SHOGUN
v1.1.0
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Template class StringKernel, is the base class of all String Kernels.
For a (very complex) example see e.g. CWeightedDegreeStringKernel
Definition at line 24 of file StringKernel.h.
Public Member Functions | |
CStringKernel (int32_t cachesize=0) | |
CStringKernel (CFeatures *l, CFeatures *r) | |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
virtual const char * | get_name () const |
virtual EKernelType | get_kernel_type ()=0 |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
template<> | |
EFeatureType | get_feature_type () |
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CKernel () | |
CKernel (int32_t size) | |
CKernel (CFeatures *l, CFeatures *r, int32_t size) | |
virtual | ~CKernel () |
float64_t | kernel (int32_t idx_a, int32_t idx_b) |
SGMatrix< float64_t > | get_kernel_matrix () |
virtual SGVector< float64_t > | get_kernel_col (int32_t j) |
virtual SGVector< float64_t > | get_kernel_row (int32_t i) |
template<class T > | |
SGMatrix< T > | get_kernel_matrix () |
virtual bool | set_normalizer (CKernelNormalizer *normalizer) |
virtual CKernelNormalizer * | get_normalizer () |
virtual bool | init_normalizer () |
virtual void | cleanup () |
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 | |
void | set_cache_size (int32_t size) |
int32_t | get_cache_size () |
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 void | set_subkernel_weights (SGVector< float64_t > weights) |
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CSGObject () | |
CSGObject (const CSGObject &orig) | |
virtual | ~CSGObject () |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
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 () |
SGVector< char * > | get_modelsel_names () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
Additional Inherited Members | |
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SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
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void | set_property (EKernelProperty p) |
void | unset_property (EKernelProperty p) |
void | set_is_initialized (bool p_init) |
virtual float64_t | compute (int32_t x, int32_t y)=0 |
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 () |
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template<class T > | |
static void * | get_kernel_matrix_helper (void *p) |
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int32_t | cache_size |
cache_size in MB | |
KERNELCACHE_ELEM * | kernel_matrix |
CFeatures * | lhs |
feature vectors to occur on left hand side | |
CFeatures * | rhs |
feature vectors to occur on right hand side | |
bool | lhs_equals_rhs |
lhs | |
int32_t | num_lhs |
number of feature vectors on left hand side | |
int32_t | num_rhs |
number of feature vectors on right hand side | |
float64_t | combined_kernel_weight |
bool | optimization_initialized |
EOptimizationType | opt_type |
uint64_t | properties |
CKernelNormalizer * | normalizer |
CStringKernel | ( | int32_t | cachesize = 0 | ) |
CStringKernel | ( | CFeatures * | l, |
CFeatures * | r | ||
) |
constructor
l | features of left-hand side |
r | features of right-hand side |
Definition at line 38 of file StringKernel.h.
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virtual |
return feature class the kernel can deal with
Implements CKernel.
Definition at line 69 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 95 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 97 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 99 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 101 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 103 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 105 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Definition at line 107 of file StringKernel.h.
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pure virtual |
return what type of kernel we are, e.g. Linear,Polynomial, Gaussian,...
abstract base method
Implements CKernel.
Implemented in CWeightedCommWordStringKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CSpectrumMismatchRBFKernel, CSalzbergWordStringKernel, CCommUlongStringKernel, CSpectrumRBFKernel, CSNPStringKernel, CPolyMatchStringKernel, CPolyMatchWordStringKernel, CSimpleLocalityImprovedStringKernel, CGaussianMatchStringKernel, CFixedDegreeStringKernel, CLocalityImprovedStringKernel, CMatchWordStringKernel, CRegulatoryModulesStringKernel, CDistantSegmentsKernel, COligoStringKernel, CHistogramWordStringKernel, CSparseSpatialSampleStringKernel, CLocalAlignmentStringKernel, and CLinearStringKernel.
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virtual |
Returns the name of the SGSerializable instance. It MUST BE the CLASS NAME without the prefixed `C'.
Implements CSGObject.
Reimplemented in CSNPStringKernel, CWeightedCommWordStringKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CSparseSpatialSampleStringKernel, CCommWordStringKernel, CSpectrumMismatchRBFKernel, CSalzbergWordStringKernel, CCommUlongStringKernel, CSpectrumRBFKernel, CPolyMatchStringKernel, CSimpleLocalityImprovedStringKernel, CPolyMatchWordStringKernel, CGaussianMatchStringKernel, CFixedDegreeStringKernel, CDistantSegmentsKernel, CLocalityImprovedStringKernel, CMatchWordStringKernel, CRegulatoryModulesStringKernel, COligoStringKernel, CLocalAlignmentStringKernel, CHistogramWordStringKernel, and CLinearStringKernel.
Definition at line 82 of file StringKernel.h.
initialize kernel e.g. setup lhs/rhs of kernel, precompute normalization constants etc. make sure to check that your kernel can deal with the supplied features (!)
l | features for left-hand side |
r | features for right-hand side |
Reimplemented from CKernel.
Reimplemented in CWeightedDegreePositionStringKernel, CWeightedDegreeStringKernel, CCommWordStringKernel, CSpectrumMismatchRBFKernel, CWeightedCommWordStringKernel, CSalzbergWordStringKernel, CCommUlongStringKernel, CSNPStringKernel, CPolyMatchStringKernel, CPolyMatchWordStringKernel, CLocalityImprovedStringKernel, CMatchWordStringKernel, CRegulatoryModulesStringKernel, CSimpleLocalityImprovedStringKernel, CSpectrumRBFKernel, CDistantSegmentsKernel, CGaussianMatchStringKernel, CFixedDegreeStringKernel, COligoStringKernel, CHistogramWordStringKernel, CSparseSpatialSampleStringKernel, CLocalAlignmentStringKernel, and CLinearStringKernel.
Definition at line 53 of file StringKernel.h.