Detailed Description

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.

Definition at line 50 of file WeightedCommWordStringKernel.h.

Inheritance diagram for CWeightedCommWordStringKernel:

[legend]

List of all members.

Public Member Functions
	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)
Protected Member Functions
virtual float64_t	compute_helper (int32_t idx_a, int32_t idx_b, bool do_sort)
Protected Attributes
int32_t	degree
float64_t *	weights

Constructor & Destructor Documentation

CWeightedCommWordStringKernel ( )

default constructor

Definition at line 18 of file WeightedCommWordStringKernel.cpp.

CWeightedCommWordStringKernel	(	int32_t	size,
		bool	use_sign
	)

constructor

Parameters:

	size	cache size
	use_sign	if sign shall be used

Definition at line 24 of file WeightedCommWordStringKernel.cpp.

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

constructor

Parameters:

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

Definition at line 32 of file WeightedCommWordStringKernel.cpp.

~CWeightedCommWordStringKernel ( ) [virtual]

Definition at line 43 of file WeightedCommWordStringKernel.cpp.

Member Function Documentation

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

add to normal

Parameters:

	idx	where to add
	weight	what to add

Reimplemented from CCommWordStringKernel.

Definition at line 191 of file WeightedCommWordStringKernel.cpp.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CCommWordStringKernel.

Definition at line 59 of file WeightedCommWordStringKernel.cpp.

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

helper for compute

Parameters:

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

Reimplemented from CCommWordStringKernel.

Definition at line 96 of file WeightedCommWordStringKernel.cpp.

float64_t compute_optimized ( int32_t idx ) [virtual]

compute optimized

Parameters:

idx

index to compute

Returns:: optimized value at given index

Reimplemented from CCommWordStringKernel.

Definition at line 253 of file WeightedCommWordStringKernel.cpp.

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

Parameters:

	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