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 50 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) |
void | get_kernel_row (int32_t docnum, int32_t *active2dnum, float64_t *buffer, bool full_line=false) |
virtual float64_t | sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true) |
virtual float64_t | sum_block (index_t block_begin_row, index_t block_begin_col, index_t block_size_row, index_t block_size_col, bool no_diag=false) |
virtual SGVector< float64_t > | row_wise_sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true) |
virtual SGMatrix< float64_t > | row_wise_sum_squared_sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true) |
virtual SGVector< float64_t > | row_col_wise_sum_block (index_t block_begin_row, index_t block_begin_col, index_t block_size_row, index_t block_size_col, bool no_diag=false) |
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 | cache_reset () |
int32_t | get_max_elems_cache () |
int32_t | get_activenum_cache () |
void | cache_kernel_row (int32_t x) |
void | cache_multiple_kernel_rows (int32_t *key, int32_t varnum) |
void | kernel_cache_reset_lru () |
void | kernel_cache_shrink (int32_t totdoc, int32_t num_shrink, int32_t *after) |
void | resize_kernel_cache (KERNELCACHE_IDX size, bool regression_hack=false) |
void | set_time (int32_t t) |
int32_t | kernel_cache_touch (int32_t cacheidx) |
int32_t | kernel_cache_check (int32_t cacheidx) |
int32_t | kernel_cache_space_available () |
void | kernel_cache_init (int32_t size, bool regression_hack=false) |
void | kernel_cache_cleanup () |
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 SGVector< float64_t > | get_parameter_gradient_diagonal (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="") |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
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 |
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 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 , |
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int32_t | mkl_stepsize = 1 |
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) |
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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add to normal
idx | where to add |
weight | what to add |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 212 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 597 行定义.
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inherited |
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void cleanup_POIM2 | ( | ) |
cleanup POIM2
在文件 WeightedDegreePositionStringKernel.cpp 第 1867 行定义.
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clear normal subkernel functionality
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 186 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 714 行定义.
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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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helper for compute batch
p | thread parameter |
在文件 WeightedDegreePositionStringKernel.cpp 第 1172 行定义.
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compute by subkernel
idx | index |
subkernel_contrib | subkernel contribution |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 236 行定义.
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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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compute optimized
idx | index to compute |
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 154 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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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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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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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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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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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.cpp 第 198 行定义.
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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 475 行定义.
bool delete_position_weights_lhs | ( | ) |
delete position weights left-hand side
在文件 WeightedDegreePositionStringKernel.h 第 486 行定义.
bool delete_position_weights_rhs | ( | ) |
delete position weights right-hand side
在文件 WeightedDegreePositionStringKernel.h 第 497 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 618 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 337 行定义.
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return feature class the kernel can deal with
实现了 CKernel.
在文件 StringKernel.h 第 71 行定义.
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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 1292 行定义.
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get kernel row
docnum | docnum |
active2dnum | active2dnum |
buffer | buffer |
full_line | full line |
在文件 Kernel.cpp 第 238 行定义.
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return what type of kernel we are
在文件 WeightedDegreePositionStringKernel.h 第 107 行定义.
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int32_t get_max_mismatch | ( | ) |
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在文件 SGObject.cpp 第 498 行定义.
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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 522 行定义.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
在文件 SGObject.cpp 第 535 行定义.
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return the kernel's name
在文件 WeightedDegreePositionStringKernel.h 第 113 行定义.
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get number of subkernels
重载 CKernel .
在文件 WeightedDegreePositionStringKernel.h 第 222 行定义.
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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 , 以及 CPeriodicKernel 重载.
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virtualinherited |
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 368 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 253 行定义.
get subkernel weights (swig compatible)
被 CCombinedKernel 重载.
在文件 Kernel.cpp 第 880 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 349 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 122 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 296 行定义.
bool is_tree_initialized | ( | ) |
check if tree is initialized
在文件 WeightedDegreePositionStringKernel.h 第 318 行定义.
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inherited |
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inherited |
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inherited |
cleanup kernel cache
在文件 Kernel.cpp 第 567 行定义.
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inherited |
initialize kernel cache
size | size to initialize to |
regression_hack | if hack for regression shall be applied |
在文件 Kernel.cpp 第 181 行定义.
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inherited |
kernel cache reset lru
在文件 Kernel.cpp 第 554 行定义.
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inherited |
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inherited |
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inherited |
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inherited |
list kernel
在文件 Kernel.cpp 第 708 行定义.
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inherited |
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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 |
在文件 SGObject.cpp 第 369 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 occurs. |
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 421 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 896 行定义.
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virtualinherited |
在文件 SGObject.cpp 第 262 行定义.
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inherited |
prints all parameter registered for model selection and their type
在文件 SGObject.cpp 第 474 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 951 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 693 行定义.
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inherited |
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virtualinherited |
Computes row-wise/col-wise sum of kernel values. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.
block_begin_row | the row index at which the block starts |
block_begin_col | the col index at which the block starts |
block_size_row | the number of rows in the block |
block_size_col | the number of cols in the block |
For Example, block_begin_row 0, block_begin_col 4 and block_size_row 5, block_size_col 6 represents the block that starts at index (0,4) in the kernel matrix and goes upto (0+5-1,4+6-1) i.e. (4,9) both inclusive
no_diag | if true (default is false), the diagonal elements are excluded from the row/col-wise sum, provided that block_size_row and block_size_col are same (i.e. the block is square). Otherwise, these are always added |
\[ v[i]=\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]
and rest block_size_col entries col-wise sum of kernel values computed as\[ v[\text{block-size-row}+j]=\sum_{i}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]
where \(i\in[0,\text{block-size-row}-1]\) and \(j\in[0,\text{block-size-col}-1]\)在文件 Kernel.cpp 第 1238 行定义.
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virtualinherited |
Computes row-wise/col-wise sum and squared sum of kernel values from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.
block_begin | the row and col index at which the block starts |
block_size | the number of rows and cols in the block |
For Example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive
no_diag | if true (default), the diagonal elements are excluded from the row/col-wise sum |
\[ v_0[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
and second column contains the row-wise sum of squared kernel values\[ v_1[i]=\sum_{j}^k^2(i+\text{block-begin}, j+\text{block-begin}) \]
where \(i,j\in[0,\text{block-size}-1]\)在文件 Kernel.cpp 第 1179 行定义.
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virtualinherited |
Computes row-wise/col-wise sum from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.
block_begin | the row and col index at which the block starts |
block_size | the number of rows and cols in the block |
For Example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive
no_diag | if true (default), the diagonal elements are excluded from the row/col-wise sum |
\[ v[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
where \(i,j\in[0,\text{block-size}-1]\)在文件 Kernel.cpp 第 1125 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 |
在文件 SGObject.cpp 第 314 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 943 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 935 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.
|
inherited |
在文件 SGObject.cpp 第 81 行定义.
|
inherited |
在文件 SGObject.cpp 第 86 行定义.
|
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.
|
inherited |
在文件 SGObject.cpp 第 101 行定义.
|
inherited |
在文件 SGObject.cpp 第 106 行定义.
|
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 |
|
protectedinherited |
|
virtualinherited |
set the current kernel normalizer
被 CWeightedDegreeStringKernel 重载.
在文件 Kernel.cpp 第 150 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 | ) |
|
virtual |
|
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.cpp 第 192 行定义.
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virtualinherited |
Computes sum of kernel values from a specified block. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.
block_begin_row | the row index at which the block starts |
block_begin_col | the col index at which the block starts |
block_size_row | the number of rows in the block |
block_size_col | the number of cols in the block |
For example, block_begin_row 0, block_begin_col 4 and block_size_row 5, block_size_col 6 represents the block that starts at index (0,4) in the kernel matrix and goes upto (0+5-1,4+6-1) i.e. (4,9) both inclusive
no_diag | if true (default is false), the diagonal elements are excluded from the sum, provided that block_size_row and block_size_col are same (i.e. the block is square). Otherwise, these are always added |
\[ \sum_{i}\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]
where \(i\in[0,\text{block-size-row}-1]\) and \(j\in[0,\text{block-size-col}-1]\)在文件 Kernel.cpp 第 1079 行定义.
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virtualinherited |
Computes sum from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.
block_begin | the row and col index at which the block starts |
block_size | the number of rows and cols in the block |
For example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive
no_diag | if true (default), the diagonal elements are excluded from the sum |
\[ \sum_{i}\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
where \(i,j\in[0,\text{block-size}-1]\)在文件 Kernel.cpp 第 1026 行定义.
|
inherited |
unset generic type
this has to be called in classes specializing a template class
在文件 SGObject.cpp 第 303 行定义.
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protectedinherited |
|
virtualinherited |
Updates the hash of current parameter combination
在文件 SGObject.cpp 第 248 行定义.
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protected |
alphabet of features
在文件 WeightedDegreePositionStringKernel.h 第 778 行定义.
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protected |
if block computation is used
在文件 WeightedDegreePositionStringKernel.h 第 746 行定义.
|
protected |
(internal) block weights
在文件 WeightedDegreePositionStringKernel.h 第 749 行定义.
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protected |
degree
在文件 WeightedDegreePositionStringKernel.h 第 729 行定义.
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inherited |
io
在文件 SGObject.h 第 369 行定义.
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protectedinherited |
|
protected |
length
在文件 WeightedDegreePositionStringKernel.h 第 731 行定义.
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protectedinherited |
|
inherited |
parameters wrt which we can compute gradients
在文件 SGObject.h 第 384 行定义.
|
inherited |
Hash of parameter values
在文件 SGObject.h 第 387 行定义.
|
inherited |
model selection parameters
在文件 SGObject.h 第 381 行定义.
|
inherited |
parameters
在文件 SGObject.h 第 378 行定义.
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protected |
temporary memory for the interface to the poim functions
在文件 WeightedDegreePositionStringKernel.h 第 768 行定义.
|
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 |
length of string (==num_feat)
在文件 WeightedDegreePositionStringKernel.h 第 773 行定义.
|
protected |
number of symbols
在文件 WeightedDegreePositionStringKernel.h 第 771 行定义.
|
protected |
total size of poim array
在文件 WeightedDegreePositionStringKernel.h 第 775 行定义.
|
protected |
maximum mismatch
在文件 WeightedDegreePositionStringKernel.h 第 734 行定义.
|
protected |
maximum shift
在文件 WeightedDegreePositionStringKernel.h 第 743 行定义.
|
protected |
MKL stepsize
在文件 WeightedDegreePositionStringKernel.h 第 726 行定义.
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protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
inherited |
parallel
在文件 SGObject.h 第 372 行定义.
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protected |
POIM tries
在文件 WeightedDegreePositionStringKernel.h 第 758 行定义.
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protected |
position mask
在文件 WeightedDegreePositionStringKernel.h 第 721 行定义.
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protected |
position weights
在文件 WeightedDegreePositionStringKernel.h 第 708 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 710 行定义.
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protected |
position weights left-hand side
在文件 WeightedDegreePositionStringKernel.h 第 713 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 715 行定义.
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protected |
position weights right-hand side
在文件 WeightedDegreePositionStringKernel.h 第 717 行定义.
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protected |
position weights len
在文件 WeightedDegreePositionStringKernel.h 第 719 行定义.
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protectedinherited |
|
protected |
length of sequence
在文件 WeightedDegreePositionStringKernel.h 第 736 行定义.
|
protected |
shifts
在文件 WeightedDegreePositionStringKernel.h 第 739 行定义.
|
protected |
length of shifts
在文件 WeightedDegreePositionStringKernel.h 第 741 行定义.
|
protected |
if tree is initialized
在文件 WeightedDegreePositionStringKernel.h 第 761 行定义.
|
protected |
tries
在文件 WeightedDegreePositionStringKernel.h 第 756 行定义.
|
protected |
WeightedDegree kernel type
在文件 WeightedDegreePositionStringKernel.h 第 751 行定义.
|
protected |
makes add_example_to_tree (ONLY!) use POIMTrie
在文件 WeightedDegreePositionStringKernel.h 第 763 行定义.
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inherited |
version
在文件 SGObject.h 第 375 行定义.
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protected |
weights
在文件 WeightedDegreePositionStringKernel.h 第 701 行定义.
|
protected |
weights buffer
在文件 WeightedDegreePositionStringKernel.h 第 724 行定义.
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protected |
degree
在文件 WeightedDegreePositionStringKernel.h 第 703 行定义.
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protected |
length
在文件 WeightedDegreePositionStringKernel.h 第 705 行定义.
|
protected |
which degree
在文件 WeightedDegreePositionStringKernel.h 第 753 行定义.