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SpectrumRBFKernel.cpp
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00001 /*
00002  * This program is free software; you can redistribute it and/or modify
00003  * it under the terms of the GNU General Public License as published by
00004  * the Free Software Foundation; either version 3 of the License, or
00005  * (at your option) any later version.
00006  *
00007  * Written (W) 1999-2009 Soeren Sonnenburg
00008  * Written (W) 1999-2008 Gunnar Raetsch
00009  * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
00010  */
00011 
00012 #include <vector>
00013 
00014 #include <shogun/lib/common.h>
00015 #include <shogun/io/SGIO.h>
00016 #include <shogun/lib/Signal.h>
00017 #include <shogun/lib/Trie.h>
00018 #include <shogun/base/Parallel.h>
00019 
00020 #include <shogun/kernel/string/SpectrumRBFKernel.h>
00021 #include <shogun/features/Features.h>
00022 #include <shogun/features/StringFeatures.h>
00023 #include <shogun/lib/SGStringList.h>
00024 #include <math.h>
00025 
00026 #include <vector>
00027 #include <string>
00028 #include <fstream>
00029 #include <cmath>
00030 
00031 #include <assert.h>
00032 
00033 #ifdef HAVE_PTHREAD
00034 #include <pthread.h>
00035 #endif
00036 
00037 
00038 using namespace shogun;
00039 
00040 CSpectrumRBFKernel::CSpectrumRBFKernel()
00041   : CStringKernel<char>(0)
00042 {
00043     init();
00044     register_param();
00045 }
00046 
00047 CSpectrumRBFKernel::CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t degree_, float64_t width_)
00048   : CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
00049 {
00050     init();
00051     register_param();
00052 
00053     target_letter_0=-1 ;
00054 
00055     AA_matrix=SGMatrix<float64_t>(128,128);
00056 
00057     memcpy(AA_matrix.matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00058 
00059     read_profiles_and_sequences();
00060     SGStringList<char> string_list;
00061     string_list.strings = sequences;
00062     string_list.num_strings = nof_sequences;
00063     string_list.max_string_length = max_sequence_length;
00064 
00065     //string_features = new CStringFeatures<char>(sequences, nof_sequences, max_sequence_length, PROTEIN);
00066     string_features = new CStringFeatures<char>(string_list, IUPAC_AMINO_ACID);
00067     SG_REF(string_features)
00068     init(string_features, string_features);
00069 }
00070 
00071 CSpectrumRBFKernel::CSpectrumRBFKernel(
00072     CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_, int32_t degree_, float64_t width_)
00073 : CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
00074 {
00075     target_letter_0=-1 ;
00076 
00077     AA_matrix=SGMatrix<float64_t>(128,128);
00078     memcpy(AA_matrix.matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00079 
00080     init(l, r);
00081     register_param();
00082 }
00083 
00084 CSpectrumRBFKernel::~CSpectrumRBFKernel()
00085 {
00086     cleanup();
00087     SG_UNREF(string_features);
00088     SG_FREE(sequences);
00089 }
00090 
00091 void CSpectrumRBFKernel::read_profiles_and_sequences()
00092 {
00093 
00094         int32_t aa_to_index[128];//profile
00095         aa_to_index[(uint8_t) 'A'] = 0;
00096         aa_to_index[(uint8_t) 'R'] = 1;
00097         aa_to_index[(uint8_t) 'N'] = 2;
00098         aa_to_index[(uint8_t) 'D'] = 3;
00099         aa_to_index[(uint8_t) 'C'] = 4;
00100         aa_to_index[(uint8_t) 'Q'] = 5;
00101         aa_to_index[(uint8_t) 'E'] = 6;
00102         aa_to_index[(uint8_t) 'G'] = 7;
00103         aa_to_index[(uint8_t) 'H'] = 8;
00104         aa_to_index[(uint8_t) 'I'] = 9;
00105         aa_to_index[(uint8_t) 'L'] = 10;
00106         aa_to_index[(uint8_t) 'K'] = 11;
00107         aa_to_index[(uint8_t) 'M'] = 12;
00108         aa_to_index[(uint8_t) 'F'] = 13;
00109         aa_to_index[(uint8_t) 'P'] = 14;
00110         aa_to_index[(uint8_t) 'S'] = 15;
00111         aa_to_index[(uint8_t) 'T'] = 16;
00112         aa_to_index[(uint8_t) 'W'] = 17;
00113         aa_to_index[(uint8_t) 'Y'] = 18;
00114         aa_to_index[(uint8_t) 'V'] = 19;
00115     SG_DEBUG("initializing background\n")
00116     double background[20]; // profile
00117     background[0]=0.0799912015849807; //A
00118     background[1]=0.0484482507611578;//R
00119     background[2]=0.044293531582512;//N
00120     background[3]=0.0578891399707563;//D
00121     background[4]=0.0171846021407367;//C
00122     background[5]=0.0380578923048682;//Q
00123     background[6]=0.0638169929675978;//E
00124     background[7]=0.0760659374742852;//G
00125     background[8]=0.0223465499452473;//H
00126     background[9]=0.0550905793661343;//I
00127     background[10]=0.0866897071203864;//L
00128     background[11]=0.060458245507428;//K
00129     background[12]=0.0215379186368154;//M
00130     background[13]=0.0396348024787477;//F
00131     background[14]=0.0465746314476874;//P
00132     background[15]=0.0630028230885602;//S
00133     background[16]=0.0580394726014824;//T
00134     background[17]=0.0144991866213453;//W
00135     background[18]=0.03635438623143;//Y
00136     background[19]=0.0700241481678408;//V
00137 
00138 
00139     std::vector<std::string> seqs;
00140     //int32_t nof_sequences = 7329;
00141 
00142     double C = 0.8;
00143     const char *filename="/fml/ag-raetsch/home/toussaint/scp/aawd_compbio_workshop/code_nora/data/profile/profiles";
00144     std::ifstream fin(filename);
00145 
00146     SG_DEBUG("Reading profiles from %s\n", filename)
00147     std::string line;
00148     while (!fin.eof())
00149     {
00150         std::getline(fin, line);
00151 
00152         if (line[0] == '>') // new sequence
00153         {
00154             int idx = line.find_first_of(' ');
00155             sequence_labels.push_back(line.substr(1,idx-1));
00156             std::getline(fin, line);
00157             std::string orig_sequence = line;
00158             std::string sequence="";
00159 
00160             int len_line = line.length();
00161 
00162             // skip 3 lines
00163 
00164             std::getline(fin, line);
00165             std::getline(fin, line);
00166             std::getline(fin, line);
00167 
00168             profiles.push_back(std::vector<double>());
00169 
00170             std::vector<double>& curr_profile = profiles.back();
00171             for (int i=0; i < len_line; ++i)
00172             {
00173                     std::getline(fin, line);
00174                     int a = line.find_first_not_of(' '); // index position
00175                     int b = line.find_first_of(' ', a); // index position
00176                     a = line.find_first_not_of(' ', b); // aa position
00177                     b = line.find_first_of(' ', a); // aa position
00178                     std::string aa=line.substr(a,b-a);
00179                     if (0) //(aa =="B" || aa == "X" || aa == "Z")
00180                     {
00181                         int pos = seqs.size()+1;
00182                         SG_DEBUG("Skipping aa in sequence %d\n", pos)
00183                     continue;
00184             }
00185                     else
00186                     {
00187                         sequence += aa;
00188 
00189                         a = line.find_first_not_of(' ', b); // beginning of block to ignore
00190                         b = line.find_first_of(' ', a); // aa position
00191 
00192                         for (int j=0; j < 19; ++j)
00193                         {
00194                             a = line.find_first_not_of(' ', b);
00195                             b = line.find_first_of(' ', a);
00196                         }
00197 
00198                         int all_zeros = 1;
00199                         // interesting block
00200                         for (int j=0; j < 20; ++j)
00201                         {
00202                             a = line.find_first_not_of(' ', b);
00203                             b = line.find_first_of(' ', a);
00204                             double p = atof(line.substr(a, b-a).c_str());
00205                             if (p > 0)
00206                             {
00207                                 all_zeros = 0;
00208                             }
00209                             double value = -1* std::log(C*(p/100)+(1-C)*background[j]); // taken from Leslie's example, C actually corresponds to 1/(1+C)
00210                             curr_profile.push_back(value);
00211                             //SG_DEBUG("seq %d aa %d value %f p %f  bg %f\n", i, j, value,p, background[j])
00212                         }
00213 
00214                         if (all_zeros)
00215                         {
00216                             SG_DEBUG(">>>>>>>>>>>>>>> all zeros")
00217                             if (aa !="B" && aa != "X" && aa != "Z")
00218                             {
00219                                 //profile[i][temp_profile_index]=-log(C+(1-C)*background[re_candidate[temp_profile_index]]);
00220                                 int32_t aa_index = aa_to_index[(int)aa.c_str()[0]];
00221                                 double value = -1* std::log(C+(1-C)*background[aa_index]); // taken from Leslie's example, C actually corresponds to 1/(1+C)
00222                                 SG_DEBUG("before %f\n", profiles.back()[(i-1) * 20 + aa_index])
00223                                 curr_profile[(i*20) + aa_index] = value;
00224                                 SG_DEBUG(">>> aa %c \t %d \t %f\n", aa.c_str()[0], aa_index, value)
00225 
00226                                 /*
00227                                 for (int z=0; z <20; ++z)
00228                                 {
00229                                     SG_DEBUG(" %d \t %f\t", z, curr_profile[z])
00230                                 }
00231                                 SG_DEBUG("\n")
00232                                 */
00233                             }
00234                         }
00235                     }
00236             }
00237 
00238             if (curr_profile.size() != 20 * sequence.length())
00239         {
00240                 SG_ERROR("Something's wrong with the profile.\n")
00241                 break;
00242             }
00243 
00244             seqs.push_back(sequence);
00245 
00246 
00247             /*
00248             // 6 irrelevant lines
00249             for (int i=0; i < 6; ++i)
00250             {
00251                 std::getline(fin, line);
00252             }
00253             //
00254             */
00255         }
00256     }
00257 
00258     fin.close();
00259 
00260     nof_sequences = seqs.size();
00261     sequences = SG_MALLOC(SGString<char>, nof_sequences);
00262 
00263     int max_len = 0;
00264     for (int i=0; i < nof_sequences; ++i)
00265     {
00266         int len = seqs[i].length();
00267         sequences[i].string = SG_MALLOC(char, len+1);
00268         sequences[i].slen = len;
00269         strcpy(sequences[i].string, seqs[i].c_str());
00270 
00271         if (len > max_len) max_len = len;
00272     }
00273 
00274     max_sequence_length = max_len;
00275     //string_features = new CStringFeatures<char>(sequences, nof_sequences, max_sequence_length, PROTEIN);
00276 
00277 }
00278 
00279 bool CSpectrumRBFKernel::init(CFeatures* l, CFeatures* r)
00280 {
00281     // >> profile
00282 /*
00283     read_profiles_and_sequences();
00284     l = string_features;
00285     r = string_features;
00286     */
00287     // << profile
00288 
00289     int32_t lhs_changed=(lhs!=l);
00290     int32_t rhs_changed=(rhs!=r);
00291 
00292     CStringKernel<char>::init(l,r);
00293 
00294     SG_DEBUG("lhs_changed: %i\n", lhs_changed)
00295     SG_DEBUG("rhs_changed: %i\n", rhs_changed)
00296 
00297     CStringFeatures<char>* sf_l=(CStringFeatures<char>*) l;
00298     CStringFeatures<char>* sf_r=(CStringFeatures<char>*) r;
00299 
00300     SG_UNREF(alphabet);
00301     alphabet=sf_l->get_alphabet();
00302     CAlphabet* ralphabet=sf_r->get_alphabet();
00303 
00304     if (!((alphabet->get_alphabet()==DNA) || (alphabet->get_alphabet()==RNA)))
00305         properties &= ((uint64_t) (-1)) ^ (KP_LINADD | KP_BATCHEVALUATION);
00306 
00307     ASSERT(ralphabet->get_alphabet()==alphabet->get_alphabet())
00308     SG_UNREF(ralphabet);
00309 
00310 
00311     return init_normalizer();
00312 }
00313 
00314 void CSpectrumRBFKernel::cleanup()
00315 {
00316 
00317     SG_UNREF(alphabet);
00318     alphabet=NULL;
00319 
00320     CKernel::cleanup();
00321 }
00322 
00323 inline bool isaa(char c)
00324 {
00325   if (c<65 || c>89 || c=='B' || c=='J' || c=='O' || c=='U' || c=='X' || c=='Z')
00326     return false ;
00327   return true ;
00328 }
00329 
00330 float64_t CSpectrumRBFKernel::AA_helper(const char* path, const int seq_degree, const char* joint_seq, unsigned int index)
00331 {
00332     //const char* AA = "ARNDCQEGHILKMFPSTWYV";
00333   float64_t diff=0.0 ;
00334 
00335   for (int i=0; i<seq_degree; i++)
00336     {
00337       if (!isaa(path[i])||!isaa(joint_seq[index+i]))
00338     diff+=1.4 ;
00339       else
00340     {
00341       diff += AA_matrix.matrix[ (path[i]-1)*128 + path[i] - 1] ;
00342       diff -= 2*AA_matrix.matrix[ (path[i]-1)*128 + joint_seq[index+i] - 1] ;
00343       diff += AA_matrix.matrix[ (joint_seq[index+i]-1)*128 + joint_seq[index+i] - 1] ;
00344       if (CMath::is_nan(diff))
00345         fprintf(stderr, "nan occurred: '%c' '%c'\n", path[i], joint_seq[index+i]) ;
00346     }
00347     }
00348 
00349   return exp( - diff/width) ;
00350 }
00351 
00352 float64_t CSpectrumRBFKernel::compute(int32_t idx_a, int32_t idx_b)
00353 {
00354     int32_t alen, blen;
00355     bool afree, bfree;
00356 
00357     char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, afree);
00358     char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, bfree);
00359 
00360     float64_t result=0;
00361     for (int32_t i=0; i<alen; i++)
00362       {
00363         for (int32_t j=0; j<blen; j++)
00364           {
00365         if ((i+degree<=alen) && (j+degree<=blen))
00366           result += AA_helper(&(avec[i]), degree, bvec, j) ;
00367           }
00368       }
00369 
00370     ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, afree);
00371     ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, bfree);
00372     return result;
00373 }
00374 
00375 bool CSpectrumRBFKernel::set_AA_matrix(
00376     float64_t* AA_matrix_)
00377 {
00378 
00379     if (AA_matrix_)
00380     {
00381         SG_DEBUG("Setting AA_matrix\n")
00382         memcpy(AA_matrix.matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00383         return true ;
00384     }
00385 
00386     return false;
00387 }
00388 
00389 void CSpectrumRBFKernel::register_param()
00390 {
00391     SG_ADD(&degree, "degree", "degree of the kernel", MS_AVAILABLE);
00392     SG_ADD(&AA_matrix, "AA_matrix", "128*128 scalar product matrix", MS_NOT_AVAILABLE);
00393     SG_ADD(&width, "width", "width of Gaussian", MS_AVAILABLE);
00394     SG_ADD(&nof_sequences, "nof_sequences", "length of the sequence",
00395         MS_NOT_AVAILABLE);
00396     m_parameters->add_vector(&sequences, &nof_sequences, "sequences", "the sequences as a part of profile");
00397     SG_ADD(&max_sequence_length,
00398         "max_sequence_length", "max length of the sequence", MS_NOT_AVAILABLE);
00399 }
00400 
00401 void CSpectrumRBFKernel::register_alphabet()
00402 {
00403     SG_ADD((CSGObject**)&alphabet, "alphabet", "the alphabet used by kernel",
00404         MS_NOT_AVAILABLE);
00405 }
00406 
00407 void CSpectrumRBFKernel::init()
00408 {
00409     alphabet = NULL;
00410     degree = 0;
00411     width = 0.0;
00412     sequences = NULL;
00413     string_features = NULL;
00414     nof_sequences = 0;
00415     max_sequence_length = 0;
00416 
00417     initialized = false;
00418 
00419     max_mismatch = 0;
00420     target_letter_0 = 0;
00421 }
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