GaussianProcessMachine.cpp

Go to the documentation of this file.

/*
 * Copyright (c) The Shogun Machine Learning Toolbox
 * Written (w) 2014 Wu Lin
 * Written (W) 2013 Roman Votyakov
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * The views and conclusions contained in the software and documentation are those
 * of the authors and should not be interpreted as representing official policies,
 * either expressed or implied, of the Shogun Development Team.
 *
 * Code adapted from
 * Gaussian Process Machine Learning Toolbox
 * http://www.gaussianprocess.org/gpml/code/matlab/doc/
 * and
 * https://gist.github.com/yorkerlin/8a36e8f9b298aa0246a4
 */

#include <shogun/lib/config.h>

#ifdef HAVE_EIGEN3

#include <shogun/machine/GaussianProcessMachine.h>
#include <shogun/mathematics/Math.h>
#include <shogun/kernel/Kernel.h>
#include <shogun/machine/gp/SingleFITCLaplacianBase.h>

#include <shogun/mathematics/eigen3.h>

using namespace shogun;
using namespace Eigen;

CGaussianProcessMachine::CGaussianProcessMachine()
{
    init();
}

CGaussianProcessMachine::CGaussianProcessMachine(CInferenceMethod* method)
{
    init();
    set_inference_method(method);
}

void CGaussianProcessMachine::init()
{
    m_method=NULL;

    SG_ADD((CSGObject**) &m_method, "inference_method", "Inference method",
        MS_AVAILABLE);
}

CGaussianProcessMachine::~CGaussianProcessMachine()
{
    SG_UNREF(m_method);
}

SGVector<float64_t> CGaussianProcessMachine::get_posterior_means(CFeatures* data)
{
    REQUIRE(m_method, "Inference method should not be NULL\n")

    CFeatures* feat;

    CSingleSparseInferenceBase* sparse_method=
        dynamic_cast<CSingleSparseInferenceBase *>(m_method);
    // use inducing features for sparse inference method
    if (sparse_method)
    {
        sparse_method->optimize_inducing_features();
        feat=sparse_method->get_inducing_features();
    }
    else
        feat=m_method->get_features();

    // get kernel and compute kernel matrix: K(feat, data)*scale^2
    CKernel* training_kernel=m_method->get_kernel();
    CKernel* kernel=CKernel::obtain_from_generic(training_kernel->clone());
    SG_UNREF(training_kernel);

    kernel->init(feat, data);

    // get kernel matrix and create eigen representation of it
    SGMatrix<float64_t> k_trts=kernel->get_kernel_matrix();
    Map<MatrixXd> eigen_Ks(k_trts.matrix, k_trts.num_rows, k_trts.num_cols);

    // compute Ks=Ks*scale^2
    eigen_Ks*=CMath::sq(m_method->get_scale());

    // cleanup
    SG_UNREF(feat);
    SG_UNREF(kernel);

    // get alpha and create eigen representation of it
    SGVector<float64_t> alpha=m_method->get_alpha();
    Map<VectorXd> eigen_alpha(alpha.vector, alpha.vlen);

    // get mean and create eigen representation of it
    CMeanFunction* mean_function=m_method->get_mean();
    SGVector<float64_t> mean=mean_function->get_mean_vector(data);
    Map<VectorXd> eigen_mean(mean.vector, mean.vlen);
    SG_UNREF(mean_function);

    const index_t C=alpha.vlen/k_trts.num_rows;
    const index_t n=k_trts.num_rows;
    const index_t m=k_trts.num_cols;

    // compute mean: mu=Ks'*alpha+m
    SGVector<float64_t> mu(C*m);
    Map<MatrixXd> eigen_mu_matrix(mu.vector,C,m);

    for(index_t bl=0; bl<C; bl++)
        eigen_mu_matrix.block(bl,0,1,m)=(eigen_Ks.adjoint()*eigen_alpha.block(bl*n,0,n,1)+eigen_mean).transpose();

    return mu;
}

SGVector<float64_t> CGaussianProcessMachine::get_posterior_variances(
        CFeatures* data)
{
    REQUIRE(m_method, "Inference method should not be NULL\n")

    CFeatures* feat;

    bool is_sparse=false;
    CSingleSparseInferenceBase* sparse_method=
        dynamic_cast<CSingleSparseInferenceBase *>(m_method);
    // use inducing features for sparse inference method
    if (sparse_method)
    {
        sparse_method->optimize_inducing_features();
        feat=sparse_method->get_inducing_features();
        is_sparse=true;
    }
    else
        feat=m_method->get_features();

    SG_REF(data);

    // get kernel and compute kernel matrix: K(data, data)*scale^2
    CKernel* training_kernel=m_method->get_kernel();
    CKernel* kernel=CKernel::obtain_from_generic(training_kernel->clone());
    SG_UNREF(training_kernel);
    kernel->init(data, data);

    // get kernel matrix and create eigen representation of it
    SGVector<float64_t> k_tsts=kernel->get_kernel_diagonal();
    Map<VectorXd> eigen_Kss_diag(k_tsts.vector, k_tsts.vlen);

    // compute Kss=Kss*scale^2
    eigen_Kss_diag*=CMath::sq(m_method->get_scale());

    // compute kernel matrix: K(feat, data)*scale^2
    kernel->init(feat, data);

    // get kernel matrix and create eigen representation of it
    SGMatrix<float64_t> k_trts=kernel->get_kernel_matrix();
    Map<MatrixXd> eigen_Ks(k_trts.matrix, k_trts.num_rows, k_trts.num_cols);

    // compute Ks=Ks*scale^2
    eigen_Ks*=CMath::sq(m_method->get_scale());

    // cleanup
    SG_UNREF(kernel);
    SG_UNREF(feat);
    SG_UNREF(data);

    // get shogun representation of cholesky and create eigen representation
    SGMatrix<float64_t> L=m_method->get_cholesky();
    Map<MatrixXd> eigen_L(L.matrix, L.num_rows, L.num_cols);

    SGVector<float64_t> alpha=m_method->get_alpha();
    const index_t n=k_trts.num_rows;
    const index_t m=k_tsts.vlen;
    const index_t C=alpha.vlen/n;
    // result variance vector
    SGVector<float64_t> s2(m*C*C);
    Map<VectorXd> eigen_s2(s2.vector, s2.vlen);

    if (eigen_L.isUpperTriangular() && !is_sparse)
    {
        if (alpha.vlen==L.num_rows)
        {
            //binary case
            // get shogun of diagonal sigma vector and create eigen representation
            SGVector<float64_t> sW=m_method->get_diagonal_vector();
            Map<VectorXd> eigen_sW(sW.vector, sW.vlen);
            // solve L' * V = sW * Ks and compute V.^2
            MatrixXd eigen_V=eigen_L.triangularView<Upper>().adjoint().solve(
                eigen_sW.asDiagonal()*eigen_Ks);
            MatrixXd eigen_sV=eigen_V.cwiseProduct(eigen_V);

            eigen_s2=eigen_Kss_diag-eigen_sV.colwise().sum().adjoint();
        }
        else
        {
            if (m_method->supports_multiclass())
            {
                //multiclass case
                //see the reference code of the gist link, which is based on the algorithm 3.4 of the GPML textbook
                Map<MatrixXd> &eigen_M=eigen_L;
                eigen_s2.fill(0);

                SGMatrix<float64_t> E=m_method->get_multiclass_E();
                Map<MatrixXd> eigen_E(E.matrix, E.num_rows, E.num_cols);
                ASSERT(E.num_cols==alpha.vlen);
                for(index_t bl_i=0; bl_i<C; bl_i++)
                {
                    //n by m
                    MatrixXd bi=eigen_E.block(0,bl_i*n,n,n)*eigen_Ks;
                    MatrixXd c_cav=eigen_M.triangularView<Upper>().adjoint().solve(bi);
                    c_cav=eigen_M.triangularView<Upper>().solve(c_cav);

                    for(index_t bl_j=0; bl_j<C; bl_j++)
                    {
                        MatrixXd bj=eigen_E.block(0,bl_j*n,n,n)*eigen_Ks;
                        for (index_t idx_m=0; idx_m<m; idx_m++)
                            eigen_s2[bl_j+(bl_i+idx_m*C)*C]=(bj.block(0,idx_m,n,1).array()*c_cav.block(0,idx_m,n,1).array()).sum();
                    }
                    for (index_t idx_m=0; idx_m<m; idx_m++)
                        eigen_s2[bl_i+(bl_i+idx_m*C)*C]+=eigen_Kss_diag(idx_m)-(eigen_Ks.block(0,idx_m,n,1).array()*bi.block(0,idx_m,n,1).array()).sum();
                }
            }
            else
            {
                SG_ERROR("Unsupported inference method!\n");
                return s2;
            }
        }
    }
    else
    {
        // M = Ks .* (L * Ks)
        MatrixXd eigen_M=eigen_Ks.cwiseProduct(eigen_L*eigen_Ks);
        eigen_s2=eigen_Kss_diag+eigen_M.colwise().sum().adjoint();
    }

    return s2;
}

#endif /* HAVE_EIGEN3 */