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WeightedDegreePositionStringKernel.cpp
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WeightedDegreePositionStringKernel.cpp
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/*
* This software is distributed under BSD 3-clause license (see LICENSE file).
*
* Authors: Giovanni De Toni, Soeren Sonnenburg, Sergey Lisitsyn,
* Heiko Strathmann, Viktor Gal, Weijie Lin, Björn Esser
*/
#include <shogun/base/Parallel.h>
#include <shogun/base/progress.h>
#include <shogun/io/SGIO.h>
#include <shogun/lib/Signal.h>
#include <shogun/lib/Trie.h>
#include <shogun/lib/common.h>
#include <shogun/kernel/string/WeightedDegreePositionStringKernel.h>
#include <shogun/kernel/normalizer/SqrtDiagKernelNormalizer.h>
#include <shogun/features/Features.h>
#include <shogun/features/StringFeatures.h>
#include <shogun/classifier/svm/SVM.h>
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
using namespace shogun;
#define TRIES(X) ((use_poim_tries) ? (poim_tries.X) : (tries.X))
#ifndef DOXYGEN_SHOULD_SKIP_THIS
template <class Trie> struct S_THREAD_PARAM_WDS
{
int32_t* vec;
float64_t* result;
float64_t* weights;
CWeightedDegreePositionStringKernel* kernel;
CTrie<Trie>* tries;
float64_t factor;
int32_t j;
int32_t start;
int32_t end;
int32_t length;
int32_t max_shift;
int32_t* shift;
int32_t* vec_idx;
};
#endif // DOXYGEN_SHOULD_SKIP_THIS
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
void)
: CStringKernel<char>()
{
init();
}
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
int32_t size, int32_t d, int32_t mm, int32_t mkls)
: CStringKernel<char>(size)
{
init();
mkl_stepsize=mkls;
degree=d;
max_mismatch=mm;
tries=CTrie<DNATrie>(d);
poim_tries=CTrie<POIMTrie>(d);
set_wd_weights();
ASSERT(weights)
}
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
int32_t size, SGVector<float64_t> w, int32_t d, int32_t mm, SGVector<int32_t> s,
int32_t mkls)
: CStringKernel<char>(size)
{
init();
mkl_stepsize=mkls;
degree=d;
max_mismatch=mm;
tries=CTrie<DNATrie>(d);
poim_tries=CTrie<POIMTrie>(d);
weights=SG_MALLOC(float64_t, d*(1+max_mismatch));
weights_degree=degree;
weights_length=(1+max_mismatch);
for (int32_t i=0; i<d*(1+max_mismatch); i++)
weights[i]=w[i];
set_shifts(s);
}
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel(
CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t d)
: CStringKernel<char>()
{
init();
mkl_stepsize=1;
degree=d;
tries=CTrie<DNATrie>(d);
poim_tries=CTrie<POIMTrie>(d);
set_wd_weights();
ASSERT(weights)
init(l, r);
}
CWeightedDegreePositionStringKernel::~CWeightedDegreePositionStringKernel()
{
cleanup();
cleanup_POIM2();
SG_FREE(shift);
shift=NULL;
SG_FREE(weights);
weights=NULL;
weights_degree=0;
weights_length=0;
SG_FREE(block_weights);
block_weights=NULL;
SG_FREE(position_weights);
position_weights=NULL;
SG_FREE(position_weights_lhs);
position_weights_lhs=NULL;
SG_FREE(position_weights_rhs);
position_weights_rhs=NULL;
SG_FREE(weights_buffer);
weights_buffer=NULL;
}
void CWeightedDegreePositionStringKernel::remove_lhs()
{
SG_DEBUG("deleting CWeightedDegreePositionStringKernel optimization\n")
delete_optimization();
tries.destroy();
poim_tries.destroy();
CKernel::remove_lhs();
}
void CWeightedDegreePositionStringKernel::create_empty_tries()
{
ASSERT(lhs)
seq_length = ((CStringFeatures<char>*) lhs)->get_max_vector_length();
if (opt_type==SLOWBUTMEMEFFICIENT)
{
tries.create(seq_length, true);
poim_tries.create(seq_length, true);
}
else if (opt_type==FASTBUTMEMHUNGRY)
{
tries.create(seq_length, false); // still buggy
poim_tries.create(seq_length, false); // still buggy
}
else
SG_ERROR("unknown optimization type\n")
}
bool CWeightedDegreePositionStringKernel::init(CFeatures* l, CFeatures* r)
{
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;
/* set shift */
if (shift_len==0) {
shift_len=sf_l->get_vector_length(0);
int32_t *shifts=SG_MALLOC(int32_t, shift_len);
for (int32_t i=0; i<shift_len; i++) {
shifts[i]=1;
}
set_shifts(SGVector<int32_t>(shifts, shift_len, false));
SG_FREE(shifts);
}
int32_t len=sf_l->get_max_vector_length();
if (lhs_changed && !sf_l->have_same_length(len))
SG_ERROR("All strings in WD kernel must have same length (lhs wrong)!\n")
if (rhs_changed && !sf_r->have_same_length(len))
SG_ERROR("All strings in WD kernel must have same length (rhs wrong)!\n")
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);
//whenever init is called also init tries and block weights
create_empty_tries();
init_block_weights();
return init_normalizer();
}
void CWeightedDegreePositionStringKernel::cleanup()
{
SG_DEBUG("deleting CWeightedDegreePositionStringKernel optimization\n")
delete_optimization();
SG_FREE(block_weights);
block_weights=NULL;
tries.destroy();
poim_tries.destroy();
seq_length = 0;
tree_initialized = false;
SG_UNREF(alphabet);
alphabet=NULL;
CKernel::cleanup();
}
bool CWeightedDegreePositionStringKernel::init_optimization(
int32_t p_count, int32_t * IDX, float64_t * alphas, int32_t tree_num,
int32_t upto_tree)
{
ASSERT(position_weights_lhs==NULL)
ASSERT(position_weights_rhs==NULL)
if (upto_tree<0)
upto_tree=tree_num;
if (max_mismatch!=0)
{
SG_ERROR("CWeightedDegreePositionStringKernel optimization not implemented for mismatch!=0\n")
return false ;
}
if (tree_num<0)
SG_DEBUG("deleting CWeightedDegreePositionStringKernel optimization\n")
delete_optimization();
if (tree_num<0)
SG_DEBUG("initializing CWeightedDegreePositionStringKernel optimization\n")
for (auto i : progress(range(p_count), *this->io))
{
if (tree_num<0)
{
add_example_to_tree(IDX[i], alphas[i]);
}
else
{
for (int32_t t=tree_num; t<=upto_tree; t++)
add_example_to_single_tree(IDX[i], alphas[i], t);
}
}
set_is_initialized(true) ;
return true ;
}
bool CWeightedDegreePositionStringKernel::delete_optimization()
{
if ((opt_type==FASTBUTMEMHUNGRY) && (tries.get_use_compact_terminal_nodes()))
{
tries.set_use_compact_terminal_nodes(false) ;
SG_DEBUG("disabling compact trie nodes with FASTBUTMEMHUNGRY\n")
}
if (get_is_initialized())
{
if (opt_type==SLOWBUTMEMEFFICIENT)
tries.delete_trees(true);
else if (opt_type==FASTBUTMEMHUNGRY)
tries.delete_trees(false); // still buggy
else {
SG_ERROR("unknown optimization type\n")
}
set_is_initialized(false);
return true;
}
return false;
}
float64_t CWeightedDegreePositionStringKernel::compute_with_mismatch(
char* avec, int32_t alen, char* bvec, int32_t blen)
{
float64_t* max_shift_vec= SG_MALLOC(float64_t, max_shift);
float64_t sum0=0 ;
for (int32_t i=0; i<max_shift; i++)
max_shift_vec[i]=0 ;
// no shift
for (int32_t i=0; i<alen; i++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0))
continue ;
int32_t mismatches=0;
float64_t sumi = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j<alen); j++)
{
if (avec[i+j]!=bvec[i+j])
{
mismatches++ ;
if (mismatches>max_mismatch)
break ;
} ;
sumi += weights[j+degree*mismatches];
}
if (position_weights!=NULL)
sum0 += position_weights[i]*sumi ;
else
sum0 += sumi ;
} ;
for (int32_t i=0; i<alen; i++)
{
for (int32_t k=1; (k<=shift[i]) && (i+k<alen); k++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0) && (position_weights[i+k]==0.0))
continue ;
float64_t sumi1 = 0.0 ;
// shift in sequence a
int32_t mismatches=0;
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j+k]!=bvec[i+j])
{
mismatches++ ;
if (mismatches>max_mismatch)
break ;
} ;
sumi1 += weights[j+degree*mismatches];
}
float64_t sumi2 = 0.0 ;
// shift in sequence b
mismatches=0;
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j]!=bvec[i+j+k])
{
mismatches++ ;
if (mismatches>max_mismatch)
break ;
} ;
sumi2 += weights[j+degree*mismatches];
}
if (position_weights!=NULL)
max_shift_vec[k-1] += position_weights[i]*sumi1 + position_weights[i+k]*sumi2 ;
else
max_shift_vec[k-1] += sumi1 + sumi2 ;
} ;
}
float64_t result = sum0 ;
for (int32_t i=0; i<max_shift; i++)
result += max_shift_vec[i]/(2*(i+1)) ;
SG_FREE(max_shift_vec);
return result ;
}
float64_t CWeightedDegreePositionStringKernel::compute_without_mismatch(
char* avec, int32_t alen, char* bvec, int32_t blen)
{
float64_t* max_shift_vec = SG_MALLOC(float64_t, max_shift);
float64_t sum0=0 ;
for (int32_t i=0; i<max_shift; i++)
max_shift_vec[i]=0 ;
// no shift
for (int32_t i=0; i<alen; i++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0))
continue ;
float64_t sumi = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j<alen); j++)
{
if (avec[i+j]!=bvec[i+j])
break ;
sumi += weights[j];
}
if (position_weights!=NULL)
sum0 += position_weights[i]*sumi ;
else
sum0 += sumi ;
} ;
for (int32_t i=0; i<alen; i++)
{
for (int32_t k=1; (k<=shift[i]) && (i+k<alen); k++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0) && (position_weights[i+k]==0.0))
continue ;
float64_t sumi1 = 0.0 ;
// shift in sequence a
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j+k]!=bvec[i+j])
break ;
sumi1 += weights[j];
}
float64_t sumi2 = 0.0 ;
// shift in sequence b
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j]!=bvec[i+j+k])
break ;
sumi2 += weights[j];
}
if (position_weights!=NULL)
max_shift_vec[k-1] += position_weights[i]*sumi1 + position_weights[i+k]*sumi2 ;
else
max_shift_vec[k-1] += sumi1 + sumi2 ;
} ;
}
float64_t result = sum0 ;
for (int32_t i=0; i<max_shift; i++)
result += max_shift_vec[i]/(2*(i+1)) ;
SG_FREE(max_shift_vec);
return result ;
}
float64_t CWeightedDegreePositionStringKernel::compute_without_mismatch_matrix(
char* avec, int32_t alen, char* bvec, int32_t blen)
{
float64_t* max_shift_vec = SG_MALLOC(float64_t, max_shift);
float64_t sum0=0 ;
for (int32_t i=0; i<max_shift; i++)
max_shift_vec[i]=0 ;
// no shift
for (int32_t i=0; i<alen; i++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0))
continue ;
float64_t sumi = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j<alen); j++)
{
if (avec[i+j]!=bvec[i+j])
break ;
sumi += weights[i*degree+j];
}
if (position_weights!=NULL)
sum0 += position_weights[i]*sumi ;
else
sum0 += sumi ;
} ;
for (int32_t i=0; i<alen; i++)
{
for (int32_t k=1; (k<=shift[i]) && (i+k<alen); k++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0) && (position_weights[i+k]==0.0))
continue ;
float64_t sumi1 = 0.0 ;
// shift in sequence a
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j+k]!=bvec[i+j])
break ;
sumi1 += weights[i*degree+j];
}
float64_t sumi2 = 0.0 ;
// shift in sequence b
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
if (avec[i+j]!=bvec[i+j+k])
break ;
sumi2 += weights[i*degree+j];
}
if (position_weights!=NULL)
max_shift_vec[k-1] += position_weights[i]*sumi1 + position_weights[i+k]*sumi2 ;
else
max_shift_vec[k-1] += sumi1 + sumi2 ;
} ;
}
float64_t result = sum0 ;
for (int32_t i=0; i<max_shift; i++)
result += max_shift_vec[i]/(2*(i+1)) ;
SG_FREE(max_shift_vec);
return result ;
}
float64_t CWeightedDegreePositionStringKernel::compute_without_mismatch_position_weights(
char* avec, float64_t* pos_weights_lhs, int32_t alen, char* bvec,
float64_t* pos_weights_rhs, int32_t blen)
{
float64_t* max_shift_vec = SG_MALLOC(float64_t, max_shift);
float64_t sum0=0 ;
for (int32_t i=0; i<max_shift; i++)
max_shift_vec[i]=0 ;
// no shift
for (int32_t i=0; i<alen; i++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0))
continue ;
float64_t sumi = 0.0 ;
float64_t posweight_lhs = 0.0 ;
float64_t posweight_rhs = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j<alen); j++)
{
posweight_lhs += pos_weights_lhs[i+j] ;
posweight_rhs += pos_weights_rhs[i+j] ;
if (avec[i+j]!=bvec[i+j])
break ;
sumi += weights[j]*(posweight_lhs/(j+1))*(posweight_rhs/(j+1)) ;
}
if (position_weights!=NULL)
sum0 += position_weights[i]*sumi ;
else
sum0 += sumi ;
} ;
for (int32_t i=0; i<alen; i++)
{
for (int32_t k=1; (k<=shift[i]) && (i+k<alen); k++)
{
if ((position_weights!=NULL) && (position_weights[i]==0.0) && (position_weights[i+k]==0.0))
continue ;
// shift in sequence a
float64_t sumi1 = 0.0 ;
float64_t posweight_lhs = 0.0 ;
float64_t posweight_rhs = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
posweight_lhs += pos_weights_lhs[i+j+k] ;
posweight_rhs += pos_weights_rhs[i+j] ;
if (avec[i+j+k]!=bvec[i+j])
break ;
sumi1 += weights[j]*(posweight_lhs/(j+1))*(posweight_rhs/(j+1)) ;
}
// shift in sequence b
float64_t sumi2 = 0.0 ;
posweight_lhs = 0.0 ;
posweight_rhs = 0.0 ;
for (int32_t j=0; (j<degree) && (i+j+k<alen); j++)
{
posweight_lhs += pos_weights_lhs[i+j] ;
posweight_rhs += pos_weights_rhs[i+j+k] ;
if (avec[i+j]!=bvec[i+j+k])
break ;
sumi2 += weights[j]*(posweight_lhs/(j+1))*(posweight_rhs/(j+1)) ;
}
if (position_weights!=NULL)
max_shift_vec[k-1] += position_weights[i]*sumi1 + position_weights[i+k]*sumi2 ;
else
max_shift_vec[k-1] += sumi1 + sumi2 ;
} ;
}
float64_t result = sum0 ;
for (int32_t i=0; i<max_shift; i++)
result += max_shift_vec[i]/(2*(i+1)) ;
SG_FREE(max_shift_vec);
return result ;
}
float64_t CWeightedDegreePositionStringKernel::compute(
int32_t idx_a, int32_t idx_b)
{
int32_t alen, blen;
bool free_avec, free_bvec;
char* avec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
char* bvec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);
// can only deal with strings of same length
ASSERT(alen==blen)
ASSERT(shift_len==alen)
float64_t result = 0 ;
if (position_weights_lhs!=NULL || position_weights_rhs!=NULL)
{
ASSERT(max_mismatch==0)
float64_t* position_weights_rhs_ = position_weights_rhs ;
if (lhs==rhs)
position_weights_rhs_ = position_weights_lhs ;
result = compute_without_mismatch_position_weights(avec, &position_weights_lhs[idx_a*alen], alen, bvec, &position_weights_rhs_[idx_b*blen], blen) ;
}
else if (max_mismatch > 0)
result = compute_with_mismatch(avec, alen, bvec, blen) ;
else if (length==0)
result = compute_without_mismatch(avec, alen, bvec, blen) ;
else
result = compute_without_mismatch_matrix(avec, alen, bvec, blen) ;
((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
return result ;
}
void CWeightedDegreePositionStringKernel::add_example_to_tree(
int32_t idx, float64_t alpha)
{
ASSERT(position_weights_lhs==NULL)
ASSERT(position_weights_rhs==NULL)
ASSERT(alphabet)
ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA)
int32_t len=0;
bool free_vec;
char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
ASSERT(max_mismatch==0)
int32_t *vec = SG_MALLOC(int32_t, len);
for (int32_t i=0; i<len; i++)
vec[i]=alphabet->remap_to_bin(char_vec[i]);
((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
if (opt_type==FASTBUTMEMHUNGRY)
{
//TRIES(set_use_compact_terminal_nodes(false)) ;
ASSERT(!TRIES(get_use_compact_terminal_nodes()))
}
for (int32_t i=0; i<len; i++)
{
int32_t max_s=-1;
if (opt_type==SLOWBUTMEMEFFICIENT)
max_s=0;
else if (opt_type==FASTBUTMEMHUNGRY)
max_s=shift[i];
else {
SG_ERROR("unknown optimization type\n")
}
for (int32_t s=max_s; s>=0; s--)
{
float64_t alpha_pw = normalizer->normalize_lhs((s==0) ? (alpha) : (alpha/(2.0*s)), idx);
TRIES(add_to_trie(i, s, vec, alpha_pw, weights, (length!=0))) ;
if ((s==0) || (i+s>=len))
continue;
TRIES(add_to_trie(i+s, -s, vec, alpha_pw, weights, (length!=0))) ;
}
}
SG_FREE(vec);
tree_initialized=true ;
}
void CWeightedDegreePositionStringKernel::add_example_to_single_tree(
int32_t idx, float64_t alpha, int32_t tree_num)
{
ASSERT(position_weights_lhs==NULL)
ASSERT(position_weights_rhs==NULL)
ASSERT(alphabet)
ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA)
int32_t len=0;
bool free_vec;
char* char_vec=((CStringFeatures<char>*) lhs)->get_feature_vector(idx, len, free_vec);
ASSERT(max_mismatch==0)
int32_t *vec=SG_MALLOC(int32_t, len);
int32_t max_s=-1;
if (opt_type==SLOWBUTMEMEFFICIENT)
max_s=0;
else if (opt_type==FASTBUTMEMHUNGRY)
{
ASSERT(!tries.get_use_compact_terminal_nodes())
max_s=shift[tree_num];
}
else {
SG_ERROR("unknown optimization type\n")
}
for (int32_t i=CMath::max(0,tree_num-max_shift);
i<CMath::min(len,tree_num+degree+max_shift); i++)
{
vec[i]=alphabet->remap_to_bin(char_vec[i]);
}
((CStringFeatures<char>*) lhs)->free_feature_vector(char_vec, idx, free_vec);
for (int32_t s=max_s; s>=0; s--)
{
float64_t alpha_pw = normalizer->normalize_lhs((s==0) ? (alpha) : (alpha/(2.0*s)), idx);
tries.add_to_trie(tree_num, s, vec, alpha_pw, weights, (length!=0)) ;
}
if (opt_type==FASTBUTMEMHUNGRY)
{
for (int32_t i=CMath::max(0,tree_num-max_shift); i<CMath::min(len,tree_num+max_shift+1); i++)
{
int32_t s=tree_num-i;
if ((i+s<len) && (s>=1) && (s<=shift[i]))
{
float64_t alpha_pw = normalizer->normalize_lhs((s==0) ? (alpha) : (alpha/(2.0*s)), idx);
tries.add_to_trie(tree_num, -s, vec, alpha_pw, weights, (length!=0)) ;
}
}
}
SG_FREE(vec);
tree_initialized=true ;
}
float64_t CWeightedDegreePositionStringKernel::compute_by_tree(int32_t idx)
{
ASSERT(position_weights_lhs==NULL)
ASSERT(position_weights_rhs==NULL)
ASSERT(alphabet)
ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA)
float64_t sum=0;
int32_t len=0;
bool free_vec;
char* char_vec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx, len, free_vec);
ASSERT(max_mismatch==0)
int32_t *vec=SG_MALLOC(int32_t, len);
for (int32_t i=0; i<len; i++)
vec[i]=alphabet->remap_to_bin(char_vec[i]);
((CStringFeatures<char>*) rhs)->free_feature_vector(char_vec, idx, free_vec);
for (int32_t i=0; i<len; i++)
sum += tries.compute_by_tree_helper(vec, len, i, i, i, weights, (length!=0)) ;
if (opt_type==SLOWBUTMEMEFFICIENT)
{
for (int32_t i=0; i<len; i++)
{
for (int32_t s=1; (s<=shift[i]) && (i+s<len); s++)
{
sum+=tries.compute_by_tree_helper(vec, len, i, i+s, i, weights, (length!=0))/(2*s) ;
sum+=tries.compute_by_tree_helper(vec, len, i+s, i, i+s, weights, (length!=0))/(2*s) ;
}
}
}
SG_FREE(vec);
return normalizer->normalize_rhs(sum, idx);
}
void CWeightedDegreePositionStringKernel::compute_by_tree(
int32_t idx, float64_t* LevelContrib)
{
ASSERT(position_weights_lhs==NULL)
ASSERT(position_weights_rhs==NULL)
ASSERT(alphabet)
ASSERT(alphabet->get_alphabet()==DNA || alphabet->get_alphabet()==RNA)
int32_t len=0;
bool free_vec;
char* char_vec=((CStringFeatures<char>*) rhs)->get_feature_vector(idx, len, free_vec);
ASSERT(max_mismatch==0)
int32_t *vec=SG_MALLOC(int32_t, len);
for (int32_t i=0; i<len; i++)
vec[i]=alphabet->remap_to_bin(char_vec[i]);
((CStringFeatures<char>*) rhs)->free_feature_vector(char_vec, idx, free_vec);
for (int32_t i=0; i<len; i++)
{
tries.compute_by_tree_helper(vec, len, i, i, i, LevelContrib,
normalizer->normalize_rhs(1.0, idx), mkl_stepsize, weights,
(length!=0));
}
if (opt_type==SLOWBUTMEMEFFICIENT)
{
for (int32_t i=0; i<len; i++)
for (int32_t k=1; (k<=shift[i]) && (i+k<len); k++)
{
tries.compute_by_tree_helper(vec, len, i, i+k, i, LevelContrib,
normalizer->normalize_rhs(1.0/(2*k), idx), mkl_stepsize,
weights, (length!=0)) ;
tries.compute_by_tree_helper(vec, len, i+k, i, i+k,
LevelContrib, normalizer->normalize_rhs(1.0/(2*k), idx),
mkl_stepsize, weights, (length!=0)) ;
}
}
SG_FREE(vec);
}
float64_t* CWeightedDegreePositionStringKernel::compute_abs_weights(
int32_t &len)
{
return tries.compute_abs_weights(len);
}
void CWeightedDegreePositionStringKernel::set_shifts(SGVector<int32_t> shifts)
{
SG_FREE(shift);
shift_len = shifts.vlen;
shift = SG_MALLOC(int32_t, shift_len);
if (shift)
{
max_shift = 0 ;
for (int32_t i=0; i<shift_len; i++)
{
shift[i] = shifts.vector[i] ;
max_shift = CMath::max(shift[i], max_shift);
}
ASSERT(max_shift>=0 && max_shift<=shift_len)
}
}
bool CWeightedDegreePositionStringKernel::set_wd_weights()
{
ASSERT(degree>0)
SG_FREE(weights);
weights=SG_MALLOC(float64_t, degree);
weights_degree=degree;
weights_length=1;
if (weights)
{
int32_t i;
float64_t sum=0;
for (i=0; i<degree; i++)
{
weights[i]=degree-i;
sum+=weights[i];
}
for (i=0; i<degree; i++)
weights[i]/=sum;
for (i=0; i<degree; i++)
{
for (int32_t j=1; j<=max_mismatch; j++)
{
if (j<i+1)
{
int32_t nk=CMath::nchoosek(i+1, j);
weights[i+j*degree]=weights[i]/(nk*CMath::pow(3.0,j));
}
else
weights[i+j*degree]= 0;
}
}
return true;
}
else
return false;
}
bool CWeightedDegreePositionStringKernel::set_weights(SGMatrix<float64_t> new_weights)
{
float64_t* ws=new_weights.matrix;
int32_t d=new_weights.num_rows;
int32_t len=new_weights.num_cols;
if (d!=degree || len<0)
SG_ERROR("WD: Dimension mismatch (should be (seq_length | 1) x degree) got (%d x %d)\n", len, degree)
degree=d;
length=len;
if (len <= 0)
len=1;
weights_degree=degree;
weights_length=len+max_mismatch;
SG_DEBUG("Creating weights of size %dx%d\n", weights_degree, weights_length)
int32_t num_weights=weights_degree*weights_length;
SG_FREE(weights);
weights=SG_MALLOC(float64_t, num_weights);
for (int32_t i=0; i<degree*len; i++)
weights[i]=ws[i];
return true;
}
void CWeightedDegreePositionStringKernel::set_position_weights(SGVector<float64_t> pws)
{
if (seq_length==0)
seq_length=pws.vlen;
if (seq_length!=pws.vlen)
SG_ERROR("seq_length = %i, position_weights_length=%i\n", seq_length, pws.vlen)
SG_FREE(position_weights);
position_weights=SG_MALLOC(float64_t, pws.vlen);
position_weights_len=pws.vlen;
tries.set_position_weights(position_weights);
for (int32_t i=0; i<pws.vlen; i++)
position_weights[i]=pws.vector[i];
}
bool CWeightedDegreePositionStringKernel::set_position_weights_lhs(float64_t* pws, int32_t len, int32_t num)
{
if (position_weights_rhs==position_weights_lhs)
position_weights_rhs=NULL;
else
delete_position_weights_rhs();
if (len==0)
{
return delete_position_weights_lhs();
}
if (seq_length!=len)
{
SG_ERROR("seq_length = %i, position_weights_length=%i\n", seq_length, len)
return false;
}
SG_FREE(position_weights_lhs);
position_weights_lhs=SG_MALLOC(float64_t, len*num);
position_weights_lhs_len=len*num;
for (int32_t i=0; i<len*num; i++)
position_weights_lhs[i]=pws[i];
return true;
}
bool CWeightedDegreePositionStringKernel::set_position_weights_rhs(
float64_t* pws, int32_t len, int32_t num)
{
if (len==0)
{
if (position_weights_rhs==position_weights_lhs)
{
position_weights_rhs=NULL;
return true;
}
return delete_position_weights_rhs();
}
if (seq_length!=len)
{
SG_ERROR("seq_length = %i, position_weights_length=%i\n", seq_length, len)
return false;
}
SG_FREE(position_weights_rhs);
position_weights_rhs=SG_MALLOC(float64_t, len*num);
position_weights_rhs_len=len*num;
for (int32_t i=0; i<len*num; i++)
position_weights_rhs[i]=pws[i];
return true;
}
bool CWeightedDegreePositionStringKernel::init_block_weights_from_wd()
{
SG_FREE(block_weights);
block_weights=SG_MALLOC(float64_t, CMath::max(seq_length,degree));
if (block_weights)