Detailed Description

spectrum mismatch rbf kernel

Definition at line 42 of file SpectrumMismatchRBFKernel.h.

Inheritance diagram for CSpectrumMismatchRBFKernel:

Public Member Functions
	CSpectrumMismatchRBFKernel ()
	CSpectrumMismatchRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
	CSpectrumMismatchRBFKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
virtual	~CSpectrumMismatchRBFKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
bool	set_max_mismatch (int32_t max)
int32_t	get_max_mismatch () const
bool	set_degree (int32_t deg)
int32_t	get_degree () const
bool	set_AA_matrix (float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128)
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 (std::string &path, const char *joint_seq, unsigned int index)
float64_t	compute_helper (const char *joint_seq, std::vector< unsigned int > joint_index, std::vector< unsigned int > joint_mismatch, std::string path, unsigned int d, const int &alen)
void	compute_helper_all (const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d)
void	compute_all ()
float64_t	compute (int32_t idx_a, int32_t idx_b)
virtual void	remove_lhs ()
virtual void	register_params ()
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
bool	initialized
CArray2< float64_t >	kernel_matrix
int32_t	kernel_matrix_length
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

CSpectrumMismatchRBFKernel ( )

default constructor

Definition at line 36 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel	(	int32_t	size,
		float64_t *	AA_matrix_,
		int32_t	nr_,
		int32_t	nc_,
		int32_t	degree,
		int32_t	max_mismatch,
		float64_t	width
	)

constructor

Parameters

size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 43 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	size,
		float64_t *	AA_matrix_,
		int32_t	nr_,
		int32_t	nc_,
		int32_t	degree,
		int32_t	max_mismatch,
		float64_t	width
	)

constructor

Parameters

l	features of left-hand side
r	features of right-hand side
size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 58 of file SpectrumMismatchRBFKernel.cpp.

~CSpectrumMismatchRBFKernel ( )

virtual

destructor

Definition at line 70 of file SpectrumMismatchRBFKernel.cpp.

Member Function Documentation

float64_t AA_helper	(	std::string &	path,
		const char *	joint_seq,
		unsigned int	index
	)

protected

AA helper

Parameters

path
joint_seq
index

Returns: AA helper

Definition at line 120 of file SpectrumMismatchRBFKernel.cpp.

void cleanup ( )

virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 111 of file SpectrumMismatchRBFKernel.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 360 of file SpectrumMismatchRBFKernel.cpp.

void compute_all ( )

protected

computer all

Definition at line 324 of file SpectrumMismatchRBFKernel.cpp.

float64_t compute_helper	(	const char *	joint_seq,
		std::vector< unsigned int >	joint_index,
		std::vector< unsigned int >	joint_mismatch,
		std::string	path,
		unsigned int	d,
		const int &	alen
	)