LocalityImprovedStringKernel.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
 * Written (W) 1999-2008 Soeren Sonnenburg
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

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

using namespace shogun;

CLocalityImprovedStringKernel::CLocalityImprovedStringKernel()
: CStringKernel<char>(0)
{
    init();
}

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

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

    SG_INFO( "LIK with parms: l=%d, id=%d, od=%d created!\n", l, id, od);
}

CLocalityImprovedStringKernel::CLocalityImprovedStringKernel(
    CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t len,
    int32_t id, int32_t od)
: CStringKernel<char>(10)
{
    init();

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

    SG_INFO( "LIK with parms: l=%d, id=%d, od=%d created!\n", len, id, od);

    init(l, r);
}

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

bool CLocalityImprovedStringKernel::init(CFeatures* l, CFeatures* r)
{
    CStringKernel<char>::init(l,r);
    return init_normalizer();
}

float64_t CLocalityImprovedStringKernel::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 && alen>0);

    int32_t i,t;
    float64_t* match=SG_MALLOC(float64_t, alen);

    // initialize match table 1 -> match;  0 -> no match
    for (i = 0; i<alen; i++)
        match[i] = (avec[i] == bvec[i])? 1 : 0;

    float64_t outer_sum = 0;

    for (t = 0; t<alen-length; t++)
    {
        float64_t sum = 0;
        for (i = 0; i<length && t+i+length+1<alen; i++)
            sum += (i+1)*match[t+i]+(length-i)*match[t+i+length+1];
        //add middle element + normalize with sum_i=0^2l+1 i = (2l+1)(l+1)
        float64_t inner_sum = (sum + (length+1)*match[t+length]) / ((2*length+1)*(length+1));
        inner_sum = pow(inner_sum, inner_degree + 1);
        outer_sum += inner_sum;
    }
    SG_FREE(match);

    ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
    ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
    return pow(outer_sum, outer_degree + 1);
}

void CLocalityImprovedStringKernel::init()
{
    length = 0;
    inner_degree = 0;
    outer_degree = 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.");
}