org.lambda3.indra.core.function.JensenShannonRelatednessFunction.java Source code

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Here is the source code for org.lambda3.indra.core.function.JensenShannonRelatednessFunction.java

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package org.lambda3.indra.core.function;

/*-
 * ==========================License-Start=============================
 * Indra Core Module
 * --------------------------------------------------------------------
 * Copyright (C) 2016 - 2017 Lambda^3
 * --------------------------------------------------------------------
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 * ==========================License-End===============================
 */

import org.apache.commons.math3.linear.RealVector;

public class JensenShannonRelatednessFunction implements RelatednessFunction {

    @Override
    public double sim(RealVector r1, RealVector r2, boolean sparse) {
        if (r1.getDimension() != r2.getDimension()) {
            return 0;
        }

        double divergence = 0.0;
        double avr = 0.0;

        for (int i = 0; i < r1.getDimension(); ++i) {
            avr = (r1.getEntry(i) + r2.getEntry(i)) / 2;

            if (r1.getEntry(i) > 0.0 && avr > 0.0) {
                divergence += r1.getEntry(i) * Math.log(r1.getEntry(i) / avr);
            }
        }
        for (int i = 0; i < r2.getDimension(); ++i) {
            avr = (r1.getEntry(i) + r2.getEntry(i)) / 2;

            if (r2.getEntry(i) > 0.0 && avr > 0.0) {
                divergence += r1.getEntry(i) * Math.log(r2.getEntry(i) / avr);
            }
        }

        double result = 1 - (divergence / (2 * Math.sqrt(2 * Math.log(2))));
        return Math.abs(result);
    }
}