详细描述

The CommWordString kernel may be used to compute the spectrum kernel from strings that have been mapped into unsigned 16bit integers.

These 16bit integers correspond to k-mers. To applicable in this kernel they need to be sorted (e.g. via the SortWordString pre-processor).

It basically uses the algorithm in the unix "comm" command (hence the name) to compute:

$k({\bf x},({\bf x'})= \Phi_k({\bf x})\cdot \Phi_k({\bf x'})$

where $\Phi_k$ maps a sequence ${\bf x}$ that consists of letters in $\Sigma$ to a feature vector of size $|\Sigma|^k$ . In this feature vector each entry denotes how often the k-mer appears in that ${\bf x}$ .

Note that this representation is especially tuned to small alphabets (like the 2-bit alphabet DNA), for which it enables spectrum kernels of order up to 8.

For this kernel the linadd speedups are quite efficiently implemented using direct maps.

在文件CommWordStringKernel.h第46行定义。

继承图，类CCommWordStringKernel

[图例]

所有成员的列表。

公有成员
	CCommWordStringKernel (int32_t size, bool use_sign)
	CCommWordStringKernel (CStringFeatures< uint16_t > l, CStringFeatures< uint16_t > r, bool use_sign=false, int32_t size=10)
virtual	~CCommWordStringKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
virtual bool	init_dictionary (int32_t size)
virtual bool	init_optimization (int32_t count, int32_t IDX, float64_t weights)
virtual bool	delete_optimization ()
virtual float64_t	compute_optimized (int32_t idx)
virtual void	add_to_normal (int32_t idx, float64_t weight)
virtual void	clear_normal ()
virtual EFeatureType	get_feature_type ()
void	get_dictionary (int32_t &dsize, float64_t *&dweights)
virtual 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 *alphas, bool do_init=true)
char *	compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t IDX, float64_t alphas)
void	set_use_dict_diagonal_optimization (bool flag)
bool	get_use_dict_diagonal_optimization ()
保护成员
virtual float64_t	compute (int32_t idx_a, int32_t idx_b)
virtual float64_t	compute_helper (int32_t idx_a, int32_t idx_b, bool do_sort)
virtual float64_t	compute_diag (int32_t idx_a)
保护属性
int32_t	dictionary_size
float64_t *	dictionary_weights
bool	use_sign
bool	use_dict_diagonal_optimization
int32_t *	dict_diagonal_optimization
友元
class	CVarianceKernelNormalizer
class	CSqrtDiagKernelNormalizer
class	CAvgDiagKernelNormalizer
class	CRidgeKernelNormalizer
class	CFirstElementKernelNormalizer
class	CTanimotoKernelNormalizer
class	CDiceKernelNormalizer

构造及析构函数文档

CCommWordStringKernel	(	int32_t	size,
		bool	use_sign
	)

constructor

参数:

	size	cache size
	use_sign	if sign shall be used

在文件CommWordStringKernel.cpp第19行定义。

CCommWordStringKernel	(	CStringFeatures< uint16_t > *	l,
		CStringFeatures< uint16_t > *	r,
		bool	use_sign = `false`,
		int32_t	size = `10`
	)

constructor

参数:

	l	features of left-hand side
	r	features of right-hand side
	use_sign	if sign shall be used
	size	cache size

在文件CommWordStringKernel.cpp第28行定义。

~CCommWordStringKernel ( ) [virtual]

在文件CommWordStringKernel.cpp第53行定义。

成员函数文档

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。

被CWeightedCommWordStringKernel重载。

在文件CommWordStringKernel.cpp第237行定义。

void cleanup ( ) [virtual]

clean up kernel

重载CKernel。

被CWeightedCommWordStringKernel重载。

在文件CommWordStringKernel.cpp第75行定义。

void clear_normal ( ) [virtual]

clear normal

重载CKernel。

在文件CommWordStringKernel.cpp第282行定义。

virtual 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CommWordStringKernel.h第212行定义。

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

compute consensus

参数:

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

返回:: computed consensus

在文件CommWordStringKernel.cpp第494行定义。

float64_t compute_diag ( int32_t idx_a ) [protected, virtual]

helper to compute only diagonal normalization for training

参数:

idx_a

index a

返回:: unnormalized diagonal value

在文件CommWordStringKernel.cpp第81行定义。

float64_t compute_helper	(	int32_t	idx_a,
		int32_t	idx_b,
		bool	do_sort
	)			`[protected, virtual]`

helper for compute

参数:

	idx_a	index a
	idx_b	index b
	do_sort	if sorting shall be performed

返回:: computed value

被CWeightedCommWordStringKernel重载。

在文件CommWordStringKernel.cpp第125行定义。

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。

被CWeightedCommWordStringKernel重载。

在文件CommWordStringKernel.cpp第322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 *	alphas,
		bool	do_init = `true`
	)			`[virtual]`

compute scoring

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
	alphas	alphas
	do_init	if initialization shall be performed