SHOGUN v0.9.0
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The Weighted Degree String kernel.
The WD kernel of order d compares two sequences and
of length L by summing all contributions of k-mer matches of lengths
, weighted by coefficients
. It is defined as
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.
在文件WeightedDegreeStringKernel.h第52行定义。
default constructor
在文件WeightedDegreeStringKernel.cpp第48行定义。
CWeightedDegreeStringKernel | ( | int32_t | degree, |
EWDKernType | type = E_WD |
||
) |
constructor
degree | degree |
type | weighted degree kernel type |
在文件WeightedDegreeStringKernel.cpp第55行定义。
CWeightedDegreeStringKernel | ( | float64_t * | weights, |
int32_t | degree | ||
) |
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 |
在文件WeightedDegreeStringKernel.cpp第85行定义。
~CWeightedDegreeStringKernel | ( | ) | [virtual] |
在文件WeightedDegreeStringKernel.cpp第97行定义。
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 |
void 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 |
void add_example_to_tree | ( | int32_t | idx, |
float64_t | weight | ||
) | [protected] |
void add_example_to_tree_mismatch | ( | int32_t | idx, |
float64_t | weight | ||
) | [protected] |
virtual void add_to_normal | ( | int32_t | idx, |
float64_t | weight | ||
) | [virtual] |
add to normal
idx | where to add |
weight | what to add |
重载CKernel。
在文件WeightedDegreeStringKernel.h第231行定义。
void cleanup | ( | ) | [virtual] |
virtual void clear_normal | ( | ) | [virtual] |
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 |
实现了CKernel。
float64_t * compute_abs_weights | ( | int32_t & | len | ) |
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 |
重载CKernel。
void * compute_batch_helper | ( | void * | p | ) | [static] |
void compute_by_subkernel | ( | int32_t | idx, |
float64_t * | subkernel_contrib | ||
) | [virtual] |
compute by subkernel
idx | index |
subkernel_contrib | subkernel contribution |
重载CKernel。
在文件WeightedDegreeStringKernel.h第265行定义。
void compute_by_tree | ( | int32_t | idx, |
float64_t * | LevelContrib | ||
) |
compute by tree
idx | index |
LevelContrib | level contribution |
float64_t compute_by_tree | ( | int32_t | idx | ) | [protected] |
virtual float64_t compute_optimized | ( | int32_t | idx | ) | [virtual] |
compute optimized
idx | index to compute |
重载CKernel。
在文件WeightedDegreeStringKernel.h第180行定义。
float64_t 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 |
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 |
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 |
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 |
void create_empty_tries | ( | ) | [protected] |
create emtpy tries
bool delete_optimization | ( | ) | [virtual] |
bool delete_position_weights | ( | ) |
int32_t get_degree | ( | ) | const |
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 |
在文件WeightedDegreeStringKernel.h第407行定义。
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
在文件WeightedDegreeStringKernel.h第133行定义。
int32_t get_max_mismatch | ( | ) | const |
get the number of mismatches that are allowed in WD kernel computation
在文件WeightedDegreeStringKernel.h第124行定义。
int32_t get_max_mismatch | ( | ) |
int32_t get_mkl_stepsize | ( | ) |
virtual const char* get_name | ( | void | ) | const [virtual] |
virtual int32_t get_num_subkernels | ( | ) | [virtual] |
float64_t* get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
在文件WeightedDegreeStringKernel.h第442行定义。
const float64_t* get_subkernel_weights | ( | int32_t & | num_weights | ) | [virtual] |
get subkernel weights
num_weights | number of weights will be stored here |
重载CKernel。
在文件WeightedDegreeStringKernel.h第287行定义。
EWDKernType get_type | ( | ) | const |
get WD kernel weighting type
在文件WeightedDegreeStringKernel.h第105行定义。
bool get_use_block_computation | ( | ) |
check if block computation is performed
在文件WeightedDegreeStringKernel.h第588行定义。
float64_t* get_weights | ( | int32_t & | num_weights | ) |
get weights
num_weights | number of weights will be stored here |
在文件WeightedDegreeStringKernel.h第419行定义。
int32_t get_which_degree | ( | ) |
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
bool init_block_weights | ( | ) |
initialize block weights
bool init_block_weights_const | ( | ) |
initialize block weights constant
bool init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
bool init_block_weights_exp | ( | ) |
initialize block weights exponential
bool init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
bool init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
bool init_block_weights_linear | ( | ) |
initialize block weights linear
bool init_block_weights_log | ( | ) |
initialize block weights logarithmic
bool init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
virtual bool init_optimization | ( | int32_t | count, |
int32_t * | IDX, | ||
float64_t * | alphas | ||
) | [virtual] |
initialize optimization
count | count |
IDX | index |
alphas | alphas |
重载CKernel。
在文件WeightedDegreeStringKernel.h第150行定义。
bool 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 |
bool is_tree_initialized | ( | ) |
void remove_lhs | ( | ) | [protected, virtual] |
bool set_degree | ( | int32_t | deg | ) |
bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
bool set_mkl_stepsize | ( | int32_t | step | ) |
set MKL steps ize
step | new step size |
在文件WeightedDegreeStringKernel.h第595行定义。
virtual bool set_normalizer | ( | CKernelNormalizer * | normalizer_ | ) | [virtual] |
set the current kernel normalizer
重载CKernel。
在文件WeightedDegreeStringKernel.h第363行定义。
bool set_position_weights | ( | float64_t * | pws, |
int32_t | len = 0 |
||
) |
set position weights
pws | new position weights |
len | number of position weights |
void set_subkernel_weights | ( | float64_t * | weights2, |
int32_t | num_weights2 | ||
) | [virtual] |
set subkernel weights
weights2 | weights |
num_weights2 | number of weights |
重载CKernel。
在文件WeightedDegreeStringKernel.h第313行定义。
bool set_use_block_computation | ( | bool | block | ) |
set if block computation shall be performed
block | if block computation shall be performed |
在文件WeightedDegreeStringKernel.h第578行定义。
void set_wd_weights | ( | float64_t * | p_weights, |
int32_t | d | ||
) |
set wd weights
p_weights | new eights |
d | degree |
在文件WeightedDegreeStringKernel.h第461行定义。
bool 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
bool set_weights | ( | float64_t * | weights, |
int32_t | d, | ||
int32_t | len | ||
) |
set weights
weights | new weights |
d | degree |
len | number of weights |
bool set_which_degree | ( | int32_t | which | ) |
set which degree
which | which degree |
在文件WeightedDegreeStringKernel.h第614行定义。
alphabet of features
在文件WeightedDegreeStringKernel.h第780行定义。
bool block_computation [protected] |
if block computation is used
在文件WeightedDegreeStringKernel.h第764行定义。
float64_t* block_weights [protected] |
(internal) block weights
在文件WeightedDegreeStringKernel.h第767行定义。
int32_t degree [protected] |
degree
在文件WeightedDegreeStringKernel.h第751行定义。
bool initialized [protected] |
if kernel is initialized
在文件WeightedDegreeStringKernel.h第761行定义。
int32_t length [protected] |
length
在文件WeightedDegreeStringKernel.h第753行定义。
int32_t max_mismatch [protected] |
maximum mismatch
在文件WeightedDegreeStringKernel.h第756行定义。
int32_t mkl_stepsize [protected] |
MKL step size
在文件WeightedDegreeStringKernel.h第749行定义。
float64_t* position_weights [protected] |
position weights
在文件WeightedDegreeStringKernel.h第743行定义。
int32_t position_weights_len [protected] |
position weights
在文件WeightedDegreeStringKernel.h第745行定义。
int32_t seq_length [protected] |
sequence length
在文件WeightedDegreeStringKernel.h第758行定义。
bool tree_initialized [protected] |
if tree is initialized
在文件WeightedDegreeStringKernel.h第777行定义。
tries
在文件WeightedDegreeStringKernel.h第774行定义。
EWDKernType type [protected] |
WeightedDegree kernel type
在文件WeightedDegreeStringKernel.h第769行定义。
degree*length weights length must match seq_length if != 0
在文件WeightedDegreeStringKernel.h第735行定义。
float64_t* weights_buffer [protected] |
weights buffer
在文件WeightedDegreeStringKernel.h第747行定义。
int32_t weights_degree [protected] |
degree
在文件WeightedDegreeStringKernel.h第737行定义。
int32_t weights_length [protected] |
length
在文件WeightedDegreeStringKernel.h第739行定义。
int32_t which_degree [protected] |
which degree
在文件WeightedDegreeStringKernel.h第771行定义。