CWeightedDegreeStringKernel Class Reference

Detailed Description

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.

Definition at line 52 of file WeightedDegreeStringKernel.h.

Inheritance diagram for CWeightedDegreeStringKernel:

[legend]

List of all members.

Public Member Functions
	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)
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 ()
Static Public Member Functions
static void *	compute_batch_helper (void *p)
Protected Member Functions
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 ()
Protected Attributes
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

Constructor & Destructor Documentation

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

constructor

Parameters:

	degree	degree
	type	weighted degree kernel type

Definition at line 54 of file WeightedDegreeStringKernel.cpp.

CWeightedDegreeStringKernel	(	float64_t *	weights,
		int32_t	degree
	)

constructor

Parameters:

	weights	kernel's weights
	degree	degree

Definition at line 73 of file WeightedDegreeStringKernel.cpp.

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

constructor

Parameters:

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

Definition at line 92 of file WeightedDegreeStringKernel.cpp.

~CWeightedDegreeStringKernel ( ) [virtual]

Definition at line 108 of file WeightedDegreeStringKernel.cpp.

Member Function Documentation

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

add example to single tree

Parameters:

	idx	index
	weight	weight
	tree_num	which tree

Definition at line 445 of file WeightedDegreeStringKernel.cpp.

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

add example to single tree mismatch

Parameters:

	idx	index
	weight	weight
	tree_num	which tree

Definition at line 496 of file WeightedDegreeStringKernel.cpp.

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

add example to tree

Parameters:

	idx	index
	weight	weight

Definition at line 399 of file WeightedDegreeStringKernel.cpp.

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

add example to tree mismatch

Parameters:

	idx	index
	weight	weight

Definition at line 470 of file WeightedDegreeStringKernel.cpp.

virtual 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 CKernel.

Definition at line 219 of file WeightedDegreeStringKernel.h.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 192 of file WeightedDegreeStringKernel.cpp.

virtual void clear_normal ( ) [virtual]

clear normal subkernel functionality

Reimplemented from CKernel.

Definition at line 205 of file WeightedDegreeStringKernel.h.

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

Parameters:

	idx_a	index a
	idx_b	index b

Returns:: computed kernel function at indices a,b

Implements CKernel.

Definition at line 373 of file WeightedDegreeStringKernel.cpp.

float64_t * compute_abs_weights ( int32_t & len )

compute abs weights

Parameters:

len

len

Returns:: computed abs weights

Definition at line 575 of file WeightedDegreeStringKernel.cpp.

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

Parameters:

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

Reimplemented from CKernel.

Definition at line 914 of file WeightedDegreeStringKernel.cpp.

void * compute_batch_helper ( void * p ) [static]

helper for compute batch

Parameters:

p

thread parameter

Definition at line 878 of file WeightedDegreeStringKernel.cpp.

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

compute by subkernel

Parameters:

	idx	index
	subkernel_contrib	subkernel contribution

Reimplemented from CKernel.

Definition at line 247 of file WeightedDegreeStringKernel.h.

float64_t compute_by_tree ( int32_t idx ) [protected]

compute by tree

Parameters:

idx

index

Returns:: computed value

Definition at line 524 of file WeightedDegreeStringKernel.cpp.

void compute_by_tree	(	int32_t	idx,
		float64_t *	LevelContrib
	)

compute by tree

Parameters:

	idx	index
	LevelContrib	level contribution

Returns:: computed value

Definition at line 548 of file WeightedDegreeStringKernel.cpp.

virtual float64_t compute_optimized ( int32_t idx ) [virtual]

compute optimized

Parameters:

idx

index to compute

Returns:: optimized value at given index

Reimplemented from CKernel.

Definition at line 172 of file WeightedDegreeStringKernel.h.

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

compute using block

Parameters:

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

Returns:: computed value

Definition at line 300 of file WeightedDegreeStringKernel.cpp.

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

compute with mismatch

Parameters:

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

Returns:: computed value

Definition at line 272 of file WeightedDegreeStringKernel.cpp.

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

compute without mismatch

Parameters:

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

Returns:: computed value

Definition at line 326 of file WeightedDegreeStringKernel.cpp.

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

compute without mismatch matrix

Parameters:

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

Returns:: computed value

Definition at line 349 of file WeightedDegreeStringKernel.cpp.

void create_empty_tries ( ) [protected]

create emtpy tries

Definition at line 137 of file WeightedDegreeStringKernel.cpp.

bool delete_optimization ( ) [virtual]

delete optimization

Returns:: if deleting was successful

Reimplemented from CKernel.

Definition at line 258 of file WeightedDegreeStringKernel.cpp.

bool delete_position_weights ( )

delete position weights

Returns:: if deleting was successful

Definition at line 490 of file WeightedDegreeStringKernel.h.

int32_t get_degree ( )

get degree

Returns:: degree

Definition at line 521 of file WeightedDegreeStringKernel.h.

int32_t get_degree ( ) const

get degree of WD kernel

Returns:: degree of the kernel

Definition at line 108 of file WeightedDegreeStringKernel.h.

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

get degree weights

Parameters:

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

Definition at line 355 of file WeightedDegreeStringKernel.h.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:: kernel type WEIGHTEDDEGREE

Implements CKernel.

Definition at line 127 of file WeightedDegreeStringKernel.h.

int32_t get_max_mismatch ( )

get maximum mismatch

Returns:: maximum mismatch

Definition at line 508 of file WeightedDegreeStringKernel.h.

int32_t get_max_mismatch ( ) const

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

Returns:: number of mismatches

Definition at line 118 of file WeightedDegreeStringKernel.h.

int32_t get_mkl_stepsize ( )

get MKL step size

Returns:: MKL step size

Definition at line 557 of file WeightedDegreeStringKernel.h.

virtual const char* get_name ( ) const [virtual]

return the kernel's name

Returns:: name WeightedDegree

Implements CSGObject.

Definition at line 133 of file WeightedDegreeStringKernel.h.

virtual int32_t get_num_subkernels ( ) [virtual]

get number of subkernels

Returns:: number of subkernels

Reimplemented from CKernel.

Definition at line 233 of file WeightedDegreeStringKernel.h.

float64_t* get_position_weights ( int32_t & len )

get position weights

Parameters:

len

number of position weights will be stored here

Returns:: position weights

Definition at line 386 of file WeightedDegreeStringKernel.h.

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

get subkernel weights

Parameters:

num_weights

number of weights will be stored here

Returns:: subkernel weights

Reimplemented from CKernel.

Definition at line 264 of file WeightedDegreeStringKernel.h.

EWDKernType get_type ( ) const

get WD kernel weighting type

Returns:: weighting type

See also:: EWDKernType

Definition at line 99 of file WeightedDegreeStringKernel.h.

bool get_use_block_computation ( )

check if block computation is performed

Returns:: if block computation is performed

Definition at line 538 of file WeightedDegreeStringKernel.h.

float64_t* get_weights ( int32_t & num_weights )

get weights

Parameters:

num_weights

number of weights will be stored here

Returns:: weights

Definition at line 367 of file WeightedDegreeStringKernel.h.

int32_t get_which_degree ( )

get which degree

Returns:: which degree

Definition at line 574 of file WeightedDegreeStringKernel.h.

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

initialize kernel

Parameters:

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

Returns:: if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 150 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights ( )

initialize block weights

Returns:: if initialization was successful

Definition at line 850 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_const ( )

initialize block weights constant

Returns:: if initialization was successful

Definition at line 735 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_cubicpoly ( )

initialize block weights cubic polynomial

Returns:: if initialization was successful

Definition at line 780 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_exp ( )

initialize block weights exponential

Returns:: if initialization was successful

Definition at line 797 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_external ( )

initialize block weights external

Returns:: if initialization was successful

Definition at line 831 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_from_wd ( )

initialize block weights from weighted degree

Returns:: if initialization was successful

Definition at line 687 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_from_wd_external ( )

initialize block weights from external weighted degree

Returns:: if initialization was successful

Definition at line 707 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_linear ( )

initialize block weights linear

Returns:: if initialization was successful

Definition at line 749 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_log ( )

initialize block weights logarithmic

Returns:: if initialization was successful

Definition at line 814 of file WeightedDegreeStringKernel.cpp.

bool init_block_weights_sqpoly ( )

initialize block weights squared polynomial

Returns:: if initialization was successful

Definition at line 763 of file WeightedDegreeStringKernel.cpp.

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

Parameters:

	count	count
	IDX	IDX
	alphas	alphas
	tree_num	which tree

Returns:: if initializing was successful

Definition at line 216 of file WeightedDegreeStringKernel.cpp.

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

initialize optimization

Parameters:

	count	count
	IDX	index
	alphas	alphas

Returns:: if initializing was successful

Reimplemented from CKernel.

Definition at line 142 of file WeightedDegreeStringKernel.h.

bool is_tree_initialized ( )

check if tree is initialized

Returns:: if tree is initialized

Definition at line 348 of file WeightedDegreeStringKernel.h.

void remove_lhs ( ) [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 126 of file WeightedDegreeStringKernel.cpp.

bool set_degree ( int32_t deg )

set degree

Parameters:

deg

new degree

Returns:: if setting was successful

Definition at line 515 of file WeightedDegreeStringKernel.h.

bool set_max_mismatch ( int32_t max )

set maximum mismatch

Parameters:

max

new maximum mismatch

Returns:: if setting was successful

Definition at line 1018 of file WeightedDegreeStringKernel.cpp.

bool set_mkl_stepsize ( int32_t step )

set MKL steps ize

Parameters:

step

new step size

Returns:: if setting was successful

Definition at line 545 of file WeightedDegreeStringKernel.h.

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

set position weights

Parameters:

	position_weights	new position weights
	len	number of position weights

Returns:: if setting was successful

Definition at line 658 of file WeightedDegreeStringKernel.cpp.

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

set subkernel weights

Parameters:

	weights2	weights
	num_weights2	number of weights

Reimplemented from CKernel.

Definition at line 286 of file WeightedDegreeStringKernel.h.

bool set_use_block_computation ( bool block )

set if block computation shall be performed

Parameters:

block

if block computation shall be performed

Returns:: if setting was successful

Definition at line 528 of file WeightedDegreeStringKernel.h.

void set_wd_weights	(	float64_t *	p_weights,
		int32_t	d
	)

set wd weights

Parameters:

	p_weights	new eights
	d	degree

Returns:: if setting was successful

Definition at line 405 of file WeightedDegreeStringKernel.h.

bool set_wd_weights_by_type ( EWDKernType type )

set wd weights

Parameters:

type

weighted degree kernel type

Returns:: if setting was successful

if we know a better weighting later on do a switch

Definition at line 581 of file WeightedDegreeStringKernel.cpp.

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

set weights

Parameters:

	weights	new weights
	d	degree
	len	number of weights

Definition at line 631 of file WeightedDegreeStringKernel.cpp.

bool set_which_degree ( int32_t which )

set which degree

Parameters:

which

which degree

Returns:: if setting was successful

Definition at line 564 of file WeightedDegreeStringKernel.h.

Member Data Documentation

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 887 of file WeightedDegreeStringKernel.h.

bool block_computation [protected]

if block computation is used

Definition at line 866 of file WeightedDegreeStringKernel.h.

float64_t* block_weights [protected]

(internal) block weights

Definition at line 874 of file WeightedDegreeStringKernel.h.

float64_t* block_weights_external [protected]

external block weights

Definition at line 871 of file WeightedDegreeStringKernel.h.

int32_t degree [protected]

degree

Definition at line 853 of file WeightedDegreeStringKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 863 of file WeightedDegreeStringKernel.h.

int32_t length [protected]

length

Definition at line 855 of file WeightedDegreeStringKernel.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 858 of file WeightedDegreeStringKernel.h.

int32_t mkl_stepsize [protected]

MKL step size

Definition at line 851 of file WeightedDegreeStringKernel.h.

int32_t num_block_weights_external [protected]

number of external block weights

Definition at line 869 of file WeightedDegreeStringKernel.h.

float64_t* position_weights [protected]

position weights

Definition at line 847 of file WeightedDegreeStringKernel.h.

int32_t seq_length [protected]

sequence length

Definition at line 860 of file WeightedDegreeStringKernel.h.

bool tree_initialized [protected]

if tree is initialized

Definition at line 884 of file WeightedDegreeStringKernel.h.

CTrie<DNATrie>* tries [protected]

tries

Definition at line 881 of file WeightedDegreeStringKernel.h.

EWDKernType type [protected]

WeightedDegree kernel type

Definition at line 876 of file WeightedDegreeStringKernel.h.

float64_t* weights [protected]

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

Definition at line 845 of file WeightedDegreeStringKernel.h.

float64_t* weights_buffer [protected]

weights buffer

Definition at line 849 of file WeightedDegreeStringKernel.h.

int32_t which_degree [protected]

which degree

Definition at line 878 of file WeightedDegreeStringKernel.h.

The documentation for this class was generated from the following files:

CWeightedDegreeStringKernel Class Reference

Detailed Description

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation