The Weighted Degree Position String kernel (Weighted Degree kernel with shifts).
The WD-shift kernel of order d compares two sequences \({\bf x}\) and \({\bf x'}\) of length L by summing all contributions of k-mer matches of lengths \(k\in\{1,\dots,d\}\), weighted by coefficients \(\beta_k\) allowing for a positional tolerance of up to shift s.
It is formally defined as
\begin{eqnarray*} &&\!\!\!\!\!\!\!k({\bf x}_i,{\bf x}_j)=\sum_{k=1}^d\beta_k\sum_{l=1}^{\!\!\!\!L-k+1\!\!\!\!}\gamma_l\sum_{\begin{array}{c}s=0\\ \!\!\!\!s+l\leq L\!\!\!\!\end{array}}^{S(l)} \delta_s\;\mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}},\\ &&\!\!\!\!\!\!\!\!\!\! {\footnotesize \mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}}\!\!\! =\!\! I({\bf u}_{k,l+s}({\bf x}_i)\! =\!{\bf u}_{k,l}({\bf x}_j))\! +\!I({\bf u}_{k,l}({\bf x}_i)\! =\!{\bf u}_{k,l+s}({\bf x}_j))},\nonumber \end{eqnarray*}
where \(\beta_j\) are the weighting coefficients of the j-mers, \(\gamma_l\) is a weighting over the position in the sequence, \(\delta_s=1/(2(s+1))\) is the weight assigned to shifts (in either direction) of extent s, and S(l) determines the shift range at position l.
在文件 WeightedDegreePositionStringKernel.h 第 48 行定义.
Public 成员函数 | |
CWeightedDegreePositionStringKernel () | |
CWeightedDegreePositionStringKernel (int32_t size, int32_t degree, int32_t max_mismatch=0, int32_t mkl_stepsize=1) | |
CWeightedDegreePositionStringKernel (int32_t size, SGVector< float64_t > weights, int32_t degree, int32_t max_mismatch, SGVector< int32_t > shifts, 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) |
virtual void | set_subkernel_weights (SGVector< float64_t > w) |
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) |
void | set_shifts (SGVector< int32_t > shifts) |
bool | set_weights (SGMatrix< float64_t > new_weights) |
virtual bool | set_wd_weights () |
virtual void | set_position_weights (SGVector< float64_t > pws) |
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 | 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 (SGMatrix< float64_t > distrib) |
void | compute_POIM2 (int32_t max_degree, CSVM *svm) |
SGVector< float64_t > | get_POIM2 () |
void | cleanup_POIM2 () |
cleanup POIM2 更多... | |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
float64_t | kernel (int32_t idx_a, int32_t idx_b) |
SGMatrix< float64_t > | get_kernel_matrix () |
template<class T > | |
SGMatrix< T > | get_kernel_matrix () |
SGVector< float64_t > | get_kernel_diagonal (SGVector< float64_t > preallocated=SGVector< float64_t >()) |
virtual SGVector< float64_t > | get_kernel_col (int32_t j) |
virtual SGVector< float64_t > | get_kernel_row (int32_t i) |
virtual bool | set_normalizer (CKernelNormalizer *normalizer) |
virtual CKernelNormalizer * | get_normalizer () |
virtual bool | init_normalizer () |
void | load (CFile *loader) |
void | save (CFile *writer) |
CFeatures * | get_lhs () |
CFeatures * | get_rhs () |
virtual int32_t | get_num_vec_lhs () |
virtual int32_t | get_num_vec_rhs () |
virtual bool | has_features () |
bool | get_lhs_equals_rhs () |
virtual void | remove_lhs_and_rhs () |
virtual void | remove_rhs () |
takes all necessary steps if the rhs is removed from kernel 更多... | |
void | set_cache_size (int32_t size) |
int32_t | get_cache_size () |
void | list_kernel () |
bool | has_property (EKernelProperty p) |
EOptimizationType | get_optimization_type () |
virtual void | set_optimization_type (EOptimizationType t) |
bool | get_is_initialized () |
bool | init_optimization_svm (CSVM *svm) |
float64_t | get_combined_kernel_weight () |
void | set_combined_kernel_weight (float64_t nw) |
virtual SGVector< float64_t > | get_subkernel_weights () |
virtual SGMatrix< float64_t > | get_parameter_gradient (const TParameter *param, index_t index=-1) |
virtual CSGObject * | shallow_copy () const |
virtual CSGObject * | deep_copy () const |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
template<> | |
void | set_generic () |
void | unset_generic () |
virtual void | print_serializable (const char *prefix="") |
virtual bool | save_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter()) |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter()) |
DynArray< TParameter * > * | load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") |
DynArray< TParameter * > * | load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") |
void | map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos) |
void | set_global_io (SGIO *io) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_global_version () |
SGStringList< char > | get_modelsel_names () |
void | print_modsel_params () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
void | build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict) |
virtual void | update_parameter_hash () |
virtual bool | parameter_hash_changed () |
virtual bool | equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) |
virtual CSGObject * | clone () |
静态 Public 成员函数 | |
static void * | compute_batch_helper (void *p) |
static CKernel * | obtain_from_generic (CSGObject *kernel) |
Public 属性 | |
SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
Parameter * | m_gradient_parameters |
ParameterMap * | m_parameter_map |
uint32_t | m_hash |
Protected 成员函数 | |
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 () |
virtual void | load_serializable_post () throw (ShogunException) |
void | set_property (EKernelProperty p) |
void | unset_property (EKernelProperty p) |
void | set_is_initialized (bool p_init) |
int32_t | compute_row_start (int64_t offs, int32_t n, bool symmetric) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
virtual void | register_params () |
virtual TParameter * | migrate (DynArray< TParameter * > *param_base, const SGParamInfo *target) |
virtual void | one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) |
virtual void | load_serializable_pre () throw (ShogunException) |
静态 Protected 成员函数 | |
template<class T > | |
static void * | get_kernel_matrix_helper (void *p) |
CWeightedDegreePositionStringKernel | ( | void | ) |
default constructor
在文件 WeightedDegreePositionStringKernel.cpp 第 52 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 59 行定义.
CWeightedDegreePositionStringKernel | ( | int32_t | size, |
SGVector< float64_t > | weights, | ||
int32_t | degree, | ||
int32_t | max_mismatch, | ||
SGVector< int32_t > | shifts, | ||
int32_t | mkl_stepsize = 1 |
||
) |
constructor
size | cache size |
weights | weights |
degree | degree |
max_mismatch | maximum mismatch |
shifts | position shifts |
mkl_stepsize | MKL stepsize |
在文件 WeightedDegreePositionStringKernel.cpp 第 76 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 100 行定义.
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virtual |
在文件 WeightedDegreePositionStringKernel.cpp 第 119 行定义.
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protected |
add example to single tree
idx | index |
weight | weight |
tree_num | which tree |
在文件 WeightedDegreePositionStringKernel.cpp 第 695 行定义.
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protectedvirtual |
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virtual |
add to normal
idx | where to add |
weight | what to add |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 210 行定义.
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inherited |
Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.
dict | dictionary of parameters to be built. |
在文件 SGObject.cpp 第 1174 行定义.
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virtual |
void cleanup_POIM2 | ( | ) |
cleanup POIM2
在文件 WeightedDegreePositionStringKernel.cpp 第 1867 行定义.
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virtual |
clear normal subkernel functionality
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 184 行定义.
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virtualinherited |
Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.
在文件 SGObject.cpp 第 1291 行定义.
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protectedvirtual |
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.
在文件 WeightedDegreePositionStringKernel.cpp 第 608 行定义.
float64_t * compute_abs_weights | ( | int32_t & | len | ) |
compute abs weights
len | len |
在文件 WeightedDegreePositionStringKernel.cpp 第 831 行定义.
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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 .
在文件 WeightedDegreePositionStringKernel.cpp 第 1230 行定义.
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static |
helper for compute batch
p | thread parameter |
在文件 WeightedDegreePositionStringKernel.cpp 第 1172 行定义.
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virtual |
compute by subkernel
idx | index |
subkernel_contrib | subkernel contribution |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 234 行定义.
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virtual |
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virtual |
compute by tree
idx | index |
LevelContrib | level contribution |
在文件 WeightedDegreePositionStringKernel.cpp 第 788 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 1499 行定义.
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virtual |
compute optimized
idx | index to compute |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 152 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 1679 行定义.
void compute_POIM2 | ( | int32_t | max_degree, |
CSVM * | svm | ||
) |
compute POIM2
max_degree | maximum degree |
svm | SVM |
在文件 WeightedDegreePositionStringKernel.cpp 第 1826 行定义.
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protectedinherited |
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 1343 行定义.
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protected |
compute with mismatch
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
在文件 WeightedDegreePositionStringKernel.cpp 第 318 行定义.
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protected |
compute without mismatch
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
在文件 WeightedDegreePositionStringKernel.cpp 第 398 行定义.
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protected |
compute without mismatch matrix
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
在文件 WeightedDegreePositionStringKernel.cpp 第 464 行定义.
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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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 528 行定义.
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protected |
create emtpy tries
在文件 WeightedDegreePositionStringKernel.cpp 第 159 行定义.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
在文件 SGObject.h 第 126 行定义.
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virtual |
delete optimization
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.cpp 第 293 行定义.
bool delete_position_weights | ( | ) |
delete position weights
在文件 WeightedDegreePositionStringKernel.h 第 473 行定义.
bool delete_position_weights_lhs | ( | ) |
delete position weights left-hand side
在文件 WeightedDegreePositionStringKernel.h 第 484 行定义.
bool delete_position_weights_rhs | ( | ) |
delete position weights right-hand side
在文件 WeightedDegreePositionStringKernel.h 第 495 行定义.
Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!
May be overwritten but please do with care! Should not be necessary in most cases.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
在文件 SGObject.cpp 第 1195 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 1616 行定义.
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inherited |
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inherited |
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 WeightedDegreePositionStringKernel.h 第 335 行定义.
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virtualinherited |
return feature class the kernel can deal with
实现了 CKernel.
在文件 StringKernel.h 第 69 行定义.
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virtualinherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
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staticprotectedinherited |
helper for computing the kernel matrix in a parallel way
p | thread parameters |
在文件 Kernel.cpp 第 522 行定义.
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virtual |
return what type of kernel we are
在文件 WeightedDegreePositionStringKernel.h 第 105 行定义.
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inherited |
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inherited |
int32_t get_max_mismatch | ( | ) |
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inherited |
在文件 SGObject.cpp 第 1066 行定义.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
在文件 SGObject.cpp 第 1090 行定义.
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inherited |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
在文件 SGObject.cpp 第 1103 行定义.
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virtual |
return the kernel's name
在文件 WeightedDegreePositionStringKernel.h 第 111 行定义.
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virtualinherited |
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virtual |
get number of subkernels
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 220 行定义.
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virtualinherited |
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virtualinherited |
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inherited |
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virtualinherited |
return derivative with respect to specified parameter
param | the parameter |
index | the index of the element if parameter is a vector |
被 CCombinedKernel, CProductKernel, CGaussianKernel, CLinearARDKernel , 以及 CGaussianARDKernel 重载.
float64_t* get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
在文件 WeightedDegreePositionStringKernel.h 第 366 行定义.
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inherited |
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virtual |
get subkernel weights
num_weights | number of weights will be stored here |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 251 行定义.
get subkernel weights (swig compatible)
被 CCombinedKernel 重载.
在文件 Kernel.cpp 第 378 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 WeightedDegreePositionStringKernel.h 第 347 行定义.
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virtualinherited |
test whether features have been assigned to lhs and rhs
被 CCustomKernel, CCombinedKernel , 以及 CProductKernel 重载.
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inherited |
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
在文件 WeightedDegreePositionStringKernel.cpp 第 178 行定义.
bool init_block_weights | ( | ) |
initialize block weights
在文件 WeightedDegreePositionStringKernel.cpp 第 1146 行定义.
bool init_block_weights_const | ( | ) |
initialize block weights constant
在文件 WeightedDegreePositionStringKernel.cpp 第 1050 行定义.
bool init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
在文件 WeightedDegreePositionStringKernel.cpp 第 1095 行定义.
bool init_block_weights_exp | ( | ) |
initialize block weights exponential
在文件 WeightedDegreePositionStringKernel.cpp 第 1112 行定义.
bool init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
在文件 WeightedDegreePositionStringKernel.cpp 第 1002 行定义.
bool init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
在文件 WeightedDegreePositionStringKernel.cpp 第 1022 行定义.
bool init_block_weights_linear | ( | ) |
initialize block weights linear
在文件 WeightedDegreePositionStringKernel.cpp 第 1064 行定义.
bool init_block_weights_log | ( | ) |
initialize block weights logarithmic
在文件 WeightedDegreePositionStringKernel.cpp 第 1129 行定义.
bool init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
在文件 WeightedDegreePositionStringKernel.cpp 第 1078 行定义.
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virtualinherited |
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virtual |
initialize optimization
p_count | count |
IDX | index |
alphas | alphas |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 120 行定义.
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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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 247 行定义.
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inherited |
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virtualinherited |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
在文件 SGObject.cpp 第 234 行定义.
bool is_tree_initialized | ( | ) |
check if tree is initialized
在文件 WeightedDegreePositionStringKernel.h 第 316 行定义.
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inherited |
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inherited |
list kernel
在文件 Kernel.cpp 第 210 行定义.
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inherited |
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inherited |
maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 639 行定义.
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inherited |
loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned
param_info | information of parameter |
file_version | parameter version of the file, must be <= provided parameter version |
file | file to load from |
prefix | prefix for members |
在文件 SGObject.cpp 第 480 行定义.
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virtualinherited |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
在文件 SGObject.cpp 第 311 行定义.
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protectedvirtual |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.cpp 第 1878 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
被 CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool > , 以及 CDynamicObjectArray 重载.
在文件 SGObject.cpp 第 990 行定义.
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inherited |
Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
param_base | set of TParameter instances that are mapped to the provided target parameter infos |
base_version | version of the parameter base |
target_param_infos | set of SGParamInfo instances that specify the target parameter base |
在文件 SGObject.cpp 第 677 行定义.
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protectedvirtualinherited |
creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
在文件 SGObject.cpp 第 884 行定义.
Obtains a kernel from a generic SGObject with error checking. Note that if passing NULL, result will be NULL
kernel | Object to cast to CKernel, is not SG_REFed |
在文件 Kernel.cpp 第 394 行定义.
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protectedvirtualinherited |
This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
replacement | (used as output) here the TParameter instance which is returned by migration is created into |
to_migrate | the only source that is used for migration |
old_name | with this parameter, a name change may be specified |
在文件 SGObject.cpp 第 824 行定义.
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virtualinherited |
在文件 SGObject.cpp 第 200 行定义.
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inherited |
prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 1042 行定义.
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virtualinherited |
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protectedvirtualinherited |
Separate the function of parameter registration This can be the first stage of a general framework for cross-validation or other parameter-based operations
被 CSpectrumMismatchRBFKernel, CSNPStringKernel, CANOVAKernel, CSubsequenceStringKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel , 以及 CHistogramIntersectionKernel 重载.
在文件 Kernel.cpp 第 449 行定义.
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protectedvirtual |
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virtualinherited |
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virtualinherited |
takes all necessary steps if the rhs is removed from kernel
remove rhs from kernel
被 CCombinedKernel, CCommUlongStringKernel , 以及 CProductKernel 重载.
在文件 Kernel.cpp 第 197 行定义.
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inherited |
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virtualinherited |
Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
在文件 SGObject.cpp 第 252 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
重载 CSGObject .
在文件 Kernel.cpp 第 441 行定义.
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protectedvirtualinherited |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
重载 CSGObject .
在文件 Kernel.cpp 第 433 行定义.
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inherited |
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inherited |
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inherited |
在文件 SGObject.cpp 第 41 行定义.
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inherited |
在文件 SGObject.cpp 第 46 行定义.
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inherited |
在文件 SGObject.cpp 第 51 行定义.
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inherited |
在文件 SGObject.cpp 第 56 行定义.
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inherited |
在文件 SGObject.cpp 第 61 行定义.
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inherited |
在文件 SGObject.cpp 第 66 行定义.
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inherited |
在文件 SGObject.cpp 第 71 行定义.
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inherited |
在文件 SGObject.cpp 第 76 行定义.
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inherited |
在文件 SGObject.cpp 第 81 行定义.
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inherited |
在文件 SGObject.cpp 第 86 行定义.
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inherited |
在文件 SGObject.cpp 第 91 行定义.
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inherited |
在文件 SGObject.cpp 第 96 行定义.
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inherited |
在文件 SGObject.cpp 第 101 行定义.
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inherited |
在文件 SGObject.cpp 第 106 行定义.
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inherited |
在文件 SGObject.cpp 第 111 行定义.
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inherited |
set generic type to T
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inherited |
|
inherited |
|
inherited |
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protectedinherited |
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virtualinherited |
set the current kernel normalizer
被 CWeightedDegreeStringKernel 重载.
在文件 Kernel.cpp 第 124 行定义.
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virtualinherited |
set position weights
pws | new position weights |
在文件 WeightedDegreePositionStringKernel.cpp 第 928 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 945 行定义.
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 |
在文件 WeightedDegreePositionStringKernel.cpp 第 973 行定义.
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protectedinherited |
void set_shifts | ( | SGVector< int32_t > | shifts | ) |
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virtual |
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virtualinherited |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
被 CGaussianKernel 重载.
在文件 SGObject.h 第 117 行定义.
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inherited |
unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 241 行定义.
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protectedinherited |
|
virtualinherited |
Updates the hash of current parameter combination
在文件 SGObject.cpp 第 187 行定义.
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protected |
alphabet of features
在文件 WeightedDegreePositionStringKernel.h 第 776 行定义.
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protected |
if block computation is used
在文件 WeightedDegreePositionStringKernel.h 第 744 行定义.
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protected |
(internal) block weights
在文件 WeightedDegreePositionStringKernel.h 第 747 行定义.
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protected |
degree
在文件 WeightedDegreePositionStringKernel.h 第 727 行定义.
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inherited |
io
在文件 SGObject.h 第 473 行定义.
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protectedinherited |
|
protected |
length
在文件 WeightedDegreePositionStringKernel.h 第 729 行定义.
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protectedinherited |
|
inherited |
parameters wrt which we can compute gradients
在文件 SGObject.h 第 488 行定义.
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inherited |
Hash of parameter values
在文件 SGObject.h 第 494 行定义.
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inherited |
model selection parameters
在文件 SGObject.h 第 485 行定义.
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inherited |
map for different parameter versions
在文件 SGObject.h 第 491 行定义.
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inherited |
parameters
在文件 SGObject.h 第 482 行定义.
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protected |
temporary memory for the interface to the poim functions
在文件 WeightedDegreePositionStringKernel.h 第 766 行定义.
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protected |
temporary memory for the interface to the poim functions
在文件 WeightedDegreePositionStringKernel.h 第 764 行定义.
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protected |
length of string (==num_feat)
在文件 WeightedDegreePositionStringKernel.h 第 771 行定义.
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protected |
number of symbols
在文件 WeightedDegreePositionStringKernel.h 第 769 行定义.
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protected |
total size of poim array
在文件 WeightedDegreePositionStringKernel.h 第 773 行定义.
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protected |
maximum mismatch
在文件 WeightedDegreePositionStringKernel.h 第 732 行定义.
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protected |
maximum shift
在文件 WeightedDegreePositionStringKernel.h 第 741 行定义.
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protected |
MKL stepsize
在文件 WeightedDegreePositionStringKernel.h 第 724 行定义.
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protectedinherited |
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protectedinherited |
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protectedinherited |
|
protectedinherited |
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protectedinherited |
|
inherited |
parallel
在文件 SGObject.h 第 476 行定义.
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protected |
POIM tries
在文件 WeightedDegreePositionStringKernel.h 第 756 行定义.
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protected |
position mask
在文件 WeightedDegreePositionStringKernel.h 第 719 行定义.
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protected |
position weights
在文件 WeightedDegreePositionStringKernel.h 第 706 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 708 行定义.
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protected |
position weights left-hand side
在文件 WeightedDegreePositionStringKernel.h 第 711 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 713 行定义.
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protected |
position weights right-hand side
在文件 WeightedDegreePositionStringKernel.h 第 715 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 717 行定义.
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protectedinherited |
|
protected |
length of sequence
在文件 WeightedDegreePositionStringKernel.h 第 734 行定义.
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protected |
shifts
在文件 WeightedDegreePositionStringKernel.h 第 737 行定义.
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protected |
length of shifts
在文件 WeightedDegreePositionStringKernel.h 第 739 行定义.
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protected |
if tree is initialized
在文件 WeightedDegreePositionStringKernel.h 第 759 行定义.
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protected |
tries
在文件 WeightedDegreePositionStringKernel.h 第 754 行定义.
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protected |
WeightedDegree kernel type
在文件 WeightedDegreePositionStringKernel.h 第 749 行定义.
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protected |
makes add_example_to_tree (ONLY!) use POIMTrie
在文件 WeightedDegreePositionStringKernel.h 第 761 行定义.
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inherited |
version
在文件 SGObject.h 第 479 行定义.
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protected |
weights
在文件 WeightedDegreePositionStringKernel.h 第 699 行定义.
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protected |
weights buffer
在文件 WeightedDegreePositionStringKernel.h 第 722 行定义.
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protected |
degree
在文件 WeightedDegreePositionStringKernel.h 第 701 行定义.
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protected |
length
在文件 WeightedDegreePositionStringKernel.h 第 703 行定义.
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protected |
which degree
在文件 WeightedDegreePositionStringKernel.h 第 751 行定义.