smile.stat.distribution.Mixture Maven / Gradle / Ivy
/*******************************************************************************
* Copyright (c) 2010-2020 Haifeng Li. All rights reserved.
*
* Smile is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, either version 3 of
* the License, or (at your option) any later version.
*
* Smile is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Smile. If not, see .
******************************************************************************/
package smile.stat.distribution;
import java.io.Serializable;
import java.util.Arrays;
import java.util.stream.Collectors;
import smile.math.MathEx;
/**
* A finite mixture model is a probabilistic model for density estimation
* using a mixture distribution. A mixture model can be regarded as a type of
* unsupervised learning or clustering.
*
* The Expectation-maximization algorithm can be used to compute the
* parameters of a parametric mixture model distribution. The EM algorithm is
* a method for finding maximum likelihood estimates of parameters, where the
* model depends on unobserved latent variables. EM is an iterative method which
* alternates between performing an expectation (E) step, which computes the
* expectation of the log-likelihood evaluated using the current estimate for
* the latent variables, and a maximization (M) step, which computes parameters
* maximizing the expected log-likelihood found on the E step. These parameter
* estimates are then used to determine the distribution of the latent variables
* in the next E step.
*
* @author Haifeng Li
*/
public class Mixture extends AbstractDistribution {
private static final long serialVersionUID = 2L;
/**
* A component in the mixture distribution is defined by a distribution
* and its weight in the mixture.
*/
public static class Component implements Serializable {
private static final long serialVersionUID = 2L;
/**
* The priori probability of component.
*/
public final double priori;
/**
* The distribution of component.
*/
public final Distribution distribution;
/**
* Constructor.
* @param priori the priori probability of component.
* @param distribution the distribution of component.
*/
public Component(double priori, Distribution distribution) {
this.priori = priori;
this.distribution = distribution;
}
}
/** The components of finite mixture model. */
public final Component[] components;
/**
* Constructor.
* @param components a list of distributions.
*/
public Mixture(Component... components) {
if (components.length == 0) {
throw new IllegalStateException("Empty mixture!");
}
double sum = 0.0;
for (Component component : components) {
sum += component.priori;
}
if (Math.abs(sum - 1.0) > 1E-3) {
throw new IllegalArgumentException("The sum of priori is not equal to 1.");
}
this.components = components;
}
/** Returns the posteriori probabilities. */
public double[] posteriori(double x) {
int k = components.length;
double[] prob = new double[k];
for (int i = 0; i < k; i++) {
Component c = components[i];
prob[i] = c.priori * c.distribution.p(x);
}
double p = MathEx.sum(prob);
for (int i = 0; i < k; i++) {
prob[i] /= p;
}
return prob;
}
/** Returns the index of component with maximum a posteriori probability. */
public int map(double x) {
int k = components.length;
double[] prob = new double[k];
for (int i = 0; i < k; i++) {
Component c = components[i];
prob[i] = c.priori * c.distribution.p(x);
}
return MathEx.whichMax(prob);
}
@Override
public double mean() {
double mu = 0.0;
for (Component c : components)
mu += c.priori * c.distribution.mean();
return mu;
}
@Override
public double variance() {
double variance = 0.0;
for (Component c : components)
variance += c.priori * c.priori * c.distribution.variance();
return variance;
}
/**
* Shannon entropy. Not supported.
*/
@Override
public double entropy() {
throw new UnsupportedOperationException("Mixture does not support entropy()");
}
@Override
public double p(double x) {
double p = 0.0;
for (Component c : components)
p += c.priori * c.distribution.p(x);
return p;
}
@Override
public double logp(double x) {
return Math.log(p(x));
}
@Override
public double cdf(double x) {
double p = 0.0;
for (Component c : components)
p += c.priori * c.distribution.cdf(x);
return p;
}
@Override
public double rand() {
double r = MathEx.random();
double p = 0.0;
for (Component g : components) {
p += g.priori;
if (r <= p)
return g.distribution.rand();
}
// we should not arrive here.
throw new IllegalStateException();
}
@Override
public double quantile(double p) {
if (p < 0.0 || p > 1.0) {
throw new IllegalArgumentException("Invalid p: " + p);
}
// Starting guess near peak of density.
// Expand interval until we bracket.
double xl, xu, inc = 1;
double x = (int) mean();
if (p < cdf(x)) {
do {
x -= inc;
inc *= 2;
} while (p < cdf(x));
xl = x;
xu = x + inc / 2;
} else {
do {
x += inc;
inc *= 2;
} while (p > cdf(x));
xu = x;
xl = x - inc / 2;
}
return quantile(p, xl, xu);
}
@Override
public int length() {
int length = components.length - 1; // independent priori parameters
for (Component component : components)
length += component.distribution.length();
return length;
}
/**
* Returns the number of components in the mixture.
*/
public int size() {
return components.length;
}
/**
* The BIC score of the mixture for given data.
*/
public double bic(double[] data) {
int n = data.length;
double logLikelihood = 0.0;
for (double x : data) {
double p = p(x);
if (p > 0) logLikelihood += Math.log(p);
}
return logLikelihood - 0.5 * length() * Math.log(n);
}
@Override
public String toString() {
return Arrays.stream(components)
.map(component -> String.format("%.2f x %s", component.priori, component.distribution))
.collect(Collectors.joining(" + ", String.format("Mixture(%d)[", components.length), "]"));
}
}