The Weighted Degree Position String kernel (Weighted Degree kernel with shifts).
The WD-shift kernel of order d compares two sequences and
of length L by summing all contributions of k-mer matches of lengths
, weighted by coefficients
allowing for a positional tolerance of up to shift s.
It is formally defined as
where are the weighting coefficients of the j-mers,
is a weighting over the position in the sequence,
is the weight assigned to shifts (in either direction) of extent s, and S(l) determines the shift range at position l.
Definition at line 48 of file WeightedDegreePositionStringKernel.h.
Public Member Functions | |
CWeightedDegreePositionStringKernel (int32_t size, int32_t degree, int32_t max_mismatch=0, int32_t mkl_stepsize=1) | |
CWeightedDegreePositionStringKernel (int32_t size, float64_t *weights, int32_t degree, int32_t max_mismatch, int32_t *shift, int32_t shift_len, int32_t mkl_stepsize=1) | |
CWeightedDegreePositionStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t degree) | |
virtual | ~CWeightedDegreePositionStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
virtual bool | init_optimization (int32_t p_count, int32_t *IDX, float64_t *alphas) |
virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *alphas, int32_t tree_num, int32_t upto_tree=-1) |
virtual bool | delete_optimization () |
virtual float64_t | compute_optimized (int32_t idx) |
virtual void | 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 void | clear_normal () |
virtual void | add_to_normal (int32_t idx, float64_t weight) |
virtual int32_t | get_num_subkernels () |
void | compute_by_subkernel (int32_t idx, float64_t *subkernel_contrib) |
const float64_t * | get_subkernel_weights (int32_t &num_weights) |
void | set_subkernel_weights (float64_t *weights2, int32_t num_weights2) |
float64_t * | compute_abs_weights (int32_t &len) |
bool | is_tree_initialized () |
int32_t | get_max_mismatch () |
int32_t | get_degree () |
float64_t * | get_degree_weights (int32_t &d, int32_t &len) |
float64_t * | get_weights (int32_t &num_weights) |
float64_t * | get_position_weights (int32_t &len) |
bool | set_shifts (int32_t *shifts, int32_t len) |
virtual bool | set_weights (float64_t *weights, int32_t d, int32_t len=0) |
virtual bool | set_wd_weights () |
virtual bool | set_position_weights (float64_t *pws, int32_t len) |
bool | set_position_weights_lhs (float64_t *pws, int32_t len, int32_t num) |
bool | set_position_weights_rhs (float64_t *pws, int32_t len, int32_t num) |
bool | init_block_weights () |
bool | init_block_weights_from_wd () |
bool | init_block_weights_from_wd_external () |
bool | init_block_weights_const () |
bool | init_block_weights_linear () |
bool | init_block_weights_sqpoly () |
bool | init_block_weights_cubicpoly () |
bool | init_block_weights_exp () |
bool | init_block_weights_log () |
bool | init_block_weights_external () |
bool | delete_position_weights () |
bool | delete_position_weights_lhs () |
bool | delete_position_weights_rhs () |
virtual float64_t | compute_by_tree (int32_t idx) |
virtual void | compute_by_tree (int32_t idx, float64_t *LevelContrib) |
float64_t * | compute_scoring (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *weights) |
char * | compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t *IDX, float64_t *alphas) |
float64_t * | extract_w (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *w_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas) |
float64_t * | compute_POIM (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *poim_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t *distrib) |
void | prepare_POIM2 (float64_t *distrib, int32_t num_sym, int32_t num_feat) |
void | compute_POIM2 (int32_t max_degree, CSVM *svm) |
void | get_POIM2 (float64_t **poim, int32_t *result_len) |
void | cleanup_POIM2 () |
cleanup POIM2 | |
Static Public Member Functions | |
static void * | compute_batch_helper (void *p) |
Protected Member Functions | |
void | create_empty_tries () |
virtual void | add_example_to_tree (int32_t idx, float64_t weight) |
void | add_example_to_single_tree (int32_t idx, float64_t weight, int32_t tree_num) |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
float64_t | compute_with_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_without_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_without_mismatch_matrix (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_without_mismatch_position_weights (char *avec, float64_t *posweights_lhs, int32_t alen, char *bvec, float64_t *posweights_rhs, int32_t blen) |
virtual void | remove_lhs () |
Protected Attributes | |
float64_t * | weights |
float64_t * | position_weights |
float64_t * | position_weights_lhs |
float64_t * | position_weights_rhs |
bool * | position_mask |
float64_t * | weights_buffer |
int32_t | mkl_stepsize |
int32_t | degree |
int32_t | length |
int32_t | max_mismatch |
int32_t | seq_length |
int32_t * | shift |
int32_t | shift_len |
int32_t | max_shift |
bool | block_computation |
int32_t | num_block_weights_external |
float64_t * | block_weights_external |
float64_t * | block_weights |
EWDKernType | type |
int32_t | which_degree |
CTrie< DNATrie > | tries |
CTrie< POIMTrie > | poim_tries |
bool | tree_initialized |
bool | use_poim_tries |
float64_t * | m_poim_distrib |
float64_t * | m_poim |
int32_t | m_poim_num_sym |
int32_t | m_poim_num_feat |
int32_t | m_poim_result_len |
CAlphabet * | alphabet |
CWeightedDegreePositionStringKernel | ( | int32_t | size, | |
int32_t | degree, | |||
int32_t | max_mismatch = 0 , |
|||
int32_t | mkl_stepsize = 1 | |||
) |
constructor
size | cache size | |
degree | degree | |
max_mismatch | maximum mismatch | |
mkl_stepsize | MKL stepsize |
Definition at line 52 of file WeightedDegreePositionStringKernel.cpp.
CWeightedDegreePositionStringKernel | ( | int32_t | size, | |
float64_t * | weights, | |||
int32_t | degree, | |||
int32_t | max_mismatch, | |||
int32_t * | shift, | |||
int32_t | shift_len, | |||
int32_t | mkl_stepsize = 1 | |||
) |
constructor
size | cache size | |
weights | weights | |
degree | degree | |
max_mismatch | maximum mismatch | |
shift | position shifts | |
shift_len | number of shifts | |
mkl_stepsize | MKL stepsize |
Definition at line 71 of file WeightedDegreePositionStringKernel.cpp.
CWeightedDegreePositionStringKernel | ( | 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 95 of file WeightedDegreePositionStringKernel.cpp.
~CWeightedDegreePositionStringKernel | ( | ) | [virtual] |
Definition at line 116 of file WeightedDegreePositionStringKernel.cpp.
void 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 700 of file WeightedDegreePositionStringKernel.cpp.
void add_example_to_tree | ( | int32_t | idx, | |
float64_t | weight | |||
) | [protected, virtual] |
add example to tree
idx | index | |
weight | weight |
Definition at line 646 of file WeightedDegreePositionStringKernel.cpp.
virtual void 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 208 of file WeightedDegreePositionStringKernel.h.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 222 of file WeightedDegreePositionStringKernel.cpp.
void cleanup_POIM2 | ( | ) |
cleanup POIM2
Definition at line 1946 of file WeightedDegreePositionStringKernel.cpp.
virtual void clear_normal | ( | ) | [virtual] |
clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 182 of file WeightedDegreePositionStringKernel.h.
float64_t 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 603 of file WeightedDegreePositionStringKernel.cpp.
float64_t * compute_abs_weights | ( | int32_t & | len | ) |
compute abs weights
len | len |
Definition at line 838 of file WeightedDegreePositionStringKernel.cpp.
void 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 1305 of file WeightedDegreePositionStringKernel.cpp.
void * compute_batch_helper | ( | void * | p | ) | [static] |
helper for compute batch
p | thread parameter |
Definition at line 1247 of file WeightedDegreePositionStringKernel.cpp.
void 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 232 of file WeightedDegreePositionStringKernel.h.
void compute_by_tree | ( | int32_t | idx, | |
float64_t * | LevelContrib | |||
) | [virtual] |
compute by tree
idx | index | |
LevelContrib | level contribution |
Definition at line 795 of file WeightedDegreePositionStringKernel.cpp.
float64_t compute_by_tree | ( | int32_t | idx | ) | [virtual] |
compute by tree
idx | index |
Definition at line 756 of file WeightedDegreePositionStringKernel.cpp.
char * compute_consensus | ( | int32_t & | num_feat, | |
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | alphas | |||
) |
compute consensus string
num_feat | number of features | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas |
Definition at line 1574 of file WeightedDegreePositionStringKernel.cpp.
virtual float64_t compute_optimized | ( | int32_t | idx | ) | [virtual] |
compute optimized
idx | index to compute |
Reimplemented from CKernel.
Definition at line 150 of file WeightedDegreePositionStringKernel.h.
float64_t * compute_POIM | ( | int32_t | max_degree, | |
int32_t & | num_feat, | |||
int32_t & | num_sym, | |||
float64_t * | poim_result, | |||
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | alphas, | |||
float64_t * | distrib | |||
) |
compute POIM
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
poim_result | poim | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas | |
distrib | distribution |
Definition at line 1754 of file WeightedDegreePositionStringKernel.cpp.
void compute_POIM2 | ( | int32_t | max_degree, | |
CSVM * | svm | |||
) |
compute POIM2
max_degree | maximum degree | |
svm | SVM |
Definition at line 1902 of file WeightedDegreePositionStringKernel.cpp.
float64_t * compute_scoring | ( | int32_t | max_degree, | |
int32_t & | num_feat, | |||
int32_t & | num_sym, | |||
float64_t * | target, | |||
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | weights | |||
) |
compute positional scoring function, which assigns a weight per position, per symbol in the sequence
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
target | target | |
num_suppvec | number of support vectors | |
IDX | IDX | |
weights | weights |
Definition at line 1418 of file WeightedDegreePositionStringKernel.cpp.
float64_t 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 313 of file WeightedDegreePositionStringKernel.cpp.
float64_t 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 393 of file WeightedDegreePositionStringKernel.cpp.
float64_t 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 458 of file WeightedDegreePositionStringKernel.cpp.
float64_t compute_without_mismatch_position_weights | ( | char * | avec, | |
float64_t * | posweights_lhs, | |||
int32_t | alen, | |||
char * | bvec, | |||
float64_t * | posweights_rhs, | |||
int32_t | blen | |||
) | [protected] |
compute without mismatch position weights
avec | vector a | |
posweights_lhs | position weights left-hand side | |
alen | length of vector a | |
bvec | vector b | |
posweights_rhs | position weights right-hand side | |
blen | length of vector b |
Definition at line 522 of file WeightedDegreePositionStringKernel.cpp.
void create_empty_tries | ( | ) | [protected] |
create emtpy tries
Definition at line 154 of file WeightedDegreePositionStringKernel.cpp.
bool delete_optimization | ( | ) | [virtual] |
delete optimization
Reimplemented from CKernel.
Definition at line 288 of file WeightedDegreePositionStringKernel.cpp.
bool delete_position_weights | ( | ) |
delete position weights
Definition at line 480 of file WeightedDegreePositionStringKernel.h.
bool delete_position_weights_lhs | ( | ) |
delete position weights left-hand side
Definition at line 491 of file WeightedDegreePositionStringKernel.h.
bool delete_position_weights_rhs | ( | ) |
delete position weights right-hand side
Definition at line 502 of file WeightedDegreePositionStringKernel.h.
float64_t * extract_w | ( | int32_t | max_degree, | |
int32_t & | num_feat, | |||
int32_t & | num_sym, | |||
float64_t * | w_result, | |||
int32_t | num_suppvec, | |||
int32_t * | IDX, | |||
float64_t * | alphas | |||
) |
extract w
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
w_result | w | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas |
Definition at line 1691 of file WeightedDegreePositionStringKernel.cpp.
int32_t get_degree | ( | ) |
float64_t* 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 332 of file WeightedDegreePositionStringKernel.h.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 103 of file WeightedDegreePositionStringKernel.h.
int32_t get_max_mismatch | ( | ) |
get maximum mismatch
Definition at line 319 of file WeightedDegreePositionStringKernel.h.
virtual const char* get_name | ( | ) | const [virtual] |
return the kernel's name
Implements CSGObject.
Definition at line 109 of file WeightedDegreePositionStringKernel.h.
virtual int32_t get_num_subkernels | ( | ) | [virtual] |
get number of subkernels
Reimplemented from CKernel.
Definition at line 218 of file WeightedDegreePositionStringKernel.h.
void get_POIM2 | ( | float64_t ** | poim, | |
int32_t * | result_len | |||
) |
get POIM2
poim | POIMs (returned) | |
result_len | (returned) |
Definition at line 1937 of file WeightedDegreePositionStringKernel.cpp.
float64_t* get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
Definition at line 363 of file WeightedDegreePositionStringKernel.h.
const float64_t* 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 249 of file WeightedDegreePositionStringKernel.h.
float64_t* get_weights | ( | int32_t & | num_weights | ) |
get weights
num_weights | number of weights will be stored here |
Definition at line 344 of file WeightedDegreePositionStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 173 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights | ( | ) |
initialize block weights
Definition at line 1218 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_const | ( | ) |
initialize block weights constant
Definition at line 1103 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
Definition at line 1148 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_exp | ( | ) |
initialize block weights exponential
Definition at line 1165 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_external | ( | ) |
initialize block weights external
Definition at line 1199 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
Definition at line 1055 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
Definition at line 1075 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_linear | ( | ) |
initialize block weights linear
Definition at line 1117 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_log | ( | ) |
initialize block weights logarithmic
Definition at line 1182 of file WeightedDegreePositionStringKernel.cpp.
bool init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
Definition at line 1131 of file WeightedDegreePositionStringKernel.cpp.
bool init_optimization | ( | int32_t | count, | |
int32_t * | IDX, | |||
float64_t * | alphas, | |||
int32_t | tree_num, | |||
int32_t | upto_tree = -1 | |||
) | [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 | |
upto_tree | up to this tree |
Definition at line 242 of file WeightedDegreePositionStringKernel.cpp.
virtual bool init_optimization | ( | int32_t | p_count, | |
int32_t * | IDX, | |||
float64_t * | alphas | |||
) | [virtual] |
initialize optimization
p_count | count | |
IDX | index | |
alphas | alphas |
Reimplemented from CKernel.
Definition at line 118 of file WeightedDegreePositionStringKernel.h.
bool is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 313 of file WeightedDegreePositionStringKernel.h.
void prepare_POIM2 | ( | float64_t * | distrib, | |
int32_t | num_sym, | |||
int32_t | num_feat | |||
) |
prepare POIM2
num_feat | number of features | |
num_sym | number of symbols | |
distrib | distribution |
Definition at line 1890 of file WeightedDegreePositionStringKernel.cpp.
void remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 143 of file WeightedDegreePositionStringKernel.cpp.
bool set_position_weights | ( | float64_t * | pws, | |
int32_t | len | |||
) | [virtual] |
set position weights
pws | new position weights | |
len | number of position weights |
Definition at line 930 of file WeightedDegreePositionStringKernel.cpp.
bool set_position_weights_lhs | ( | float64_t * | pws, | |
int32_t | len, | |||
int32_t | num | |||
) |
set position weights for left-hand side
pws | new position weights | |
len | len | |
num | num |
Definition at line 955 of file WeightedDegreePositionStringKernel.cpp.
bool set_position_weights_rhs | ( | float64_t * | pws, | |
int32_t | len, | |||
int32_t | num | |||
) |
set position weights for right-hand side
pws | new position weights | |
len | len | |
num | num |
Definition at line 1001 of file WeightedDegreePositionStringKernel.cpp.
bool set_shifts | ( | int32_t * | shifts, | |
int32_t | len | |||
) |
set shifts
shifts | new shifts | |
len | number of shifts |
Definition at line 844 of file WeightedDegreePositionStringKernel.cpp.
void 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 271 of file WeightedDegreePositionStringKernel.h.
bool set_wd_weights | ( | ) | [virtual] |
set wd weights
Definition at line 869 of file WeightedDegreePositionStringKernel.cpp.
bool set_weights | ( | float64_t * | weights, | |
int32_t | d, | |||
int32_t | len = 0 | |||
) | [virtual] |
set weights
weights | new weights | |
d | degree | |
len | number of weights |
Definition at line 907 of file WeightedDegreePositionStringKernel.cpp.
alphabet of features
Definition at line 765 of file WeightedDegreePositionStringKernel.h.
bool block_computation [protected] |
if block computation is used
Definition at line 728 of file WeightedDegreePositionStringKernel.h.
float64_t* block_weights [protected] |
(internal) block weights
Definition at line 736 of file WeightedDegreePositionStringKernel.h.
float64_t* block_weights_external [protected] |
external block weights
Definition at line 733 of file WeightedDegreePositionStringKernel.h.
int32_t degree [protected] |
degree
Definition at line 711 of file WeightedDegreePositionStringKernel.h.
int32_t length [protected] |
length
Definition at line 713 of file WeightedDegreePositionStringKernel.h.
temporary memory for the interface to the poim functions
Definition at line 755 of file WeightedDegreePositionStringKernel.h.
float64_t* m_poim_distrib [protected] |
temporary memory for the interface to the poim functions
Definition at line 753 of file WeightedDegreePositionStringKernel.h.
int32_t m_poim_num_feat [protected] |
length of string (==num_feat)
Definition at line 760 of file WeightedDegreePositionStringKernel.h.
int32_t m_poim_num_sym [protected] |
number of symbols
Definition at line 758 of file WeightedDegreePositionStringKernel.h.
int32_t m_poim_result_len [protected] |
total size of poim array
Definition at line 762 of file WeightedDegreePositionStringKernel.h.
int32_t max_mismatch [protected] |
maximum mismatch
Definition at line 716 of file WeightedDegreePositionStringKernel.h.
int32_t max_shift [protected] |
maximum shift
Definition at line 725 of file WeightedDegreePositionStringKernel.h.
int32_t mkl_stepsize [protected] |
MKL stepsize
Definition at line 708 of file WeightedDegreePositionStringKernel.h.
int32_t num_block_weights_external [protected] |
number of external block weights
Definition at line 731 of file WeightedDegreePositionStringKernel.h.
CTrie<POIMTrie> poim_tries [protected] |
POIM tries
Definition at line 745 of file WeightedDegreePositionStringKernel.h.
bool* position_mask [protected] |
position mask
Definition at line 703 of file WeightedDegreePositionStringKernel.h.
float64_t* position_weights [protected] |
position weights
Definition at line 697 of file WeightedDegreePositionStringKernel.h.
float64_t* position_weights_lhs [protected] |
position weights left-hand side
Definition at line 699 of file WeightedDegreePositionStringKernel.h.
float64_t* position_weights_rhs [protected] |
position weights right-hand side
Definition at line 701 of file WeightedDegreePositionStringKernel.h.
int32_t seq_length [protected] |
length of sequence
Definition at line 718 of file WeightedDegreePositionStringKernel.h.
int32_t* shift [protected] |
shifts
Definition at line 721 of file WeightedDegreePositionStringKernel.h.
int32_t shift_len [protected] |
length of shifts
Definition at line 723 of file WeightedDegreePositionStringKernel.h.
bool tree_initialized [protected] |
if tree is initialized
Definition at line 748 of file WeightedDegreePositionStringKernel.h.
tries
Definition at line 743 of file WeightedDegreePositionStringKernel.h.
EWDKernType type [protected] |
WeightedDegree kernel type
Definition at line 738 of file WeightedDegreePositionStringKernel.h.
bool use_poim_tries [protected] |
makes add_example_to_tree (ONLY!) use POIMTrie
Definition at line 750 of file WeightedDegreePositionStringKernel.h.
weights
Definition at line 695 of file WeightedDegreePositionStringKernel.h.
float64_t* weights_buffer [protected] |
weights buffer
Definition at line 706 of file WeightedDegreePositionStringKernel.h.
int32_t which_degree [protected] |
which degree
Definition at line 740 of file WeightedDegreePositionStringKernel.h.