CDistantSegmentsKernel Class Reference

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Detailed Description

The distant segments kernel is a string kernel, which counts the number of substrings, so-called segments, at a certain distance from each other.

The implementation is taken from http://www.retrovirology.com/content/5/1/110/ and only adjusted to work with shogun. See that page for any details.

Reference: Sebastien Boisvert, Mario Marchand, Francois Laviolette, and Jacques Corbeil. Hiv-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology, 5(1):110, Dec 2008.

Definition at line 34 of file DistantSegmentsKernel.h.

Inheritance diagram for CDistantSegmentsKernel:

List of all members.

Public Member Functions
	CDistantSegmentsKernel ()
	CDistantSegmentsKernel (int32_t size, int32_t delta, int32_t theta)
	CDistantSegmentsKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, int32_t delta, int32_t theta)
virtual bool	init (CFeatures *l, CFeatures *r)
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
Protected Member Functions
virtual float64_t	compute (int32_t idx_a, int32_t idx_b)
Protected Attributes
int32_t	m_delta
int32_t	m_theta

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Constructor & Destructor Documentation

CDistantSegmentsKernel

(

)

default constructor

Definition at line 17 of file DistantSegmentsKernel.cpp.

CDistantSegmentsKernel	(	int32_t	size,
		int32_t	delta,
		int32_t	theta
	)

constructor

Parameters:

	size	cache size
	delta	-parameter of the DS-kernel
	theta	-parameter of the DS-kernel

Definition at line 23 of file DistantSegmentsKernel.cpp.

CDistantSegmentsKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	size,
		int32_t	delta,
		int32_t	theta
	)

constructor

Parameters:

	l	features of left-side
	r	features of right-side
	size	cache size
	delta	-parameter of the DS-kernel
	theta	-parameter of the DS-kernel

Definition at line 29 of file DistantSegmentsKernel.cpp.

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Member Function Documentation

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 49 of file DistantSegmentsKernel.cpp.

virtual EKernelType get_kernel_type

(

)

[virtual]

Returns:

kernel type

Implements CStringKernel< char >.

Definition at line 70 of file DistantSegmentsKernel.h.

virtual const char* get_name

(

)

const [virtual]

Returns:

name of kernel

Reimplemented from CStringKernel< char >.

Definition at line 78 of file DistantSegmentsKernel.h.

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

initialize kernel with features

Parameters:

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

Returns:

true if successful

Reimplemented from CStringKernel< char >.

Definition at line 37 of file DistantSegmentsKernel.cpp.

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Member Data Documentation

int32_t m_delta [protected]

delta parameter of DS-kernel

Definition at line 123 of file DistantSegmentsKernel.h.

int32_t m_theta [protected]

theta parameter of DS-kernel

Definition at line 126 of file DistantSegmentsKernel.h.

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

• DistantSegmentsKernel.h
• DistantSegmentsKernel.cpp