SimpleLocalityImprovedStringKernel.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) 1999-2008 Gunnar Raetsch
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#include <shogun/lib/common.h>
#include <shogun/io/SGIO.h>
#include <shogun/kernel/SimpleLocalityImprovedStringKernel.h>
#include <shogun/features/Features.h>
#include <shogun/features/StringFeatures.h>

using namespace shogun;

CSimpleLocalityImprovedStringKernel::CSimpleLocalityImprovedStringKernel()
: CStringKernel<char>()
{
    init();
}

CSimpleLocalityImprovedStringKernel::CSimpleLocalityImprovedStringKernel(
    int32_t size, int32_t l, int32_t id, int32_t od)
: CStringKernel<char>(size)
{
    init();

    length=l;
    inner_degree=id;
    outer_degree=od;
}

CSimpleLocalityImprovedStringKernel::CSimpleLocalityImprovedStringKernel(
    CStringFeatures<char>* l, CStringFeatures<char>* r,
    int32_t len, int32_t id, int32_t od)
: CStringKernel<char>()
{
    init();

    length=len;
    inner_degree=id;
    outer_degree=od;

    init(l, r);
}

CSimpleLocalityImprovedStringKernel::~CSimpleLocalityImprovedStringKernel()
{
    cleanup();
}

bool CSimpleLocalityImprovedStringKernel::init(CFeatures* l, CFeatures* r)
{
    bool result = CStringKernel<char>::init(l,r);

    if (!result)
        return false;
    const int32_t num_features = ((CStringFeatures<char>*) l)->get_max_vector_length();
    const int32_t PYRAL = 2 * length - 1; // total window length
    const int32_t pyra_len  = num_features-PYRAL+1;
    const int32_t pyra_len2 = (int32_t) pyra_len/2;

    SG_FREE(pyramid_weights);

    pyramid_weights = SG_MALLOC(float64_t, pyra_len);
    num_pyramid_weights=pyra_len;

    SG_INFO("initializing pyramid weights: size=%ld length=%i\n",
        num_features, length);

    float64_t PYRAL_pot;
    int32_t DEGREE1_1  = (inner_degree & 0x1)==0;
    int32_t DEGREE1_1n = (inner_degree & ~0x1)!=0;
    int32_t DEGREE1_2  = (inner_degree & 0x2)!=0;
    int32_t DEGREE1_3  = (inner_degree & ~0x3)!=0;
    int32_t DEGREE1_4  = (inner_degree & 0x4)!=0;
    {
    float64_t PYRAL_ = PYRAL;
    PYRAL_pot = DEGREE1_1 ? 1.0 : PYRAL_;
    if (DEGREE1_1n)
    {
        PYRAL_ *= PYRAL_;
        if (DEGREE1_2)
            PYRAL_pot *= PYRAL_;
        if (DEGREE1_3)
        {
            PYRAL_ *= PYRAL_;
            if (DEGREE1_4)
                PYRAL_pot *= PYRAL_;
        }
    }
    }

    {
    int32_t j;
    for (j = 0; j < pyra_len; j++)
        pyramid_weights[j] = 4*((float64_t)((j < pyra_len2)? j+1 : pyra_len-j))/((float64_t)pyra_len);
    for (j = 0; j < pyra_len; j++)
        pyramid_weights[j] /= PYRAL_pot;
    }

    return init_normalizer();
}

void CSimpleLocalityImprovedStringKernel::cleanup()
{
    SG_FREE(pyramid_weights);
    pyramid_weights = NULL;
    num_pyramid_weights = 0;

    CKernel::cleanup();
}

float64_t CSimpleLocalityImprovedStringKernel::dot_pyr (const char* const x1,
         const char* const x2, const int32_t NOF_NTS, const int32_t NTWIDTH,
         const int32_t DEGREE1, const int32_t DEGREE2, float64_t *pyra)
{
    const int32_t PYRAL = 2*NTWIDTH-1; // total window length
    int32_t pyra_len, pyra_len2;
    float64_t pot, PYRAL_pot;
    float64_t sum;
    int32_t DEGREE1_1 = (DEGREE1 & 0x1)==0;
    int32_t DEGREE1_1n = (DEGREE1 & ~0x1)!=0;
    int32_t DEGREE1_2 = (DEGREE1 & 0x2)!=0;
    int32_t DEGREE1_3 = (DEGREE1 & ~0x3)!=0;
    int32_t DEGREE1_4 = (DEGREE1 & 0x4)!=0;
    {
    float64_t PYRAL_ = PYRAL;
    PYRAL_pot = DEGREE1_1 ? 1.0 : PYRAL_;
    if (DEGREE1_1n)
    {
        PYRAL_ *= PYRAL_;
        if (DEGREE1_2) PYRAL_pot *= PYRAL_;
        if (DEGREE1_3)
        {
            PYRAL_ *= PYRAL_;
            if (DEGREE1_4) PYRAL_pot *= PYRAL_;
        }
    }
    }

    ASSERT((DEGREE1 & ~0x7) == 0);
    ASSERT((DEGREE2 & ~0x7) == 0);

    pyra_len = NOF_NTS-PYRAL+1;
    pyra_len2 = (int32_t) pyra_len/2;
    {
    int32_t j;
    for (j = 0; j < pyra_len; j++)
        pyra[j] = 4*((float64_t)((j < pyra_len2) ? j+1 : pyra_len-j))/((float64_t)pyra_len);
    for (j = 0; j < pyra_len; j++)
        pyra[j] /= PYRAL_pot;
    }

    register int32_t conv;
    register int32_t i;
    register int32_t j;

    sum = 0.0;
    conv = 0;
    for (j = 0; j < PYRAL; j++)
        conv += (x1[j] == x2[j]) ? 1 : 0;

    for (i = 0; i < NOF_NTS-PYRAL+1; i++)
    {
        register float64_t pot2;
        if (i>0)
            conv += ((x1[i+PYRAL-1] == x2[i+PYRAL-1]) ? 1 : 0 ) - 
                ((x1[i-1] == x2[i-1]) ? 1 : 0);
        { /* potencing of conv -- float64_t is faster*/
        register float64_t conv2 = conv;
        pot2 = (DEGREE1_1) ? 1.0 : conv2;
            if (DEGREE1_1n)
            {
                conv2 *= conv2;
                if (DEGREE1_2)
                    pot2 *= conv2;
                if (DEGREE1_3 && DEGREE1_4)
                    pot2 *= conv2*conv2;
            }
        }
        sum += pot2*pyra[i];
    }

    pot = ((DEGREE2 & 0x1) == 0) ? 1.0 : sum;
    if ((DEGREE2 & ~0x1) != 0)
    {
        sum *= sum;
        if ((DEGREE2 & 0x2) != 0)
            pot *= sum;
        if ((DEGREE2 & ~0x3) != 0)
        {
            sum *= sum;
            if ((DEGREE2 & 0x4) != 0)
                pot *= sum;
        }
    }
    return pot;
}

float64_t CSimpleLocalityImprovedStringKernel::compute(
    int32_t idx_a, int32_t idx_b)
{
    int32_t alen, blen;
    bool free_avec, free_bvec;

    char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
    char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);

    // can only deal with strings of same length
    ASSERT(alen==blen);

    float64_t dpt;

    dpt = dot_pyr(avec, bvec, alen, length, inner_degree, outer_degree, pyramid_weights);
    dpt = dpt / pow((float64_t) alen, (float64_t) outer_degree);

    ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
    ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
    return (float64_t) dpt;
}

void CSimpleLocalityImprovedStringKernel::init()
{
    length = 3;
    inner_degree = 3;
    outer_degree = 1;
    pyramid_weights=NULL;
    num_pyramid_weights=0;

    m_parameters->add(&length, "length", "Window Length.");
    m_parameters->add(&inner_degree, "inner_degree", "Inner degree.");
    m_parameters->add(&outer_degree, "outer_degree", "Outer degree.");

    m_parameters->add_vector(&pyramid_weights, &num_pyramid_weights,
            "pyramid_weights", "Pyramid weights.");
}