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:

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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_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)
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)

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
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters
Static Protected Member Functions inherited from CKernel
template<class T >
static void *	get_kernel_matrix_helper (void *p)

Constructor & Destructor Documentation

CDistantSegmentsKernel ( )

default constructor

Definition at line 17 of file DistantSegmentsKernel.cpp.

CDistantSegmentsKernel	(	int32_t	size,
		int32_t	delta,
		int32_t	theta
	)

constructor

Parameters

size	cache 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

l	features of left-side
r	features of right-side
size	cache 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_a	index a
idx_b	index 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

l	features of left-side
r	features 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:

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation