LaplacianEigenmaps.cpp

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2011 Sergey Lisitsyn
 * Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
 */

#include <shogun/converter/LaplacianEigenmaps.h>
#include <shogun/converter/EmbeddingConverter.h>
#ifdef HAVE_LAPACK
#include <shogun/mathematics/arpack.h>
#include <shogun/mathematics/lapack.h>
#include <shogun/lib/FibonacciHeap.h>
#include <shogun/mathematics/Math.h>
#include <shogun/io/SGIO.h>
#include <shogun/distance/Distance.h>
#include <shogun/lib/Signal.h>

using namespace shogun;

CLaplacianEigenmaps::CLaplacianEigenmaps() :
        CEmbeddingConverter()
{
    m_k = 3;
    m_tau = 1.0;

    init();
}

void CLaplacianEigenmaps::init()
{
    SG_ADD(&m_k, "k", "number of neighbors", MS_AVAILABLE);
    SG_ADD(&m_tau, "tau", "heat distribution coefficient", MS_AVAILABLE);
}

CLaplacianEigenmaps::~CLaplacianEigenmaps()
{
}

void CLaplacianEigenmaps::set_k(int32_t k)
{
    ASSERT(k>0);
    m_k = k;
}

int32_t CLaplacianEigenmaps::get_k() const
{
    return m_k;
}

void CLaplacianEigenmaps::set_tau(float64_t tau)
{
    m_tau = tau;
}

float64_t CLaplacianEigenmaps::get_tau() const
{
    return m_tau;
}

const char* CLaplacianEigenmaps::get_name() const
{
    return "LaplacianEigenmaps";
};

CFeatures* CLaplacianEigenmaps::apply(CFeatures* features)
{
    // shorthand for simplefeatures
    SG_REF(features);

    // get dimensionality and number of vectors of data
    int32_t N = features->get_num_vectors();
    ASSERT(m_k<N);
    ASSERT(m_target_dim<N);

    // compute distance matrix
    ASSERT(m_distance);
    m_distance->init(features,features);
    CDenseFeatures<float64_t>* embedding = embed_distance(m_distance,features);
    m_distance->remove_lhs_and_rhs();
    SG_UNREF(features);
    return (CFeatures*)embedding;
}

CDenseFeatures<float64_t>* CLaplacianEigenmaps::embed_distance(CDistance* distance, CFeatures* features)
{
    int32_t i,j;
    SGMatrix<float64_t> W_sgmatrix = distance->get_distance_matrix();
    ASSERT(W_sgmatrix.num_rows==W_sgmatrix.num_cols);
    int32_t N = W_sgmatrix.num_rows;
    // shorthand
    float64_t* W_matrix = W_sgmatrix.matrix;

    // init heap to use
    CFibonacciHeap* heap = new CFibonacciHeap(N);
    float64_t tmp;
    // for each object
    for (i=0; i<N; i++)
    {
        // fill heap
        for (j=0; j<N; j++)
            heap->insert(j,W_matrix[i*N+j]);

        // rearrange heap with extracting ith object itself
        heap->extract_min(tmp);

        // extract nearest neighbors, takes ~O(k*log n), and change sign for them
        for (j=0; j<m_k; j++)
            W_matrix[i*N+heap->extract_min(tmp)] *= -1.0;

        // remove all 'positive' distances and change 'negative' ones to positive
        for (j=0; j<N; j++)
        {
            if (W_matrix[i*N+j]>0.0)
                W_matrix[i*N+j] = 0.0;
            else
                W_matrix[i*N+j] *= -1.0;
        }

        // clear heap to reuse
        heap->clear();
    }
    delete heap;
    // make distance matrix symmetric with mutual kNN relation
    for (i=0; i<N; i++)
    {
        // check only upper triangle
        for (j=i; j<N; j++)
        {
            // make kNN relation symmetric
            if (W_matrix[i*N+j]!=0.0 || W_matrix[j*N+i]==0.0)
            {
                W_matrix[j*N+i] = W_matrix[i*N+j];
            }
            if (W_matrix[j*N+i]!=0.0 || W_matrix[i*N+j]==0.0)
            {
                W_matrix[i*N+j] = W_matrix[j*N+i];
            }

            if (W_matrix[i*N+j] != 0.0)
            {
                // compute heat, exp(-d^2/tau)
                tmp = CMath::exp(-CMath::sq(W_matrix[i*N+j])/m_tau);
                W_matrix[i*N+j] = tmp;
                W_matrix[j*N+i] = tmp;
            }
        }
    }

    // compute D
    CDenseFeatures<float64_t>* embedding = construct_embedding(features,W_sgmatrix);

    return embedding;
}

CDenseFeatures<float64_t>* CLaplacianEigenmaps::construct_embedding(CFeatures* features,
                                                                     SGMatrix<float64_t> W_matrix)
{
    int32_t i,j;
    int32_t N = W_matrix.num_cols;

    float64_t* D_diag_vector = SG_CALLOC(float64_t, N);
    for (i=0; i<N; i++)
    {
        for (j=0; j<N; j++)
            D_diag_vector[i] += W_matrix[i*N+j];
    }

    // W = -W
    for (i=0; i<N*N; i++)
        if (W_matrix[i]>0.0)
            W_matrix[i] *= -1.0;
    // W = W + D
    for (i=0; i<N; i++)
        W_matrix[i*N+i] += D_diag_vector[i];

#ifdef HAVE_ARPACK
    // using ARPACK DS{E,A}UPD
    int eigenproblem_status = 0;
    float64_t* eigenvalues_vector = SG_MALLOC(float64_t,m_target_dim+1);
    arpack_dsxupd(W_matrix.matrix,D_diag_vector,true,N,m_target_dim+1,"LA",true,3,false,false,-1e-9,0.0,
                  eigenvalues_vector,W_matrix.matrix,eigenproblem_status);

    if (eigenproblem_status!=0)
        SG_ERROR("DSXUPD failed with code %d\n",eigenproblem_status);

    SG_FREE(eigenvalues_vector);
#else /* HAVE_ARPACK */
    // using LAPACK DSYGVX
    // requires 2x memory because of dense rhs matrix usage
    int eigenproblem_status = 0;
    float64_t* eigenvalues_vector = SG_MALLOC(float64_t,N);
    float64_t* rhs = SG_CALLOC(float64_t,N*N);
    // fill rhs with diag (for safety reasons zeros will be replaced with 1e-3)
    for (i=0; i<N; i++)
        rhs[i*N+i] = D_diag_vector[i];

    wrap_dsygvx(1,'V','U',N,W_matrix.matrix,N,rhs,N,1,m_target_dim+2,eigenvalues_vector,W_matrix.matrix,&eigenproblem_status);

    if (eigenproblem_status)
        SG_ERROR("DSYGVX failed with code: %d.\n",eigenproblem_status);

    SG_FREE(rhs);
    SG_FREE(eigenvalues_vector);

#endif /* HAVE_ARPACK */
    SG_FREE(D_diag_vector);

    SGMatrix<float64_t> new_features = SGMatrix<float64_t>(m_target_dim,N);
    // fill features according to used solver
    for (i=0; i<m_target_dim; i++)
    {
        for (j=0; j<N; j++)
        {
            #ifdef HAVE_ARPACK
                new_features[j*m_target_dim+i] = W_matrix[j*(m_target_dim+1)+i+1];
            #else
                new_features[j*m_target_dim+i] = W_matrix[(i+1)*N+j];
            #endif
        }
    }
    return new CDenseFeatures<float64_t>(new_features);
}

#endif /* HAVE_LAPACK */