Here, is the string of length k starting at position l of the sequence
and
is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.
Definition at line 48 of file WeightedDegreeStringKernel.h.
CWeightedDegreeStringKernel::CWeightedDegreeStringKernel | ( | int32_t | degree, | |
EWDKernType | type = E_WD | |||
) |
constructor
degree | degree | |
type | weighted degree kernel type |
Definition at line 42 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel::CWeightedDegreeStringKernel | ( | float64_t * | weights, | |
int32_t | degree | |||
) |
constructor
weights | kernel's weights | |
degree | degree |
Definition at line 61 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel::CWeightedDegreeStringKernel | ( | CStringFeatures< char > * | l, | |
CStringFeatures< char > * | r, | |||
int32_t | degree | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
degree | degree |
Definition at line 80 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel::~CWeightedDegreeStringKernel | ( | ) | [virtual] |
Definition at line 96 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::add_example_to_single_tree | ( | int32_t | idx, | |
float64_t | weight, | |||
int32_t | tree_num | |||
) | [protected] |
add example to single tree
idx | index | |
weight | weight | |
tree_num | which tree |
Definition at line 436 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::add_example_to_single_tree_mismatch | ( | int32_t | idx, | |
float64_t | weight, | |||
int32_t | tree_num | |||
) | [protected] |
add example to single tree mismatch
idx | index | |
weight | weight | |
tree_num | which tree |
Definition at line 482 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::add_example_to_tree | ( | int32_t | idx, | |
float64_t | weight | |||
) | [protected] |
add example to tree
idx | index | |
weight | weight |
Definition at line 392 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::add_example_to_tree_mismatch | ( | int32_t | idx, | |
float64_t | weight | |||
) | [protected] |
add example to tree mismatch
idx | index | |
weight | weight |
Definition at line 458 of file WeightedDegreeStringKernel.cpp.
virtual void CWeightedDegreeStringKernel::add_to_normal | ( | int32_t | idx, | |
float64_t | weight | |||
) | [virtual] |
add to normal
idx | where to add | |
weight | what to add |
Reimplemented from CKernel.
Definition at line 197 of file WeightedDegreeStringKernel.h.
void CWeightedDegreeStringKernel::cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 177 of file WeightedDegreeStringKernel.cpp.
virtual void CWeightedDegreeStringKernel::clear_normal | ( | ) | [virtual] |
clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 183 of file WeightedDegreeStringKernel.h.
float64_t CWeightedDegreeStringKernel::compute | ( | int32_t | idx_a, | |
int32_t | idx_b | |||
) | [protected, virtual] |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a | |
idx_b | index b |
Implements CKernel.
Definition at line 369 of file WeightedDegreeStringKernel.cpp.
float64_t * CWeightedDegreeStringKernel::compute_abs_weights | ( | int32_t & | len | ) |
compute abs weights
len | len |
Definition at line 555 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::compute_batch | ( | int32_t | num_vec, | |
int32_t * | vec_idx, | |||
float64_t * | target, | |||
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | alphas, | |||
float64_t | factor = 1.0 | |||
) | [virtual] |
compute batch
num_vec | number of vectors | |
vec_idx | vector index | |
target | target | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas | |
factor | factor |
Reimplemented from CKernel.
Definition at line 890 of file WeightedDegreeStringKernel.cpp.
void * CWeightedDegreeStringKernel::compute_batch_helper | ( | void * | p | ) | [static] |
helper for compute batch
p | thread parameter |
Definition at line 856 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::compute_by_subkernel | ( | int32_t | idx, | |
float64_t * | subkernel_contrib | |||
) | [virtual] |
compute by subkernel
idx | index | |
subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 225 of file WeightedDegreeStringKernel.h.
float64_t CWeightedDegreeStringKernel::compute_by_tree | ( | int32_t | idx | ) | [protected] |
compute by tree
idx | index |
Definition at line 508 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::compute_by_tree | ( | int32_t | idx, | |
float64_t * | LevelContrib | |||
) |
compute by tree
idx | index | |
LevelContrib | level contribution |
Definition at line 530 of file WeightedDegreeStringKernel.cpp.
virtual float64_t CWeightedDegreeStringKernel::compute_optimized | ( | int32_t | idx | ) | [virtual] |
compute optimized
idx | index to compute |
Reimplemented from CKernel.
Definition at line 150 of file WeightedDegreeStringKernel.h.
float64_t CWeightedDegreeStringKernel::compute_using_block | ( | char * | avec, | |
int32_t | alen, | |||
char * | bvec, | |||
int32_t | blen | |||
) | [protected] |
compute using block
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 296 of file WeightedDegreeStringKernel.cpp.
float64_t CWeightedDegreeStringKernel::compute_with_mismatch | ( | char * | avec, | |
int32_t | alen, | |||
char * | bvec, | |||
int32_t | blen | |||
) | [protected] |
compute with mismatch
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 268 of file WeightedDegreeStringKernel.cpp.
float64_t CWeightedDegreeStringKernel::compute_without_mismatch | ( | char * | avec, | |
int32_t | alen, | |||
char * | bvec, | |||
int32_t | blen | |||
) | [protected] |
compute without mismatch
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 322 of file WeightedDegreeStringKernel.cpp.
float64_t CWeightedDegreeStringKernel::compute_without_mismatch_matrix | ( | char * | avec, | |
int32_t | alen, | |||
char * | bvec, | |||
int32_t | blen | |||
) | [protected] |
compute without mismatch matrix
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 345 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::create_empty_tries | ( | ) | [protected] |
create emtpy tries
Definition at line 125 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::delete_optimization | ( | ) | [virtual] |
delete optimization
Reimplemented from CKernel.
Definition at line 254 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::delete_position_weights | ( | ) |
delete position weights
Definition at line 468 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::get_degree | ( | ) |
float64_t* CWeightedDegreeStringKernel::get_degree_weights | ( | int32_t & | d, | |
int32_t & | len | |||
) |
get degree weights
d | degree weights will be stored here | |
len | number of degree weights will be stored here |
Definition at line 333 of file WeightedDegreeStringKernel.h.
virtual EKernelType CWeightedDegreeStringKernel::get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 105 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::get_max_mismatch | ( | ) |
get maximum mismatch
Definition at line 486 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::get_mkl_stepsize | ( | ) |
get MKL step size
Definition at line 533 of file WeightedDegreeStringKernel.h.
virtual const char* CWeightedDegreeStringKernel::get_name | ( | ) | [virtual] |
return the kernel's name
Implements CKernel.
Definition at line 111 of file WeightedDegreeStringKernel.h.
virtual int32_t CWeightedDegreeStringKernel::get_num_subkernels | ( | ) | [virtual] |
get number of subkernels
Reimplemented from CKernel.
Definition at line 211 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
Definition at line 364 of file WeightedDegreeStringKernel.h.
const float64_t* CWeightedDegreeStringKernel::get_subkernel_weights | ( | int32_t & | num_weights | ) | [virtual] |
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented from CKernel.
Definition at line 242 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::get_use_block_computation | ( | ) |
check if block computation is performed
Definition at line 516 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::get_weights | ( | int32_t & | num_weights | ) |
get weights
num_weights | number of weights will be stored here |
Definition at line 345 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::get_which_degree | ( | ) |
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 136 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights | ( | ) |
initialize block weights
Definition at line 828 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_const | ( | ) |
initialize block weights constant
Definition at line 713 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
Definition at line 758 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_exp | ( | ) |
initialize block weights exponential
Definition at line 775 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_external | ( | ) |
initialize block weights external
Definition at line 809 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
Definition at line 665 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
Definition at line 685 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_linear | ( | ) |
initialize block weights linear
Definition at line 727 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_log | ( | ) |
initialize block weights logarithmic
Definition at line 792 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
Definition at line 741 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::init_optimization | ( | int32_t | count, | |
int32_t * | IDX, | |||
float64_t * | alphas, | |||
int32_t | tree_num | |||
) | [virtual] |
initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees
count | count | |
IDX | IDX | |
alphas | alphas | |
tree_num | which tree |
Definition at line 212 of file WeightedDegreeStringKernel.cpp.
virtual bool CWeightedDegreeStringKernel::init_optimization | ( | int32_t | count, | |
int32_t * | IDX, | |||
float64_t * | alphas | |||
) | [virtual] |
initialize optimization
count | count | |
IDX | index | |
alphas | alphas |
Reimplemented from CKernel.
Definition at line 120 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 326 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::load_init | ( | FILE * | src | ) | [virtual] |
load kernel init_data
src | file to load from |
Implements CKernel.
Definition at line 201 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 114 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::save_init | ( | FILE * | dest | ) | [virtual] |
save kernel init_data
dest | file to save to |
Implements CKernel.
Definition at line 206 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 493 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
Definition at line 991 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::set_mkl_stepsize | ( | int32_t | step | ) |
set MKL steps ize
step | new step size |
Definition at line 523 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::set_position_weights | ( | float64_t * | position_weights, | |
int32_t | len = 0 | |||
) |
set position weights
position_weights | new position weights | |
len | number of position weights |
Definition at line 636 of file WeightedDegreeStringKernel.cpp.
void CWeightedDegreeStringKernel::set_subkernel_weights | ( | float64_t * | weights2, | |
int32_t | num_weights2 | |||
) | [virtual] |
set subkernel weights
weights2 | weights | |
num_weights2 | number of weights |
Reimplemented from CKernel.
Definition at line 264 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::set_use_block_computation | ( | bool | block | ) |
set if block computation shall be performed
block | if block computation shall be performed |
Definition at line 506 of file WeightedDegreeStringKernel.h.
void CWeightedDegreeStringKernel::set_wd_weights | ( | float64_t * | p_weights, | |
int32_t | d | |||
) |
set wd weights
p_weights | new eights | |
d | degree |
Definition at line 383 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::set_wd_weights_by_type | ( | EWDKernType | type | ) |
set wd weights
type | weighted degree kernel type |
if we know a better weighting later on do a switch
Definition at line 561 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::set_weights | ( | float64_t * | weights, | |
int32_t | d, | |||
int32_t | len | |||
) |
set weights
weights | new weights | |
d | degree | |
len | number of weights |
Definition at line 611 of file WeightedDegreeStringKernel.cpp.
bool CWeightedDegreeStringKernel::set_which_degree | ( | int32_t | which | ) |
set which degree
which | which degree |
Definition at line 540 of file WeightedDegreeStringKernel.h.
CAlphabet* CWeightedDegreeStringKernel::alphabet [protected] |
alphabet of features
Definition at line 698 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::block_computation [protected] |
if block computation is used
Definition at line 677 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::block_weights [protected] |
(internal) block weights
Definition at line 685 of file WeightedDegreeStringKernel.h.
external block weights
Definition at line 682 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::degree [protected] |
degree
Definition at line 664 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::initialized [protected] |
if kernel is initialized
Definition at line 674 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::length [protected] |
length
Definition at line 666 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::max_mismatch [protected] |
maximum mismatch
Definition at line 669 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::mkl_stepsize [protected] |
MKL step size
Definition at line 662 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::num_block_weights_external [protected] |
number of external block weights
Definition at line 680 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::position_weights [protected] |
position weights
Definition at line 658 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::seq_length [protected] |
sequence length
Definition at line 671 of file WeightedDegreeStringKernel.h.
bool CWeightedDegreeStringKernel::tree_initialized [protected] |
if tree is initialized
Definition at line 695 of file WeightedDegreeStringKernel.h.
CTrie<DNATrie>* CWeightedDegreeStringKernel::tries [protected] |
tries
Definition at line 692 of file WeightedDegreeStringKernel.h.
EWDKernType CWeightedDegreeStringKernel::type [protected] |
WeightedDegree kernel type
Definition at line 687 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::weights [protected] |
degree*length weights length must match seq_length if != 0
Definition at line 656 of file WeightedDegreeStringKernel.h.
float64_t* CWeightedDegreeStringKernel::weights_buffer [protected] |
weights buffer
Definition at line 660 of file WeightedDegreeStringKernel.h.
int32_t CWeightedDegreeStringKernel::which_degree [protected] |
which degree
Definition at line 689 of file WeightedDegreeStringKernel.h.