LinearHMM.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) 1999-2009 Soeren Sonnenburg
 * 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/base/Parameter.h>

#include <shogun/distributions/LinearHMM.h>
#include <shogun/features/StringFeatures.h>

using namespace shogun;

CLinearHMM::CLinearHMM() : CDistribution()
{
    init();
}

CLinearHMM::CLinearHMM(CStringFeatures<uint16_t>* f)
: CDistribution()
{
    init();

    set_features(f);
    sequence_length = f->get_vector_length(0);
    num_symbols     = (int32_t) f->get_num_symbols();
    num_params      = sequence_length*num_symbols;
}

CLinearHMM::CLinearHMM(int32_t p_num_features, int32_t p_num_symbols)
: CDistribution()
{
    init();

    sequence_length = p_num_features;
    num_symbols     = p_num_symbols;
    num_params      = sequence_length*num_symbols;
}

CLinearHMM::~CLinearHMM()
{
    SG_FREE(transition_probs);
    SG_FREE(log_transition_probs);
}

bool CLinearHMM::train(CFeatures* data)
{
    if (data)
    {
        if (data->get_feature_class() != C_STRING ||
                data->get_feature_type() != F_WORD)
        {
            SG_ERROR("Expected features of class string type word!\n");
        }
        set_features(data);
    }
    SG_FREE(transition_probs);
    SG_FREE(log_transition_probs);
    int32_t* int_transition_probs=SG_MALLOC(int32_t, num_params);

    int32_t vec;
    int32_t i;

    for (i=0; i< num_params; i++)
        int_transition_probs[i]=0;

    for (vec=0; vec<features->get_num_vectors(); vec++)
    {
        int32_t len;
        bool free_vec;

        uint16_t* vector=((CStringFeatures<uint16_t>*) features)->
            get_feature_vector(vec, len, free_vec);

        //just count the symbols per position -> transition_probsogram
        for (int32_t feat=0; feat<len ; feat++)
            int_transition_probs[feat*num_symbols+vector[feat]]++;

        ((CStringFeatures<uint16_t>*) features)->
            free_feature_vector(vector, vec, free_vec);
    }

    //trade memory for speed
    transition_probs=SG_MALLOC(float64_t, num_params);
    log_transition_probs=SG_MALLOC(float64_t, num_params);

    for (i=0;i<sequence_length;i++)
    {
        for (int32_t j=0; j<num_symbols; j++)
        {
            float64_t sum=0;
            int32_t offs=i*num_symbols+
                ((CStringFeatures<uint16_t> *) features)->
                    get_masked_symbols((uint16_t)j,(uint8_t) 254);
            int32_t original_num_symbols=(int32_t)
                ((CStringFeatures<uint16_t> *) features)->
                    get_original_num_symbols();

            for (int32_t k=0; k<original_num_symbols; k++)
                sum+=int_transition_probs[offs+k];

            transition_probs[i*num_symbols+j]=
                (int_transition_probs[i*num_symbols+j]+pseudo_count)/
                (sum+((CStringFeatures<uint16_t> *) features)->
                    get_original_num_symbols()*pseudo_count);
            log_transition_probs[i*num_symbols+j]=
                log(transition_probs[i*num_symbols+j]);
        }
    }

    SG_FREE(int_transition_probs);
    return true;
}

bool CLinearHMM::train(
    const int32_t* indizes, int32_t num_indizes, float64_t pseudo)
{
    SG_FREE(transition_probs);
    SG_FREE(log_transition_probs);
    int32_t* int_transition_probs=SG_MALLOC(int32_t, num_params);
    int32_t vec;
    int32_t i;

    for (i=0; i< num_params; i++)
        int_transition_probs[i]=0;

    for (vec=0; vec<num_indizes; vec++)
    {
        int32_t len;
        bool free_vec;

        ASSERT(indizes[vec]>=0 &&
            indizes[vec]<((CStringFeatures<uint16_t>*) features)->
                get_num_vectors());
        uint16_t* vector=((CStringFeatures<uint16_t>*) features)->
            get_feature_vector(indizes[vec], len, free_vec);
        ((CStringFeatures<uint16_t>*) features)->
            free_feature_vector(vector, indizes[vec], free_vec);

        //just count the symbols per position -> transition_probsogram
        //
        for (int32_t feat=0; feat<len ; feat++)
            int_transition_probs[feat*num_symbols+vector[feat]]++;
    }

    //trade memory for speed
    transition_probs=SG_MALLOC(float64_t, num_params);
    log_transition_probs=SG_MALLOC(float64_t, num_params);

    for (i=0;i<sequence_length;i++)
    {
        for (int32_t j=0; j<num_symbols; j++)
        {
            float64_t sum=0;
            int32_t original_num_symbols=(int32_t)
                ((CStringFeatures<uint16_t> *) features)->
                    get_original_num_symbols();
            for (int32_t k=0; k<original_num_symbols; k++)
            {
                sum+=int_transition_probs[i*num_symbols+
                    ((CStringFeatures<uint16_t>*) features)->
                        get_masked_symbols((uint16_t)j,(uint8_t) 254)+k];
            }

            transition_probs[i*num_symbols+j]=
                (int_transition_probs[i*num_symbols+j]+pseudo)/
                (sum+((CStringFeatures<uint16_t>*) features)->
                    get_original_num_symbols()*pseudo);
            log_transition_probs[i*num_symbols+j]=
                log(transition_probs[i*num_symbols+j]);
        }
    }

    SG_FREE(int_transition_probs);
    return true;
}

float64_t CLinearHMM::get_log_likelihood_example(uint16_t* vector, int32_t len)
{
    float64_t result=log_transition_probs[vector[0]];

    for (int32_t i=1; i<len; i++)
        result+=log_transition_probs[i*num_symbols+vector[i]];
    
    return result;
}

float64_t CLinearHMM::get_log_likelihood_example(int32_t num_example)
{
    int32_t len;
    bool free_vec;
    uint16_t* vector=((CStringFeatures<uint16_t>*) features)->
        get_feature_vector(num_example, len, free_vec);
    float64_t result=log_transition_probs[vector[0]];

    for (int32_t i=1; i<len; i++)
        result+=log_transition_probs[i*num_symbols+vector[i]];

    ((CStringFeatures<uint16_t>*) features)->
        free_feature_vector(vector, num_example, free_vec);

    return result;
}

float64_t CLinearHMM::get_likelihood_example(uint16_t* vector, int32_t len)
{
    float64_t result=transition_probs[vector[0]];

    for (int32_t i=1; i<len; i++)
        result*=transition_probs[i*num_symbols+vector[i]];
    
    return result;
}

float64_t CLinearHMM::get_log_derivative(int32_t num_param, int32_t num_example)
{
    int32_t len;
    bool free_vec;
    uint16_t* vector=((CStringFeatures<uint16_t>*) features)->
        get_feature_vector(num_example, len, free_vec);
    float64_t result=0;
    int32_t position=num_param/num_symbols;
    ASSERT(position>=0 && position<len);
    uint16_t sym=(uint16_t) (num_param-position*num_symbols);

    if (vector[position]==sym && transition_probs[num_param]!=0)
        result=1.0/transition_probs[num_param];
    ((CStringFeatures<uint16_t>*) features)->
        free_feature_vector(vector, num_example, free_vec);

    return result;
}

SGVector<float64_t> CLinearHMM::get_transition_probs()
{
    return SGVector<float64_t>(transition_probs, num_params);   
}

bool CLinearHMM::set_transition_probs(SGVector<float64_t> probs)
{
    ASSERT(probs.vlen == num_params);   

    if (!log_transition_probs)
        log_transition_probs=SG_MALLOC(float64_t, num_params);

    if (!transition_probs)
        transition_probs=SG_MALLOC(float64_t, num_params);

    for (int32_t i=0; i<num_params; i++)
    {
        transition_probs[i]=probs.vector[i];
        log_transition_probs[i]=log(transition_probs[i]);
    }

    return true;
}

SGVector<float64_t> CLinearHMM::get_log_transition_probs()
{
    return SGVector<float64_t>(log_transition_probs, num_params);
}

bool CLinearHMM::set_log_transition_probs(SGVector<float64_t> probs)
{
    ASSERT(probs.vlen == num_params);

    if (!log_transition_probs)
        log_transition_probs=SG_MALLOC(float64_t, num_params);

    if (!transition_probs)
        transition_probs=SG_MALLOC(float64_t, num_params);

    for (int32_t i=0; i<num_params; i++)
    {
        log_transition_probs[i]=probs.vector[i];
        transition_probs[i]=exp(log_transition_probs[i]);
    }

    return true;
}

void CLinearHMM::load_serializable_post() throw (ShogunException)
{
    CSGObject::load_serializable_post();

    num_params = sequence_length*num_symbols;
}

void CLinearHMM::init()
{
    sequence_length = 0;
    num_symbols = 0;
    num_params = 0;
    transition_probs = NULL;
    log_transition_probs = NULL;

    m_parameters->add_matrix(&transition_probs, &num_symbols, &sequence_length,
            "transition_probs", "Transition probabilities.");
    m_parameters->add_matrix(&log_transition_probs, &num_symbols, &sequence_length,
            "log_transition_probs", "Transition probabilities (logspace).");
}