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CStringKernel< ST > Class Template Referenceabstract

Detailed Description

template<class ST>
class shogun::CStringKernel< ST >

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.

Inheritance diagram for CStringKernel< ST >:
Inheritance graph
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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 ()
 
- Public Member Functions inherited from CKernel
 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 More...
 
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)
 
- Public Member Functions inherited from CSGObject
 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)
 
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 ()
 

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIO * io
 
Parallel * parallel
 
Version * version
 
Parameter * m_parameters
 
Parameter * m_model_selection_parameters
 
- Protected Member Functions inherited from CKernel
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 ()
 
- Protected Member Functions inherited from CSGObject
virtual void load_serializable_pre () throw (ShogunException)
 
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)
 
- Protected Attributes inherited from CKernel
int32_t cache_size
 cache_size in MB 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
 

Constructor & Destructor Documentation

CStringKernel ( int32_t  cachesize = 0)

constructor

Parameters
cachesizecache size

Definition at line 31 of file StringKernel.h.

CStringKernel ( CFeatures *  l,
CFeatures *  r 
)

constructor

Parameters
lfeatures of left-hand side
rfeatures of right-hand side

Definition at line 38 of file StringKernel.h.

Member Function Documentation

virtual EFeatureClass get_feature_class ( )
virtual

return feature class the kernel can deal with

Returns
feature class STRING

Implements CKernel.

Definition at line 69 of file StringKernel.h.

virtual EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

Returns
templated feature type

Implements CKernel.

Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 95 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 97 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 99 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 101 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 103 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 105 of file StringKernel.h.

EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

abstract base method

Returns
feature type

Implements CKernel.

Definition at line 107 of file StringKernel.h.

virtual EKernelType get_kernel_type ( )
pure virtual

return what type of kernel we are, e.g. Linear,Polynomial, Gaussian,...

abstract base method

Returns
kernel type

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.

virtual const char* get_name ( ) const
virtual

Returns the name of the SGSerializable instance. It MUST BE the CLASS NAME without the prefixed `C'.

Returns
name of the SGSerializable

Implements CSGObject.

Reimplemented in CSNPStringKernel, CWeightedCommWordStringKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CSparseSpatialSampleStringKernel, CCommWordStringKernel, CSpectrumMismatchRBFKernel, CSalzbergWordStringKernel, CCommUlongStringKernel, CSpectrumRBFKernel, CPolyMatchStringKernel, CPolyMatchWordStringKernel, CSimpleLocalityImprovedStringKernel, CGaussianMatchStringKernel, CFixedDegreeStringKernel, CDistantSegmentsKernel, CLocalityImprovedStringKernel, CMatchWordStringKernel, CRegulatoryModulesStringKernel, COligoStringKernel, CHistogramWordStringKernel, CLocalAlignmentStringKernel, and CLinearStringKernel.

Definition at line 82 of file StringKernel.h.

virtual bool init ( CFeatures *  l,
CFeatures *  r 
)
virtual

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 (!)

Parameters
lfeatures for left-hand side
rfeatures for right-hand side
Returns
if init was successful

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.

The documentation for this class was generated from the following file:
SHOGUN Machine Learning Toolbox - Documentation