详细描述

The WeightedCommWordString kernel may be used to compute the weighted spectrum kernel (i.e. a spectrum kernel for 1 to K-mers, where each k-mer length is weighted by some coefficient $\beta_k$ ) 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:

$k({\bf x},({\bf x'})= \sum_{k=1}^K\beta_k\Phi_k({\bf x})\cdot \Phi_k({\bf x'})$

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 8.

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

在文件WeightedCommWordStringKernel.h第50行定义。

继承图，类CWeightedCommWordStringKernel

[图例]

所有成员的列表。

公有成员
	CWeightedCommWordStringKernel ()
	CWeightedCommWordStringKernel (int32_t size, bool use_sign)
	CWeightedCommWordStringKernel (CStringFeatures< uint16_t > l, CStringFeatures< uint16_t > r, bool use_sign=false, int32_t size=10)
virtual	~CWeightedCommWordStringKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual float64_t	compute_optimized (int32_t idx)
virtual void	add_to_normal (int32_t idx, float64_t weight)
void	merge_normal ()
bool	set_wd_weights ()
bool	set_weights (float64_t *w, int32_t d)
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
virtual EFeatureType	get_feature_type ()
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)
保护成员
virtual float64_t	compute_helper (int32_t idx_a, int32_t idx_b, bool do_sort)
保护属性
int32_t	degree
float64_t *	weights

构造及析构函数文档

CWeightedCommWordStringKernel ( )

default constructor

在文件WeightedCommWordStringKernel.cpp第18行定义。

CWeightedCommWordStringKernel	(	int32_t	size,
		bool	use_sign
	)

constructor

参数:

size	cache size
use_sign	if sign shall be used

在文件WeightedCommWordStringKernel.cpp第24行定义。

CWeightedCommWordStringKernel	(	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WeightedCommWordStringKernel.cpp第32行定义。

~CWeightedCommWordStringKernel ( ) [virtual]

在文件WeightedCommWordStringKernel.cpp第43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CCommWordStringKernel。

在文件WeightedCommWordStringKernel.cpp第191行定义。

void cleanup ( ) [virtual]

clean up kernel

重载CCommWordStringKernel。

在文件WeightedCommWordStringKernel.cpp第59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

重载CCommWordStringKernel。

在文件WeightedCommWordStringKernel.cpp第96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CCommWordStringKernel。

在文件WeightedCommWordStringKernel.cpp第253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