smile.mds.MDS Maven / Gradle / Ivy
/*******************************************************************************
* Copyright (c) 2010 Haifeng Li
*
* Licensed 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.
*******************************************************************************/
package smile.mds;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import smile.math.Math;
import smile.math.matrix.Matrix;
import smile.math.matrix.DenseMatrix;
import smile.math.matrix.EVD;
/**
* Classical multidimensional scaling, also known as principal coordinates
* analysis. Given a matrix of dissimilarities (e.g. pairwise distances), MDS
* finds a set of points in low dimensional space that well-approximates the
* dissimilarities in A. We are not restricted to using a Euclidean
* distance metric. However, when Euclidean distances are used MDS is
* equivalent to PCA.
*
* @see smile.projection.PCA
* @see SammonMapping
*
* @author Haifeng Li
*/
public class MDS {
private static final Logger logger = LoggerFactory.getLogger(MDS.class);
/**
* Component scores.
*/
private double[] eigenvalues;
/**
* Coordinate matrix.
*/
private double[][] coordinates;
/**
* The proportion of variance contained in each principal component.
*/
private double[] proportion;
/**
* Returns the component scores, ordered from largest to smallest.
*/
public double[] getEigenValues() {
return eigenvalues;
}
/**
* Returns the proportion of variance contained in each eigenvectors,
* ordered from largest to smallest.
*/
public double[] getProportion() {
return proportion;
}
/**
* Returns the principal coordinates of projected data.
*/
public double[][] getCoordinates() {
return coordinates;
}
/**
* Constructor. Learn the classical multidimensional scaling.
* Map original data into 2-dimensional Euclidean space.
* @param proximity the nonnegative proximity matrix of dissimilarities. The
* diagonal should be zero and all other elements should be positive and
* symmetric. For pairwise distances matrix, it should be just the plain
* distance, not squared.
*/
public MDS(double[][] proximity) {
this(proximity, 2);
}
/**
* Constructor. Learn the classical multidimensional scaling.
* @param proximity the nonnegative proximity matrix of dissimilarities. The
* diagonal should be zero and all other elements should be positive and
* symmetric. For pairwise distances matrix, it should be just the plain
* distance, not squared.
* @param k the dimension of the projection.
*/
public MDS(double[][] proximity, int k) {
this(proximity, k, false);
}
/**
* Constructor. Learn the classical multidimensional scaling.
* @param proximity the nonnegative proximity matrix of dissimilarities. The
* diagonal should be zero and all other elements should be positive and
* symmetric. For pairwise distances matrix, it should be just the plain
* distance, not squared.
* @param k the dimension of the projection.
* @param add true to estimate an appropriate constant to be added
* to all the dissimilarities, apart from the self-dissimilarities, that
* makes the learning matrix positive semi-definite. The other formulation of
* the additive constant problem is as follows. If the proximity is
* measured in an interval scale, where there is no natural origin, then there
* is not a sympathy of the dissimilarities to the distances in the Euclidean
* space used to represent the objects. In this case, we can estimate a constant c
* such that proximity + c may be taken as ratio data, and also possibly
* to minimize the dimensionality of the Euclidean space required for
* representing the objects.
*/
public MDS(double[][] proximity, int k, boolean add) {
int m = proximity.length;
int n = proximity[0].length;
if (m != n) {
throw new IllegalArgumentException("The proximity matrix is not square.");
}
if (k < 1 || k >= n) {
throw new IllegalArgumentException("Invalid k = " + k);
}
DenseMatrix A = Matrix.zeros(n, n);
DenseMatrix B = Matrix.zeros(n, n);
for (int i = 0; i < n; i++) {
for (int j = 0; j < i; j++) {
double x = -0.5 * Math.sqr(proximity[i][j]);
A.set(i, j, x);
A.set(j, i, x);
}
}
double[] mean = A.rowMeans();
double mu = Math.mean(mean);
for (int i = 0; i < n; i++) {
for (int j = 0; j <= i; j++) {
double x = A.get(i, j) - mean[i] - mean[j] + mu;
B.set(i, j, x);
B.set(j, i, x);;
}
}
if (add) {
DenseMatrix Z = Matrix.zeros(2 * n, 2 * n);
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
Z.set(i, n + j, 2 * B.get(i, j));
}
}
for (int i = 0; i < n; i++) {
Z.set(n + i, i, -1);
}
mean = Math.rowMeans(proximity);
mu = Math.mean(mean);
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
Z.set(n + i, n + j, 2 * (proximity[i][j] - mean[i] - mean[j] + mu));
}
}
double[] evalues = Z.eig();
double c = Math.max(evalues);
for (int i = 0; i < n; i++) {
B.set(i, i, 0.0);
for (int j = 0; j < i; j++) {
double x = -0.5 * Math.sqr(proximity[i][j] + c);
B.set(i, j, x);
B.set(j, i, x);
}
}
}
B.setSymmetric(true);
EVD eigen = B.eigen(k);
if (eigen.getEigenValues().length < k) {
logger.warn("eigen({}) returns only {} eigen vectors", k, eigen.getEigenValues().length);
k = eigen.getEigenValues().length;
}
coordinates = new double[n][k];
for (int j = 0; j < k; j++) {
if (eigen.getEigenValues()[j] < 0) {
throw new IllegalArgumentException(String.format("Some of the first %d eigenvalues are < 0.", k));
}
double scale = Math.sqrt(eigen.getEigenValues()[j]);
for (int i = 0; i < n; i++) {
coordinates[i][j] = eigen.getEigenVectors().get(i, j) * scale;
}
}
eigenvalues = eigen.getEigenValues();
proportion = eigenvalues.clone();
Math.unitize1(proportion);
}
}
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