smile.classification.RDA 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.classification;
import java.io.Serializable;
import java.util.Arrays;
import smile.math.Math;
import smile.math.matrix.Matrix;
import smile.math.matrix.DenseMatrix;
import smile.math.matrix.EVD;
/**
* Regularized discriminant analysis. RDA is a compromise between LDA and QDA,
* which allows one to shrink the separate covariances of QDA toward a common
* variance as in LDA. This method is very similar in flavor to ridge regression.
* The regularized covariance matrices of each class is
* Σk(α) = α Σk + (1 - α) Σ.
* The quadratic discriminant function is defined using the shrunken covariance
* matrices Σk(α). The parameter α in [0, 1]
* controls the complexity of the model. When α is one, RDA becomes QDA.
* While α is zero, RDA is equivalent to LDA. Therefore, the
* regularization factor α allows a continuum of models between LDA and QDA.
*
* @see LDA
* @see QDA
*
* @author Haifeng Li
*/
public class RDA implements SoftClassifier, Serializable {
private static final long serialVersionUID = 1L;
/**
* The dimensionality of data.
*/
private int p;
/**
* The number of classes.
*/
private int k;
/**
* Constant term of discriminant function of each class.
*/
private final double[] ct;
/**
* A priori probabilities of each class.
*/
private double[] priori;
/**
* Mean vectors of each class.
*/
private double[][] mu;
/**
* Eigen vectors of each covariance matrix, which transforms observations
* to discriminant functions, normalized so that within groups covariance
* matrix is spherical.
*/
private DenseMatrix[] scaling;
/**
* Eigen values of each covariance matrix.
*/
private double[][] ev;
/**
* Trainer for regularized discriminant analysis.
*/
public static class Trainer extends ClassifierTrainer {
/**
* Regularization factor in [0, 1] allows a continuum of models
* between LDA and QDA.
*/
private double alpha;
/**
* A priori probabilities of each class.
*/
private double[] priori;
/**
* A tolerance to decide if a covariance matrix is singular. The trainer
* will reject variables whose variance is less than tol2.
*/
private double tol = 1E-4;
/**
* Constructor. The default tolerance to covariance matrix singularity
* is 1E-4.
*
* @param alpha regularization factor in [0, 1] allows a continuum of
* models between LDA and QDA.
*/
public Trainer(double alpha) {
if (alpha < 0.0 || alpha > 1.0) {
throw new IllegalArgumentException("Invalid regularization factor: " + alpha);
}
this.alpha = alpha;
}
/**
* Sets a priori probabilities of each class.
* @param priori a priori probabilities of each class.
*/
public Trainer setPriori(double[] priori) {
this.priori = priori;
return this;
}
/**
* Sets covariance matrix singular tolerance.
*
* @param tol a tolerance to decide if a covariance matrix is singular.
* The trainer will reject variables whose variance is less than tol2.
*/
public Trainer setTolerance(double tol) {
if (tol < 0.0) {
throw new IllegalArgumentException("Invalid tol: " + tol);
}
this.tol = tol;
return this;
}
@Override
public RDA train(double[][] x, int[] y) {
return new RDA(x, y, priori, alpha, tol);
}
}
/**
* Constructor. Learn regularized discriminant analysis.
* @param x training samples.
* @param y training labels in [0, k), where k is the number of classes.
* @param alpha regularization factor in [0, 1] allows a continuum of models
* between LDA and QDA.
*/
public RDA(double[][] x, int[] y, double alpha) {
this(x, y, null, alpha);
}
/**
* Constructor. Learn regularized discriminant analysis.
* @param x training samples.
* @param y training labels in [0, k), where k is the number of classes.
* @param alpha regularization factor in [0, 1] allows a continuum of models
* between LDA and QDA.
* @param priori the priori probability of each class.
*/
public RDA(double[][] x, int[] y, double[] priori, double alpha) {
this(x, y, priori, alpha, 1E-4);
}
/**
* Constructor. Learn regularized discriminant analysis.
* @param x training samples.
* @param y training labels in [0, k), where k is the number of classes.
* @param alpha regularization factor in [0, 1] allows a continuum of models
* between LDA and QDA.
* @param priori the priori probability of each class.
* @param tol tolerance to decide if a covariance matrix is singular; it
* will reject variables whose variance is less than tol2.
*/
public RDA(double[][] x, int[] y, double[] priori, double alpha, double tol) {
if (x.length != y.length) {
throw new IllegalArgumentException(String.format("The sizes of X and Y don't match: %d != %d", x.length, y.length));
}
if (alpha < 0.0 || alpha > 1.0) {
throw new IllegalArgumentException("Invalid regularization factor: " + alpha);
}
if (priori != null) {
if (priori.length < 2) {
throw new IllegalArgumentException("Invalid number of priori probabilities: " + priori.length);
}
double sum = 0.0;
for (double pr : priori) {
if (pr <= 0.0 || pr >= 1.0) {
throw new IllegalArgumentException("Invalid priori probability: " + pr);
}
sum += pr;
}
if (Math.abs(sum - 1.0) > 1E-10) {
throw new IllegalArgumentException("The sum of priori probabilities is not one: " + sum);
}
}
// class label set.
int[] labels = Math.unique(y);
Arrays.sort(labels);
for (int i = 0; i < labels.length; i++) {
if (labels[i] < 0) {
throw new IllegalArgumentException("Negative class label: " + labels[i]);
}
if (i > 0 && labels[i] - labels[i-1] > 1) {
throw new IllegalArgumentException("Missing class: " + labels[i]+1);
}
}
k = labels.length;
if (k < 2) {
throw new IllegalArgumentException("Only one class.");
}
if (priori != null && k != priori.length) {
throw new IllegalArgumentException("The number of classes and the number of priori probabilities don't match.");
}
if (tol < 0.0) {
throw new IllegalArgumentException("Invalid tol: " + tol);
}
final int n = x.length;
if (n <= k) {
throw new IllegalArgumentException(String.format("Sample size is too small: %d <= %d", n, k));
}
p = x[0].length;
// The number of instances in each class.
int[] ni = new int[k];
// Common mean vector.
double[] mean = Math.colMeans(x);
// Common covariance.
DenseMatrix C = Matrix.zeros(p, p);
// Class mean vectors.
mu = new double[k][p];
// Class covarainces.
DenseMatrix[] cov = new DenseMatrix[k];
for (int i = 0; i < n; i++) {
int c = y[i];
ni[c]++;
for (int j = 0; j < p; j++) {
mu[c][j] += x[i][j];
}
}
for (int i = 0; i < k; i++) {
if (ni[i] <= 1) {
throw new IllegalArgumentException(String.format("Class %d has only one sample.", i));
}
cov[i] = Matrix.zeros(p, p);
for (int j = 0; j < p; j++) {
mu[i][j] /= ni[i];
}
}
if (priori == null) {
priori = new double[k];
for (int i = 0; i < k; i++) {
priori[i] = (double) ni[i] / n;
}
}
this.priori = priori;
for (int i = 0; i < n; i++) {
int c = y[i];
for (int j = 0; j < p; j++) {
for (int l = 0; l <= j; l++) {
cov[c].add(j, l, (x[i][j] - mu[c][j]) * (x[i][l] - mu[c][l]));
C.add(j, l, (x[i][j] - mean[j]) * (x[i][l] - mean[l]));
}
}
}
tol = tol * tol;
for (int j = 0; j < p; j++) {
for (int l = 0; l <= j; l++) {
C.div(j, l, (n - k));
C.set(l, j, C.get(j, l));
}
if (C.get(j, j) < tol) {
throw new IllegalArgumentException(String.format("Covariance matrix (variable %d) is close to singular.", j));
}
}
ev = new double[k][];
for (int i = 0; i < k; i++) {
for (int j = 0; j < p; j++) {
for (int l = 0; l <= j; l++) {
cov[i].div(j, l, (ni[i] - 1));
cov[i].set(j, l, alpha * cov[i].get(j, l) + (1 - alpha) * C.get(j, l));
cov[i].set(l, j, cov[i].get(j, l));
}
if (cov[i].get(j, j) < tol) {
throw new IllegalArgumentException(String.format("Class %d covariance matrix (variable %d) is close to singular.", i, j));
}
}
cov[i].setSymmetric(true);
EVD eigen = cov[i].eigen();
for (double s : eigen.getEigenValues()) {
if (s < tol) {
throw new IllegalArgumentException(String.format("Class %d covariance matrix is close to singular.", i));
}
}
ev[i] = eigen.getEigenValues();
cov[i] = eigen.getEigenVectors();
}
scaling = cov;
ct = new double[k];
for (int i = 0; i < k; i++) {
double logev = 0.0;
for (int j = 0; j < p; j++) {
logev += Math.log(ev[i][j]);
}
ct[i] = Math.log(priori[i]) - 0.5 * logev;
}
}
/**
* Returns a priori probabilities.
*/
public double[] getPriori() {
return priori;
}
@Override
public int predict(double[] x) {
return predict(x, null);
}
@Override
public int predict(double[] x, double[] posteriori) {
if (x.length != p) {
throw new IllegalArgumentException(String.format("Invalid input vector size: %d, expected: %d", x.length, p));
}
if (posteriori != null && posteriori.length != k) {
throw new IllegalArgumentException(String.format("Invalid posteriori vector size: %d, expected: %d", posteriori.length, k));
}
int y = 0;
double max = Double.NEGATIVE_INFINITY;
double[] d = new double[p];
double[] ux = new double[p];
for (int i = 0; i < k; i++) {
for (int j = 0; j < p; j++) {
d[j] = x[j] - mu[i][j];
}
scaling[i].atx(d, ux);
double f = 0.0;
for (int j = 0; j < p; j++) {
f += ux[j] * ux[j] / ev[i][j];
}
f = ct[i] - 0.5 * f;
if (max < f) {
max = f;
y = i;
}
if (posteriori != null) {
posteriori[i] = f;
}
}
if (posteriori != null) {
double sum = 0.0;
for (int i = 0; i < k; i++) {
posteriori[i] = Math.exp(posteriori[i] - max);
sum += posteriori[i];
}
for (int i = 0; i < k; i++) {
posteriori[i] /= sum;
}
}
return y;
}
}
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