public void compute() {
int n = A.columns();
// Distances to centroids
DoubleMatrix2D D = new DenseDoubleMatrix2D(k, n);
// Object-cluster assignments
V = new DenseDoubleMatrix2D(n, k);
// Initialize the centroids with some document vectors
U = new DenseDoubleMatrix2D(A.rows(), k);
U.assign(A.viewPart(0, 0, A.rows(), k));
int[] minIndices = new int[D.columns()];
double[] minValues = new double[D.columns()];
for (iterationsCompleted = 0; iterationsCompleted < maxIterations; iterationsCompleted++) {
// Calculate cosine distances
U.zMult(A, D, 1, 0, true, false);
V.assign(0);
U.assign(0);
// For each object
MatrixUtils.maxInColumns(D, minIndices, minValues);
for (int i = 0; i < minIndices.length; i++) {
V.setQuick(i, minIndices[i], 1);
}
// Update centroids
for (int c = 0; c < V.columns(); c++) {
// Sum
int count = 0;
for (int d = 0; d < V.rows(); d++) {
if (V.getQuick(d, c) != 0) {
count++;
U.viewColumn(c).assign(A.viewColumn(d), Functions.PLUS);
}
}
// Divide
U.viewColumn(c).assign(Mult.div(count));
MatrixUtils.normalizeColumnL2(U, null);
}
}
}
/**
* Builds a sparse term-document-like matrix for the provided matrixWordIndices in the same term
* space as the original term-document matrix.
*/
static DoubleMatrix2D buildAlignedMatrix(
VectorSpaceModelContext vsmContext, int[] featureIndex, ITermWeighting termWeighting) {
final IntIntHashMap stemToRowIndex = vsmContext.stemToRowIndex;
if (featureIndex.length == 0) {
return new DenseDoubleMatrix2D(stemToRowIndex.size(), 0);
}
final DoubleMatrix2D phraseMatrix =
new SparseDoubleMatrix2D(stemToRowIndex.size(), featureIndex.length);
final PreprocessingContext preprocessingContext = vsmContext.preprocessingContext;
final int[] wordsStemIndex = preprocessingContext.allWords.stemIndex;
final int[] stemsTf = preprocessingContext.allStems.tf;
final int[][] stemsTfByDocument = preprocessingContext.allStems.tfByDocument;
final int[][] phrasesWordIndices = preprocessingContext.allPhrases.wordIndices;
final int documentCount = preprocessingContext.documents.size();
final int wordCount = wordsStemIndex.length;
for (int i = 0; i < featureIndex.length; i++) {
final int feature = featureIndex[i];
final int[] wordIndices;
if (feature < wordCount) {
wordIndices = new int[] {feature};
} else {
wordIndices = phrasesWordIndices[feature - wordCount];
}
for (int wordIndex = 0; wordIndex < wordIndices.length; wordIndex++) {
final int stemIndex = wordsStemIndex[wordIndices[wordIndex]];
final int index = stemToRowIndex.indexOf(stemIndex);
if (stemToRowIndex.indexExists(index)) {
final int rowIndex = stemToRowIndex.indexGet(index);
double weight =
termWeighting.calculateTermWeight(
stemsTf[stemIndex], stemsTfByDocument[stemIndex].length / 2, documentCount);
phraseMatrix.setQuick(rowIndex, i, weight);
}
}
}
return phraseMatrix;
}
/**
* Builds a term-phrase matrix in the same space as the main term-document matrix. If the
* processing context contains no phrases, {@link VectorSpaceModelContext#termPhraseMatrix} will
* remain <code>null</code>.
*/
public void buildTermPhraseMatrix(VectorSpaceModelContext context) {
final PreprocessingContext preprocessingContext = context.preprocessingContext;
final IntIntHashMap stemToRowIndex = context.stemToRowIndex;
final int[] labelsFeatureIndex = preprocessingContext.allLabels.featureIndex;
final int firstPhraseIndex = preprocessingContext.allLabels.firstPhraseIndex;
if (firstPhraseIndex >= 0 && stemToRowIndex.size() > 0) {
// Build phrase matrix
int[] phraseFeatureIndices = new int[labelsFeatureIndex.length - firstPhraseIndex];
for (int featureIndex = 0; featureIndex < phraseFeatureIndices.length; featureIndex++) {
phraseFeatureIndices[featureIndex] = labelsFeatureIndex[featureIndex + firstPhraseIndex];
}
final DoubleMatrix2D phraseMatrix =
TermDocumentMatrixBuilder.buildAlignedMatrix(
context, phraseFeatureIndices, termWeighting);
MatrixUtils.normalizeColumnL2(phraseMatrix, null);
context.termPhraseMatrix = phraseMatrix.viewDice();
}
}
/**
* A native implementation of Colt's original multiplication method method.
*
* <p>NOTE: this method will use native calls only when:
*
* <ul>
* <li>all input matrices are @link DenseDoubleMatrix2D or its subclasses (e.g. @link
* NNIDenseDoubleMatrix2D)
* <li>none of the input matrices is a view
* <li>the dynamic libraries required by the NNI are available
* </ul>
*/
public DoubleMatrix2D zMult(
DoubleMatrix2D B,
DoubleMatrix2D C,
double alpha,
double beta,
boolean transposeA,
boolean transposeB) {
// A workaround for a bug in DenseDoubleMatrix2D.
// If B is a SelectedDenseDoubleMatrix the implementation of this method
// throws a ClassCastException. The workaround is to swap and transpose
// the arguments and then transpose the result. As SelectedDenseDoubleMatrix2D is
// package-private, if it was loaded with a different class loader than
// the one used for this class it would give a VerificationError if we referred
// to it directly here. Hence the hacky string comparison here.
//
if (B.getClass().getName().endsWith("SelectedDenseDoubleMatrix2D")) {
return B.zMult(this, C, alpha, beta, !transposeB, !transposeA).viewDice();
}
// Check the sizes
int rowsB = (transposeB ? B.columns() : B.rows());
int columnsB = (transposeB ? B.rows() : B.columns());
int rowsA = (transposeA ? columns() : rows());
int columnsA = (transposeA ? rows() : columns());
if (C == null) {
C = new NNIDenseDoubleMatrix2D(rowsA, columnsB);
}
if (this == C || B == C) {
throw new IllegalArgumentException("Matrices must not be identical");
}
final int rowsC = C.rows();
final int columnsC = C.columns();
if (rowsB != columnsA) {
throw new IllegalArgumentException(
"Matrix2D inner dimensions must agree:" + toStringShort() + ", " + B.toStringShort());
}
if (rowsC != rowsA || columnsC != columnsB) {
throw new IllegalArgumentException(
"Incompatibile result matrix: "
+ toStringShort()
+ ", "
+ B.toStringShort()
+ ", "
+ C.toStringShort());
}
// Need native BLAS, dense matrices and no views to operate
// Default to Colt's implementation otherwise
if (!NNIInterface.isNativeBlasAvailable()
|| (!(B instanceof NNIDenseDoubleMatrix2D))
|| (!(C instanceof NNIDenseDoubleMatrix2D))
|| isView()
|| ((NNIDenseDoubleMatrix2D) B).isView()
|| ((NNIDenseDoubleMatrix2D) C).isView()) {
return super.zMult(B, C, alpha, beta, transposeA, transposeB);
}
NNIInterface.getBlas()
.gemm(
this,
(NNIDenseDoubleMatrix2D) B,
(NNIDenseDoubleMatrix2D) C,
transposeA,
transposeB,
columnsA,
alpha,
columns,
beta);
return C;
}
/**
* Builds a term document matrix from data provided in the <code>context</code>, stores the result
* in there.
*/
public void buildTermDocumentMatrix(VectorSpaceModelContext vsmContext) {
final PreprocessingContext preprocessingContext = vsmContext.preprocessingContext;
final int documentCount = preprocessingContext.documents.size();
final int[] stemsTf = preprocessingContext.allStems.tf;
final int[][] stemsTfByDocument = preprocessingContext.allStems.tfByDocument;
final byte[] stemsFieldIndices = preprocessingContext.allStems.fieldIndices;
if (documentCount == 0) {
vsmContext.termDocumentMatrix = new DenseDoubleMatrix2D(0, 0);
vsmContext.stemToRowIndex = new IntIntHashMap();
return;
}
// Determine the index of the title field
int titleFieldIndex = -1;
final String[] fieldsName = preprocessingContext.allFields.name;
for (int i = 0; i < fieldsName.length; i++) {
if (Document.TITLE.equals(fieldsName[i])) {
titleFieldIndex = i;
break;
}
}
// Determine the stems we, ideally, should include in the matrix
int[] stemsToInclude = computeRequiredStemIndices(preprocessingContext);
// Sort stems by weight, so that stems get included in the matrix in the order
// of frequency
final double[] stemsWeight = new double[stemsToInclude.length];
for (int i = 0; i < stemsToInclude.length; i++) {
final int stemIndex = stemsToInclude[i];
stemsWeight[i] =
termWeighting.calculateTermWeight(
stemsTf[stemIndex], stemsTfByDocument[stemIndex].length / 2, documentCount)
* getWeightBoost(titleFieldIndex, stemsFieldIndices[stemIndex]);
}
final int[] stemWeightOrder =
IndirectSort.mergesort(
0, stemsWeight.length, new IndirectComparator.DescendingDoubleComparator(stemsWeight));
// Calculate the number of terms we can include to fulfill the max matrix size
final int maxRows = maximumMatrixSize / documentCount;
final DoubleMatrix2D tdMatrix =
new DenseDoubleMatrix2D(Math.min(maxRows, stemsToInclude.length), documentCount);
for (int i = 0; i < stemWeightOrder.length && i < maxRows; i++) {
final int stemIndex = stemsToInclude[stemWeightOrder[i]];
final int[] tfByDocument = stemsTfByDocument[stemIndex];
final int df = tfByDocument.length / 2;
final byte fieldIndices = stemsFieldIndices[stemIndex];
for (int j = 0; j < df; j++) {
double weight =
termWeighting.calculateTermWeight(tfByDocument[j * 2 + 1], df, documentCount);
weight *= getWeightBoost(titleFieldIndex, fieldIndices);
tdMatrix.set(i, tfByDocument[j * 2], weight);
}
}
// Convert stemsToInclude into tdMatrixStemIndices
final IntIntHashMap stemToRowIndex = new IntIntHashMap();
for (int i = 0; i < stemWeightOrder.length && i < tdMatrix.rows(); i++) {
stemToRowIndex.put(stemsToInclude[stemWeightOrder[i]], i);
}
// Store the results
vsmContext.termDocumentMatrix = tdMatrix;
vsmContext.stemToRowIndex = stemToRowIndex;
}