source: src/main/java/agents/anac/y2015/Phoenix/GP/CovSEiso.java

package agents.anac.y2015.Phoenix.GP;/* This file is part of the jgpml Project.
 * http://github.com/renzodenardi/jgpml
 *
 * Copyright (c) 2011 Renzo De Nardi and Hugo Gravato-Marques
 *
 * 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.
 */

import static agents.anac.y2015.Phoenix.GP.MatrixOperations.*;

import java.util.Arrays;

import agents.Jama.Matrix;

/**
 * Squared Exponential covariance function with isotropic distance measure. The
 * covariance function is parameterized as:
 * <P><DD>
 * k(x^p,x^q) = sf2 * exp(-(x^p - x^q)'*inv(P)*(x^p - x^q)/2)
 * </DD>
 * where the P matrix is ell^2 times the unit matrix and sf2 is the signal
 * variance. The hyperparameters are:
 * <P>
 * [ log(ell)
 * log(sqrt(sf2)) ]
 */

public class CovSEiso implements CovarianceFunction{

    public CovSEiso(){}


    /**
     * Returns the number of hyperparameters of this<code>PhoenixAlpha.CovarianceFunction</code>
     *
     * @return number of hyperparameters
     */
    public int numParameters() {
        return 2;
    }

    /**
     * Compute covariance matrix of a dataset X
     *
     * @param loghyper column <code>Matrix</code> of hyperparameters
     * @param X        input dataset
     * @return K covariance <code>Matrix</code>
     */
    public Matrix compute(Matrix loghyper, Matrix X) {

        if(loghyper.getColumnDimension()!=1 || loghyper.getRowDimension()!=numParameters())
            throw new IllegalArgumentException("Wrong number of hyperparameters, "+loghyper.getRowDimension()+" instead of "+numParameters());

        double ell = Math.exp(loghyper.get(0,0));
        double sf2 = Math.exp(2*loghyper.get(1,0));

        Matrix K = exp(squareDist(X.transpose().times(1/ell)).times(-0.5)).times(sf2);

        return K;
    }

    /**
     * Compute compute test set covariances
     *
     * @param loghyper column <code>Matrix</code> of hyperparameters
     * @param X        input dataset
     * @param Xstar    test set
     * @return [K(Xstar,Xstar) K(X,Xstar)]
     */
    public Matrix[] compute(Matrix loghyper, Matrix X, Matrix Xstar) {

        if(loghyper.getColumnDimension()!=1 || loghyper.getRowDimension()!=numParameters())
            throw new IllegalArgumentException("Wrong number of hyperparameters, "+loghyper.getRowDimension()+" instead of "+numParameters());


        double ell = Math.exp(loghyper.get(0,0));
        double sf2 = Math.exp(2*loghyper.get(1,0));
        double[] a = new double[Xstar.getRowDimension()];
        Arrays.fill(a,sf2);
        Matrix A = new Matrix(a,a.length);

        Matrix B = exp(squareDist(X.transpose().times(1/ell),Xstar.transpose().times(1/ell)).times(-0.5)).times(sf2);

        return new Matrix[]{A,B};
    }

    /**
     * Coompute the derivatives of this <code>PhoenixAlpha.CovarianceFunction</code> with respect
     * to the hyperparameter with index <code>idx</code>
     *
     * @param loghyper hyperparameters
     * @param X        input dataset
     * @param index    hyperparameter index
     * @return <code>Matrix</code> of derivatives
     */
    public Matrix computeDerivatives(Matrix loghyper, Matrix X, int index) {

        if(loghyper.getColumnDimension()!=1 || loghyper.getRowDimension()!=numParameters())
            throw new IllegalArgumentException("Wrong number of hyperparameters, "+loghyper.getRowDimension()+" instead of "+numParameters());
        if(index>numParameters()-1)
            throw new IllegalArgumentException("Wrong hyperparameters index "+index+" it should be smaller or equal to "+(numParameters()-1));

        double ell = Math.exp(loghyper.get(0,0));
        double sf2 = Math.exp(2*loghyper.get(1,0));

        Matrix tmp = squareDist(X.transpose().times(1/ell));
        Matrix A = null;
        if(index==0){
            A = exp(tmp.times(-0.5)).arrayTimes(tmp).times(sf2);
        } else {
            A = exp(tmp.times(-0.5)).times(2*sf2);
        }

        return A;
    }


    private static Matrix squareDist(Matrix a){
        return squareDist(a,a);
    }

    private static Matrix squareDist(Matrix a, Matrix b){
        Matrix C = new Matrix(a.getColumnDimension(),b.getColumnDimension());
        final int m = a.getColumnDimension();
        final int n = b.getColumnDimension();
        final int d = a.getRowDimension();

        for (int i=0; i<m; i++){
            for (int j=0; j<n; j++) {
                double z = 0.0;
                for (int k=0; k<d; k++) { double t = a.get(k,i) - b.get(k,j); z += t*t; }
                C.set(i,j,z);
            }
        }

        return C;
    }

    public static void main(String[] args) {

        CovSEiso cf = new CovSEiso();

        Matrix X = Matrix.identity(6,6);
        Matrix logtheta = new Matrix(new double[][]{{0.1},{0.2}});

//        Matrix z = new Matrix(new double[][]{{1,2,3,4,5,6},{1,2,3,4,5,6}});
//
//            System.out.println("");
//            Matrix K = cf.compute(logtheta,X);
//            K.print(K.getColumnDimension(), 8);
//
//            Matrix[] res = cf.compute(logtheta,X,z);
//
//            res[0].print(res[0].getColumnDimension(), 20);
//            res[1].print(res[1].getColumnDimension(), 20);

        Matrix d = cf.computeDerivatives(logtheta,X,1);

        d.print(d.getColumnDimension(), 8);
    }
}

//    private static Matrix squareDist(Matrix a, Matrix b, Matrix Q){
//
//        if(a.getColumnDimension()!=Q.getRowDimension() || b.getColumnDimension()!=Q.getColumnDimension())
//            throw new IllegalArgumentException("Wrong size of for Q "+Q.getRowDimension()+"x"+Q.getColumnDimension()+" instead of "+a.getColumnDimension()+"x"+b.getColumnDimension());
//
//        Matrix C = new Matrix(D,1);
//
//        for (int i=0; i<b.getColumnDimension(); i++) {
//            for (int j=0; j<a.getColumnDimension(); j++) {
//                double t = Q.get(i,j);
//                for (int k=0; k<D; k++) {
//                    double z = a.get(i,k) - b.get(j,k);
//                    C.set(k,0,C.get(k,0)+ t*z*z);
//                }
//            }
//        }
//
//        return C;
//    }