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/*
* File: MultivariatePolyaDistribution.java
* Authors: Kevin R. Dixon
* Company: Sandia National Laboratories
* Project: Cognitive Foundry
*
* Copyright May 15, 2010, Sandia Corporation.
* Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive
* license for use of this work by or on behalf of the U.S. Government.
* Export of this program may require a license from the United States
* Government. See CopyrightHistory.txt for complete details.
*
*/
package gov.sandia.cognition.statistics.distribution;
import gov.sandia.cognition.annotation.PublicationReference;
import gov.sandia.cognition.annotation.PublicationType;
import gov.sandia.cognition.math.MathUtil;
import gov.sandia.cognition.math.matrix.Vector;
import gov.sandia.cognition.math.matrix.VectorFactory;
import gov.sandia.cognition.math.matrix.VectorInputEvaluator;
import gov.sandia.cognition.statistics.AbstractDistribution;
import gov.sandia.cognition.statistics.ClosedFormComputableDiscreteDistribution;
import gov.sandia.cognition.statistics.ProbabilityMassFunction;
import gov.sandia.cognition.statistics.ProbabilityMassFunctionUtil;
import gov.sandia.cognition.util.ObjectUtil;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Random;
/**
* A multivariate Polya Distribution, also known as a Dirichlet-Multinomial
* model, is a compound distribution where the parameters of a multinomial
* are drawn from a Dirichlet distribution with fixed parameters and a constant
* number of trials and then the observations are generated by this
* multinomial. This is the multivariate generalization of the Beta-Binomial
* Distribution and is the predictive posterior distribution for a
* Multinomial Bayesian estimator using its conjugate prior Dirichlet
* distribution.
* @author Kevin R. Dixon
* @since 3.0
*/
@PublicationReference(
author="Wikipedia",
title="Multivariate Polya Distribution",
type=PublicationType.WebPage,
year=2010,
url="http://en.wikipedia.org/wiki/Multivariate_Polya_distribution"
)
public class MultivariatePolyaDistribution
extends AbstractDistribution
implements ClosedFormComputableDiscreteDistribution
{
/**
* Default number of trials, {@value}.
*/
public static final int DEFAULT_NUM_TRIALS =
MultinomialDistribution.DEFAULT_NUM_TRIALS;
/**
* Default dimensionality, {@value}.
*/
public static final int DEFAULT_DIMENSIONALITY = 2;
/**
* Parameters of the Dirichlet distribution, must be at least 2-dimensional
* and each element must be positive.
*/
protected Vector parameters;
/**
* Number of trials in the distribution, must be greater than 0.
*/
private int numTrials;
/**
* Creates a new instance of DirichletDistribution
*/
public MultivariatePolyaDistribution()
{
this( DEFAULT_DIMENSIONALITY, DEFAULT_NUM_TRIALS );
}
/**
* Creates a new instance of MultivariatePolyaDistribution
* @param dimensionality
* Dimensionality of the distribution
* @param numTrials
* Number of trials in the distribution, must be greater than 0.
*/
public MultivariatePolyaDistribution(
final int dimensionality,
final int numTrials )
{
this( VectorFactory.getDefault().createVector(dimensionality,1.0), numTrials );
}
/**
* Creates a new instance of MultivariatePolyaDistribution
* @param parameters
* Parameters of the Dirichlet distribution, must be at least 2-dimensional
* and each element must be positive.
* @param numTrials
* Number of trials in the distribution, must be greater than 0.
*/
public MultivariatePolyaDistribution(
final Vector parameters,
final int numTrials )
{
this.setParameters(parameters);
this.setNumTrials(numTrials);
}
/**
* Copy Constructor.
* @param other
* MultivariatePolyaDistribution to copy.
*/
public MultivariatePolyaDistribution(
MultivariatePolyaDistribution other )
{
this( ObjectUtil.cloneSafe( other.getParameters() ), other.getNumTrials() );
}
@Override
public MultivariatePolyaDistribution clone()
{
MultivariatePolyaDistribution clone =
(MultivariatePolyaDistribution) super.clone();
clone.setParameters( ObjectUtil.cloneSafe(this.getParameters()) );
return clone;
}
@Override
public Vector getMean()
{
return this.parameters.scale( this.numTrials / this.parameters.norm1() );
}
@Override
public void sampleInto(
final Random random,
final int sampleCount,
final Collection output)
{
DirichletDistribution prior =
new DirichletDistribution( this.parameters );
ArrayList dirichletSamples = prior.sample(random, sampleCount);
final int dim = this.getInputDimensionality();
final int N = this.getNumTrials();
MultinomialDistribution conditional =
new MultinomialDistribution( dim, N );
conditional.setNumTrials(N);
for( int i = 0; i < sampleCount; i++ )
{
conditional.setParameters(dirichletSamples.get(i));
output.add( conditional.sample(random) );
}
}
/**
* Getter for numTrials
* @return
* Number of trials in the distribution, must be greater than 0.
*/
public int getNumTrials()
{
return this.numTrials;
}
/**
* Setter for numTrials
* @param numTrials
* Number of trials in the distribution, must be greater than 0.
*/
public void setNumTrials(
final int numTrials)
{
if( numTrials <= 0 )
{
throw new IllegalArgumentException( "numTrials must be > 0" );
}
this.numTrials = numTrials;
}
@Override
public MultivariatePolyaDistribution.PMF getProbabilityFunction()
{
return new MultivariatePolyaDistribution.PMF( this );
}
@Override
public Vector convertToVector()
{
return ObjectUtil.cloneSafe(this.getParameters());
}
@Override
public void convertFromVector(
final Vector parameters)
{
parameters.assertSameDimensionality( this.getParameters() );
this.setParameters( ObjectUtil.cloneSafe(parameters) );
}
/**
* Gets the dimensionality of the parameters
* @return
* Number of parameters in the distribution.
*/
public int getInputDimensionality()
{
return (this.parameters != null) ? this.parameters.getDimensionality() : 0;
}
/**
* Getter for parameters
* @return
* Parameters of the Dirichlet distribution, must be at least 2-dimensional
* and each element must be positive.
*/
public Vector getParameters()
{
return this.parameters;
}
/**
* Setter for parameters
* @param parameters
* Parameters of the Dirichlet distribution, must be at least 2-dimensional
* and each element must be positive.
*/
public void setParameters(
final Vector parameters)
{
final int N = parameters.getDimensionality();
if( N < 2 )
{
throw new IllegalArgumentException( "Dimensionality must be >= 2" );
}
for( int i = 0; i < N; i++ )
{
if( parameters.getElement(i) <= 0.0 )
{
throw new IllegalArgumentException(
"All parameter elements must be > 0.0" );
}
}
this.parameters = parameters;
}
@Override
public MultinomialDistribution.Domain getDomain()
{
return new MultinomialDistribution.Domain(
this.getInputDimensionality(), this.getNumTrials() );
}
@Override
public int getDomainSize()
{
return this.getDomain().size();
}
@Override
public String toString()
{
return "N = " + this.getNumTrials() + ", Parameters = " + this.getParameters();
}
/**
* PMF of the MultivariatePolyaDistribution
*/
public static class PMF
extends MultivariatePolyaDistribution
implements ProbabilityMassFunction,
VectorInputEvaluator
{
/**
* Creates a new instance of DirichletDistribution
*/
public PMF()
{
super();
}
/**
* Creates a new instance of MultivariatePolyaDistribution
* @param dimensionality
* Dimensionality of the distribution
* @param numTrials
* Number of trials in the distribution, must be greater than 0.
*/
public PMF(
final int dimensionality,
final int numTrials )
{
super( dimensionality, numTrials );
}
/**
* Creates a new instance of MultivariatePolyaDistribution
* @param parameters
* Parameters of the Dirichlet distribution, must be at least 2-dimensional
* and each element must be positive.
* @param numTrials
* Number of trials in the distribution, must be greater than 0.
*
*/
public PMF(
final Vector parameters,
final int numTrials )
{
super( parameters, numTrials );
}
/**
* Copy Constructor.
* @param other
* MultivariatePolyaDistribution to copy.
*/
public PMF(
MultivariatePolyaDistribution other )
{
super( other );
}
@Override
public MultivariatePolyaDistribution.PMF getProbabilityFunction()
{
return this;
}
@Override
public double logEvaluate(
final Vector input)
{
final int dim = this.getInputDimensionality();
input.assertDimensionalityEquals(dim);
final int ni = (int) Math.round( input.norm1() );
final int N = this.getNumTrials();
final double A = this.parameters.norm1();
if( ni != N )
{
return Math.log(0.0);
}
double logSum = 0.0;
logSum += Math.log(ni);
logSum += MathUtil.logBetaFunction(A, ni);
for( int i = 0; i < dim; i++ )
{
double pi = this.parameters.getElement(i);
double xi = input.getElement(i);
if( (pi > 0.0) && (xi > 0.0) )
{
logSum -= Math.log(xi);
logSum -= MathUtil.logBetaFunction( pi, xi );
}
}
return logSum;
}
@Override
public Double evaluate(
final Vector input)
{
return Math.exp( this.logEvaluate(input) );
}
@Override
public double getEntropy()
{
return ProbabilityMassFunctionUtil.getEntropy(this);
}
}
}