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SHOGUN
4.2.0
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SHOGUN
4.2.0
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The WeightedCommWordString kernel may be used to compute the weighted spectrum kernel (i.e. a spectrum kernel for 1 to K-mers, where each k-mer length is weighted by some coefficient \(\beta_k\)) from strings that have been mapped into unsigned 16bit integers.
These 16bit integers correspond to k-mers. To applicable in this kernel they need to be sorted (e.g. via the SortWordString pre-processor).
It basically uses the algorithm in the unix "comm" command (hence the name) to compute:
\[ k({\bf x},({\bf x'})= \sum_{k=1}^K\beta_k\Phi_k({\bf x})\cdot \Phi_k({\bf x'}) \]
where \(\Phi_k\) maps a sequence \({\bf x}\) that consists of letters in \(\Sigma\) to a feature vector of size \(|\Sigma|^k\). In this feature vector each entry denotes how often the k-mer appears in that \({\bf x}\).
Note that this representation is especially tuned to small alphabets (like the 2-bit alphabet DNA), for which it enables spectrum kernels of order 8.
For this kernel the linadd speedups are quite efficiently implemented using direct maps.
Definition at line 52 of file WeightedCommWordStringKernel.h.
Public Member Functions | |
| CWeightedCommWordStringKernel () | |
| CWeightedCommWordStringKernel (int32_t size, bool use_sign) | |
| CWeightedCommWordStringKernel (CStringFeatures< uint16_t > *l, CStringFeatures< uint16_t > *r, bool use_sign=false, int32_t size=10) | |
| virtual | ~CWeightedCommWordStringKernel () |
| virtual bool | init (CFeatures *l, CFeatures *r) |
| virtual void | cleanup () |
| virtual float64_t | compute_optimized (int32_t idx) |
| virtual void | add_to_normal (int32_t idx, float64_t weight) |
| void | merge_normal () |
| bool | set_wd_weights () |
| bool | set_weights (SGVector< float64_t > weights) |
| virtual EKernelType | get_kernel_type () |
| virtual const char * | get_name () const |
| virtual EFeatureType | get_feature_type () |
| virtual 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 *alphas, bool do_init=true) |
| virtual bool | init_dictionary (int32_t size) |
| virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
| virtual bool | delete_optimization () |
| virtual void | clear_normal () |
| void | get_dictionary (int32_t &dsize, float64_t *&dweights) |
| char * | compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t *IDX, float64_t *alphas) |
| void | set_use_dict_diagonal_optimization (bool flag) |
| bool | get_use_dict_diagonal_optimization () |
| virtual EFeatureClass | get_feature_class () |
| 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_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) |
| EOptimizationType | get_optimization_type () |
| virtual void | set_optimization_type (EOptimizationType t) |
| bool | get_is_initialized () |
| bool | init_optimization_svm (CSVM *svm) |
| 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) |
| 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 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_helper (int32_t idx_a, int32_t idx_b, bool do_sort) |
| virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
| virtual float64_t | compute_diag (int32_t idx_a) |
| 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) |
Protected Attributes | |
| int32_t | degree |
| float64_t * | weights |
| int32_t | dictionary_size |
| float64_t * | dictionary_weights |
| bool | use_sign |
| bool | use_dict_diagonal_optimization |
| int32_t * | dict_diagonal_optimization |
| 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 |
default constructor
Definition at line 18 of file WeightedCommWordStringKernel.cpp.
| CWeightedCommWordStringKernel | ( | int32_t | size, |
| bool | use_sign | ||
| ) |
constructor
| size | cache size |
| use_sign | if sign shall be used |
Definition at line 24 of file WeightedCommWordStringKernel.cpp.
| CWeightedCommWordStringKernel | ( | CStringFeatures< uint16_t > * | l, |
| CStringFeatures< uint16_t > * | r, | ||
| bool | use_sign = false, |
||
| int32_t | size = 10 |
||
| ) |
constructor
| l | features of left-hand side |
| r | features of right-hand side |
| use_sign | if sign shall be used |
| size | cache size |
Definition at line 32 of file WeightedCommWordStringKernel.cpp.
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virtual |
Definition at line 43 of file WeightedCommWordStringKernel.cpp.
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virtual |
add to normal
| idx | where to add |
| weight | what to add |
Reimplemented from CCommWordStringKernel.
Definition at line 191 of file WeightedCommWordStringKernel.cpp.
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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 CCommWordStringKernel.
Definition at line 59 of file WeightedCommWordStringKernel.cpp.
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virtualinherited |
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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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protectedvirtualinherited |
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 217 of file CommWordStringKernel.h.
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virtualinherited |
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 847 of file Kernel.cpp.
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virtualinherited |
compute by subkernel
| vector_idx | index |
| subkernel_contrib | subkernel contribution |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 869 of file Kernel.cpp.
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inherited |
compute consensus
| num_feat | number of features |
| num_suppvec | number of support vectors |
| IDX | IDX |
| alphas | alphas |
Definition at line 498 of file CommWordStringKernel.cpp.
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protectedvirtualinherited |
helper to compute only diagonal normalization for training
| idx_a | index a |
Definition at line 85 of file CommWordStringKernel.cpp.
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protectedvirtual |
helper for compute
| idx_a | index a |
| idx_b | index b |
| do_sort | if sorting shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 96 of file WeightedCommWordStringKernel.cpp.
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virtual |
compute optimized
| idx | index to compute |
Reimplemented from CCommWordStringKernel.
Definition at line 253 of file WeightedCommWordStringKernel.cpp.
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protectedinherited |
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virtual |
compute scoring
| max_degree | maximum degree |
| num_feat | number of features |
| num_sym | number of symbols |
| target | target |
| num_suppvec | number of support vectors |
| IDX | IDX |
| alphas | alphas |
| do_init | if initialization shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 288 of file WeightedCommWordStringKernel.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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delete optimization
Reimplemented from CKernel.
Definition at line 318 of file CommWordStringKernel.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 651 of file SGObject.cpp.
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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 |
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inherited |
get dictionary
| dsize | dictionary size will be stored in here |
| dweights | dictionary weights will be stored in here |
Definition at line 155 of file CommWordStringKernel.h.
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return feature class the kernel can deal with
Implements CKernel.
Definition at line 71 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
Reimplemented from CCommWordStringKernel.
Definition at line 135 of file WeightedCommWordStringKernel.h.
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inherited |
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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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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
Reimplemented from CCommWordStringKernel.
Definition at line 123 of file WeightedCommWordStringKernel.h.
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inherited |
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inherited |
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inherited |
Definition at line 531 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 555 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 568 of file SGObject.cpp.
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return the kernel's name
Reimplemented from CCommWordStringKernel.
Definition at line 129 of file WeightedCommWordStringKernel.h.
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virtualinherited |
obtain the current kernel normalizer
Definition at line 162 of file Kernel.cpp.
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virtualinherited |
get number of subkernels
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, and CProductKernel.
Definition at line 864 of file Kernel.cpp.
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virtualinherited |
get number of vectors of lhs features
Reimplemented in CCustomKernel.
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get number of vectors of rhs features
Reimplemented in CCustomKernel.
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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 |
Reimplemented in CCombinedKernel, CProductKernel, CGaussianKernel, and CPeriodicKernel.
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virtualinherited |
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inherited |
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virtualinherited |
get subkernel weights
| num_weights | number of weights will be stored here |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 875 of file Kernel.cpp.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 881 of file Kernel.cpp.
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inherited |
get.use.dict.diagonal.optimization
Definition at line 203 of file CommWordStringKernel.h.
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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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initialize kernel
| l | features of left-hand side |
| r | features of right-hand side |
Reimplemented from CCommWordStringKernel.
Definition at line 48 of file WeightedCommWordStringKernel.cpp.
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virtualinherited |
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virtualinherited |
initialize the current kernel normalizer
Definition at line 168 of file Kernel.cpp.
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virtualinherited |
initialize optimization
| count | count |
| IDX | index |
| weights | weights |
Reimplemented from CKernel.
Definition at line 292 of file CommWordStringKernel.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.
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inherited |
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inherited |
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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 |
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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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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.
| void merge_normal | ( | ) |
merge normal
Definition at line 221 of file WeightedCommWordStringKernel.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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virtualinherited |
remove lhs from kernel
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 679 of file Kernel.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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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 1239 of file Kernel.cpp.
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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.
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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.
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save kernel matrix
| writer | File object via which to save data |
Definition at line 652 of file Kernel.cpp.
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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.
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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::SAVE_SERIALIZABLE_POST is called.
| ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 944 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::SAVE_SERIALIZABLE_PRE is called.
| ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 936 of file Kernel.cpp.
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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.
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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.
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Definition at line 74 of file SGObject.cpp.
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Definition at line 79 of file SGObject.cpp.
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Definition at line 84 of file SGObject.cpp.
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Definition at line 89 of file SGObject.cpp.
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Definition at line 94 of file SGObject.cpp.
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Definition at line 99 of file SGObject.cpp.
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Definition at line 104 of file SGObject.cpp.
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Definition at line 109 of file SGObject.cpp.
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Definition at line 114 of file SGObject.cpp.
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Definition at line 119 of file SGObject.cpp.
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Definition at line 124 of file SGObject.cpp.
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Definition at line 129 of file SGObject.cpp.
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Definition at line 134 of file SGObject.cpp.
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Definition at line 139 of file SGObject.cpp.
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Definition at line 144 of file SGObject.cpp.
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set generic type to T
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set the parallel object
| parallel | parallel object to use |
Definition at line 274 of file SGObject.cpp.
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set the version object
| version | version object to use |
Definition at line 316 of file SGObject.cpp.
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set the current kernel normalizer
Reimplemented in CWeightedDegreeStringKernel.
Definition at line 150 of file Kernel.cpp.
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set subkernel weights
| weights | new subkernel weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 888 of file Kernel.cpp.
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set_use_dict_diagonal_optimization
| flag | enable diagonal optimization |
Definition at line 194 of file CommWordStringKernel.h.
| bool set_wd_weights | ( | ) |
set weighted degree weights
Definition at line 67 of file WeightedCommWordStringKernel.cpp.
set custom weights (swig compatible)
| weights | weights |
Definition at line 85 of file WeightedCommWordStringKernel.cpp.
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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.
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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.
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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 1027 of file Kernel.cpp.
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unset generic type
this has to be called in classes specializing a template class
Definition at line 336 of file SGObject.cpp.
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Updates the hash of current parameter combination
Definition at line 281 of file SGObject.cpp.
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degree
Definition at line 169 of file WeightedCommWordStringKernel.h.
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array to hold counters for all strings
Definition at line 255 of file CommWordStringKernel.h.
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size of dictionary (number of possible strings)
Definition at line 244 of file CommWordStringKernel.h.
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dictionary weights - array to hold counters for all possible strings
Definition at line 247 of file CommWordStringKernel.h.
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io
Definition at line 537 of file SGObject.h.
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parameters wrt which we can compute gradients
Definition at line 552 of file SGObject.h.
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Hash of parameter values
Definition at line 555 of file SGObject.h.
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model selection parameters
Definition at line 549 of file SGObject.h.
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parameters
Definition at line 546 of file SGObject.h.
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parallel
Definition at line 540 of file SGObject.h.
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whether diagonal optimization shall be used
Definition at line 253 of file CommWordStringKernel.h.
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if sign shall be used
Definition at line 250 of file CommWordStringKernel.h.
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version
Definition at line 543 of file SGObject.h.
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weights for each of the subkernels of degree 1...d
Definition at line 172 of file WeightedCommWordStringKernel.h.