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00012 #include <vector>
00013
00014 #include "lib/common.h"
00015 #include "lib/io.h"
00016 #include "lib/Signal.h"
00017 #include "lib/Trie.h"
00018 #include "base/Parallel.h"
00019
00020 #include "kernel/SpectrumRBFKernel.h"
00021 #include "features/Features.h"
00022 #include "features/StringFeatures.h"
00023 #include <math.h>
00024
00025 #include <vector>
00026 #include <string>
00027 #include <fstream>
00028 #include <cmath>
00029
00030 #include <assert.h>
00031
00032 #ifndef WIN32
00033 #include <pthread.h>
00034 #endif
00035
00036
00037 using namespace shogun;
00038
00039 CSpectrumRBFKernel::CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t degree_, float64_t width_)
00040 : CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
00041 {
00042 lhs=NULL;
00043 rhs=NULL;
00044
00045 target_letter_0=-1 ;
00046
00047 AA_matrix=new float64_t[128*128];
00048
00049
00050 memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00051
00052 read_profiles_and_sequences();
00053
00054
00055 string_features = new CStringFeatures<char>(sequences, nof_sequences, max_sequence_length, IUPAC_AMINO_ACID);
00056 init(string_features, string_features);
00057 }
00058
00059 CSpectrumRBFKernel::CSpectrumRBFKernel(
00060 CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_, int32_t degree_, float64_t width_)
00061 : CStringKernel<char>(size), alphabet(NULL), degree(degree_), width(width_), sequences(NULL), string_features(NULL), nof_sequences(0), max_sequence_length(0)
00062 {
00063 target_letter_0=-1 ;
00064
00065 AA_matrix=new float64_t[128*128];
00066 memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00067
00068 init(l, r);
00069 }
00070
00071 CSpectrumRBFKernel::~CSpectrumRBFKernel()
00072 {
00073 cleanup();
00074 delete[] AA_matrix ;
00075 }
00076
00077
00078 void CSpectrumRBFKernel::remove_lhs()
00079 {
00080
00081 CKernel::remove_lhs();
00082 }
00083
00084 void CSpectrumRBFKernel::read_profiles_and_sequences()
00085 {
00086
00087 int32_t aa_to_index[128];
00088 aa_to_index['A'] = 0;
00089 aa_to_index['R'] = 1;
00090 aa_to_index['N'] = 2;
00091 aa_to_index['D'] = 3;
00092 aa_to_index['C'] = 4;
00093 aa_to_index['Q'] = 5;
00094 aa_to_index['E'] = 6;
00095 aa_to_index['G'] = 7;
00096 aa_to_index['H'] = 8;
00097 aa_to_index['I'] = 9;
00098 aa_to_index['L'] = 10;
00099 aa_to_index['K'] = 11;
00100 aa_to_index['M'] = 12;
00101 aa_to_index['F'] = 13;
00102 aa_to_index['P'] = 14;
00103 aa_to_index['S'] = 15;
00104 aa_to_index['T'] = 16;
00105 aa_to_index['W'] = 17;
00106 aa_to_index['Y'] = 18;
00107 aa_to_index['V'] = 19;
00108 SG_DEBUG("initializing background\n");
00109 double background[20];
00110 background[0]=0.0799912015849807;
00111 background[1]=0.0484482507611578;
00112 background[2]=0.044293531582512;
00113 background[3]=0.0578891399707563;
00114 background[4]=0.0171846021407367;
00115 background[5]=0.0380578923048682;
00116 background[6]=0.0638169929675978;
00117 background[7]=0.0760659374742852;
00118 background[8]=0.0223465499452473;
00119 background[9]=0.0550905793661343;
00120 background[10]=0.0866897071203864;
00121 background[11]=0.060458245507428;
00122 background[12]=0.0215379186368154;
00123 background[13]=0.0396348024787477;
00124 background[14]=0.0465746314476874;
00125 background[15]=0.0630028230885602;
00126 background[16]=0.0580394726014824;
00127 background[17]=0.0144991866213453;
00128 background[18]=0.03635438623143;
00129 background[19]=0.0700241481678408;
00130
00131
00132 std::vector<std::string> seqs;
00133
00134
00135 double C = 0.8;
00136 const char *filename="/fml/ag-raetsch/home/toussaint/scp/aawd_compbio_workshop/code_nora/data/profile/profiles";
00137 std::ifstream fin(filename);
00138
00139 SG_DEBUG("Reading profiles from %s\n", filename);
00140 std::string line;
00141 while (!fin.eof())
00142 {
00143 std::getline(fin, line);
00144
00145 if (line[0] == '>')
00146 {
00147 int idx = line.find_first_of(' ');
00148 sequence_labels.push_back(line.substr(1,idx-1));
00149 std::getline(fin, line);
00150 std::string orig_sequence = line;
00151 std::string sequence="";
00152
00153 int len_line = line.length();
00154
00155
00156
00157 std::getline(fin, line);
00158 std::getline(fin, line);
00159 std::getline(fin, line);
00160
00161 profiles.push_back(std::vector<double>());
00162
00163 std::vector<double>& curr_profile = profiles.back();
00164 for (int i=0; i < len_line; ++i)
00165 {
00166 std::getline(fin, line);
00167 int a = line.find_first_not_of(' ');
00168 int b = line.find_first_of(' ', a);
00169 a = line.find_first_not_of(' ', b);
00170 b = line.find_first_of(' ', a);
00171 std::string aa=line.substr(a,b-a);
00172 if (0)
00173 {
00174 int pos = seqs.size()+1;
00175 SG_DEBUG("Skipping aa in sequence %d\n", pos);
00176 continue;
00177 }
00178 else
00179 {
00180 sequence += aa;
00181
00182 a = line.find_first_not_of(' ', b);
00183 b = line.find_first_of(' ', a);
00184
00185 for (int j=0; j < 19; ++j)
00186 {
00187 a = line.find_first_not_of(' ', b);
00188 b = line.find_first_of(' ', a);
00189 }
00190
00191 int all_zeros = 1;
00192
00193 for (int j=0; j < 20; ++j)
00194 {
00195 a = line.find_first_not_of(' ', b);
00196 b = line.find_first_of(' ', a);
00197 double p = atof(line.substr(a, b-a).c_str());
00198 if (p > 0)
00199 {
00200 all_zeros = 0;
00201 }
00202 double value = -1* std::log(C*(p/100)+(1-C)*background[j]);
00203 curr_profile.push_back(value);
00204
00205 }
00206
00207 if (all_zeros)
00208 {
00209 SG_DEBUG(">>>>>>>>>>>>>>> all zeros");
00210 if (aa !="B" && aa != "X" && aa != "Z")
00211 {
00212
00213 int32_t aa_index = aa_to_index[(int)aa.c_str()[0]];
00214 double value = -1* std::log(C+(1-C)*background[aa_index]);
00215 SG_DEBUG("before %f\n", profiles.back()[(i-1) * 20 + aa_index]);
00216 curr_profile[(i*20) + aa_index] = value;
00217 SG_DEBUG(">>> aa %c \t %d \t %f\n", aa.c_str()[0], aa_index, value);
00218
00219
00220
00221
00222
00223
00224
00225
00226 }
00227 }
00228 }
00229 }
00230
00231 if (curr_profile.size() != 20 * sequence.length())
00232 {
00233 SG_ERROR("Something's wrong with the profile.\n");
00234 break;
00235 }
00236
00237 seqs.push_back(sequence);
00238
00239
00240
00241
00242
00243
00244
00245
00246
00247
00248 }
00249 }
00250
00251 fin.close();
00252
00253 nof_sequences = seqs.size();
00254 sequences = new T_STRING<char>[nof_sequences];
00255
00256 int max_len = 0;
00257 for (int i=0; i < nof_sequences; ++i)
00258 {
00259 int len = seqs[i].length();
00260 sequences[i].string = new char[len+1];
00261 sequences[i].length = len;
00262 strcpy(sequences[i].string, seqs[i].c_str());
00263
00264 if (len > max_len) max_len = len;
00265 }
00266
00267 max_sequence_length = max_len;
00268
00269
00270 }
00271
00272 bool CSpectrumRBFKernel::init(CFeatures* l, CFeatures* r)
00273 {
00274
00275
00276
00277
00278
00279
00280
00281
00282 int32_t lhs_changed=(lhs!=l);
00283 int32_t rhs_changed=(rhs!=r);
00284
00285 CStringKernel<char>::init(l,r);
00286
00287 SG_DEBUG("lhs_changed: %i\n", lhs_changed);
00288 SG_DEBUG("rhs_changed: %i\n", rhs_changed);
00289
00290 CStringFeatures<char>* sf_l=(CStringFeatures<char>*) l;
00291 CStringFeatures<char>* sf_r=(CStringFeatures<char>*) r;
00292
00293 SG_UNREF(alphabet);
00294 alphabet=sf_l->get_alphabet();
00295 CAlphabet* ralphabet=sf_r->get_alphabet();
00296
00297 if (!((alphabet->get_alphabet()==DNA) || (alphabet->get_alphabet()==RNA)))
00298 properties &= ((uint64_t) (-1)) ^ (KP_LINADD | KP_BATCHEVALUATION);
00299
00300 ASSERT(ralphabet->get_alphabet()==alphabet->get_alphabet());
00301 SG_UNREF(ralphabet);
00302
00303
00304 return init_normalizer();
00305 }
00306
00307 void CSpectrumRBFKernel::cleanup()
00308 {
00309
00310 SG_UNREF(alphabet);
00311 alphabet=NULL;
00312
00313 CKernel::cleanup();
00314 }
00315
00316 inline bool isaa(char c)
00317 {
00318 if (c<65 || c>89 || c=='B' || c=='J' || c=='O' || c=='U' || c=='X' || c=='Z')
00319 return false ;
00320 return true ;
00321 }
00322
00323 float64_t CSpectrumRBFKernel::AA_helper(const char* path, const int seq_degree, const char* joint_seq, unsigned int index)
00324 {
00325
00326 float64_t diff=0.0 ;
00327
00328 for (int i=0; i<seq_degree; i++)
00329 {
00330 if (!isaa(path[i])||!isaa(joint_seq[index+i]))
00331 diff+=1.4 ;
00332 else
00333 {
00334 diff += AA_matrix[ (path[i]-1)*128 + path[i] - 1] ;
00335 diff -= 2*AA_matrix[ (path[i]-1)*128 + joint_seq[index+i] - 1] ;
00336 diff += AA_matrix[ (joint_seq[index+i]-1)*128 + joint_seq[index+i] - 1] ;
00337 if (CMath::is_nan(diff))
00338 fprintf(stderr, "nan occurred: '%c' '%c'\n", path[i], joint_seq[index+i]) ;
00339 }
00340 }
00341
00342 return exp( - diff/width) ;
00343 }
00344
00345 float64_t CSpectrumRBFKernel::compute(int32_t idx_a, int32_t idx_b)
00346 {
00347 int32_t alen, blen;
00348 bool afree, bfree;
00349
00350 char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, afree);
00351 char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, bfree);
00352
00353 float64_t result=0;
00354 for (int32_t i=0; i<alen; i++)
00355 {
00356 for (int32_t j=0; j<blen; j++)
00357 {
00358 if ((i+degree<=alen) && (j+degree<=blen))
00359 result += AA_helper(&(avec[i]), degree, bvec, j) ;
00360 }
00361 }
00362
00363 ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, afree);
00364 ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, bfree);
00365 return result;
00366 }
00367
00368 bool CSpectrumRBFKernel::set_AA_matrix(
00369 float64_t* AA_matrix_)
00370 {
00371
00372 if (AA_matrix_)
00373 {
00374 SG_DEBUG("Setting AA_matrix\n") ;
00375 memcpy(AA_matrix, AA_matrix_, 128*128*sizeof(float64_t)) ;
00376 return true ;
00377 }
00378
00379 return false;
00380 }