详细描述

The Weighted Degree String kernel.

The WD kernel of order d compares two sequences ${\bf x}$ and ${\bf x'}$ of length L by summing all contributions of k-mer matches of lengths $k\in\{1,\dots,d\}$ , weighted by coefficients $\beta_k$ . It is defined as

$k({\bf x},{\bf x'})=\sum_{k=1}^d\beta_k\sum_{l=1}^{L-k+1}I({\bf u}_{k,l}({\bf x})={\bf u}_{k,l}({\bf x'})).$

Here, ${\bf u}_{k,l}({\bf x})$ is the string of length k starting at position l of the sequence ${\bf x}$ and $I(\cdot)$ is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.

在文件WeightedDegreeStringKernel.h第58行定义。

继承图，类CWeightedDegreeStringKernel

[图例]

所有成员的列表。

公有成员
	CWeightedDegreeStringKernel (int32_t degree, EWDKernType type=E_WD)
	CWeightedDegreeStringKernel (float64_t *weights, int32_t degree)
	CWeightedDegreeStringKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t degree)
virtual	~CWeightedDegreeStringKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
EWDKernType	get_type () const
int32_t	get_degree () const
int32_t	get_max_mismatch () const
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
virtual bool	init_optimization (int32_t count, int32_t IDX, float64_t alphas)
virtual bool	init_optimization (int32_t count, int32_t IDX, float64_t alphas, int32_t tree_num)
virtual bool	delete_optimization ()
virtual float64_t	compute_optimized (int32_t 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)
virtual void	clear_normal ()
virtual void	add_to_normal (int32_t idx, float64_t weight)
virtual int32_t	get_num_subkernels ()
void	compute_by_subkernel (int32_t idx, float64_t *subkernel_contrib)
const float64_t *	get_subkernel_weights (int32_t &num_weights)
void	set_subkernel_weights (float64_t *weights2, int32_t num_weights2)
virtual bool	set_normalizer (CKernelNormalizer *normalizer_)
float64_t *	compute_abs_weights (int32_t &len)
void	compute_by_tree (int32_t idx, float64_t *LevelContrib)
bool	is_tree_initialized ()
float64_t *	get_degree_weights (int32_t &d, int32_t &len)
float64_t *	get_weights (int32_t &num_weights)
float64_t *	get_position_weights (int32_t &len)
bool	set_wd_weights_by_type (EWDKernType type)
void	set_wd_weights (float64_t *p_weights, int32_t d)
bool	set_weights (float64_t *weights, int32_t d, int32_t len)
bool	set_position_weights (float64_t *position_weights, int32_t len=0)
bool	init_block_weights ()
bool	init_block_weights_from_wd ()
bool	init_block_weights_from_wd_external ()
bool	init_block_weights_const ()
bool	init_block_weights_linear ()
bool	init_block_weights_sqpoly ()
bool	init_block_weights_cubicpoly ()
bool	init_block_weights_exp ()
bool	init_block_weights_log ()
bool	init_block_weights_external ()
bool	delete_position_weights ()
bool	set_max_mismatch (int32_t max)
int32_t	get_max_mismatch ()
bool	set_degree (int32_t deg)
int32_t	get_degree ()
bool	set_use_block_computation (bool block)
bool	get_use_block_computation ()
bool	set_mkl_stepsize (int32_t step)
int32_t	get_mkl_stepsize ()
bool	set_which_degree (int32_t which)
int32_t	get_which_degree ()
静态公有成员
static void *	compute_batch_helper (void *p)
保护成员
void	create_empty_tries ()
void	add_example_to_tree (int32_t idx, float64_t weight)
void	add_example_to_single_tree (int32_t idx, float64_t weight, int32_t tree_num)
void	add_example_to_tree_mismatch (int32_t idx, float64_t weight)
void	add_example_to_single_tree_mismatch (int32_t idx, float64_t weight, int32_t tree_num)
float64_t	compute_by_tree (int32_t idx)
float64_t	compute (int32_t idx_a, int32_t idx_b)
float64_t	compute_with_mismatch (char avec, int32_t alen, char bvec, int32_t blen)
float64_t	compute_without_mismatch (char avec, int32_t alen, char bvec, int32_t blen)
float64_t	compute_without_mismatch_matrix (char avec, int32_t alen, char bvec, int32_t blen)
float64_t	compute_using_block (char avec, int32_t alen, char bvec, int32_t blen)
virtual void	remove_lhs ()
保护属性
float64_t *	weights
float64_t *	position_weights
float64_t *	weights_buffer
int32_t	mkl_stepsize
int32_t	degree
int32_t	length
int32_t	max_mismatch
int32_t	seq_length
bool	initialized
bool	block_computation
int32_t	num_block_weights_external
float64_t *	block_weights_external
float64_t *	block_weights
EWDKernType	type
int32_t	which_degree
CTrie< DNATrie > *	tries
bool	tree_initialized
CAlphabet *	alphabet

构造及析构函数文档

CWeightedDegreeStringKernel	(	int32_t	degree,
		EWDKernType	type = `E_WD`
	)

constructor

参数:

	degree	degree
	type	weighted degree kernel type

在文件WeightedDegreeStringKernel.cpp第55行定义。

CWeightedDegreeStringKernel	(	float64_t *	weights,
		int32_t	degree
	)

constructor

参数:

	weights	kernel's weights
	degree	degree

在文件WeightedDegreeStringKernel.cpp第74行定义。

CWeightedDegreeStringKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	degree
	)

constructor

参数:

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

在文件WeightedDegreeStringKernel.cpp第93行定义。

~CWeightedDegreeStringKernel ( ) [virtual]

在文件WeightedDegreeStringKernel.cpp第109行定义。

成员函数文档

void add_example_to_single_tree	(	int32_t	idx,
		float64_t	weight,
		int32_t	tree_num
	)			`[protected]`

add example to single tree

参数:

	idx	index
	weight	weight
	tree_num	which tree

在文件WeightedDegreeStringKernel.cpp第446行定义。

void add_example_to_single_tree_mismatch	(	int32_t	idx,
		float64_t	weight,
		int32_t	tree_num
	)			`[protected]`

add example to single tree mismatch

参数:

	idx	index
	weight	weight
	tree_num	which tree

在文件WeightedDegreeStringKernel.cpp第497行定义。

void add_example_to_tree	(	int32_t	idx,
		float64_t	weight
	)			`[protected]`

add example to tree

参数:

	idx	index
	weight	weight

在文件WeightedDegreeStringKernel.cpp第400行定义。

void add_example_to_tree_mismatch	(	int32_t	idx,
		float64_t	weight
	)			`[protected]`

add example to tree mismatch

参数:

	idx	index
	weight	weight

在文件WeightedDegreeStringKernel.cpp第471行定义。

virtual void add_to_normal	(	int32_t	idx,
		float64_t	weight
	)			`[virtual]`

add to normal

参数:

	idx	where to add
	weight	what to add

重载CKernel。

在文件WeightedDegreeStringKernel.h第229行定义。

void cleanup ( ) [virtual]

clean up kernel

重载CKernel。

在文件WeightedDegreeStringKernel.cpp第193行定义。

virtual void clear_normal ( ) [virtual]

clear normal subkernel functionality

重载CKernel。

在文件WeightedDegreeStringKernel.h第211行定义。

float64_t compute	(	int32_t	idx_a,
		int32_t	idx_b
	)			`[protected, virtual]`

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

参数:

	idx_a	index a
	idx_b	index b

返回:: computed kernel function at indices a,b

实现了CKernel。

在文件WeightedDegreeStringKernel.cpp第374行定义。

float64_t * compute_abs_weights ( int32_t & len )

compute abs weights

参数:

len

len

返回:: computed abs weights

在文件WeightedDegreeStringKernel.cpp第576行定义。

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`
	)			`[virtual]`

compute batch

参数:

	num_vec	number of vectors
	vec_idx	vector index
	target	target
	num_suppvec	number of support vectors
	IDX	IDX
	alphas	alphas
	factor	factor

重载CKernel。

在文件WeightedDegreeStringKernel.cpp第915行定义。

void * compute_batch_helper ( void * p ) [static]

helper for compute batch

参数:

p

thread parameter

在文件WeightedDegreeStringKernel.cpp第879行定义。

void compute_by_subkernel	(	int32_t	idx,
		float64_t *	subkernel_contrib
	)			`[virtual]`

compute by subkernel

参数:

	idx	index
	subkernel_contrib	subkernel contribution

重载CKernel。

在文件WeightedDegreeStringKernel.h第263行定义。

void compute_by_tree	(	int32_t	idx,
		float64_t *	LevelContrib
	)

compute by tree

参数:

	idx	index
	LevelContrib	level contribution

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第549行定义。

float64_t compute_by_tree ( int32_t idx ) [protected]

compute by tree

参数:

idx

index

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第525行定义。

virtual float64_t compute_optimized ( int32_t idx ) [virtual]

compute optimized

参数:

idx

index to compute

返回:: optimized value at given index

重载CKernel。

在文件WeightedDegreeStringKernel.h第178行定义。

float64_t compute_using_block	(	char *	avec,
		int32_t	alen,
		char *	bvec,
		int32_t	blen
	)			`[protected]`

compute using block

参数:

	avec	vector a
	alen	length of vector a
	bvec	vector b
	blen	length of vector b

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第301行定义。

float64_t compute_with_mismatch	(	char *	avec,
		int32_t	alen,
		char *	bvec,
		int32_t	blen
	)			`[protected]`

compute with mismatch

参数:

	avec	vector a
	alen	length of vector a
	bvec	vector b
	blen	length of vector b

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第273行定义。

float64_t compute_without_mismatch	(	char *	avec,
		int32_t	alen,
		char *	bvec,
		int32_t	blen
	)			`[protected]`

compute without mismatch

参数:

	avec	vector a
	alen	length of vector a
	bvec	vector b
	blen	length of vector b

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第327行定义。

float64_t compute_without_mismatch_matrix	(	char *	avec,
		int32_t	alen,
		char *	bvec,
		int32_t	blen
	)			`[protected]`

compute without mismatch matrix

参数:

	avec	vector a
	alen	length of vector a
	bvec	vector b
	blen	length of vector b

返回:: computed value

在文件WeightedDegreeStringKernel.cpp第350行定义。

void create_empty_tries ( ) [protected]

create emtpy tries

在文件WeightedDegreeStringKernel.cpp第138行定义。

bool delete_optimization ( ) [virtual]

delete optimization

返回:: if deleting was successful

重载CKernel。

在文件WeightedDegreeStringKernel.cpp第259行定义。

bool delete_position_weights ( )

delete position weights

返回:: if deleting was successful

在文件WeightedDegreeStringKernel.h第544行定义。

int32_t get_degree ( ) const

get degree of WD kernel

返回:: degree of the kernel

在文件WeightedDegreeStringKernel.h第114行定义。

int32_t get_degree ( )

get degree

返回:: degree

在文件WeightedDegreeStringKernel.h第575行定义。

float64_t* get_degree_weights	(	int32_t &	d,
		int32_t &	len
	)

get degree weights

参数:

	d	degree weights will be stored here
	len	number of degree weights will be stored here

在文件WeightedDegreeStringKernel.h第405行定义。

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

返回:: kernel type WEIGHTEDDEGREE

实现了CKernel。

在文件WeightedDegreeStringKernel.h第133行定义。

int32_t get_max_mismatch ( ) const

get the number of mismatches that are allowed in WD kernel computation

返回:: number of mismatches

在文件WeightedDegreeStringKernel.h第124行定义。

int32_t get_max_mismatch ( )

get maximum mismatch

返回:: maximum mismatch

在文件WeightedDegreeStringKernel.h第562行定义。

int32_t get_mkl_stepsize ( )

get MKL step size

返回:: MKL step size

在文件WeightedDegreeStringKernel.h第611行定义。

virtual const char* get_name ( ) const [virtual]

return the kernel's name

返回:: name WeightedDegree

实现了CSGObject。

在文件WeightedDegreeStringKernel.h第139行定义。

virtual int32_t get_num_subkernels ( ) [virtual]

get number of subkernels

返回:: number of subkernels

重载CKernel。

在文件WeightedDegreeStringKernel.h第247行定义。

float64_t* get_position_weights ( int32_t & len )

get position weights

参数:

len

number of position weights will be stored here

返回:: position weights

在文件WeightedDegreeStringKernel.h第440行定义。

const float64_t* get_subkernel_weights ( int32_t & num_weights ) [virtual]

get subkernel weights

参数:

num_weights

number of weights will be stored here

返回:: subkernel weights

重载CKernel。

在文件WeightedDegreeStringKernel.h第285行定义。

EWDKernType get_type ( ) const

get WD kernel weighting type

返回:: weighting type

参见:: EWDKernType

在文件WeightedDegreeStringKernel.h第105行定义。

bool get_use_block_computation ( )

check if block computation is performed

返回:: if block computation is performed

在文件WeightedDegreeStringKernel.h第592行定义。

float64_t* get_weights ( int32_t & num_weights )

get weights

参数:

num_weights

number of weights will be stored here

返回:: weights

在文件WeightedDegreeStringKernel.h第417行定义。

int32_t get_which_degree ( )

get which degree

返回:: which degree

在文件WeightedDegreeStringKernel.h第628行定义。

bool init	(	CFeatures *	l,
		CFeatures *	r
	)			`[virtual]`

initialize kernel

参数:

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

返回:: if initializing was successful

重载CStringKernel< char >。

在文件WeightedDegreeStringKernel.cpp第151行定义。

bool init_block_weights ( )

initialize block weights

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第851行定义。

bool init_block_weights_const ( )

initialize block weights constant

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第736行定义。

bool init_block_weights_cubicpoly ( )

initialize block weights cubic polynomial

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第781行定义。

bool init_block_weights_exp ( )

initialize block weights exponential

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第798行定义。

bool init_block_weights_external ( )

initialize block weights external

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第832行定义。

bool init_block_weights_from_wd ( )

initialize block weights from weighted degree

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第688行定义。

bool init_block_weights_from_wd_external ( )

initialize block weights from external weighted degree

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第708行定义。

bool init_block_weights_linear ( )

initialize block weights linear

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第750行定义。

bool init_block_weights_log ( )

initialize block weights logarithmic

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第815行定义。

bool init_block_weights_sqpoly ( )

initialize block weights squared polynomial

返回:: if initialization was successful

在文件WeightedDegreeStringKernel.cpp第764行定义。

virtual bool init_optimization	(	int32_t	count,
		int32_t *	IDX,
		float64_t *	alphas
	)			`[virtual]`

initialize optimization

参数:

	count	count
	IDX	index
	alphas	alphas

返回:: if initializing was successful

重载CKernel。

在文件WeightedDegreeStringKernel.h第148行定义。

bool init_optimization	(	int32_t	count,
		int32_t *	IDX,
		float64_t *	alphas,
		int32_t	tree_num
	)			`[virtual]`

initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees

参数:

	count	count
	IDX	IDX
	alphas	alphas
	tree_num	which tree

返回:: if initializing was successful

在文件WeightedDegreeStringKernel.cpp第217行定义。

bool is_tree_initialized ( )

check if tree is initialized

返回:: if tree is initialized

在文件WeightedDegreeStringKernel.h第398行定义。

void remove_lhs ( ) [protected, virtual]

remove lhs from kernel

重载CKernel。

在文件WeightedDegreeStringKernel.cpp第127行定义。

bool set_degree ( int32_t deg )

set degree

参数:

deg

new degree

返回:: if setting was successful

在文件WeightedDegreeStringKernel.h第569行定义。

bool set_max_mismatch ( int32_t max )

set maximum mismatch

参数:

max

new maximum mismatch

返回:: if setting was successful

在文件WeightedDegreeStringKernel.cpp第1019行定义。

bool set_mkl_stepsize ( int32_t step )

set MKL steps ize

参数:

step

new step size

返回:: if setting was successful

在文件WeightedDegreeStringKernel.h第599行定义。

virtual bool set_normalizer ( CKernelNormalizer * normalizer_ ) [virtual]

set the current kernel normalizer

返回:: if successful

重载CKernel。

在文件WeightedDegreeStringKernel.h第361行定义。

bool set_position_weights	(	float64_t *	position_weights,
		int32_t	len = `0`
	)

set position weights

参数:

	position_weights	new position weights
	len	number of position weights

返回:: if setting was successful

在文件WeightedDegreeStringKernel.cpp第659行定义。

void set_subkernel_weights	(	float64_t *	weights2,
		int32_t	num_weights2
	)			`[virtual]`

set subkernel weights

参数:

	weights2	weights
	num_weights2	number of weights

重载CKernel。

在文件WeightedDegreeStringKernel.h第311行定义。

bool set_use_block_computation ( bool block )

set if block computation shall be performed

参数:

block

if block computation shall be performed

返回:: if setting was successful

在文件WeightedDegreeStringKernel.h第582行定义。

void set_wd_weights	(	float64_t *	p_weights,
		int32_t	d
	)

set wd weights

参数:

	p_weights	new eights
	d	degree

返回:: if setting was successful

在文件WeightedDegreeStringKernel.h第459行定义。

bool set_wd_weights_by_type ( EWDKernType type )

set wd weights

参数:

type

weighted degree kernel type

返回:: if setting was successful

if we know a better weighting later on do a switch

在文件WeightedDegreeStringKernel.cpp第582行定义。

bool set_weights	(	float64_t *	weights,
		int32_t	d,
		int32_t	len
	)

set weights

参数:

	weights	new weights
	d	degree
	len	number of weights

在文件WeightedDegreeStringKernel.cpp第632行定义。

bool set_which_degree ( int32_t which )

set which degree

参数:

which

which degree

返回:: if setting was successful

在文件WeightedDegreeStringKernel.h第618行定义。

成员数据文档

CAlphabet* alphabet [protected]

alphabet of features

在文件WeightedDegreeStringKernel.h第930行定义。

bool block_computation [protected]

if block computation is used

在文件WeightedDegreeStringKernel.h第909行定义。

float64_t* block_weights [protected]

(internal) block weights

在文件WeightedDegreeStringKernel.h第917行定义。

float64_t* block_weights_external [protected]

external block weights

在文件WeightedDegreeStringKernel.h第914行定义。

int32_t degree [protected]

degree

在文件WeightedDegreeStringKernel.h第896行定义。

bool initialized [protected]

if kernel is initialized

在文件WeightedDegreeStringKernel.h第906行定义。

int32_t length [protected]

length

在文件WeightedDegreeStringKernel.h第898行定义。

int32_t max_mismatch [protected]

maximum mismatch

在文件WeightedDegreeStringKernel.h第901行定义。

int32_t mkl_stepsize [protected]

MKL step size

在文件WeightedDegreeStringKernel.h第894行定义。

int32_t num_block_weights_external [protected]

number of external block weights

在文件WeightedDegreeStringKernel.h第912行定义。

float64_t* position_weights [protected]

position weights

在文件WeightedDegreeStringKernel.h第890行定义。

int32_t seq_length [protected]

sequence length

在文件WeightedDegreeStringKernel.h第903行定义。

bool tree_initialized [protected]

if tree is initialized

在文件WeightedDegreeStringKernel.h第927行定义。

CTrie<DNATrie>* tries [protected]

tries

在文件WeightedDegreeStringKernel.h第924行定义。

EWDKernType type [protected]

WeightedDegree kernel type

在文件WeightedDegreeStringKernel.h第919行定义。

float64_t* weights [protected]

degree*length weights length must match seq_length if != 0

在文件WeightedDegreeStringKernel.h第888行定义。

float64_t* weights_buffer [protected]

weights buffer

在文件WeightedDegreeStringKernel.h第892行定义。

int32_t which_degree [protected]

which degree

在文件WeightedDegreeStringKernel.h第921行定义。

该类的文档由以下文件生成：

CWeightedDegreeStringKernel类参考

详细描述

公有成员

静态公有成员

保护成员

保护属性

构造及析构函数文档

成员函数文档

成员数据文档