WeightedDegreeStringKernel.cpp

Go to the documentation of this file.
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 "lib/common.h"
00013 #include "lib/io.h"
00014 #include "lib/Signal.h"
00015 #include "lib/Trie.h"
00016 #include "base/Parameter.h"
00017 #include "base/Parallel.h"
00018 
00019 #include "kernel/WeightedDegreeStringKernel.h"
00020 #include "kernel/FirstElementKernelNormalizer.h"
00021 #include "features/Features.h"
00022 #include "features/StringFeatures.h"
00023 
00024 #ifndef WIN32
00025 #include <pthread.h>
00026 #endif
00027 
00028 using namespace shogun;
00029 
00030 #ifndef DOXYGEN_SHOULD_SKIP_THIS
00031 struct S_THREAD_PARAM
00032 {
00033 
00034     int32_t* vec;
00035     float64_t* result;
00036     float64_t* weights;
00037     CWeightedDegreeStringKernel* kernel;
00038     CTrie<DNATrie>* tries;
00039     float64_t factor;
00040     int32_t j;
00041     int32_t start;
00042     int32_t end;
00043     int32_t length;
00044     int32_t* vec_idx;
00045 };
00046 #endif // DOXYGEN_SHOULD_SKIP_THIS
00047 
00048 CWeightedDegreeStringKernel::CWeightedDegreeStringKernel ()
00049 : CStringKernel<char>()
00050 {
00051     init();
00052 }
00053 
00054 
00055 CWeightedDegreeStringKernel::CWeightedDegreeStringKernel (
00056     int32_t d, EWDKernType t)
00057 : CStringKernel<char>()
00058 {
00059     init();
00060 
00061     degree=d;
00062     type=t;
00063 
00064     if (type!=E_EXTERNAL)
00065         set_wd_weights_by_type(type);
00066 }
00067 
00068 CWeightedDegreeStringKernel::CWeightedDegreeStringKernel (
00069     float64_t *w, int32_t d)
00070 : CStringKernel<char>(10)
00071 {
00072     init();
00073 
00074     type=E_EXTERNAL;
00075     degree=d;
00076 
00077     weights=new float64_t[degree*(1+max_mismatch)];
00078     weights_degree=degree;
00079     weights_length=(1+max_mismatch);
00080 
00081     for (int32_t i=0; i<degree*(1+max_mismatch); i++)
00082         weights[i]=w[i];
00083 }
00084 
00085 CWeightedDegreeStringKernel::CWeightedDegreeStringKernel(
00086     CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t d)
00087 : CStringKernel<char>(10)
00088 {
00089     init();
00090     degree=d;
00091     type=E_WD;
00092     set_wd_weights_by_type(type);
00093     set_normalizer(new CFirstElementKernelNormalizer());
00094     init(l, r);
00095 }
00096 
00097 CWeightedDegreeStringKernel::~CWeightedDegreeStringKernel()
00098 {
00099     cleanup();
00100 
00101     delete[] weights;
00102     weights=NULL;
00103     weights_degree=0;
00104     weights_length=0;
00105 
00106     delete[] block_weights;
00107     block_weights=NULL;
00108 
00109     delete[] position_weights;
00110     position_weights=NULL;
00111 
00112     delete[] weights_buffer;
00113     weights_buffer=NULL;
00114 }
00115 
00116 
00117 void CWeightedDegreeStringKernel::remove_lhs()
00118 {
00119     SG_DEBUG( "deleting CWeightedDegreeStringKernel optimization\n");
00120     delete_optimization();
00121 
00122     if (tries!=NULL)
00123         tries->destroy();
00124 
00125     CKernel::remove_lhs();
00126 }
00127 
00128 void CWeightedDegreeStringKernel::create_empty_tries()
00129 {
00130     ASSERT(lhs);
00131 
00132     seq_length=((CStringFeatures<char>*) lhs)->get_max_vector_length();
00133 
00134     if (tries!=NULL)
00135     {
00136         tries->destroy() ;
00137         tries->create(seq_length, max_mismatch==0) ;
00138     }
00139 }
00140 
00141 bool CWeightedDegreeStringKernel::init(CFeatures* l, CFeatures* r)
00142 {
00143     int32_t lhs_changed=(lhs!=l);
00144     int32_t rhs_changed=(rhs!=r);
00145 
00146     CStringKernel<char>::init(l,r);
00147 
00148     SG_DEBUG("lhs_changed: %i\n", lhs_changed);
00149     SG_DEBUG("rhs_changed: %i\n", rhs_changed);
00150 
00151     CStringFeatures<char>* sf_l=(CStringFeatures<char>*) l;
00152     CStringFeatures<char>* sf_r=(CStringFeatures<char>*) r;
00153 
00154     int32_t len=sf_l->get_max_vector_length();
00155     if (lhs_changed && !sf_l->have_same_length(len))
00156         SG_ERROR("All strings in WD kernel must have same length (lhs wrong)!\n");
00157 
00158     if (rhs_changed && !sf_r->have_same_length(len))
00159         SG_ERROR("All strings in WD kernel must have same length (rhs wrong)!\n");
00160 
00161     SG_UNREF(alphabet);
00162     alphabet=sf_l->get_alphabet();
00163     CAlphabet* ralphabet=sf_r->get_alphabet();
00164 
00165     if (!((alphabet->get_alphabet()==DNA) || (alphabet->get_alphabet()==RNA)))
00166         properties &= ((uint64_t) (-1)) ^ (KP_LINADD | KP_BATCHEVALUATION);
00167 
00168     ASSERT(ralphabet->get_alphabet()==alphabet->get_alphabet());
00169     SG_UNREF(ralphabet);
00170 
00171     if (tries!=NULL) {
00172         tries->delete_trees(max_mismatch==0);
00173         SG_UNREF(tries);
00174     }
00175     tries=new CTrie<DNATrie>(degree, max_mismatch==0);
00176     create_empty_tries();
00177 
00178     init_block_weights();
00179 
00180     return init_normalizer();
00181 }
00182 
00183 void CWeightedDegreeStringKernel::cleanup()
00184 {
00185     SG_DEBUG("deleting CWeightedDegreeStringKernel optimization\n");
00186     delete_optimization();
00187 
00188     delete[] block_weights;
00189     block_weights=NULL;
00190 
00191     if (tries!=NULL)
00192     {
00193         tries->destroy();
00194         SG_UNREF(tries);
00195         tries=NULL;
00196     }
00197 
00198     seq_length=0;
00199     tree_initialized = false;
00200 
00201     SG_UNREF(alphabet);
00202     alphabet=NULL;
00203 
00204     CKernel::cleanup();
00205 }
00206 
00207 bool CWeightedDegreeStringKernel::init_optimization(int32_t count, int32_t* IDX, float64_t* alphas, int32_t tree_num)
00208 {
00209     if (tree_num<0)
00210         SG_DEBUG( "deleting CWeightedDegreeStringKernel optimization\n");
00211 
00212     delete_optimization();
00213 
00214     if (tree_num<0)
00215         SG_DEBUG( "initializing CWeightedDegreeStringKernel optimization\n") ;
00216 
00217     for (int32_t i=0; i<count; i++)
00218     {
00219         if (tree_num<0)
00220         {
00221             if ( (i % (count/10+1)) == 0)
00222                 SG_PROGRESS(i, 0, count);
00223 
00224             if (max_mismatch==0)
00225                 add_example_to_tree(IDX[i], alphas[i]) ;
00226             else
00227                 add_example_to_tree_mismatch(IDX[i], alphas[i]) ;
00228 
00229             //SG_DEBUG( "number of used trie nodes: %i\n", tries.get_num_used_nodes()) ;
00230         }
00231         else
00232         {
00233             if (max_mismatch==0)
00234                 add_example_to_single_tree(IDX[i], alphas[i], tree_num) ;
00235             else
00236                 add_example_to_single_tree_mismatch(IDX[i], alphas[i], tree_num) ;
00237         }
00238     }
00239 
00240     if (tree_num<0)
00241         SG_DONE();
00242 
00243     //tries.compact_nodes(NO_CHILD, 0, weights) ;
00244 
00245     set_is_initialized(true) ;
00246     return true ;
00247 }
00248 
00249 bool CWeightedDegreeStringKernel::delete_optimization()
00250 {
00251     if (get_is_initialized())
00252     {
00253         if (tries!=NULL)
00254             tries->delete_trees(max_mismatch==0);
00255         set_is_initialized(false);
00256         return true;
00257     }
00258 
00259     return false;
00260 }
00261 
00262 
00263 float64_t CWeightedDegreeStringKernel::compute_with_mismatch(
00264     char* avec, int32_t alen, char* bvec, int32_t blen)
00265 {
00266     float64_t sum = 0.0;
00267 
00268     for (int32_t i=0; i<alen; i++)
00269     {
00270         float64_t sumi = 0.0;
00271         int32_t mismatches=0;
00272 
00273         for (int32_t j=0; (i+j<alen) && (j<degree); j++)
00274         {
00275             if (avec[i+j]!=bvec[i+j])
00276             {
00277                 mismatches++ ;
00278                 if (mismatches>max_mismatch)
00279                     break ;
00280             } ;
00281             sumi += weights[j+degree*mismatches];
00282         }
00283         if (position_weights!=NULL)
00284             sum+=position_weights[i]*sumi ;
00285         else
00286             sum+=sumi ;
00287     }
00288     return sum ;
00289 }
00290 
00291 float64_t CWeightedDegreeStringKernel::compute_using_block(
00292     char* avec, int32_t alen, char* bvec, int32_t blen)
00293 {
00294     ASSERT(alen==blen);
00295 
00296     float64_t sum=0;
00297     int32_t match_len=-1;
00298 
00299     for (int32_t i=0; i<alen; i++)
00300     {
00301         if (avec[i]==bvec[i])
00302             match_len++;
00303         else
00304         {
00305             if (match_len>=0)
00306                 sum+=block_weights[match_len];
00307             match_len=-1;
00308         }
00309     }
00310 
00311     if (match_len>=0)
00312         sum+=block_weights[match_len];
00313 
00314     return sum;
00315 }
00316 
00317 float64_t CWeightedDegreeStringKernel::compute_without_mismatch(
00318     char* avec, int32_t alen, char* bvec, int32_t blen)
00319 {
00320     float64_t sum = 0.0;
00321 
00322     for (int32_t i=0; i<alen; i++)
00323     {
00324         float64_t sumi = 0.0;
00325 
00326         for (int32_t j=0; (i+j<alen) && (j<degree); j++)
00327         {
00328             if (avec[i+j]!=bvec[i+j])
00329                 break ;
00330             sumi += weights[j];
00331         }
00332         if (position_weights!=NULL)
00333             sum+=position_weights[i]*sumi ;
00334         else
00335             sum+=sumi ;
00336     }
00337     return sum ;
00338 }
00339 
00340 float64_t CWeightedDegreeStringKernel::compute_without_mismatch_matrix(
00341     char* avec, int32_t alen, char* bvec, int32_t blen)
00342 {
00343     float64_t sum = 0.0;
00344 
00345     for (int32_t i=0; i<alen; i++)
00346     {
00347         float64_t sumi=0.0;
00348         for (int32_t j=0; (i+j<alen) && (j<degree); j++)
00349         {
00350             if (avec[i+j]!=bvec[i+j])
00351                 break;
00352             sumi += weights[i*degree+j];
00353         }
00354         if (position_weights!=NULL)
00355             sum += position_weights[i]*sumi ;
00356         else
00357             sum += sumi ;
00358     }
00359 
00360     return sum ;
00361 }
00362 
00363 
00364 float64_t CWeightedDegreeStringKernel::compute(int32_t idx_a, int32_t idx_b)
00365 {
00366     int32_t alen, blen;
00367     bool free_avec, free_bvec;
00368     char* avec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
00369     char* bvec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);
00370     float64_t result=0;
00371 
00372     if (max_mismatch==0 && length==0 && block_computation)
00373         result=compute_using_block(avec, alen, bvec, blen);
00374     else
00375     {
00376         if (max_mismatch>0)
00377             result=compute_with_mismatch(avec, alen, bvec, blen);
00378         else if (length==0)
00379             result=compute_without_mismatch(avec, alen, bvec, blen);
00380         else
00381             result=compute_without_mismatch_matrix(avec, alen, bvec, blen);
00382     }
00383     ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
00384     ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
00385 
00386     return result;
00387 }
00388 
00389 
00390 void CWeightedDegreeStringKernel::add_example_to_tree(
00391     int32_t idx, float64_t alpha)
00392 {
00393     ASSERT(alphabet);
00394     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00395 
00396     int32_t len=0;
00397     bool free_vec;
00398     char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
00399     ASSERT(max_mismatch==0);
00400     int32_t *vec=new int32_t[len];
00401 
00402     for (int32_t i=0; i<len; i++)
00403         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00404     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00405 
00406     if (length == 0 || max_mismatch > 0)
00407     {
00408         for (int32_t i=0; i<len; i++)
00409         {
00410             float64_t alpha_pw=alpha;
00411             /*if (position_weights!=NULL)
00412               alpha_pw *= position_weights[i] ;*/
00413             if (alpha_pw==0.0)
00414                 continue;
00415             ASSERT(tries);
00416             tries->add_to_trie(i, 0, vec, normalizer->normalize_lhs(alpha_pw, idx), weights, (length!=0));
00417         }
00418     }
00419     else
00420     {
00421         for (int32_t i=0; i<len; i++)
00422         {
00423             float64_t alpha_pw=alpha;
00424             /*if (position_weights!=NULL)
00425               alpha_pw = alpha*position_weights[i] ;*/
00426             if (alpha_pw==0.0)
00427                 continue ;
00428             ASSERT(tries);
00429             tries->add_to_trie(i, 0, vec, normalizer->normalize_lhs(alpha_pw, idx), weights, (length!=0));
00430         }
00431     }
00432     delete[] vec ;
00433     tree_initialized=true ;
00434 }
00435 
00436 void CWeightedDegreeStringKernel::add_example_to_single_tree(
00437     int32_t idx, float64_t alpha, int32_t tree_num)
00438 {
00439     ASSERT(alphabet);
00440     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00441 
00442     int32_t len;
00443     bool free_vec;
00444     char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
00445     ASSERT(max_mismatch==0);
00446     int32_t *vec = new int32_t[len] ;
00447 
00448     for (int32_t i=tree_num; i<tree_num+degree && i<len; i++)
00449         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00450     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00451 
00452 
00453     ASSERT(tries);
00454     if (alpha!=0.0)
00455         tries->add_to_trie(tree_num, 0, vec, normalizer->normalize_lhs(alpha, idx), weights, (length!=0));
00456 
00457     delete[] vec ;
00458     tree_initialized=true ;
00459 }
00460 
00461 void CWeightedDegreeStringKernel::add_example_to_tree_mismatch(int32_t idx, float64_t alpha)
00462 {
00463     ASSERT(tries);
00464     ASSERT(alphabet);
00465     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00466 
00467     int32_t len ;
00468     bool free_vec;
00469     char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
00470 
00471     int32_t *vec = new int32_t[len] ;
00472 
00473     for (int32_t i=0; i<len; i++)
00474         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00475     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00476 
00477     for (int32_t i=0; i<len; i++)
00478     {
00479         if (alpha!=0.0)
00480             tries->add_example_to_tree_mismatch_recursion(NO_CHILD, i, normalizer->normalize_lhs(alpha, idx), &vec[i], len-i, 0, 0, max_mismatch, weights);
00481     }
00482 
00483     delete[] vec ;
00484     tree_initialized=true ;
00485 }
00486 
00487 void CWeightedDegreeStringKernel::add_example_to_single_tree_mismatch(
00488     int32_t idx, float64_t alpha, int32_t tree_num)
00489 {
00490     ASSERT(tries);
00491     ASSERT(alphabet);
00492     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00493 
00494     int32_t len=0;
00495     bool free_vec;
00496     char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
00497     int32_t *vec=new int32_t[len];
00498 
00499     for (int32_t i=tree_num; i<len && i<tree_num+degree; i++)
00500         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00501     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00502 
00503     if (alpha!=0.0)
00504     {
00505         tries->add_example_to_tree_mismatch_recursion(
00506             NO_CHILD, tree_num, normalizer->normalize_lhs(alpha, idx), &vec[tree_num], len-tree_num,
00507             0, 0, max_mismatch, weights);
00508     }
00509 
00510     delete[] vec;
00511     tree_initialized=true;
00512 }
00513 
00514 
00515 float64_t CWeightedDegreeStringKernel::compute_by_tree(int32_t idx)
00516 {
00517     ASSERT(alphabet);
00518     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00519 
00520     int32_t len=0;
00521     bool free_vec;
00522     char* char_vec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx, len, free_vec);
00523     ASSERT(char_vec && len>0);
00524     int32_t *vec=new int32_t[len];
00525 
00526     for (int32_t i=0; i<len; i++)
00527         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00528     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00529 
00530     float64_t sum=0;
00531     ASSERT(tries);
00532     for (int32_t i=0; i<len; i++)
00533         sum+=tries->compute_by_tree_helper(vec, len, i, i, i, weights, (length!=0));
00534 
00535     delete[] vec;
00536     return normalizer->normalize_rhs(sum, idx);
00537 }
00538 
00539 void CWeightedDegreeStringKernel::compute_by_tree(
00540     int32_t idx, float64_t* LevelContrib)
00541 {
00542     ASSERT(alphabet);
00543     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00544 
00545     int32_t len ;
00546     bool free_vec;
00547     char* char_vec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx, len, free_vec);
00548 
00549     int32_t *vec = new int32_t[len] ;
00550 
00551     for (int32_t i=0; i<len; i++)
00552         vec[i]=alphabet->remap_to_bin(char_vec[i]);
00553     ((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
00554 
00555     ASSERT(tries);
00556     for (int32_t i=0; i<len; i++)
00557     {
00558         tries->compute_by_tree_helper(vec, len, i, i, i, LevelContrib,
00559                 normalizer->normalize_rhs(1.0, idx),
00560                 mkl_stepsize, weights, (length!=0));
00561     }
00562 
00563     delete[] vec ;
00564 }
00565 
00566 float64_t *CWeightedDegreeStringKernel::compute_abs_weights(int32_t &len)
00567 {
00568     ASSERT(tries);
00569     return tries->compute_abs_weights(len);
00570 }
00571 
00572 bool CWeightedDegreeStringKernel::set_wd_weights_by_type(EWDKernType p_type)
00573 {
00574     ASSERT(degree>0);
00575     ASSERT(p_type==E_WD); 
00576 
00577     delete[] weights;
00578     weights=new float64_t[degree];
00579     weights_degree=degree;
00580     weights_length=1;
00581 
00582     if (weights)
00583     {
00584         int32_t i;
00585         float64_t sum=0;
00586         for (i=0; i<degree; i++)
00587         {
00588             weights[i]=degree-i;
00589             sum+=weights[i];
00590         }
00591         for (i=0; i<degree; i++)
00592             weights[i]/=sum;
00593 
00594         for (i=0; i<degree; i++)
00595         {
00596             for (int32_t j=1; j<=max_mismatch; j++)
00597             {
00598                 if (j<i+1)
00599                 {
00600                     int32_t nk=CMath::nchoosek(i+1, j);
00601                     weights[i+j*degree]=weights[i]/(nk*CMath::pow(3.0,j));
00602                 }
00603                 else
00604                     weights[i+j*degree]= 0;
00605             }
00606         }
00607 
00608         if (which_degree>=0)
00609         {
00610             ASSERT(which_degree<degree);
00611             for (i=0; i<degree; i++)
00612             {
00613                 if (i!=which_degree)
00614                     weights[i]=0;
00615                 else
00616                     weights[i]=1;
00617             }
00618         }
00619         return true;
00620     }
00621     else
00622         return false;
00623 }
00624 
00625 bool CWeightedDegreeStringKernel::set_weights(
00626     float64_t* ws, int32_t d, int32_t len)
00627 {
00628     if (d!=degree || len<0)
00629         SG_ERROR("WD: Dimension mismatch (should be (seq_length | 1) x degree) got (%d x %d)\n", len, degree);
00630 
00631     degree=d;
00632     length=len;
00633 
00634     if (len <= 0)
00635         len=1;
00636 
00637     weights_degree=degree;
00638     weights_length=len+max_mismatch;
00639 
00640 
00641     SG_DEBUG("Creating weights of size %dx%d\n", weights_degree, weights_length);
00642     int32_t num_weights=weights_degree*weights_length;
00643     delete[] weights;
00644     weights=new float64_t[num_weights];
00645 
00646     for (int32_t i=0; i<degree*len; i++)
00647         weights[i]=ws[i];
00648 
00649     return true;
00650 }
00651 
00652 bool CWeightedDegreeStringKernel::set_position_weights(
00653     float64_t* pws, int32_t len)
00654 {
00655     if (len==0)
00656     {
00657         delete[] position_weights;
00658         position_weights=NULL;
00659         ASSERT(tries);
00660         tries->set_position_weights(position_weights);
00661     }
00662 
00663     if (seq_length!=len)
00664         SG_ERROR("seq_length = %i, position_weights_length=%i\n", seq_length, len);
00665 
00666     delete[] position_weights;
00667     position_weights=new float64_t[len];
00668     position_weights_len=len;
00669     ASSERT(tries);
00670     tries->set_position_weights(position_weights);
00671 
00672     if (position_weights)
00673     {
00674         for (int32_t i=0; i<len; i++)
00675             position_weights[i]=pws[i];
00676         return true;
00677     }
00678     else
00679         return false;
00680 }
00681 
00682 bool CWeightedDegreeStringKernel::init_block_weights_from_wd()
00683 {
00684     delete[] block_weights;
00685     block_weights=new float64_t[CMath::max(seq_length,degree)];
00686 
00687     int32_t k;
00688     float64_t d=degree; // use float to evade rounding errors below
00689 
00690     for (k=0; k<degree; k++)
00691         block_weights[k]=
00692             (-CMath::pow(k, 3)+(3*d-3)*CMath::pow(k, 2)+(9*d-2)*k+6*d)/(3*d*(d+1));
00693     for (k=degree; k<seq_length; k++)
00694         block_weights[k]=(-d+3*k+4)/3;
00695 
00696     return true;
00697 }
00698 
00699 bool CWeightedDegreeStringKernel::init_block_weights_from_wd_external()
00700 {
00701     ASSERT(weights);
00702     delete[] block_weights;
00703     block_weights=new float64_t[CMath::max(seq_length,degree)];
00704 
00705     int32_t i=0;
00706     block_weights[0]=weights[0];
00707     for (i=1; i<CMath::max(seq_length,degree); i++)
00708         block_weights[i]=0;
00709 
00710     for (i=1; i<CMath::max(seq_length,degree); i++)
00711     {
00712         block_weights[i]=block_weights[i-1];
00713 
00714         float64_t contrib=0;
00715         for (int32_t j=0; j<CMath::min(degree,i+1); j++)
00716             contrib+=weights[j];
00717 
00718         block_weights[i]+=contrib;
00719     }
00720     return true;
00721 }
00722 
00723 bool CWeightedDegreeStringKernel::init_block_weights_const()
00724 {
00725     delete[] block_weights;
00726     block_weights=new float64_t[seq_length];
00727 
00728     for (int32_t i=1; i<seq_length+1 ; i++)
00729         block_weights[i-1]=1.0/seq_length;
00730     return true;
00731 }
00732 
00733 bool CWeightedDegreeStringKernel::init_block_weights_linear()
00734 {
00735     delete[] block_weights;
00736     block_weights=new float64_t[seq_length];
00737 
00738     for (int32_t i=1; i<seq_length+1 ; i++)
00739         block_weights[i-1]=degree*i;
00740 
00741     return true;
00742 }
00743 
00744 bool CWeightedDegreeStringKernel::init_block_weights_sqpoly()
00745 {
00746     delete[] block_weights;
00747     block_weights=new float64_t[seq_length];
00748 
00749     for (int32_t i=1; i<degree+1 ; i++)
00750         block_weights[i-1]=((float64_t) i)*i;
00751 
00752     for (int32_t i=degree+1; i<seq_length+1 ; i++)
00753         block_weights[i-1]=i;
00754 
00755     return true;
00756 }
00757 
00758 bool CWeightedDegreeStringKernel::init_block_weights_cubicpoly()
00759 {
00760     delete[] block_weights;
00761     block_weights=new float64_t[seq_length];
00762 
00763     for (int32_t i=1; i<degree+1 ; i++)
00764         block_weights[i-1]=((float64_t) i)*i*i;
00765 
00766     for (int32_t i=degree+1; i<seq_length+1 ; i++)
00767         block_weights[i-1]=i;
00768     return true;
00769 }
00770 
00771 bool CWeightedDegreeStringKernel::init_block_weights_exp()
00772 {
00773     delete[] block_weights;
00774     block_weights=new float64_t[seq_length];
00775 
00776     for (int32_t i=1; i<degree+1 ; i++)
00777         block_weights[i-1]=exp(((float64_t) i/10.0));
00778 
00779     for (int32_t i=degree+1; i<seq_length+1 ; i++)
00780         block_weights[i-1]=i;
00781 
00782     return true;
00783 }
00784 
00785 bool CWeightedDegreeStringKernel::init_block_weights_log()
00786 {
00787     delete[] block_weights;
00788     block_weights=new float64_t[seq_length];
00789 
00790     for (int32_t i=1; i<degree+1 ; i++)
00791         block_weights[i-1]=CMath::pow(CMath::log((float64_t) i),2);
00792 
00793     for (int32_t i=degree+1; i<seq_length+1 ; i++)
00794         block_weights[i-1]=i-degree+1+CMath::pow(CMath::log(degree+1.0),2);
00795 
00796     return true;
00797 }
00798 
00799 bool CWeightedDegreeStringKernel::init_block_weights()
00800 {
00801     switch (type)
00802     {
00803         case E_WD:
00804             return init_block_weights_from_wd();
00805         case E_EXTERNAL:
00806             return init_block_weights_from_wd_external();
00807         case E_BLOCK_CONST:
00808             return init_block_weights_const();
00809         case E_BLOCK_LINEAR:
00810             return init_block_weights_linear();
00811         case E_BLOCK_SQPOLY:
00812             return init_block_weights_sqpoly();
00813         case E_BLOCK_CUBICPOLY:
00814             return init_block_weights_cubicpoly();
00815         case E_BLOCK_EXP:
00816             return init_block_weights_exp();
00817         case E_BLOCK_LOG:
00818             return init_block_weights_log();
00819     };
00820     return false;
00821 }
00822 
00823 
00824 void* CWeightedDegreeStringKernel::compute_batch_helper(void* p)
00825 {
00826     S_THREAD_PARAM* params = (S_THREAD_PARAM*) p;
00827     int32_t j=params->j;
00828     CWeightedDegreeStringKernel* wd=params->kernel;
00829     CTrie<DNATrie>* tries=params->tries;
00830     float64_t* weights=params->weights;
00831     int32_t length=params->length;
00832     int32_t* vec=params->vec;
00833     float64_t* result=params->result;
00834     float64_t factor=params->factor;
00835     int32_t* vec_idx=params->vec_idx;
00836 
00837     CStringFeatures<char>* rhs_feat=((CStringFeatures<char>*) wd->get_rhs());
00838     CAlphabet* alpha=wd->alphabet;
00839 
00840     for (int32_t i=params->start; i<params->end; i++)
00841     {
00842         int32_t len=0;
00843         bool free_vec;
00844         char* char_vec=rhs_feat->get_feature_vector(vec_idx[i], len, free_vec);
00845         for (int32_t k=j; k<CMath::min(len,j+wd->get_degree()); k++)
00846             vec[k]=alpha->remap_to_bin(char_vec[k]);
00847         rhs_feat->free_feature_vector(char_vec, vec_idx[i], free_vec);
00848 
00849         ASSERT(tries);
00850 
00851         result[i]+=factor*
00852             wd->normalizer->normalize_rhs(tries->compute_by_tree_helper(vec, len, j, j, j, weights, (length!=0)), vec_idx[i]);
00853     }
00854 
00855     SG_UNREF(rhs_feat);
00856 
00857     return NULL;
00858 }
00859 
00860 void CWeightedDegreeStringKernel::compute_batch(
00861     int32_t num_vec, int32_t* vec_idx, float64_t* result, int32_t num_suppvec,
00862     int32_t* IDX, float64_t* alphas, float64_t factor)
00863 {
00864     ASSERT(tries);
00865     ASSERT(alphabet);
00866     ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA);
00867     ASSERT(rhs);
00868     ASSERT(num_vec<=rhs->get_num_vectors());
00869     ASSERT(num_vec>0);
00870     ASSERT(vec_idx);
00871     ASSERT(result);
00872     create_empty_tries();
00873 
00874     int32_t num_feat=((CStringFeatures<char>*) rhs)->get_max_vector_length();
00875     ASSERT(num_feat>0);
00876     int32_t num_threads=parallel->get_num_threads();
00877     ASSERT(num_threads>0);
00878     int32_t* vec=new int32_t[num_threads*num_feat];
00879 
00880     if (num_threads < 2)
00881     {
00882 #ifdef CYGWIN
00883         for (int32_t j=0; j<num_feat; j++)
00884 #else
00885         CSignal::clear_cancel();
00886         for (int32_t j=0; j<num_feat && !CSignal::cancel_computations(); j++)
00887 #endif
00888         {
00889             init_optimization(num_suppvec, IDX, alphas, j);
00890             S_THREAD_PARAM params;
00891             params.vec=vec;
00892             params.result=result;
00893             params.weights=weights;
00894             params.kernel=this;
00895             params.tries=tries;
00896             params.factor=factor;
00897             params.j=j;
00898             params.start=0;
00899             params.end=num_vec;
00900             params.length=length;
00901             params.vec_idx=vec_idx;
00902             compute_batch_helper((void*) &params);
00903 
00904             SG_PROGRESS(j,0,num_feat);
00905         }
00906     }
00907 #ifndef WIN32
00908     else
00909     {
00910         CSignal::clear_cancel();
00911         for (int32_t j=0; j<num_feat && !CSignal::cancel_computations(); j++)
00912         {
00913             init_optimization(num_suppvec, IDX, alphas, j);
00914             pthread_t* threads = new pthread_t[num_threads-1];
00915             S_THREAD_PARAM* params = new S_THREAD_PARAM[num_threads];
00916             int32_t step= num_vec/num_threads;
00917             int32_t t;
00918 
00919             for (t=0; t<num_threads-1; t++)
00920             {
00921                 params[t].vec=&vec[num_feat*t];
00922                 params[t].result=result;
00923                 params[t].weights=weights;
00924                 params[t].kernel=this;
00925                 params[t].tries=tries;
00926                 params[t].factor=factor;
00927                 params[t].j=j;
00928                 params[t].start = t*step;
00929                 params[t].end = (t+1)*step;
00930                 params[t].length=length;
00931                 params[t].vec_idx=vec_idx;
00932                 pthread_create(&threads[t], NULL, CWeightedDegreeStringKernel::compute_batch_helper, (void*)&params[t]);
00933             }
00934             params[t].vec=&vec[num_feat*t];
00935             params[t].result=result;
00936             params[t].weights=weights;
00937             params[t].kernel=this;
00938             params[t].tries=tries;
00939             params[t].factor=factor;
00940             params[t].j=j;
00941             params[t].start=t*step;
00942             params[t].end=num_vec;
00943             params[t].length=length;
00944             params[t].vec_idx=vec_idx;
00945             compute_batch_helper((void*) &params[t]);
00946 
00947             for (t=0; t<num_threads-1; t++)
00948                 pthread_join(threads[t], NULL);
00949             SG_PROGRESS(j,0,num_feat);
00950 
00951             delete[] params;
00952             delete[] threads;
00953         }
00954     }
00955 #endif
00956 
00957     delete[] vec;
00958 
00959     //really also free memory as this can be huge on testing especially when
00960     //using the combined kernel
00961     create_empty_tries();
00962 }
00963 
00964 bool CWeightedDegreeStringKernel::set_max_mismatch(int32_t max)
00965 {
00966     if (type==E_EXTERNAL && max!=0)
00967         return false;
00968 
00969     max_mismatch=max;
00970 
00971     if (lhs!=NULL && rhs!=NULL)
00972         return init(lhs, rhs);
00973     else
00974         return true;
00975 }
00976 
00977 void CWeightedDegreeStringKernel::init()
00978 {
00979     weights=NULL;
00980     weights_degree=0;
00981     weights_length=0;
00982 
00983     position_weights=NULL;
00984     position_weights_len=0;
00985 
00986     weights_buffer=NULL;
00987     mkl_stepsize=1;
00988     degree=1;
00989     length=0;
00990 
00991     max_mismatch=0;
00992     seq_length=0;
00993 
00994     block_weights=NULL;
00995     block_computation=true;
00996     type=E_WD;
00997     which_degree=-1;
00998     tries=NULL;
00999 
01000     tree_initialized=false;
01001     alphabet=NULL;
01002 
01003     lhs=NULL;
01004     rhs=NULL;
01005 
01006     properties |= KP_LINADD | KP_KERNCOMBINATION | KP_BATCHEVALUATION;
01007 
01008     set_normalizer(new CFirstElementKernelNormalizer());
01009 
01010     m_parameters->add_matrix(&weights, &weights_degree, &weights_length,
01011             "weights", "WD Kernel weights.");
01012     m_parameters->add_vector(&position_weights, &position_weights_len,
01013             "position_weights",
01014             "Weights per position.");
01015     m_parameters->add(&mkl_stepsize, "mkl_stepsize", "MKL step size.");
01016     m_parameters->add(&degree, "degree", "Order of WD kernel.");
01017     m_parameters->add(&max_mismatch, "max_mismatch",
01018             "Number of allowed mismatches.");
01019     m_parameters->add(&block_computation, "block_computation",
01020             "If block computation shall be used.");
01021     m_parameters->add((machine_int_t*) &type, "type",
01022             "WeightedDegree kernel type.");
01023     m_parameters->add(&which_degree, "which_degree",
01024             "Unqueal -1 if just a single degree is selected.");
01025     m_parameters->add((CSGObject**) &alphabet, "alphabet",
01026             "Alphabet of Features.");
01027 }
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines

SHOGUN Machine Learning Toolbox - Documentation