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SHOGUN
4.1.0
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SHOGUN
4.1.0
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The Custom Kernel allows for custom user provided kernel matrices.
For squared training matrices it allows to store only the upper triangle of the kernel to save memory: Full symmetric kernel matrices can be stored as is or can be internally converted into (or directly given in) upper triangle representation. Also note that values are stored as 32bit floats.
The custom kernel supports subsets each on the rows and the columns. See documentation in CFeatures, CLabels how this works. The interface is similar.
Definition at line 36 of file CustomKernel.h.
Public Member Functions | |
| CCustomKernel () | |
| CCustomKernel (CKernel *k) | |
| CCustomKernel (SGMatrix< float64_t > km) | |
| CCustomKernel (SGMatrix< float32_t > km) | |
| virtual | ~CCustomKernel () |
| virtual bool | dummy_init (int32_t rows, int32_t cols) |
| virtual bool | init (CFeatures *l, CFeatures *r) |
| virtual void | cleanup () |
| void | cleanup_custom () |
| virtual EKernelType | get_kernel_type () |
| virtual EFeatureType | get_feature_type () |
| virtual EFeatureClass | get_feature_class () |
| virtual const char * | get_name () const |
| bool | set_triangle_kernel_matrix_from_triangle (SGVector< float64_t > tri_kernel_matrix) |
| template<class T > | |
| bool | set_triangle_kernel_matrix_from_triangle_generic (SGVector< T > tri_kernel_matrix) |
| bool | set_triangle_kernel_matrix_from_full (SGMatrix< float64_t > full_kernel_matrix) |
| template<class T > | |
| bool | set_triangle_kernel_matrix_from_full_generic (SGMatrix< T > full_kernel_matrix) |
| bool | set_full_kernel_matrix_from_full (SGMatrix< float32_t > full_kernel_matrix, bool check_symmetry=false) |
| bool | set_full_kernel_matrix_from_full (SGMatrix< float64_t > full_kernel_matrix, bool check_symmetry=false) |
| virtual void | add_row_subset (SGVector< index_t > subset) |
| virtual void | add_row_subset_in_place (SGVector< index_t > subset) |
| virtual void | remove_row_subset () |
| virtual void | remove_all_row_subsets () |
| virtual void | row_subset_changed_post () |
| virtual void | add_col_subset (SGVector< index_t > subset) |
| virtual void | add_col_subset_in_place (SGVector< index_t > subset) |
| virtual void | remove_col_subset () |
| virtual void | remove_all_col_subsets () |
| virtual void | col_subset_changed_post () |
| virtual int32_t | get_num_vec_lhs () |
| virtual int32_t | get_num_vec_rhs () |
| virtual bool | has_features () |
| SGMatrix< float32_t > | get_float32_kernel_matrix () |
| 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 () |
| bool | get_lhs_equals_rhs () |
| virtual void | remove_lhs_and_rhs () |
| virtual void | remove_lhs () |
| 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) |
| virtual void | clear_normal () |
| virtual void | add_to_normal (int32_t vector_idx, float64_t weight) |
| EOptimizationType | get_optimization_type () |
| virtual void | set_optimization_type (EOptimizationType t) |
| bool | get_is_initialized () |
| virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
| virtual bool | delete_optimization () |
| bool | init_optimization_svm (CSVM *svm) |
| virtual float64_t | compute_optimized (int32_t vector_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) |
| float64_t | get_combined_kernel_weight () |
| void | set_combined_kernel_weight (float64_t nw) |
| virtual int32_t | get_num_subkernels () |
| virtual void | compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib) |
| virtual const float64_t * | get_subkernel_weights (int32_t &num_weights) |
| virtual SGVector< float64_t > | get_subkernel_weights () |
| virtual void | set_subkernel_weights (SGVector< float64_t > 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 () |
Static Public Member Functions | |
| 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 | |
| virtual float64_t | compute (int32_t row, int32_t col) |
| 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) |
Static Protected Member Functions | |
| template<class T > | |
| static void * | get_kernel_matrix_helper (void *p) |
Protected Attributes | |
| SGMatrix< float32_t > | kmatrix |
| bool | upper_diagonal |
| bool | m_is_symmetric |
| CSubsetStack * | m_row_subset_stack |
| CSubsetStack * | m_col_subset_stack |
| bool | m_free_km |
| int32_t | cache_size |
| cache_size in MB More... | |
| KERNEL_CACHE | kernel_cache |
| kernel cache More... | |
| KERNELCACHE_ELEM * | kernel_matrix |
| CFeatures * | lhs |
| feature vectors to occur on left hand side More... | |
| CFeatures * | rhs |
| feature vectors to occur on right hand side More... | |
| bool | lhs_equals_rhs |
| lhs More... | |
| int32_t | num_lhs |
| number of feature vectors on left hand side More... | |
| int32_t | num_rhs |
| number of feature vectors on right hand side More... | |
| float64_t | combined_kernel_weight |
| bool | optimization_initialized |
| EOptimizationType | opt_type |
| uint64_t | properties |
| CKernelNormalizer * | normalizer |
| CCustomKernel | ( | ) |
default constructor
Definition at line 48 of file CustomKernel.cpp.
| CCustomKernel | ( | CKernel * | k | ) |
constructor
compute custom kernel from given kernel matrix
| k | kernel matrix |
Definition at line 55 of file CustomKernel.cpp.
| CCustomKernel | ( | SGMatrix< float64_t > | km | ) |
constructor
sets full kernel matrix from full kernel matrix (from double precision floats)
| km | kernel matrix |
Definition at line 76 of file CustomKernel.cpp.
| CCustomKernel | ( | SGMatrix< float32_t > | km | ) |
constructor
sets full kernel matrix from full kernel matrix (from double precision floats)
| km | kernel matrix |
Definition at line 85 of file CustomKernel.cpp.
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virtual |
Definition at line 94 of file CustomKernel.cpp.
Adds a column subset of indices on top of the current subsets (possibly subset of subset). Every call causes a new active index vector to be stored. Added subsets can be removed one-by-one. If this is not needed, add_col_subset_in_place() should be used (does not store intermediate index vectors)
Calls col_subset_changed_post() afterwards
| subset | subset of indices to add |
Definition at line 422 of file CustomKernel.cpp.
Sets/changes latest added column subset. This allows to add multiple subsets with in-place memory requirements. They cannot be removed one-by-one afterwards, only the latest active can. If this is needed, use add_col_subset(). If no subset is active, this just adds.
Calls col_subset_changed_post() afterwards
| subset | subset of indices to replace the latest one with. |
Definition at line 428 of file CustomKernel.cpp.
Adds a row subset of indices on top of the current subsets (possibly subset of subset). Every call causes a new active index vector to be stored. Added subsets can be removed one-by-one. If this is not needed, add_row_subset_in_place() should be used (does not store intermediate index vectors)
Calls row_subset_changed_post() afterwards
| subset | subset of indices to add |
Definition at line 390 of file CustomKernel.cpp.
Sets/changes latest added row subset. This allows to add multiple subsets with in-place memory requirements. They cannot be removed one-by-one afterwards, only the latest active can. If this is needed, use add_row_subset(). If no subset is active, this just adds.
Calls row_subset_changed_post() afterwards
| subset | subset of indices to replace the latest one with. |
Definition at line 396 of file CustomKernel.cpp.
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virtualinherited |
add vector*factor to 'virtual' normal vector
| vector_idx | index |
| weight | weight |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.
Definition at line 853 of file Kernel.cpp.
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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 597 of file SGObject.cpp.
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| void cleanup_custom | ( | ) |
only cleanup stuff specific to Custom kernel
Definition at line 372 of file CustomKernel.cpp.
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for optimizable kernels, i.e. kernels where the weight vector can be computed explicitly (if it fits into memory)
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 858 of file Kernel.cpp.
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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 714 of file SGObject.cpp.
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method may be overwritten to update things that depend on subset
Definition at line 446 of file CustomKernel.cpp.
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compute kernel function
works with subset
| row | row |
| col | col |
Implements CKernel.
Definition at line 580 of file CustomKernel.h.
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computes output for a batch of examples in an optimized fashion (favorable if kernel supports it, i.e. has KP_BATCHEVALUATION. to the outputvector target (of length num_vec elements) the output for the examples enumerated in vec_idx are added. therefore make sure that it is initialized with ZERO. the following num_suppvec, IDX, alphas arguments are the number of support vectors, their indices and weights
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 846 of file Kernel.cpp.
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compute by subkernel
| vector_idx | index |
| subkernel_contrib | subkernel contribution |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 868 of file Kernel.cpp.
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virtualinherited |
compute optimized
| vector_idx | index to compute |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.
Definition at line 840 of file Kernel.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 198 of file SGObject.cpp.
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delete optimization
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 834 of file Kernel.cpp.
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initialize kernel with dummy features
Kernels always need feature objects assigned. As the custom kernel does not really require this it creates some magic dummy features that only know about the number of vectors
removes subset before
| rows | features of left-hand side |
| cols | features of right-hand side |
Definition at line 103 of file CustomKernel.cpp.
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 618 of file SGObject.cpp.
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return feature class the kernel can deal with
Implements CKernel.
Definition at line 120 of file CustomKernel.h.
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return feature type the kernel can deal with
Implements CKernel.
Definition at line 114 of file CustomKernel.h.
returns kernel matrix as is (not possible with subset)
Definition at line 553 of file CustomKernel.h.
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helper for computing the kernel matrix in a parallel way
| p | thread parameters |
Definition at line 1292 of file Kernel.cpp.
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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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return what type of kernel we are
Implements CKernel.
Definition at line 108 of file CustomKernel.h.
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Definition at line 498 of file SGObject.cpp.
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Returns description of a given parameter string, if it exists. SG_ERROR otherwise
| param_name | name of the parameter |
Definition at line 522 of file SGObject.cpp.
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Returns index of model selection parameter with provided index
| param_name | name of model selection parameter |
Definition at line 535 of file SGObject.cpp.
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return the kernel's name
Implements CSGObject.
Definition at line 126 of file CustomKernel.h.
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obtain the current kernel normalizer
Definition at line 162 of file Kernel.cpp.
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get number of subkernels
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, and CProductKernel.
Definition at line 863 of file Kernel.cpp.
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get number of vectors of lhs features
works with subset
Reimplemented from CKernel.
Definition at line 520 of file CustomKernel.h.
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get number of vectors of rhs features
works with subset
Reimplemented from CKernel.
Definition at line 532 of file CustomKernel.h.
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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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get subkernel weights
| num_weights | number of weights will be stored here |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 874 of file Kernel.cpp.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 880 of file Kernel.cpp.
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test whether features have been assigned to lhs and rhs
works with subset
Reimplemented from CKernel.
Definition at line 544 of file CustomKernel.h.
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initialize kernel
removes subset before
| l | features of left-hand side |
| r | features of right-hand side |
Reimplemented from CKernel.
Definition at line 108 of file CustomKernel.cpp.
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initialize the current kernel normalizer
Definition at line 168 of file Kernel.cpp.
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initialize optimization
| count | count |
| IDX | index |
| weights | weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 827 of file Kernel.cpp.
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initialize optimization
| svm | svm model |
Definition at line 910 of file Kernel.cpp.
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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 296 of file SGObject.cpp.
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cleanup kernel cache
Definition at line 567 of file Kernel.cpp.
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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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kernel cache reset lru
Definition at line 554 of file Kernel.cpp.
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kernel cache shrink
| totdoc | totdoc |
| num_shrink | number of shrink |
| after | after |
Definition at line 495 of file Kernel.cpp.
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list kernel
Definition at line 708 of file Kernel.cpp.
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load the kernel matrix
| loader | File object via which to load data |
Definition at line 646 of file Kernel.cpp.
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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 369 of file SGObject.cpp.
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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 928 of file Kernel.cpp.
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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 421 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 896 of file Kernel.cpp.
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Definition at line 262 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 474 of file SGObject.cpp.
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prints registered parameters out
| prefix | prefix for members |
Definition at line 308 of file SGObject.cpp.
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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 951 of file Kernel.cpp.
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removes all col subsets Calls subset_changed_post() afterwards
Definition at line 440 of file CustomKernel.cpp.
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removes all row subsets Calls subset_changed_post() afterwards
Definition at line 408 of file CustomKernel.cpp.
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removes that last added col subset from subset stack, if existing Calls subset_changed_post() afterwards
Definition at line 434 of file CustomKernel.cpp.
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remove lhs from kernel
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 679 of file Kernel.cpp.
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remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 660 of file Kernel.cpp.
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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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removes that last added row subset from subset stack, if existing Calls subset_changed_post() afterwards
Definition at line 402 of file CustomKernel.cpp.
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resize kernel cache
| size | new size |
| regression_hack | hack for regression |
Definition at line 85 of file Kernel.cpp.
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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 1238 of file Kernel.cpp.
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virtual |
method may be overwritten to update things that depend on subset
Definition at line 414 of file CustomKernel.cpp.
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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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1179 of file Kernel.cpp.
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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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1125 of file Kernel.cpp.
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inherited |
save kernel matrix
| writer | File object via which to save data |
Definition at line 652 of file Kernel.cpp.
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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 |
Definition at line 314 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::SAVE_SERIALIZABLE_POST is called.
| ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 943 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::SAVE_SERIALIZABLE_PRE is called.
| ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 935 of file Kernel.cpp.
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inherited |
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inherited |
| bool set_full_kernel_matrix_from_full | ( | SGMatrix< float32_t > | full_kernel_matrix, |
| bool | check_symmetry = false |
||
| ) |
set full kernel matrix from full kernel matrix
for float32
works NOT with subset
| full_kernel_matrix | the original kernel matrix to be set from |
| check_symmetry | whether checking for symmetry of the kernel matrix is required |
Definition at line 263 of file CustomKernel.h.
| bool set_full_kernel_matrix_from_full | ( | SGMatrix< float64_t > | full_kernel_matrix, |
| bool | check_symmetry = false |
||
| ) |
set full kernel matrix from full kernel matrix
for float64
works NOT with subset
| full_kernel_matrix | the original kernel matrix to be set from |
| check_symmetry | whether checking for symmetry of the kernel matrix is required |
Definition at line 294 of file CustomKernel.h.
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inherited |
Definition at line 41 of file SGObject.cpp.
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inherited |
Definition at line 46 of file SGObject.cpp.
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inherited |
Definition at line 51 of file SGObject.cpp.
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inherited |
Definition at line 56 of file SGObject.cpp.
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inherited |
Definition at line 61 of file SGObject.cpp.
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inherited |
Definition at line 66 of file SGObject.cpp.
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inherited |
Definition at line 71 of file SGObject.cpp.
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inherited |
Definition at line 76 of file SGObject.cpp.
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inherited |
Definition at line 81 of file SGObject.cpp.
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inherited |
Definition at line 86 of file SGObject.cpp.
|
inherited |
Definition at line 91 of file SGObject.cpp.
|
inherited |
Definition at line 96 of file SGObject.cpp.
|
inherited |
Definition at line 101 of file SGObject.cpp.
|
inherited |
Definition at line 106 of file SGObject.cpp.
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inherited |
Definition at line 111 of file SGObject.cpp.
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inherited |
set generic type to T
|
inherited |
|
inherited |
set the parallel object
| parallel | parallel object to use |
Definition at line 241 of file SGObject.cpp.
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inherited |
set the version object
| version | version object to use |
Definition at line 283 of file SGObject.cpp.
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protectedinherited |
|
virtualinherited |
set the current kernel normalizer
Reimplemented in CWeightedDegreeStringKernel.
Definition at line 150 of file Kernel.cpp.
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virtualinherited |
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protectedinherited |
set subkernel weights
| weights | new subkernel weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 887 of file Kernel.cpp.
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inherited |
set kernel matrix (only elements from upper triangle) from squared matrix
for float64's
works NOT with subset
Definition at line 204 of file CustomKernel.h.
| bool set_triangle_kernel_matrix_from_full_generic | ( | SGMatrix< T > | full_kernel_matrix | ) |
set kernel matrix (only elements from upper triangle) from squared matrix
works NOT with subset
Definition at line 218 of file CustomKernel.h.
set kernel matrix (only elements from upper triangle) from elements of upper triangle (concat'd), including the main diagonal
small variant for floats64's, triangle needs to have less than 2**32 elements
works NOT with subset
| tri_kernel_matrix | tri kernel matrix |
Definition at line 139 of file CustomKernel.h.
| bool set_triangle_kernel_matrix_from_triangle_generic | ( | SGVector< T > | tri_kernel_matrix | ) |
set kernel matrix (only elements from upper triangle) from elements of upper triangle (concat'd), including the main diagonal
big variant, allowing the triangle to have more than 2**31-1 elements
works NOT with subset
| tri_kernel_matrix | tri kernel matrix |
Definition at line 162 of file CustomKernel.h.
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virtualinherited |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 192 of file SGObject.cpp.
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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 \(j\in[0,\text{block-size-col}-1]\)Definition at line 1079 of file Kernel.cpp.
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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 \(i,j\in[0,\text{block-size}-1]\)Definition at line 1026 of file Kernel.cpp.
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inherited |
unset generic type
this has to be called in classes specializing a template class
Definition at line 303 of file SGObject.cpp.
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protectedinherited |
|
virtualinherited |
Updates the hash of current parameter combination
Definition at line 248 of file SGObject.cpp.
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protectedinherited |
|
inherited |
io
Definition at line 369 of file SGObject.h.
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protectedinherited |
kernel matrix
Definition at line 608 of file CustomKernel.h.
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protectedinherited |
|
protected |
column subset stack
Definition at line 620 of file CustomKernel.h.
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protected |
indicates whether kernel matrix is to be freed in destructor
Definition at line 623 of file CustomKernel.h.
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inherited |
parameters wrt which we can compute gradients
Definition at line 384 of file SGObject.h.
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inherited |
Hash of parameter values
Definition at line 387 of file SGObject.h.
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protected |
whether the kernel matrix is symmetric
Definition at line 614 of file CustomKernel.h.
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inherited |
model selection parameters
Definition at line 381 of file SGObject.h.
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inherited |
parameters
Definition at line 378 of file SGObject.h.
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protected |
row subset stack
Definition at line 617 of file CustomKernel.h.
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protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
protectedinherited |
|
inherited |
parallel
Definition at line 372 of file SGObject.h.
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protectedinherited |
|
protected |
upper diagonal
Definition at line 611 of file CustomKernel.h.
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inherited |
version
Definition at line 375 of file SGObject.h.