InferenceMethod.cpp

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/*
 * Copyright (c) The Shogun Machine Learning Toolbox
 * Written (W) 2013 Heiko Strathmann
 * Written (W) 2013 Roman Votyakov
 * Written (W) 2012 Jacob Walker
 * 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.
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 */
#include <shogun/lib/config.h>

#ifdef HAVE_EIGEN3

#include <shogun/machine/gp/InferenceMethod.h>
#include <shogun/distributions/classical/GaussianDistribution.h>
#include <shogun/mathematics/Statistics.h>
#include <shogun/mathematics/Math.h>
#include <shogun/lib/Lock.h>

using namespace shogun;

#ifndef DOXYGEN_SHOULD_SKIP_THIS
struct GRADIENT_THREAD_PARAM
{
    CInferenceMethod* inf;
    CMap<TParameter*, SGVector<float64_t> >* grad;
    CSGObject* obj;
    TParameter* param;
    CLock* lock;
};
#endif /* DOXYGEN_SHOULD_SKIP_THIS */

CInferenceMethod::CInferenceMethod()
{
    init();
}

float64_t CInferenceMethod::get_scale() const
{
    return CMath::exp(m_log_scale);
}

void CInferenceMethod::set_scale(float64_t scale)
{
    REQUIRE(scale>0, "Scale (%f) must be positive", scale);
    m_log_scale=CMath::log(scale);
}

SGMatrix<float64_t> CInferenceMethod::get_multiclass_E()
{
    if (parameter_hash_changed())
        update();

    return SGMatrix<float64_t>(m_E);
}

CInferenceMethod::CInferenceMethod(CKernel* kernel, CFeatures* features,
    CMeanFunction* mean, CLabels* labels, CLikelihoodModel* model)
{
    init();

    set_kernel(kernel);
    set_features(features);
    set_labels(labels);
    set_model(model);
    set_mean(mean);
}

CInferenceMethod::~CInferenceMethod()
{
    SG_UNREF(m_kernel);
    SG_UNREF(m_features);
    SG_UNREF(m_labels);
    SG_UNREF(m_model);
    SG_UNREF(m_mean);
}

void CInferenceMethod::init()
{
    SG_ADD((CSGObject**)&m_kernel, "kernel", "Kernel", MS_AVAILABLE);
    SG_ADD(&m_log_scale, "log_scale", "Kernel log scale", MS_AVAILABLE, GRADIENT_AVAILABLE);
    SG_ADD((CSGObject**)&m_model, "likelihood_model", "Likelihood model",
        MS_AVAILABLE);
    SG_ADD((CSGObject**)&m_mean, "mean_function", "Mean function", MS_AVAILABLE);
    SG_ADD((CSGObject**)&m_labels, "labels", "Labels", MS_NOT_AVAILABLE);
    SG_ADD((CSGObject**)&m_features, "features", "Features", MS_NOT_AVAILABLE);
    SG_ADD(&m_gradient_update, "gradient_update", "Whether gradients are updated", MS_NOT_AVAILABLE);
    

    m_kernel=NULL;
    m_model=NULL;
    m_labels=NULL;
    m_features=NULL;
    m_mean=NULL;
    m_log_scale=0.0;
    m_gradient_update=false;

    SG_ADD(&m_alpha, "alpha", "alpha vector used in process mean calculation", MS_NOT_AVAILABLE);
    SG_ADD(&m_L, "L", "upper triangular factor of Cholesky decomposition", MS_NOT_AVAILABLE);
    SG_ADD(&m_E, "E", "the matrix used for multi classification", MS_NOT_AVAILABLE);
}

float64_t CInferenceMethod::get_marginal_likelihood_estimate(
        int32_t num_importance_samples, float64_t ridge_size)
{
    /* sample from Gaussian approximation to q(f|y) */
    SGMatrix<float64_t> cov=get_posterior_covariance();

    /* add ridge */
    for (index_t i=0; i<cov.num_rows; ++i)
        cov(i,i)+=ridge_size;

    SGVector<float64_t> mean=get_posterior_mean();

    CGaussianDistribution* post_approx=new CGaussianDistribution(mean, cov);
    SGMatrix<float64_t> samples=post_approx->sample(num_importance_samples);

    /* evaluate q(f^i|y), p(f^i|\theta), p(y|f^i), i.e.,
     * log pdf of approximation, prior and likelihood */

    /* log pdf q(f^i|y) */
    SGVector<float64_t> log_pdf_post_approx=post_approx->log_pdf_multiple(samples);

    /* dont need gaussian anymore, free memory */
    SG_UNREF(post_approx);
    post_approx=NULL;

    /* log pdf p(f^i|\theta) and free memory afterwise. Scale kernel before */
    SGMatrix<float64_t> scaled_kernel(m_ktrtr.num_rows, m_ktrtr.num_cols);
    memcpy(scaled_kernel.matrix, m_ktrtr.matrix,
            sizeof(float64_t)*m_ktrtr.num_rows*m_ktrtr.num_cols);
    for (index_t i=0; i<m_ktrtr.num_rows*m_ktrtr.num_cols; ++i)
        scaled_kernel.matrix[i]*=CMath::exp(m_log_scale*2.0);

    /* add ridge */
    for (index_t i=0; i<cov.num_rows; ++i)
        scaled_kernel(i,i)+=ridge_size;

    CGaussianDistribution* prior=new CGaussianDistribution(
            m_mean->get_mean_vector(m_features), scaled_kernel);
    SGVector<float64_t> log_pdf_prior=prior->log_pdf_multiple(samples);
    SG_UNREF(prior);
    prior=NULL;

    /* p(y|f^i) */
    SGVector<float64_t> log_likelihood=m_model->get_log_probability_fmatrix(
            m_labels, samples);

    /* combine probabilities */
    ASSERT(log_likelihood.vlen==num_importance_samples);
    ASSERT(log_likelihood.vlen==log_pdf_prior.vlen);
    ASSERT(log_likelihood.vlen==log_pdf_post_approx.vlen);
    SGVector<float64_t> sum(log_likelihood);
    for (index_t i=0; i<log_likelihood.vlen; ++i)
        sum[i]=log_likelihood[i]+log_pdf_prior[i]-log_pdf_post_approx[i];

    /* use log-sum-exp (in particular, log-mean-exp) trick to combine values */
    return CMath::log_mean_exp(sum);
}

CMap<TParameter*, SGVector<float64_t> >* CInferenceMethod::
get_negative_log_marginal_likelihood_derivatives(CMap<TParameter*, CSGObject*>* params)
{
    REQUIRE(params->get_num_elements(), "Number of parameters should be greater "
            "than zero\n")

    compute_gradient();

    // get number of derivatives
    const index_t num_deriv=params->get_num_elements();

    // create map of derivatives
    CMap<TParameter*, SGVector<float64_t> >* result=
        new CMap<TParameter*, SGVector<float64_t> >(num_deriv, num_deriv);

    SG_REF(result);

    // create lock object
    CLock lock;

#ifdef HAVE_PTHREAD
    if (num_deriv<2)
    {
#endif /* HAVE_PTHREAD */
        for (index_t i=0; i<num_deriv; i++)
        {
            CMapNode<TParameter*, CSGObject*>* node=params->get_node_ptr(i);

            GRADIENT_THREAD_PARAM thread_params;

            thread_params.inf=this;
            thread_params.obj=node->data;
            thread_params.param=node->key;
            thread_params.grad=result;
            thread_params.lock=&lock;

            get_derivative_helper((void*) &thread_params);
        }
#ifdef HAVE_PTHREAD
    }
    else
    {
        pthread_t* threads=SG_MALLOC(pthread_t, num_deriv);
        GRADIENT_THREAD_PARAM* thread_params=SG_MALLOC(GRADIENT_THREAD_PARAM,
                num_deriv);

        for (index_t t=0; t<num_deriv; t++)
        {
            CMapNode<TParameter*, CSGObject*>* node=params->get_node_ptr(t);

            thread_params[t].inf=this;
            thread_params[t].obj=node->data;
            thread_params[t].param=node->key;
            thread_params[t].grad=result;
            thread_params[t].lock=&lock;

            pthread_create(&threads[t], NULL, CInferenceMethod::get_derivative_helper,
                    (void*)&thread_params[t]);
        }

        for (index_t t=0; t<num_deriv; t++)
            pthread_join(threads[t], NULL);

        SG_FREE(thread_params);
        SG_FREE(threads);
    }
#endif /* HAVE_PTHREAD */

    return result;
}

void* CInferenceMethod::get_derivative_helper(void *p)
{
    GRADIENT_THREAD_PARAM* thread_param=(GRADIENT_THREAD_PARAM*)p;

    CInferenceMethod* inf=thread_param->inf;
    CSGObject* obj=thread_param->obj;
    CMap<TParameter*, SGVector<float64_t> >* grad=thread_param->grad;
    TParameter* param=thread_param->param;
    CLock* lock=thread_param->lock;

    REQUIRE(param, "Parameter should not be NULL\n");
    REQUIRE(obj, "Object of the parameter should not be NULL\n");

    SGVector<float64_t> gradient;

    if (obj==inf)
    {
        // try to find dervative wrt InferenceMethod.parameter
        gradient=inf->get_derivative_wrt_inference_method(param);
    }
    else if (obj==inf->m_model)
    {
        // try to find derivative wrt LikelihoodModel.parameter
        gradient=inf->get_derivative_wrt_likelihood_model(param);
    }
    else if (obj==inf->m_kernel)
    {
        // try to find derivative wrt Kernel.parameter
        gradient=inf->get_derivative_wrt_kernel(param);
    }
    else if (obj==inf->m_mean)
    {
        // try to find derivative wrt MeanFunction.parameter
        gradient=inf->get_derivative_wrt_mean(param);
    }
    else
    {
        SG_SERROR("Can't compute derivative of negative log marginal "
                "likelihood wrt %s.%s", obj->get_name(), param->m_name);
    }

    lock->lock();
    grad->add(param, gradient);
    lock->unlock();

    return NULL;
}

void CInferenceMethod::update()
{
    check_members();
    update_train_kernel();
}

void CInferenceMethod::check_members() const
{
    REQUIRE(m_features, "Training features should not be NULL\n")
    REQUIRE(m_features->get_num_vectors(),
            "Number of training features must be greater than zero\n")
    REQUIRE(m_labels, "Labels should not be NULL\n")
    REQUIRE(m_labels->get_num_labels(),
            "Number of labels must be greater than zero\n")
    REQUIRE(m_labels->get_num_labels()==m_features->get_num_vectors(),
            "Number of training vectors (%d) must match number of labels (%d)\n",
            m_labels->get_num_labels(), m_features->get_num_vectors())
    REQUIRE(m_kernel, "Kernel should not be NULL\n")
    REQUIRE(m_mean, "Mean function should not be NULL\n")
}

void CInferenceMethod::update_train_kernel()
{
    m_kernel->init(m_features, m_features);
    m_ktrtr=m_kernel->get_kernel_matrix();
}

void CInferenceMethod::compute_gradient()
{
    if (parameter_hash_changed())
        update();
}
#endif /* HAVE_EIGEN3 */