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SHOGUN
4.2.0
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SHOGUN
4.2.0
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The Weighted Degree String kernel.
The WD 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 \(\beta_k\). It is defined as
\[ k({\bf x},{\bf x'})=\sum_{k=1}^d\beta_k\sum_{l=1}^{L-k+1}I({\bf u}_{k,l}({\bf x})={\bf u}_{k,l}({\bf x'})). \]
Here, \({\bf u}_{k,l}({\bf x})\) is the string of length k starting at position l of the sequence \({\bf x}\) and \(I(\cdot)\) is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.
Definition at line 55 of file WeightedDegreeStringKernel.h.
Public Member Functions | |
| CWeightedDegreeStringKernel () | |
| CWeightedDegreeStringKernel (int32_t degree, EWDKernType type=E_WD) | |
| CWeightedDegreeStringKernel (SGVector< float64_t > weights) | |
| CWeightedDegreeStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t degree) | |
| virtual | ~CWeightedDegreeStringKernel () |
| virtual bool | init (CFeatures *l, CFeatures *r) |
| virtual void | cleanup () |
| EWDKernType | get_type () const |
| virtual EKernelType | get_kernel_type () |
| virtual const char * | get_name () const |
| virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *alphas) |
| virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *alphas, int32_t tree_num) |
| 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) |
| virtual bool | set_normalizer (CKernelNormalizer *normalizer_) |
| float64_t * | compute_abs_weights (int32_t &len) |
| void | compute_by_tree (int32_t idx, float64_t *LevelContrib) |
| bool | is_tree_initialized () |
| float64_t * | get_degree_weights (int32_t &d, int32_t &len) |
| float64_t * | get_weights (int32_t &num_weights) |
| float64_t * | get_position_weights (int32_t &len) |
| bool | set_wd_weights_by_type (EWDKernType type) |
| void | set_wd_weights (SGVector< float64_t > new_weights) |
| bool | set_weights (SGMatrix< float64_t > new_weights) |
| bool | set_position_weights (float64_t *pws, int32_t len) |
| 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 | set_max_mismatch (int32_t max) |
| int32_t | get_max_mismatch () const |
| bool | set_degree (int32_t deg) |
| int32_t | get_degree () const |
| bool | set_use_block_computation (bool block) |
| bool | get_use_block_computation () |
| bool | set_mkl_stepsize (int32_t step) |
| int32_t | get_mkl_stepsize () |
| bool | set_which_degree (int32_t which) |
| int32_t | get_which_degree () |
| 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 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 More... | |
| 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) |
| bool | has (const std::string &name) const |
| template<typename T > | |
| bool | has (const Tag< T > &tag) const |
| template<typename T , typename U = void> | |
| bool | has (const std::string &name) const |
| template<typename T > | |
| void | set (const Tag< T > &_tag, const T &value) |
| template<typename T , typename U = void> | |
| void | set (const std::string &name, const T &value) |
| template<typename T > | |
| T | get (const Tag< T > &_tag) const |
| template<typename T , typename U = void> | |
| T | get (const std::string &name) const |
| 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 () |
Static Public Member Functions | |
| static void * | compute_batch_helper (void *p) |
| static CKernel * | obtain_from_generic (CSGObject *kernel) |
Public Attributes | |
| SGIO * | io |
| Parallel * | parallel |
| Version * | version |
| Parameter * | m_parameters |
| Parameter * | m_model_selection_parameters |
| Parameter * | m_gradient_parameters |
| uint32_t | m_hash |
Protected Member Functions | |
| void | create_empty_tries () |
| 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) |
| void | add_example_to_tree_mismatch (int32_t idx, float64_t weight) |
| void | add_example_to_single_tree_mismatch (int32_t idx, float64_t weight, int32_t tree_num) |
| float64_t | compute_by_tree (int32_t idx) |
| 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_using_block (char *avec, int32_t alen, char *bvec, int32_t blen) |
| virtual void | remove_lhs () |
| 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 | load_serializable_post () throw (ShogunException) |
| 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) |
| template<typename T > | |
| void | register_param (Tag< T > &_tag, const T &value) |
| template<typename T > | |
| void | register_param (const std::string &name, const T &value) |
Static Protected Member Functions | |
| template<class T > | |
| static void * | get_kernel_matrix_helper (void *p) |
default constructor
Definition at line 48 of file WeightedDegreeStringKernel.cpp.
| CWeightedDegreeStringKernel | ( | int32_t | degree, |
| EWDKernType | type = E_WD |
||
| ) |
constructor
| degree | degree |
| type | weighted degree kernel type |
Definition at line 55 of file WeightedDegreeStringKernel.cpp.
| CWeightedDegreeStringKernel | ( | SGVector< float64_t > | weights | ) |
constructor
| weights | kernel's weights |
Definition at line 68 of file WeightedDegreeStringKernel.cpp.
| CWeightedDegreeStringKernel | ( | CStringFeatures< char > * | l, |
| CStringFeatures< char > * | r, | ||
| int32_t | degree | ||
| ) |
constructor
| l | features of left-hand side |
| r | features of right-hand side |
| degree | degree |
Definition at line 84 of file WeightedDegreeStringKernel.cpp.
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virtual |
Definition at line 96 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to single tree
| idx | index |
| weight | weight |
| tree_num | which tree |
Definition at line 435 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to single tree mismatch
| idx | index |
| weight | weight |
| tree_num | which tree |
Definition at line 486 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to tree
| idx | index |
| weight | weight |
Definition at line 389 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to tree mismatch
| idx | index |
| weight | weight |
Definition at line 460 of file WeightedDegreeStringKernel.cpp.
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virtual |
add to normal
| idx | where to add |
| weight | what to add |
Reimplemented from CKernel.
Definition at line 214 of file WeightedDegreeStringKernel.h.
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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. |
Definition at line 630 of file SGObject.cpp.
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inherited |
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inherited |
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virtual |
clean up kernel
Reimplemented from CKernel.
Definition at line 182 of file WeightedDegreeStringKernel.cpp.
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clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 196 of file WeightedDegreeStringKernel.h.
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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.
Definition at line 747 of file SGObject.cpp.
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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 |
Implements CKernel.
Definition at line 363 of file WeightedDegreeStringKernel.cpp.
| float64_t * compute_abs_weights | ( | int32_t & | len | ) |
compute abs weights
| len | len |
Definition at line 565 of file WeightedDegreeStringKernel.cpp.
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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 |
Reimplemented from CKernel.
Definition at line 862 of file WeightedDegreeStringKernel.cpp.
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static |
helper for compute batch
| p | thread parameter |
Definition at line 826 of file WeightedDegreeStringKernel.cpp.
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virtual |
compute by subkernel
| idx | index |
| subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 248 of file WeightedDegreeStringKernel.h.
| void compute_by_tree | ( | int32_t | idx, |
| float64_t * | LevelContrib | ||
| ) |
compute by tree
| idx | index |
| LevelContrib | level contribution |
Definition at line 538 of file WeightedDegreeStringKernel.cpp.
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protected |
compute by tree
| idx | index |
Definition at line 514 of file WeightedDegreeStringKernel.cpp.
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virtual |
compute optimized
| idx | index to compute |
Reimplemented from CKernel.
Definition at line 163 of file WeightedDegreeStringKernel.h.
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protectedinherited |
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protected |
compute using block
| avec | vector a |
| alen | length of vector a |
| bvec | vector b |
| blen | length of vector b |
Definition at line 290 of file WeightedDegreeStringKernel.cpp.
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protected |
compute with mismatch
| avec | vector a |
| alen | length of vector a |
| bvec | vector b |
| blen | length of vector b |
Definition at line 262 of file WeightedDegreeStringKernel.cpp.
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protected |
compute without mismatch
| avec | vector a |
| alen | length of vector a |
| bvec | vector b |
| blen | length of vector b |
Definition at line 316 of file WeightedDegreeStringKernel.cpp.
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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 |
Definition at line 339 of file WeightedDegreeStringKernel.cpp.
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protected |
create emtpy tries
Definition at line 127 of file WeightedDegreeStringKernel.cpp.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
Definition at line 231 of file SGObject.cpp.
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virtual |
delete optimization
Reimplemented from CKernel.
Definition at line 248 of file WeightedDegreeStringKernel.cpp.
| bool delete_position_weights | ( | ) |
delete position weights
Definition at line 521 of file WeightedDegreeStringKernel.h.
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) |
Definition at line 651 of file SGObject.cpp.
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inherited |
Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.
| _tag | name and type information of parameter |
Definition at line 367 of file SGObject.h.
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inherited |
Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.
| name | name of the parameter |
Definition at line 388 of file SGObject.h.
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inherited |
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inherited |
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inherited |
| int32_t get_degree | ( | ) | const |
| float64_t* get_degree_weights | ( | int32_t & | d, |
| int32_t & | len | ||
| ) |
get degree weights
| d | degree weights will be stored here |
| len | number of degree weights will be stored here |
Definition at line 390 of file WeightedDegreeStringKernel.h.
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virtualinherited |
return feature class the kernel can deal with
Implements CKernel.
Definition at line 71 of file StringKernel.h.
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virtualinherited |
|
inherited |
|
inherited |
|
inherited |
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inherited |
|
inherited |
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staticprotectedinherited |
helper for computing the kernel matrix in a parallel way
| p | thread parameters |
Definition at line 1293 of file Kernel.cpp.
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inherited |
get kernel row
| docnum | docnum |
| active2dnum | active2dnum |
| buffer | buffer |
| full_line | full line |
Definition at line 238 of file Kernel.cpp.
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virtual |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 116 of file WeightedDegreeStringKernel.h.
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inherited |
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inherited |
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inherited |
| int32_t get_max_mismatch | ( | ) | const |
get maximum mismatch
Definition at line 539 of file WeightedDegreeStringKernel.h.
| int32_t get_mkl_stepsize | ( | ) |
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inherited |
Definition at line 531 of file SGObject.cpp.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
| param_name | name of the parameter |
Definition at line 555 of file SGObject.cpp.
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inherited |
Returns index of model selection parameter with provided index
| param_name | name of model selection parameter |
Definition at line 568 of file SGObject.cpp.
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virtual |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 122 of file WeightedDegreeStringKernel.h.
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virtualinherited |
obtain the current kernel normalizer
Definition at line 162 of file Kernel.cpp.
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virtual |
get number of subkernels
Reimplemented from CKernel.
Definition at line 232 of file WeightedDegreeStringKernel.h.
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virtualinherited |
get number of vectors of lhs features
Reimplemented in CCustomKernel.
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virtualinherited |
get number of vectors of rhs features
Reimplemented in CCustomKernel.
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inherited |
|
virtualinherited |
return derivative with respect to specified parameter
| param | the parameter |
| index | the index of the element if parameter is a vector |
Reimplemented in CCombinedKernel, CProductKernel, CGaussianKernel, and CPeriodicKernel.
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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 |
Definition at line 425 of file WeightedDegreeStringKernel.h.
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inherited |
|
virtual |
get subkernel weights
| num_weights | number of weights will be stored here |
Reimplemented from CKernel.
Definition at line 270 of file WeightedDegreeStringKernel.h.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 881 of file Kernel.cpp.
| EWDKernType get_type | ( | ) | const |
get WD kernel weighting type
Definition at line 107 of file WeightedDegreeStringKernel.h.
| bool get_use_block_computation | ( | ) |
check if block computation is performed
Definition at line 569 of file WeightedDegreeStringKernel.h.
| float64_t* get_weights | ( | int32_t & | num_weights | ) |
get weights
| num_weights | number of weights will be stored here |
Definition at line 402 of file WeightedDegreeStringKernel.h.
| int32_t get_which_degree | ( | ) |
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inherited |
Checks if object has a class parameter identified by a name.
| name | name of the parameter |
Definition at line 289 of file SGObject.h.
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inherited |
Checks if object has a class parameter identified by a Tag.
| tag | tag of the parameter containing name and type information |
Definition at line 301 of file SGObject.h.
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inherited |
Checks if a type exists for a class parameter identified by a name.
| name | name of the parameter |
Definition at line 312 of file SGObject.h.
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virtualinherited |
test whether features have been assigned to lhs and rhs
Reimplemented in CCustomKernel, CCombinedKernel, and CProductKernel.
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inherited |
initialize kernel
| l | features of left-hand side |
| r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 140 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights | ( | ) |
initialize block weights
Definition at line 801 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_const | ( | ) |
initialize block weights constant
Definition at line 725 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
Definition at line 760 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_exp | ( | ) |
initialize block weights exponential
Definition at line 773 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
Definition at line 684 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
Definition at line 701 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_linear | ( | ) |
initialize block weights linear
Definition at line 735 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_log | ( | ) |
initialize block weights logarithmic
Definition at line 787 of file WeightedDegreeStringKernel.cpp.
| bool init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
Definition at line 746 of file WeightedDegreeStringKernel.cpp.
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virtualinherited |
initialize the current kernel normalizer
Definition at line 168 of file Kernel.cpp.
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virtual |
initialize optimization
| count | count |
| IDX | index |
| alphas | alphas |
Reimplemented from CKernel.
Definition at line 133 of file WeightedDegreeStringKernel.h.
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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 |
Definition at line 206 of file WeightedDegreeStringKernel.cpp.
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inherited |
initialize optimization
| svm | svm model |
Definition at line 911 of file Kernel.cpp.
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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 |
Definition at line 329 of file SGObject.cpp.
| bool is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 383 of file WeightedDegreeStringKernel.h.
|
inherited |
|
inherited |
|
inherited |
cleanup kernel cache
Definition at line 567 of file Kernel.cpp.
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inherited |
initialize kernel cache
| size | size to initialize to |
| regression_hack | if hack for regression shall be applied |
Definition at line 181 of file Kernel.cpp.
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inherited |
kernel cache reset lru
Definition at line 554 of file Kernel.cpp.
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inherited |
kernel cache shrink
| totdoc | totdoc |
| num_shrink | number of shrink |
| after | after |
Definition at line 495 of file Kernel.cpp.
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inherited |
|
inherited |
|
inherited |
list kernel
Definition at line 708 of file Kernel.cpp.
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inherited |
load the kernel matrix
| loader | File object via which to load data |
Definition at line 646 of file Kernel.cpp.
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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 |
Definition at line 402 of file SGObject.cpp.
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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::LOAD_SERIALIZABLE_POST is called.
| ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Reimplemented in CWeightedDegreePositionStringKernel, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 929 of file Kernel.cpp.
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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. |
Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 454 of file SGObject.cpp.
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 |
Definition at line 897 of file Kernel.cpp.
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virtualinherited |
Definition at line 295 of file SGObject.cpp.
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inherited |
prints all parameter registered for model selection and their type
Definition at line 507 of file SGObject.cpp.
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virtualinherited |
prints registered parameters out
| prefix | prefix for members |
Definition at line 341 of file SGObject.cpp.
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protectedinherited |
Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.
| _tag | name and type information of parameter |
| value | value of the parameter |
Definition at line 439 of file SGObject.h.
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protectedinherited |
Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.
| name | name of the parameter |
| value | value of the parameter along with type information |
Definition at line 452 of file SGObject.h.
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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
Reimplemented in CSpectrumMismatchRBFKernel, CSNPStringKernel, CANOVAKernel, CSubsequenceStringKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.
Definition at line 952 of file Kernel.cpp.
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protectedvirtual |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 116 of file WeightedDegreeStringKernel.cpp.
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virtualinherited |
remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 660 of file Kernel.cpp.
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virtualinherited |
takes all necessary steps if the rhs is removed from kernel
remove rhs from kernel
Reimplemented in CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 693 of file Kernel.cpp.
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inherited |
resize kernel cache
| size | new size |
| regression_hack | hack for regression |
Definition at line 85 of file Kernel.cpp.
|
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 \(j\in[0,\text{block-size-col}-1]\)Definition at line 1239 of file Kernel.cpp.
|
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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1180 of file Kernel.cpp.
|
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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1126 of file Kernel.cpp.
|
inherited |
save kernel matrix
| writer | File object via which to save data |
Definition at line 652 of file Kernel.cpp.
|
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 |
Definition at line 347 of file SGObject.cpp.
|
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. |
Reimplemented from CSGObject.
Definition at line 944 of file Kernel.cpp.
|
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. |
Reimplemented from CSGObject.
Definition at line 936 of file Kernel.cpp.
|
inherited |
Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.
| _tag | name and type information of parameter |
| value | value of the parameter |
Definition at line 328 of file SGObject.h.
|
inherited |
Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.
| name | name of the parameter |
| value | value of the parameter along with type information |
Definition at line 354 of file SGObject.h.
|
inherited |
|
inherited |
| bool set_degree | ( | int32_t | deg | ) |
set degree
| deg | new degree |
Definition at line 546 of file WeightedDegreeStringKernel.h.
|
inherited |
Definition at line 74 of file SGObject.cpp.
|
inherited |
Definition at line 79 of file SGObject.cpp.
|
inherited |
Definition at line 84 of file SGObject.cpp.
|
inherited |
Definition at line 89 of file SGObject.cpp.
|
inherited |
Definition at line 94 of file SGObject.cpp.
|
inherited |
Definition at line 99 of file SGObject.cpp.
|
inherited |
Definition at line 104 of file SGObject.cpp.
|
inherited |
Definition at line 109 of file SGObject.cpp.
|
inherited |
Definition at line 114 of file SGObject.cpp.
|
inherited |
Definition at line 119 of file SGObject.cpp.
|
inherited |
Definition at line 124 of file SGObject.cpp.
|
inherited |
Definition at line 129 of file SGObject.cpp.
|
inherited |
Definition at line 134 of file SGObject.cpp.
|
inherited |
Definition at line 139 of file SGObject.cpp.
|
inherited |
Definition at line 144 of file SGObject.cpp.
|
inherited |
set generic type to T
|
inherited |
|
inherited |
set the parallel object
| parallel | parallel object to use |
Definition at line 274 of file SGObject.cpp.
|
inherited |
set the version object
| version | version object to use |
Definition at line 316 of file SGObject.cpp.
|
protectedinherited |
| bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
| max | new maximum mismatch |
Definition at line 966 of file WeightedDegreeStringKernel.cpp.
| bool set_mkl_stepsize | ( | int32_t | step | ) |
set MKL steps ize
| step | new step size |
Definition at line 576 of file WeightedDegreeStringKernel.h.
|
virtual |
set the current kernel normalizer
Reimplemented from CKernel.
Definition at line 346 of file WeightedDegreeStringKernel.h.
|
virtualinherited |
| bool set_position_weights | ( | float64_t * | pws, |
| int32_t | len | ||
| ) |
set position weights
| pws | new position weights |
| len | number of position weights |
Definition at line 654 of file WeightedDegreeStringKernel.cpp.
|
protectedinherited |
set subkernel weights
| w | weights |
Reimplemented from CKernel.
Definition at line 295 of file WeightedDegreeStringKernel.h.
|
inherited |
| bool set_use_block_computation | ( | bool | block | ) |
set if block computation shall be performed
| block | if block computation shall be performed |
Definition at line 559 of file WeightedDegreeStringKernel.h.
set wd weights
| new_weights | new weights |
Definition at line 442 of file WeightedDegreeStringKernel.h.
| 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
Definition at line 571 of file WeightedDegreeStringKernel.cpp.
set weights
| new_weights | new weights |
Definition at line 624 of file WeightedDegreeStringKernel.cpp.
| bool set_which_degree | ( | int32_t | which | ) |
set which degree
| which | which degree |
Definition at line 595 of file WeightedDegreeStringKernel.h.
|
virtualinherited |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 225 of file SGObject.cpp.
|
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 \(j\in[0,\text{block-size-col}-1]\)Definition at line 1080 of file Kernel.cpp.
|
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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1027 of file Kernel.cpp.
|
inherited |
unset generic type
this has to be called in classes specializing a template class
Definition at line 336 of file SGObject.cpp.
|
protectedinherited |
|
virtualinherited |
Updates the hash of current parameter combination
Definition at line 281 of file SGObject.cpp.
|
protected |
alphabet of features
Definition at line 761 of file WeightedDegreeStringKernel.h.
|
protected |
if block computation is used
Definition at line 745 of file WeightedDegreeStringKernel.h.
|
protected |
(internal) block weights
Definition at line 748 of file WeightedDegreeStringKernel.h.
|
protectedinherited |
|
protected |
degree
Definition at line 732 of file WeightedDegreeStringKernel.h.
|
protected |
if kernel is initialized
Definition at line 742 of file WeightedDegreeStringKernel.h.
|
inherited |
io
Definition at line 537 of file SGObject.h.
|
protectedinherited |
|
protected |
length
Definition at line 734 of file WeightedDegreeStringKernel.h.
|
protectedinherited |
|
inherited |
parameters wrt which we can compute gradients
Definition at line 552 of file SGObject.h.
|
inherited |
Hash of parameter values
Definition at line 555 of file SGObject.h.
|
inherited |
model selection parameters
Definition at line 549 of file SGObject.h.
|
inherited |
parameters
Definition at line 546 of file SGObject.h.
|
protected |
maximum mismatch
Definition at line 737 of file WeightedDegreeStringKernel.h.
|
protected |
MKL step size
Definition at line 730 of file WeightedDegreeStringKernel.h.
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
inherited |
parallel
Definition at line 540 of file SGObject.h.
|
protected |
position weights
Definition at line 724 of file WeightedDegreeStringKernel.h.
|
protected |
position weights
Definition at line 726 of file WeightedDegreeStringKernel.h.
|
protectedinherited |
|
protected |
sequence length
Definition at line 739 of file WeightedDegreeStringKernel.h.
|
protected |
if tree is initialized
Definition at line 758 of file WeightedDegreeStringKernel.h.
|
protected |
tries
Definition at line 755 of file WeightedDegreeStringKernel.h.
|
protected |
WeightedDegree kernel type
Definition at line 750 of file WeightedDegreeStringKernel.h.
|
inherited |
version
Definition at line 543 of file SGObject.h.
|
protected |
degree*length weights length must match seq_length if != 0
Definition at line 716 of file WeightedDegreeStringKernel.h.
|
protected |
weights buffer
Definition at line 728 of file WeightedDegreeStringKernel.h.
|
protected |
degree
Definition at line 718 of file WeightedDegreeStringKernel.h.
|
protected |
length
Definition at line 720 of file WeightedDegreeStringKernel.h.
|
protected |
which degree
Definition at line 752 of file WeightedDegreeStringKernel.h.