
// Further processing only if there are words to process
clusters = Lists.newArrayList();
if (preprocessingContext.hasLabels())
{
// Term-document matrix building and reduction
final VectorSpaceModelContext vsmContext = new VectorSpaceModelContext(
preprocessingContext);
final ReducedVectorSpaceModelContext reducedVsmContext = new ReducedVectorSpaceModelContext(
vsmContext);
matrixBuilder.buildTermDocumentMatrix(vsmContext);
matrixBuilder.buildTermPhraseMatrix(vsmContext);
// Prepare rowIndex -> stemIndex mapping for labeling
final IntIntHashMap rowToStemIndex = new IntIntHashMap();
for (IntIntCursor c : vsmContext.stemToRowIndex)
{
rowToStemIndex.put(c.value, c.key);
}
final DoubleMatrix2D tdMatrix;
if (useDimensionalityReduction && clusterCount * 2 < preprocessingContext.documents.size())
{
matrixReducer.reduce(reducedVsmContext, clusterCount * 2);
tdMatrix = reducedVsmContext.coefficientMatrix.viewDice();
}
else
{
tdMatrix = vsmContext.termDocumentMatrix;
}
// Initial selection containing all columns, initial clustering
final IntArrayList columns = new IntArrayList(tdMatrix.columns());
for (int c = 0; c < tdMatrix.columns(); c++)
{
columns.add(c);
}
final List rawClusters = Lists.newArrayList();
rawClusters.addAll(split(partitionCount, tdMatrix, columns, maxIterations));
Collections.sort(rawClusters, BY_SIZE_DESCENDING);
int largestIndex = 0;
while (rawClusters.size() < clusterCount && largestIndex < rawClusters.size())
{
// Find largest cluster to split
IntArrayList largest = rawClusters.get(largestIndex);
if (largest.size() <= partitionCount * 2)
{
// No cluster is large enough to produce a meaningful
// split (i.e. a split into subclusters with more than
// 1 member).
break;
}
final List split = split(partitionCount, tdMatrix, largest,
maxIterations);
if (split.size() > 1)
{
rawClusters.remove(largestIndex);
rawClusters.addAll(split);
Collections.sort(rawClusters, BY_SIZE_DESCENDING);
largestIndex = 0;
}
else
{
largestIndex++;
}
}
for (int i = 0; i < rawClusters.size(); i++)
{
final Cluster cluster = new Cluster();
final IntArrayList rawCluster = rawClusters.get(i);
if (rawCluster.size() > 1)
{
cluster.addPhrases(getLabels(rawCluster,
vsmContext.termDocumentMatrix, rowToStemIndex,
preprocessingContext.allStems.mostFrequentOriginalWordIndex,
preprocessingContext.allWords.image));
for (int j = 0; j < rawCluster.size(); j++)
{
cluster.addDocuments(documents.get(rawCluster.get(j)));
}
clusters.add(cluster);
}
}
}
Collections.sort(clusters, Cluster.BY_REVERSED_SIZE_AND_LABEL_COMPARATOR);
Cluster.appendOtherTopics(documents, clusters);
}
private static final Comparator BY_SIZE_DESCENDING = new Comparator()
{
@Override
public int compare(IntArrayList o1, IntArrayList o2)
{
// We don't expect very large sizes here.
return o2.size() - o1.size();
}
};
private List getLabels(IntArrayList documents,
DoubleMatrix2D termDocumentMatrix, IntIntHashMap rowToStemIndex,
int [] mostFrequentOriginalWordIndex, char [][] wordImage)
{
// Prepare a centroid. If dimensionality reduction was used,
// the centroid from k-means will not be based on real terms,
// so we need to calculate the centroid here once again based
// on the cluster's documents.
final DoubleMatrix1D centroid = new DenseDoubleMatrix1D(termDocumentMatrix.rows());
for (IntCursor d : documents)
{
centroid.assign(termDocumentMatrix.viewColumn(d.value), Functions.PLUS);
}
final List labels = Lists.newArrayListWithCapacity(labelCount);
final int [] order = IndirectSort.mergesort(0, centroid.size(),
new IndirectComparator()
{
@Override
public int compare(int a, int b)
{
final double valueA = centroid.get(a);
final double valueB = centroid.get(b);
return valueA < valueB ? -1 : valueA > valueB ? 1 : 0;
}
});
final double minValueForLabel = centroid.get(order[order.length
- Math.min(labelCount, order.length)]);
for (int i = 0; i < centroid.size(); i++)
{
if (centroid.getQuick(i) >= minValueForLabel)
{
labels.add(LabelFormatter.format(new char [] []
{
wordImage[mostFrequentOriginalWordIndex[rowToStemIndex.get(i)]]
}, new boolean []
{
false
}, false));
}
}
return labels;
}
/**
* Splits the input documents into the specified number of partitions using the
* standard k-means routine.
*/
private List split(int partitions, DoubleMatrix2D input,
IntArrayList columns, int iterations)
{
// Prepare selected matrix
final DoubleMatrix2D selected = input.viewSelection(null, columns.toArray())
.copy();
final IntIntMap selectedToInput = new IntIntHashMap(selected.columns());
for (int i = 0; i < columns.size(); i++)
{
selectedToInput.put(i, columns.get(i));
}
// Prepare results holders
List result = Lists.newArrayList();
List previousResult = null;
for (int i = 0; i < partitions; i++)
{
result.add(new IntArrayList(selected.columns()));
}
for (int i = 0; i < selected.columns(); i++)
{
result.get(i % partitions).add(i);
}
// Matrices for centroids and document-centroid similarities
final DoubleMatrix2D centroids = new DenseDoubleMatrix2D(selected.rows(),
partitions).assign(selected.viewPart(0, 0, selected.rows(), partitions));
final DoubleMatrix2D similarities = new DenseDoubleMatrix2D(partitions,
selected.columns());
// Run a fixed number of K-means iterations
for (int it = 0; it < iterations; it++)
{
// Update centroids
for (int i = 0; i < result.size(); i++)
{
final IntArrayList cluster = result.get(i);
for (int k = 0; k < selected.rows(); k++)
{
double sum = 0;
for (int j = 0; j < cluster.size(); j++)
{
sum += selected.get(k, cluster.get(j));
}
centroids.setQuick(k, i, sum / cluster.size());
}
}
previousResult = result;
result = Lists.newArrayList();
for (int i = 0; i < partitions; i++)
{
result.add(new IntArrayList(selected.columns()));
}
// Calculate similarity to centroids
centroids.zMult(selected, similarities, 1, 0, true, false);
// Assign documents to the nearest centroid
for (int c = 0; c < similarities.columns(); c++)
{
int maxRow = 0;
double max = similarities.get(0, c);
for (int r = 1; r < similarities.rows(); r++)
{
if (max < similarities.get(r, c))
{
max = similarities.get(r, c);
maxRow = r;
}
}
result.get(maxRow).add(c);
}
if (ObjectUtils.equals(previousResult, result))
{
// Unchanged result
break;
}
}
// Map the results back to the global indices
for (Iterator it = result.iterator(); it.hasNext();)
{
final IntArrayList cluster = it.next();
if (cluster.isEmpty())
{
it.remove();
}
else
{
for (int j = 0; j < cluster.size(); j++)
{
cluster.set(j, selectedToInput.get(cluster.get(j)));
}
}
}
return result;
}
}
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