Detailed Description

The class SNPStringKernel computes a variant of the polynomial kernel on strings of same length.

It is computed as FIXME

$k({\bf x},{\bf x'})= (\sum_{i=0}^{L-1} I(x_i=x'_i)+c)^d$

where I is the indicator function which evaluates to 1 if its argument is true and to 0 otherwise.

Note that additional normalisation is applied, i.e.

$k'({\bf x}, {\bf x'})=\frac{k({\bf x}, {\bf x'})}{\sqrt{k({\bf x}, {\bf x})k({\bf x'}, {\bf x'})}}$

Definition at line 36 of file SNPStringKernel.h.

Inheritance diagram for CSNPStringKernel:

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Public Member Functions
	CSNPStringKernel ()

	CSNPStringKernel (int32_t size, int32_t degree, int32_t win_len, bool inhomogene)

	CSNPStringKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t degree, int32_t win_len, bool inhomogene)

virtual	~CSNPStringKernel ()

virtual bool	init (CFeatures l, CFeatures r)

virtual void	cleanup ()

virtual EKernelType	get_kernel_type ()

void	set_minor_base_string (const char *str)

void	set_major_base_string (const char *str)

char *	get_minor_base_string ()

char *	get_major_base_string ()

void	obtain_base_strings ()

virtual const char *	get_name () const

virtual void	register_params ()

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 ()

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 ()

Protected Member Functions
virtual float64_t	compute (int32_t idx_a, int32_t idx_b)

Protected Member Functions inherited from CKernel
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)

Protected Member Functions inherited from CSGObject
virtual void	load_serializable_pre () throw (ShogunException)

Protected Attributes
int32_t	m_degree

int32_t	m_win_len

bool	m_inhomogene

int32_t	m_str_len

char *	m_str_min

char *	m_str_maj

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

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

CSNPStringKernel ( )

default constructor

Definition at line 20 of file SNPStringKernel.cpp.

CSNPStringKernel	(	int32_t	size,
		int32_t	degree,
		int32_t	win_len,
		bool	inhomogene
	)

constructor

Parameters

size	cache size
degree	degree
win_len	length of local window
inhomogene	whether inhomogeneous poly

Definition at line 29 of file SNPStringKernel.cpp.

CSNPStringKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	degree,
		int32_t	win_len,
		bool	inhomogene
	)

constructor

Parameters

l	features of left-hand side
r	features of right-hand side
degree	degree
win_len	length of local window
inhomogene	whether inhomogeneous poly

Definition at line 39 of file SNPStringKernel.cpp.

~CSNPStringKernel ( )

virtual

Definition at line 53 of file SNPStringKernel.cpp.

Member Function Documentation

void cleanup ( )

virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 64 of file SNPStringKernel.cpp.

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 123 of file SNPStringKernel.cpp.

virtual EKernelType get_kernel_type ( )

virtual

return what type of kernel we are

Returns: kernel type POLYMATCH

Implements CStringKernel< char >.

Definition at line 80 of file SNPStringKernel.h.

char* get_major_base_string ( )

get the base string for major aleles

Returns: major freq. string

Definition at line 116 of file SNPStringKernel.h.

char* get_minor_base_string ( )

get the base string for minor aleles

Returns: minor freq. string

Definition at line 107 of file SNPStringKernel.h.

virtual const char* get_name ( ) const

virtual

return the kernel's name

Returns: name PolyMatchString

Reimplemented from CStringKernel< char >.

Definition at line 128 of file SNPStringKernel.h.

bool init	(	CFeatures *	l,
		CFeatures *	r
	)

virtual

initialize kernel

Parameters

l	features of left-hand side
r	features of right-hand side

Returns: if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 58 of file SNPStringKernel.cpp.

void obtain_base_strings ( )

compute the minor / major alele base strings

Definition at line 71 of file SNPStringKernel.cpp.

void register_params ( )

virtual

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 from CKernel.

Definition at line 181 of file SNPStringKernel.cpp.

void set_major_base_string ( const char * str )

set the base string for major aleles

Parameters

str	major freq. string

Definition at line 98 of file SNPStringKernel.h.

void set_minor_base_string ( const char * str )

set the base string for minor aleles

Parameters

str	minor freq. string

Definition at line 89 of file SNPStringKernel.h.

Member Data Documentation

int32_t m_degree

protected

degree

Definition at line 147 of file SNPStringKernel.h.

bool m_inhomogene

protected

inhomogeneous poly kernel ?

Definition at line 152 of file SNPStringKernel.h.

int32_t m_str_len

protected

total string length / must match length of min/maj strings and string length of each vector

Definition at line 156 of file SNPStringKernel.h.

char* m_str_maj

protected

allele B

Definition at line 161 of file SNPStringKernel.h.

char* m_str_min

protected

allele A

Definition at line 159 of file SNPStringKernel.h.

int32_t m_win_len

protected

window length

Definition at line 149 of file SNPStringKernel.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