SpectrumRBFKernel.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 <vector>

#include <shogun/lib/common.h>
#include <shogun/io/SGIO.h>
#include <shogun/lib/Signal.h>
#include <shogun/lib/Trie.h>
#include <shogun/base/Parallel.h>

#include <shogun/kernel/string/SpectrumRBFKernel.h>
#include <shogun/features/Features.h>
#include <shogun/features/StringFeatures.h>
#include <math.h>

#include <vector>
#include <string>
#include <fstream>
#include <cmath>

#include <assert.h>

#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif


using namespace shogun;

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

CSpectrumRBFKernel::CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t degree_, float64_t width_)
  : CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
{
    lhs=NULL;
    rhs=NULL;

    target_letter_0=-1 ;

    AA_matrix=SG_MALLOC(float64_t, 128*128);


    memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;

    read_profiles_and_sequences();
    SGStringList<char> string_list;
    string_list.strings = sequences;
    string_list.num_strings = nof_sequences;
    string_list.max_string_length = max_sequence_length;

    //string_features = new CStringFeatures<char>(sequences, nof_sequences, max_sequence_length, PROTEIN);
    string_features = new CStringFeatures<char>(string_list, IUPAC_AMINO_ACID);
    init(string_features, string_features);
    register_param();
}

CSpectrumRBFKernel::CSpectrumRBFKernel(
    CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_, int32_t degree_, float64_t width_)
: CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
{
    target_letter_0=-1 ;

    AA_matrix=SG_MALLOC(float64_t, 128*128);
    memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;

    init(l, r);
    register_param();
}

CSpectrumRBFKernel::~CSpectrumRBFKernel()
{
    cleanup();
    SG_FREE(AA_matrix);
}


void CSpectrumRBFKernel::remove_lhs()
{

    CKernel::remove_lhs();
}

void CSpectrumRBFKernel::read_profiles_and_sequences()
{

        int32_t aa_to_index[128];//profile
        aa_to_index[(uint8_t) 'A'] = 0;
        aa_to_index[(uint8_t) 'R'] = 1;
        aa_to_index[(uint8_t) 'N'] = 2;
        aa_to_index[(uint8_t) 'D'] = 3;
        aa_to_index[(uint8_t) 'C'] = 4;
        aa_to_index[(uint8_t) 'Q'] = 5;
        aa_to_index[(uint8_t) 'E'] = 6;
        aa_to_index[(uint8_t) 'G'] = 7;
        aa_to_index[(uint8_t) 'H'] = 8;
        aa_to_index[(uint8_t) 'I'] = 9;
        aa_to_index[(uint8_t) 'L'] = 10;
        aa_to_index[(uint8_t) 'K'] = 11;
        aa_to_index[(uint8_t) 'M'] = 12;
        aa_to_index[(uint8_t) 'F'] = 13;
        aa_to_index[(uint8_t) 'P'] = 14;
        aa_to_index[(uint8_t) 'S'] = 15;
        aa_to_index[(uint8_t) 'T'] = 16;
        aa_to_index[(uint8_t) 'W'] = 17;
        aa_to_index[(uint8_t) 'Y'] = 18;
        aa_to_index[(uint8_t) 'V'] = 19;
    SG_DEBUG("initializing background\n");
    double background[20]; // profile
    background[0]=0.0799912015849807; //A
    background[1]=0.0484482507611578;//R
    background[2]=0.044293531582512;//N
    background[3]=0.0578891399707563;//D
    background[4]=0.0171846021407367;//C
    background[5]=0.0380578923048682;//Q
    background[6]=0.0638169929675978;//E
    background[7]=0.0760659374742852;//G
    background[8]=0.0223465499452473;//H
    background[9]=0.0550905793661343;//I
    background[10]=0.0866897071203864;//L
    background[11]=0.060458245507428;//K
    background[12]=0.0215379186368154;//M
    background[13]=0.0396348024787477;//F
    background[14]=0.0465746314476874;//P
    background[15]=0.0630028230885602;//S
    background[16]=0.0580394726014824;//T
    background[17]=0.0144991866213453;//W
    background[18]=0.03635438623143;//Y
    background[19]=0.0700241481678408;//V


    std::vector<std::string> seqs;
    //int32_t nof_sequences = 7329;

    double C = 0.8;
    const char *filename="/fml/ag-raetsch/home/toussaint/scp/aawd_compbio_workshop/code_nora/data/profile/profiles";
    std::ifstream fin(filename);

    SG_DEBUG("Reading profiles from %s\n", filename);
    std::string line;
    while (!fin.eof())
    {
        std::getline(fin, line);

        if (line[0] == '>') // new sequence
        {
            int idx = line.find_first_of(' ');
            sequence_labels.push_back(line.substr(1,idx-1));
            std::getline(fin, line);
            std::string orig_sequence = line;
            std::string sequence="";

            int len_line = line.length();

            // skip 3 lines

            std::getline(fin, line);
            std::getline(fin, line);
            std::getline(fin, line);

            profiles.push_back(std::vector<double>());

            std::vector<double>& curr_profile = profiles.back();
            for (int i=0; i < len_line; ++i)
            {
                    std::getline(fin, line);
                    int a = line.find_first_not_of(' '); // index position
                    int b = line.find_first_of(' ', a); // index position
                    a = line.find_first_not_of(' ', b); // aa position
                    b = line.find_first_of(' ', a); // aa position
                    std::string aa=line.substr(a,b-a);
                    if (0) //(aa =="B" || aa == "X" || aa == "Z")
                    {
                        int pos = seqs.size()+1;
                        SG_DEBUG("Skipping aa in sequence %d\n", pos);
                    continue;
            }
                    else
                    {
                        sequence += aa;

                        a = line.find_first_not_of(' ', b); // beginning of block to ignore
                        b = line.find_first_of(' ', a); // aa position

                        for (int j=0; j < 19; ++j)
                        {
                            a = line.find_first_not_of(' ', b);
                            b = line.find_first_of(' ', a);
                        }

                        int all_zeros = 1;
                        // interesting block
                        for (int j=0; j < 20; ++j)
                        {
                            a = line.find_first_not_of(' ', b);
                            b = line.find_first_of(' ', a);
                            double p = atof(line.substr(a, b-a).c_str());
                            if (p > 0)
                            {
                                all_zeros = 0;
                            }
                            double value = -1* std::log(C*(p/100)+(1-C)*background[j]); // taken from Leslie's example, C actually corresponds to 1/(1+C)
                            curr_profile.push_back(value);
                            //SG_DEBUG("seq %d aa %d value %f p %f  bg %f\n", i, j, value,p, background[j]);
                        }

                        if (all_zeros)
                        {
                            SG_DEBUG(">>>>>>>>>>>>>>> all zeros");
                            if (aa !="B" && aa != "X" && aa != "Z")
                            {
                                //profile[i][temp_profile_index]=-log(C+(1-C)*background[re_candidate[temp_profile_index]]);
                                int32_t aa_index = aa_to_index[(int)aa.c_str()[0]];
                                double value = -1* std::log(C+(1-C)*background[aa_index]); // taken from Leslie's example, C actually corresponds to 1/(1+C)
                                SG_DEBUG("before %f\n", profiles.back()[(i-1) * 20 + aa_index]);
                                curr_profile[(i*20) + aa_index] = value;
                                SG_DEBUG(">>> aa %c \t %d \t %f\n", aa.c_str()[0], aa_index, value);

                                /*
                                for (int z=0; z <20; ++z)
                                {
                                    SG_DEBUG(" %d \t %f\t", z, curr_profile[z]);
                                }
                                SG_DEBUG("\n");
                                */
                            }
                        }
                    }
            }

            if (curr_profile.size() != 20 * sequence.length())
        {
                SG_ERROR("Something's wrong with the profile.\n");
                break;
            }

            seqs.push_back(sequence);


            /*
            // 6 irrelevant lines
            for (int i=0; i < 6; ++i)
            {
                std::getline(fin, line);
            }
            //
            */
        }
    }

    fin.close();

    nof_sequences = seqs.size();
    sequences = SG_MALLOC(SGString<char>, nof_sequences);

    int max_len = 0;
    for (int i=0; i < nof_sequences; ++i)
    {
        int len = seqs[i].length();
        sequences[i].string = SG_MALLOC(char, len+1);
        sequences[i].slen = len;
        strcpy(sequences[i].string, seqs[i].c_str());

        if (len > max_len) max_len = len;
    }

    max_sequence_length = max_len;
    //string_features = new CStringFeatures<char>(sequences, nof_sequences, max_sequence_length, PROTEIN);

}

bool CSpectrumRBFKernel::init(CFeatures* l, CFeatures* r)
{
    // >> profile
/*
    read_profiles_and_sequences();
    l = string_features;
    r = string_features;
    */
    // << profile

    int32_t lhs_changed=(lhs!=l);
    int32_t rhs_changed=(rhs!=r);

    CStringKernel<char>::init(l,r);

    SG_DEBUG("lhs_changed: %i\n", lhs_changed);
    SG_DEBUG("rhs_changed: %i\n", rhs_changed);

    CStringFeatures<char>* sf_l=(CStringFeatures<char>*) l;
    CStringFeatures<char>* sf_r=(CStringFeatures<char>*) r;

    SG_UNREF(alphabet);
    alphabet=sf_l->get_alphabet();
    CAlphabet* ralphabet=sf_r->get_alphabet();

    if (!((alphabet->get_alphabet()==DNA) || (alphabet->get_alphabet()==RNA)))
        properties &= ((uint64_t) (-1)) ^ (KP_LINADD | KP_BATCHEVALUATION);

    ASSERT(ralphabet->get_alphabet()==alphabet->get_alphabet());
    SG_UNREF(ralphabet);


    return init_normalizer();
}

void CSpectrumRBFKernel::cleanup()
{

    SG_UNREF(alphabet);
    alphabet=NULL;

    CKernel::cleanup();
}

inline bool isaa(char c)
{
  if (c<65 || c>89 || c=='B' || c=='J' || c=='O' || c=='U' || c=='X' || c=='Z')
    return false ;
  return true ;
}

float64_t CSpectrumRBFKernel::AA_helper(const char* path, const int seq_degree, const char* joint_seq, unsigned int index)
{
    //const char* AA = "ARNDCQEGHILKMFPSTWYV";
  float64_t diff=0.0 ;

  for (int i=0; i<seq_degree; i++)
    {
      if (!isaa(path[i])||!isaa(joint_seq[index+i]))
    diff+=1.4 ;
      else
    {
      diff += AA_matrix[ (path[i]-1)*128 + path[i] - 1] ;
      diff -= 2*AA_matrix[ (path[i]-1)*128 + joint_seq[index+i] - 1] ;
      diff += AA_matrix[ (joint_seq[index+i]-1)*128 + joint_seq[index+i] - 1] ;
      if (CMath::is_nan(diff))
        fprintf(stderr, "nan occurred: '%c' '%c'\n", path[i], joint_seq[index+i]) ;
    }
    }

  return exp( - diff/width) ;
}

float64_t CSpectrumRBFKernel::compute(int32_t idx_a, int32_t idx_b)
{
    int32_t alen, blen;
    bool afree, bfree;

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

    float64_t result=0;
    for (int32_t i=0; i<alen; i++)
      {
        for (int32_t j=0; j<blen; j++)
          {
        if ((i+degree<=alen) && (j+degree<=blen))
          result += AA_helper(&(avec[i]), degree, bvec, j) ;
          }
      }

    ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, afree);
    ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, bfree);
    return result;
}

bool CSpectrumRBFKernel::set_AA_matrix(
    float64_t* AA_matrix_)
{

    if (AA_matrix_)
    {
        SG_DEBUG("Setting AA_matrix\n") ;
        memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
        return true ;
    }

    return false;
}

void CSpectrumRBFKernel::register_param()
{
    SG_ADD(&degree, "degree", "degree of the kernel", MS_AVAILABLE);
    SG_ADD(&AA_matrix_length, "AA_matrix_length", "the length of AA matrix",
        MS_NOT_AVAILABLE);
    m_parameters->add_vector(&AA_matrix, &AA_matrix_length, "AA_matrix", "128*128 scalar product matrix");
    SG_ADD(&width, "width", "width of Gaussian", MS_AVAILABLE);
    SG_ADD(&nof_sequences, "nof_sequences", "length of the sequence",
        MS_NOT_AVAILABLE);
    m_parameters->add_vector(&sequences, &nof_sequences, "the sequences as a part of profile");
    SG_ADD(&max_sequence_length,
        "max_sequence_length", "max length of the sequence", MS_NOT_AVAILABLE);
}

void CSpectrumRBFKernel::register_alphabet()
{
    SG_ADD((CSGObject**)&alphabet, "alphabet", "the alphabet used by kernel",
        MS_NOT_AVAILABLE);
}

void CSpectrumRBFKernel::init()
{
    alphabet = NULL;
    degree = 0;
    AA_matrix = NULL;
    AA_matrix_length = 128*128;
    width = 0.0;
    sequences = NULL;
    string_features = NULL;
    nof_sequences = 0;
    max_sequence_length = 0;

    initialized = false;

    max_mismatch = 0;
    target_letter_0 = 0;
}