Detailed Description

The CommUlongString kernel may be used to compute the spectrum kernel from strings that have been mapped into unsigned 64bit integers.

These 64bit integers correspond to k-mers. To be applicable in this kernel they need to be sorted (e.g. via the SortUlongString 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 enables spectrum kernels of order 8 for 8bit alphabets (like binaries) and order 32 for 2-bit alphabets like DNA.

For this kernel the linadd speedups are implemented (though there is room for improvement here when a whole set of sequences is ADDed) using sorted lists.

Definition at line 48 of file CommUlongStringKernel.h.

Inheritance diagram for CCommUlongStringKernel:

[legend]

List of all members.

Public Member Functions
	CCommUlongStringKernel (int32_t size=10, bool use_sign=false)
	CCommUlongStringKernel (CStringFeatures< uint64_t > l, CStringFeatures< uint64_t > r, bool use_sign=false, int32_t size=10)
virtual	~CCommUlongStringKernel ()
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 count, int32_t IDX, float64_t weights)
virtual bool	delete_optimization ()
virtual float64_t	compute_optimized (int32_t idx)
void	merge_dictionaries (int32_t &t, int32_t j, int32_t &k, uint64_t vec, uint64_t dic, float64_t *dic_weights, float64_t weight, int32_t vec_idx)
virtual void	add_to_normal (int32_t idx, float64_t weight)
virtual void	clear_normal ()
virtual void	remove_lhs ()
virtual void	remove_rhs ()
virtual EFeatureType	get_feature_type ()
void	get_dictionary (int32_t &dsize, uint64_t &dict, float64_t &dweights)
Protected Member Functions
float64_t	compute (int32_t idx_a, int32_t idx_b)
Protected Attributes
CDynamicArray< uint64_t >	dictionary
CDynamicArray< float64_t >	dictionary_weights
bool	use_sign

Constructor & Destructor Documentation

CCommUlongStringKernel	(	int32_t	size = `10`,
		bool	use_sign = `false`
	)

constructor

Parameters:

size	cache size
use_sign	if sign shall be used

Definition at line 19 of file CommUlongStringKernel.cpp.

CCommUlongStringKernel	(	CStringFeatures< uint64_t > *	l,
		CStringFeatures< uint64_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 28 of file CommUlongStringKernel.cpp.

~CCommUlongStringKernel ( ) [virtual]

Definition at line 39 of file CommUlongStringKernel.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 CKernel.

Definition at line 145 of file CommUlongStringKernel.cpp.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 73 of file CommUlongStringKernel.cpp.

void clear_normal ( ) [virtual]

clear normal

Reimplemented from CKernel.

Definition at line 210 of file CommUlongStringKernel.cpp.

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 80 of file CommUlongStringKernel.cpp.

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 254 of file CommUlongStringKernel.cpp.

bool delete_optimization ( ) [virtual]

delete optimization

Returns:: if deleting was successful

Reimplemented from CKernel.

Definition at line 245 of file CommUlongStringKernel.cpp.

void get_dictionary	(	int32_t &	dsize,
		uint64_t *&	dict,
		float64_t *&	dweights
	)

get dictionary

Parameters:

dsize	dictionary size will be stored in here
dict	dictionary will be stored in here
dweights	dictionary weights will be stored in here

Definition at line 183 of file CommUlongStringKernel.h.

virtual EFeatureType get_feature_type ( ) [virtual]

return feature type the kernel can deal with

Returns:: feature type ULONG

Reimplemented from CStringKernel< uint64_t >.

Definition at line 175 of file CommUlongStringKernel.h.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:: kernel type COMMULONGSTRING

Implements CStringKernel< uint64_t >.

Definition at line 87 of file CommUlongStringKernel.h.

virtual const char* get_name ( ) const [virtual]

return the kernel's name

Returns:: name CommUlongString

Reimplemented from CStringKernel< uint64_t >.

Definition at line 93 of file CommUlongStringKernel.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< uint64_t >.

Definition at line 67 of file CommUlongStringKernel.cpp.

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

initialize optimization

Parameters:

count	count
IDX	index
weights	weights

Returns:: if initializing was successful

Reimplemented from CKernel.

Definition at line 217 of file CommUlongStringKernel.cpp.

void merge_dictionaries	(	int32_t &	t,
		int32_t	j,
		int32_t &	k,
		uint64_t *	vec,
		uint64_t *	dic,
		float64_t *	dic_weights,
		float64_t	weight,
		int32_t	vec_idx
	)

merge dictionaries

Parameters:

t	t
j	j
k	k
vec	vector
dic	dictionary
dic_weights	dictionary weights
weight	weight
vec_idx	vector index

Definition at line 129 of file CommUlongStringKernel.h.

void remove_lhs ( ) [virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 44 of file CommUlongStringKernel.cpp.

void remove_rhs ( ) [virtual]

remove rhs from kernel

Reimplemented from CKernel.

Definition at line 57 of file CommUlongStringKernel.cpp.

Member Data Documentation

CDynamicArray<uint64_t> dictionary [protected]

dictionary

Definition at line 204 of file CommUlongStringKernel.h.

CDynamicArray<float64_t> dictionary_weights [protected]

dictionary weights

Definition at line 206 of file CommUlongStringKernel.h.

bool use_sign [protected]

if sign shall be used

Definition at line 209 of file CommUlongStringKernel.h.

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation