详细描述

The Weighted Degree Position String kernel (Weighted Degree kernel with shifts).

The WD-shift 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 $\beta_k$ allowing for a positional tolerance of up to shift s.

It is formally defined as

$\begin{eqnarray*} &&\!\!\!\!\!\!\!k({\bf x}_i,{\bf x}_j)=\sum_{k=1}^d\beta_k\sum_{l=1}^{\!\!\!\!L-k+1\!\!\!\!}\gamma_l\sum_{\begin{array}{c}s=0\\ \!\!\!\!s+l\leq L\!\!\!\!\end{array}}^{S(l)} \delta_s\;\mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}},\\ &&\!\!\!\!\!\!\!\!\!\! {\footnotesize \mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}}\!\!\! =\!\! I({\bf u}_{k,l+s}({\bf x}_i)\! =\!{\bf u}_{k,l}({\bf x}_j))\! +\!I({\bf u}_{k,l}({\bf x}_i)\! =\!{\bf u}_{k,l+s}({\bf x}_j))},\nonumber \end{eqnarray*}$

where $\beta_j$ are the weighting coefficients of the j-mers, $\gamma_l$ is a weighting over the position in the sequence, $\delta_s=1/(2(s+1))$ is the weight assigned to shifts (in either direction) of extent s, and S(l) determines the shift range at position l.

在文件WeightedDegreePositionStringKernel.h第48行定义。

继承图，类CWeightedDegreePositionStringKernel

[图例]

所有成员的列表。

公有成员
	CWeightedDegreePositionStringKernel (void)
	CWeightedDegreePositionStringKernel (int32_t size, int32_t degree, int32_t max_mismatch=0, int32_t mkl_stepsize=1)
	CWeightedDegreePositionStringKernel (int32_t size, float64_t weights, int32_t degree, int32_t max_mismatch, int32_t shift, int32_t shift_len, int32_t mkl_stepsize=1)
	CWeightedDegreePositionStringKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t degree)
virtual	~CWeightedDegreePositionStringKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
virtual bool	init_optimization (int32_t p_count, int32_t IDX, float64_t alphas)
virtual bool	init_optimization (int32_t count, int32_t IDX, float64_t alphas, int32_t tree_num, int32_t upto_tree=-1)
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)
float64_t *	compute_abs_weights (int32_t &len)
bool	is_tree_initialized ()
int32_t	get_max_mismatch ()
int32_t	get_degree ()
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_shifts (int32_t *shifts, int32_t len)
virtual bool	set_weights (float64_t *weights, int32_t d, int32_t len=0)
virtual bool	set_wd_weights ()
virtual bool	set_position_weights (float64_t *pws, int32_t len)
bool	set_position_weights_lhs (float64_t *pws, int32_t len, int32_t num)
bool	set_position_weights_rhs (float64_t *pws, int32_t len, int32_t num)
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	delete_position_weights ()
bool	delete_position_weights_lhs ()
bool	delete_position_weights_rhs ()
virtual float64_t	compute_by_tree (int32_t idx)
virtual void	compute_by_tree (int32_t idx, float64_t *LevelContrib)
float64_t *	compute_scoring (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t target, int32_t num_suppvec, int32_t IDX, float64_t *weights)
char *	compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t IDX, float64_t alphas)
float64_t *	extract_w (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t w_result, int32_t num_suppvec, int32_t IDX, float64_t *alphas)
float64_t *	compute_POIM (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t poim_result, int32_t num_suppvec, int32_t IDX, float64_t alphas, float64_t distrib)
void	prepare_POIM2 (float64_t *distrib, int32_t num_sym, int32_t num_feat)
void	compute_POIM2 (int32_t max_degree, CSVM *svm)
void	get_POIM2 (float64_t *poim, int32_t result_len)
void	cleanup_POIM2 ()
	cleanup POIM2
静态公有成员
static void *	compute_batch_helper (void *p)
保护成员
void	create_empty_tries ()
virtual 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)
virtual 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_without_mismatch_position_weights (char avec, float64_t posweights_lhs, int32_t alen, char bvec, float64_t posweights_rhs, int32_t blen)
virtual void	remove_lhs ()
virtual void	load_serializable_post (void) throw (ShogunException)
保护属性
float64_t *	weights
int32_t	weights_degree
int32_t	weights_length
float64_t *	position_weights
int32_t	position_weights_len
float64_t *	position_weights_lhs
int32_t	position_weights_lhs_len
float64_t *	position_weights_rhs
int32_t	position_weights_rhs_len
bool *	position_mask
float64_t *	weights_buffer
int32_t	mkl_stepsize
int32_t	degree
int32_t	length
int32_t	max_mismatch
int32_t	seq_length
int32_t *	shift
int32_t	shift_len
int32_t	max_shift
bool	block_computation
float64_t *	block_weights
EWDKernType	type
int32_t	which_degree
CTrie< DNATrie >	tries
CTrie< POIMTrie >	poim_tries
bool	tree_initialized
bool	use_poim_tries
float64_t *	m_poim_distrib
float64_t *	m_poim
int32_t	m_poim_num_sym
int32_t	m_poim_num_feat
int32_t	m_poim_result_len
CAlphabet *	alphabet

构造及析构函数文档

CWeightedDegreePositionStringKernel ( void )

default constructor

在文件WeightedDegreePositionStringKernel.cpp第52行定义。

CWeightedDegreePositionStringKernel	(	int32_t	size,
		int32_t	degree,
		int32_t	max_mismatch = `0`,
		int32_t	mkl_stepsize = `1`
	)

constructor

参数:

size	cache size
degree	degree
max_mismatch	maximum mismatch
mkl_stepsize	MKL stepsize

在文件WeightedDegreePositionStringKernel.cpp第59行定义。

CWeightedDegreePositionStringKernel	(	int32_t	size,
		float64_t *	weights,
		int32_t	degree,
		int32_t	max_mismatch,
		int32_t *	shift,
		int32_t	shift_len,
		int32_t	mkl_stepsize = `1`
	)

constructor

参数:

size	cache size
weights	weights
degree	degree
max_mismatch	maximum mismatch
shift	position shifts
shift_len	number of shifts
mkl_stepsize	MKL stepsize

在文件WeightedDegreePositionStringKernel.cpp第76行定义。

CWeightedDegreePositionStringKernel	(	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WeightedDegreePositionStringKernel.cpp第100行定义。

~CWeightedDegreePositionStringKernel ( ) [virtual]

在文件WeightedDegreePositionStringKernel.cpp第119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WeightedDegreePositionStringKernel.cpp第695行定义。

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

add example to tree

参数:

idx	index
weight	weight

在文件WeightedDegreePositionStringKernel.cpp第644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WeightedDegreePositionStringKernel.h第211行定义。

void cleanup ( ) [virtual]

clean up kernel

重载CKernel。

在文件WeightedDegreePositionStringKernel.cpp第227行定义。

void cleanup_POIM2 ( )

cleanup POIM2

在文件WeightedDegreePositionStringKernel.cpp第1880行定义。

virtual void clear_normal ( ) [virtual]

clear normal subkernel functionality

重载CKernel。

在文件WeightedDegreePositionStringKernel.h第185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WeightedDegreePositionStringKernel.cpp第608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WeightedDegreePositionStringKernel.cpp第831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WeightedDegreePositionStringKernel.cpp第1239行定义。

void * compute_batch_helper ( void * p ) [static]

helper for compute batch

参数:

p	thread parameter

在文件WeightedDegreePositionStringKernel.cpp第1181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WeightedDegreePositionStringKernel.h第235行定义。

float64_t compute_by_tree ( int32_t idx ) [virtual]

compute by tree

参数:

idx index

返回:: computed value

在文件WeightedDegreePositionStringKernel.cpp第749行定义。

void compute_by_tree	(	int32_t	idx,
		float64_t *	LevelContrib
	)		`[virtual]`

compute by tree

参数:

idx	index
LevelContrib	level contribution

在文件WeightedDegreePositionStringKernel.cpp第788行定义。

char * compute_consensus	(	int32_t &	num_feat,
		int32_t	num_suppvec,
		int32_t *	IDX,
		float64_t *	alphas
	)

compute consensus string

参数:

num_feat	number of features
num_suppvec	number of support vectors
IDX	IDX
alphas	alphas

返回:: consensus string

在文件WeightedDegreePositionStringKernel.cpp第1508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WeightedDegreePositionStringKernel.h第153行定义。

float64_t * compute_POIM	(	int32_t	max_degree,
		int32_t &	num_feat,
		int32_t &	num_sym,
		float64_t *	poim_result,
		int32_t	num_suppvec,
		int32_t *	IDX,
		float64_t *	alphas,
		float64_t *	distrib
	)

compute POIM

参数:

max_degree	maximum degree
num_feat	number of features
num_sym	number of symbols
poim_result	poim
num_suppvec	number of support vectors
IDX	IDX
alphas	alphas
distrib	distribution

返回:: computed POIMs

在文件WeightedDegreePositionStringKernel.cpp第1688行定义。

void compute_POIM2	(	int32_t	max_degree,
		CSVM *	svm
	)

compute POIM2

参数:

max_degree	maximum degree
svm	SVM

在文件WeightedDegreePositionStringKernel.cpp第1836行定义。

float64_t * compute_scoring	(	int32_t	max_degree,
		int32_t &	num_feat,
		int32_t &	num_sym,
		float64_t *	target,
		int32_t	num_suppvec,
		int32_t *	IDX,
		float64_t *	weights
	)

compute positional scoring function, which assigns a weight per position, per symbol in the sequence

参数:

max_degree	maximum degree
num_feat	number of features
num_sym	number of symbols
target	target
num_suppvec	number of support vectors
IDX	IDX
weights	weights

返回:: computed scores

在文件WeightedDegreePositionStringKernel.cpp第1352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WeightedDegreePositionStringKernel.cpp第318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WeightedDegreePositionStringKernel.cpp第398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WeightedDegreePositionStringKernel.cpp第464行定义。

float64_t compute_without_mismatch_position_weights	(	char *	avec,
		float64_t *	posweights_lhs,
		int32_t	alen,
		char *	bvec,
		float64_t *	posweights_rhs,
		int32_t	blen
	)		`[protected]`

compute without mismatch position weights

参数:

avec	vector a
posweights_lhs	position weights left-hand side
alen	length of vector a
bvec	vector b
posweights_rhs	position weights right-hand side
blen	length of vector b

返回:: computed value

在文件WeightedDegreePositionStringKernel.cpp第528行定义。

void create_empty_tries ( ) [protected]

create emtpy tries

在文件WeightedDegreePositionStringKernel.cpp第159行定义。

bool delete_optimization ( ) [virtual]

delete optimization

返回:: if deleting was successful

重载CKernel。

在文件WeightedDegreePositionStringKernel.cpp第293行定义。

bool delete_position_weights ( )

delete position weights

返回:: if deleting was successful

在文件WeightedDegreePositionStringKernel.h第477行定义。

bool delete_position_weights_lhs ( )

delete position weights left-hand side

返回:: if deleting was successful

在文件WeightedDegreePositionStringKernel.h第488行定义。

bool delete_position_weights_rhs ( )

delete position weights right-hand side

返回:: if deleting was successful

在文件WeightedDegreePositionStringKernel.h第499行定义。

float64_t * extract_w	(	int32_t	max_degree,
		int32_t &	num_feat,
		int32_t &	num_sym,
		float64_t *	w_result,
		int32_t	num_suppvec,
		int32_t *	IDX,
		float64_t *	alphas
	)

extract w

参数:

max_degree	maximum degree
num_feat	number of features
num_sym	number of symbols
w_result	w
num_suppvec	number of support vectors
IDX	IDX
alphas	alphas

返回:: w

在文件WeightedDegreePositionStringKernel.cpp第1625行定义。

int32_t get_degree ( )

get degree

返回:: the degree

在文件WeightedDegreePositionStringKernel.h第328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WeightedDegreePositionStringKernel.h第335行定义。

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

返回:: kernel type WEIGHTEDDEGREEPOS

实现了CStringKernel< char >。

在文件WeightedDegreePositionStringKernel.h第106行定义。

int32_t get_max_mismatch ( )

get maximum mismatch

返回:: maximum mismatch

在文件WeightedDegreePositionStringKernel.h第322行定义。

virtual const char* get_name ( void ) const [virtual]

return the kernel's name

返回:: name WeightedDegreePos

重载CStringKernel< char >。

在文件WeightedDegreePositionStringKernel.h第112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WeightedDegreePositionStringKernel.h第221行定义。

void get_POIM2	(	float64_t **	poim,
		int32_t *	result_len
	)

get POIM2

参数:

poim	POIMs (returned)
result_len	(returned)

在文件WeightedDegreePositionStringKernel.cpp第1871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WeightedDegreePositionStringKernel.h第366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WeightedDegreePositionStringKernel.h第252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WeightedDegreePositionStringKernel.h第347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WeightedDegreePositionStringKernel.cpp第178行定义。

bool init_block_weights ( )

initialize block weights

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1155行定义。

bool init_block_weights_const ( )

initialize block weights constant

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1059行定义。

bool init_block_weights_cubicpoly ( )

initialize block weights cubic polynomial

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1104行定义。

bool init_block_weights_exp ( )

initialize block weights exponential

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1121行定义。

bool init_block_weights_from_wd ( )

initialize block weights from weighted degree

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1011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WeightedDegreePositionStringKernel.cpp第1031行定义。

bool init_block_weights_linear ( )

initialize block weights linear

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1073行定义。

bool init_block_weights_log ( )

initialize block weights logarithmic

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1138行定义。

bool init_block_weights_sqpoly ( )

initialize block weights squared polynomial

返回:: if initialization was successful

在文件WeightedDegreePositionStringKernel.cpp第1087行定义。

bool init_optimization	(	int32_t	count,
		int32_t *	IDX,
		float64_t *	alphas,
		int32_t	tree_num,
		int32_t	upto_tree = `-1`
	)		`[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
upto_tree	up to this tree

返回:: if initializing was successful

在文件WeightedDegreePositionStringKernel.cpp第247行定义。

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

initialize optimization

参数:

p_count	count
IDX	index
alphas	alphas

返回:: if initializing was successful

重载CKernel。

在文件WeightedDegreePositionStringKernel.h第121行定义。

bool is_tree_initialized ( )

check if tree is initialized

返回:: if tree is initialized

在文件WeightedDegreePositionStringKernel.h第316行定义。

void load_serializable_post ( void ) throw (ShogunException) [protected, virtual]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

异常:

ShogunException Will be thrown if an error occurres.

重载CKernel。

在文件WeightedDegreePositionStringKernel.cpp第1891行定义。