Detailed Description

spectrum rbf kernel

Definition at line 31 of file SpectrumRBFKernel.h.

Inheritance diagram for CSpectrumRBFKernel:

Public Member Functions
	CSpectrumRBFKernel ()
	CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
	CSpectrumRBFKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
virtual	~CSpectrumRBFKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
int32_t	get_degree () const
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
bool	set_degree (int32_t deg)
int32_t	get_degree ()
bool	set_AA_matrix (float64_t *AA_matrix_)
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_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
float64_t	AA_helper (const char path, const int degree, const char joint_seq, unsigned int index)
void	read_profiles_and_sequences ()
float64_t	compute (int32_t idx_a, int32_t idx_b)
virtual void	remove_lhs ()
virtual void	register_param ()
void	register_alphabet ()

Protected Attributes
CAlphabet *	alphabet
int32_t	degree
int32_t	max_mismatch
float64_t *	AA_matrix
int32_t	AA_matrix_length
float64_t	width
std::vector< std::vector < float64_t > >	profiles
std::vector< std::string >	sequence_labels
SGString< char > *	sequences
CStringFeatures< char > *	string_features
int32_t	nof_sequences
int32_t	max_sequence_length
bool	initialized
CArray2< float64_t >	kernel_matrix
int32_t	target_letter_0

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

CSpectrumRBFKernel ( )

default constructor

Definition at line 39 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel	(	int32_t	size,
		float64_t *	AA_matrix,
		int32_t	degree,
		float64_t	width
	)

constructor

Parameters

size
AA_matrix
degree
width

Definition at line 46 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	size,
		float64_t *	AA_matrix,
		int32_t	degree,
		float64_t	width
	)

constructor

Parameters

l	features of left-hand side
r	features of right-hand side
size
AA_matrix
degree
width

Definition at line 71 of file SpectrumRBFKernel.cpp.

~CSpectrumRBFKernel ( )

virtual

destructor

Definition at line 84 of file SpectrumRBFKernel.cpp.

Member Function Documentation

float64_t AA_helper	(	const char *	path,
		const int	degree,
		const char *	joint_seq,
		unsigned int	index
	)

protected

AA helper

Parameters

path
degree
joint_seq
index

Definition at line 336 of file SpectrumRBFKernel.cpp.

void cleanup ( )

virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 320 of file SpectrumRBFKernel.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 358 of file SpectrumRBFKernel.cpp.

int32_t get_degree ( ) const

get degree

Returns: degree of the kernel

Definition at line 75 of file SpectrumRBFKernel.h.

int32_t get_degree ( )

get degree

Returns: degree

Definition at line 103 of file SpectrumRBFKernel.h.

virtual EKernelType get_kernel_type ( )

virtual

return what type of kernel we are

Returns: kernel type

Implements CStringKernel< char >.

Definition at line 84 of file SpectrumRBFKernel.h.

virtual const char* get_name ( ) const

virtual

return the kernel's name

Returns: name

Reimplemented from CStringKernel< char >.

Definition at line 90 of file SpectrumRBFKernel.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 285 of file SpectrumRBFKernel.cpp.

void read_profiles_and_sequences ( )

protected

read profiles and sequences

Definition at line 97 of file SpectrumRBFKernel.cpp.

void register_alphabet ( )

protected

register the alphabet

Definition at line 406 of file SpectrumRBFKernel.cpp.

void register_param ( )

protectedvirtual

register the parameters

Definition at line 395 of file SpectrumRBFKernel.cpp.

void remove_lhs ( )

protectedvirtual

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 91 of file SpectrumRBFKernel.cpp.

bool set_AA_matrix ( float64_t * AA_matrix_ )

set AA matrix

Parameters

AA_matrix_

Definition at line 381 of file SpectrumRBFKernel.cpp.

bool set_degree ( int32_t deg )

set degree

Parameters

deg	new degree

Returns: if setting was successful

Definition at line 97 of file SpectrumRBFKernel.h.

Member Data Documentation

float64_t* AA_matrix

protected

128x128 scalar product matrix

Definition at line 149 of file SpectrumRBFKernel.h.

int32_t AA_matrix_length

protected

length of the AA_matrix – for registration

Definition at line 151 of file SpectrumRBFKernel.h.

CAlphabet* alphabet

protected

alphabet of features

Definition at line 143 of file SpectrumRBFKernel.h.

int32_t degree

protected

degree

Definition at line 145 of file SpectrumRBFKernel.h.

bool initialized

protected

if kernel is initialized

Definition at line 172 of file SpectrumRBFKernel.h.

CArray2<float64_t> kernel_matrix

protected

kernel matrix

Definition at line 174 of file SpectrumRBFKernel.h.

int32_t max_mismatch

protected

maximum mismatch

Definition at line 147 of file SpectrumRBFKernel.h.

int32_t max_sequence_length

protected

max sequence length

Definition at line 169 of file SpectrumRBFKernel.h.

int32_t nof_sequences

protected

nof sequences

Definition at line 167 of file SpectrumRBFKernel.h.

std::vector< std::vector<float64_t> > profiles

protected

profiles

Definition at line 159 of file SpectrumRBFKernel.h.

std::vector<std::string> sequence_labels

protected

sequence labels

Definition at line 161 of file SpectrumRBFKernel.h.

SGString<char>* sequences

protected

sequences

Definition at line 163 of file SpectrumRBFKernel.h.

CStringFeatures<char>* string_features

protected

string features

Definition at line 165 of file SpectrumRBFKernel.h.

int32_t target_letter_0

protected

target letter 0

Definition at line 176 of file SpectrumRBFKernel.h.

float64_t width

protected

width of Gaussian

Definition at line 153 of file SpectrumRBFKernel.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