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CDistantSegmentsKernel Class Reference

Detailed Description

The distant segments kernel is a string kernel, which counts the number of substrings, so-called segments, at a certain distance from each other.

The implementation is taken from http://www.retrovirology.com/content/5/1/110/ and only adjusted to work with shogun. See that page for any details.

Reference: Sebastien Boisvert, Mario Marchand, Francois Laviolette, and Jacques Corbeil. Hiv-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology, 5(1):110, Dec 2008.

Definition at line 34 of file DistantSegmentsKernel.h.

Inheritance diagram for CDistantSegmentsKernel:
Inheritance graph
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Public Member Functions

 CDistantSegmentsKernel ()
 CDistantSegmentsKernel (int32_t size, int32_t delta, int32_t theta)
 CDistantSegmentsKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, int32_t delta, int32_t theta)
virtual bool init (CFeatures *l, CFeatures *r)
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
- Public Member Functions inherited from CStringKernel< char >
 CStringKernel (int32_t cachesize=0)
 CStringKernel (CFeatures *l, CFeatures *r)
virtual EFeatureClass get_feature_class ()
virtual 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_tget_kernel_matrix ()
virtual SGVector< float64_tget_kernel_col (int32_t j)
virtual SGVector< float64_tget_kernel_row (int32_t i)
template<class T >
SGMatrix< T > get_kernel_matrix ()
virtual bool set_normalizer (CKernelNormalizer *normalizer)
virtual CKernelNormalizerget_normalizer ()
virtual bool init_normalizer ()
virtual void cleanup ()
void load (CFile *loader)
void save (CFile *writer)
CFeaturesget_lhs ()
CFeaturesget_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_tget_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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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)

Protected Member Functions

virtual float64_t compute (int32_t idx_a, int32_t idx_b)

Protected Attributes

int32_t m_delta
int32_t m_theta

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)

Constructor & Destructor Documentation

default constructor

Definition at line 17 of file DistantSegmentsKernel.cpp.

CDistantSegmentsKernel ( int32_t  size,
int32_t  delta,
int32_t  theta 
)

constructor

Parameters
sizecache size
delta

\[\delta\]

-parameter of the DS-kernel
theta

\[\theta\]

-parameter of the DS-kernel

Definition at line 23 of file DistantSegmentsKernel.cpp.

CDistantSegmentsKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  size,
int32_t  delta,
int32_t  theta 
)

constructor

Parameters
lfeatures of left-side
rfeatures of right-side
sizecache size
delta

\[\delta\]

-parameter of the DS-kernel
theta

\[\theta\]

-parameter of the DS-kernel

Definition at line 29 of file DistantSegmentsKernel.cpp.

Member Function Documentation

float64_t compute ( int32_t  idx_a,
int32_t  idx_b 
)
protectedvirtual

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters
idx_aindex a
idx_bindex b
Returns
computed kernel function at indices a,b

Implements CKernel.

Definition at line 49 of file DistantSegmentsKernel.cpp.

virtual EKernelType get_kernel_type ( )
virtual
Returns
kernel type

Implements CStringKernel< char >.

Definition at line 70 of file DistantSegmentsKernel.h.

virtual const char* get_name ( ) const
virtual
Returns
name of kernel

Reimplemented from CStringKernel< char >.

Definition at line 78 of file DistantSegmentsKernel.h.

bool init ( CFeatures l,
CFeatures r 
)
virtual

initialize kernel with features

Parameters
lfeatures of left-side
rfeatures of right-side
Returns
true if successful

Reimplemented from CStringKernel< char >.

Definition at line 37 of file DistantSegmentsKernel.cpp.

Member Data Documentation

int32_t m_delta
protected

delta parameter of DS-kernel

Definition at line 123 of file DistantSegmentsKernel.h.

int32_t m_theta
protected

theta parameter of DS-kernel

Definition at line 126 of file DistantSegmentsKernel.h.


The documentation for this class was generated from the following files:

SHOGUN Machine Learning Toolbox - Documentation