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

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

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/*******************************************************************************
*   Copyright 2012 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;

/**
 * NegativeExpGamma distribution, which is a distribution over a
 * variable whose negative exponential is Gamma distributed. That is,
 * this is the negative log of a Gamma distributed variable.
 * 
 * The variables in the argument list are ordered as follows:
 * 
 * 1) Alpha: Alpha parameter of the underlying Gamma distribution (non-negative)
 * 2) Beta: Beta parameter of the underlying Gamma distribution (non-negative)
 * 3...) An arbitrary number of real variables
    
 * Alpha and Beta parameters may optionally be specified as constants in the constructor.
 * In this case, they are not included in the list of arguments.
 * 
 */
public class NegativeExpGamma extends FactorFunction {
    protected double _alpha;
    protected double _beta;
    protected double _alphaMinusOne;
    protected double _logGammaAlphaMinusAlphaLogBeta;
    protected boolean _parametersConstant = false;
    protected int _firstDirectedToIndex = 2;

    public NegativeExpGamma() {
        super();
    }

    public NegativeExpGamma(double alpha, double beta) {
        this();
        _alpha = alpha;
        _beta = beta;
        _alphaMinusOne = _alpha - 1;
        _logGammaAlphaMinusAlphaLogBeta = org.apache.commons.math3.special.Gamma.logGamma(_alpha)
                - _alpha * Math.log(_beta);
        _parametersConstant = true;
        _firstDirectedToIndex = 0;
        if (_alpha <= 0)
            throw new DimpleException("Non-positive alpha parameter. This must be a positive value.");
        if (_beta <= 0)
            throw new DimpleException("Non-positive beta parameter. This must be a positive value.");
    }

    @Override
    public final double evalEnergy(Value[] arguments) {
        int index = 0;
        if (!_parametersConstant) {
            _alpha = arguments[index++].getDouble(); // First input is alpha parameter (must be non-negative)
            if (_alpha <= 0)
                return Double.POSITIVE_INFINITY;
            _beta = arguments[index++].getDouble(); // Second input is beta parameter (must be non-negative)
            if (_beta <= 0)
                return Double.POSITIVE_INFINITY;
            _alphaMinusOne = _alpha - 1;
            _logGammaAlphaMinusAlphaLogBeta = org.apache.commons.math3.special.Gamma.logGamma(_alpha)
                    - _alpha * Math.log(_beta);
        }
        final int length = arguments.length;
        final int N = length - index; // Number of non-parameter variables
        double sum = 0;
        for (; index < length; index++) {
            final double x = arguments[index].getDouble(); // Remaining inputs are NegativeExpGamma variables
            sum += x * _alphaMinusOne + Math.exp(-x) * _beta;
        }
        return sum + N * _logGammaAlphaMinusAlphaLogBeta;
    }

    @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 hasConstantParameters() {
        return _parametersConstant;
    }

    public final double getAlphaMinusOne() {
        return _alphaMinusOne;
    }

    public final double getBeta() {
        return _beta;
    }
}