com.analog.lyric.dimple.factorfunctions.Binomial.java Source code

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Here is the source code for com.analog.lyric.dimple.factorfunctions.Binomial.java

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/*******************************************************************************
*   Copyright 2013 Analog Devices, Inc.
*
*   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 com.analog.lyric.dimple.factorfunctions;

import com.analog.lyric.dimple.exceptions.DimpleException;
import com.analog.lyric.dimple.factorfunctions.core.FactorFunction;
import com.analog.lyric.dimple.factorfunctions.core.FactorFunctionUtilities;
import com.analog.lyric.dimple.model.values.Value;

/**
 * Binomial distribution.
 * <p>
 * Corresponds to p(x | N, p),
 * where x is a count of the number of ones, N is the total count (ones and zeros),
 * and p is the probability parameter.
 * <p>
 * The conjugate prior for p is a Beta distribution.
 * Depending on the solver, it may or may not be necessary to use a
 * conjugate prior (for the Gibbs solver, for example, it is not).
 * <p>
 * The variables in the argument list are ordered as follows:
 * <ol>
 * <li>N: Parameter indicating the total count (ones and zeros)
 * <li> p: Probability parameter
 * <li>x: Count of ones
 * </ol>
 * N parameter may optionally be specified as constants in the constructor.
 * In this case, N is not included in the list of arguments.
 */
public class Binomial extends FactorFunction {
    protected int _N;
    protected double _negativeLogFactorialN;
    protected boolean _NParameterConstant = false;
    private int _firstDirectedToIndex = 2;

    public Binomial() {
        super((String) null);
    } // Variable N

    public Binomial(int N) // Fixed N
    {
        this();
        _N = N;
        if (_N < 0)
            throw new DimpleException("N must be a non-negative value.");
        _negativeLogFactorialN = -org.apache.commons.math3.special.Gamma.logGamma(_N + 1);
        _NParameterConstant = true;
        _firstDirectedToIndex = 1;
    }

    @Override
    public final double evalEnergy(Value[] arguments) {
        int index = 0;
        if (!_NParameterConstant) {
            _N = arguments[index++].getInt(); // First argument is N parameter
            if (_N < 0)
                return Double.POSITIVE_INFINITY;
            _negativeLogFactorialN = -org.apache.commons.math3.special.Gamma.logGamma(_N + 1);
        }

        final double p = arguments[index++].getDouble(); // Next argument is the probability parameter
        if (p < 0 || p > 1)
            return Double.POSITIVE_INFINITY;

        final int numOnes = arguments[index++].getInt(); // Next argument is the one-count
        if (numOnes < 0 || numOnes > _N)
            return Double.POSITIVE_INFINITY;
        int numZeros = _N - numOnes;

        if (p == 0)
            if (numOnes > 0)
                return Double.POSITIVE_INFINITY;
            else
                return 0;
        else if (p == 1)
            if (numZeros > 0)
                return Double.POSITIVE_INFINITY;
            else
                return 0;
        else
            return -(numOnes * Math.log(p) + numZeros * Math.log(1 - p)) + _negativeLogFactorialN
                    + org.apache.commons.math3.special.Gamma.logGamma(numOnes + 1)
                    + org.apache.commons.math3.special.Gamma.logGamma(numZeros + 1);
    }

    @Override
    public final boolean isDirected() {
        return true;
    }

    @Override
    public final int[] getDirectedToIndices(int numEdges) {
        // All edges except the parameter edges (if present) are directed-to edges
        return FactorFunctionUtilities.getListOfIndices(_firstDirectedToIndex, numEdges - 1);
    }

    // Factor-specific methods
    public final boolean hasConstantNParameter() {
        return _NParameterConstant;
    }

    public final int getN() {
        return _N;
    }
}