/usr/include/shogun/kernel/DistantSegmentsKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
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* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* Written (W) 2011 Heiko Strathmann
* DS-Kernel implementation Written (W) 2008 Sébastien Boisvert under GPLv3
* Copyright (C) 2011 Berlin Institute of Technology and Max-Planck-Society
*/
#ifndef DISTANTSEGMENTSKERNEL_H_
#define DISTANTSEGMENTSKERNEL_H_
#include <shogun/kernel/StringKernel.h>
namespace shogun
{
/**
* @brief 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.
*/
class CDistantSegmentsKernel: public CStringKernel<char>
{
public:
/** default constructor */
CDistantSegmentsKernel();
/** constructor
*
* @param size cache size
* @param delta \f[\delta\f]-parameter of the DS-kernel
* @param theta \f[\theta\f]-parameter of the DS-kernel
*/
CDistantSegmentsKernel(int32_t size, int32_t delta, int32_t theta);
/** constructor
*
* @param l features of left-side
* @param r features of right-side
* @param size cache size
* @param delta \f[\delta\f]-parameter of the DS-kernel
* @param theta \f[\theta\f]-parameter of the DS-kernel
*/
CDistantSegmentsKernel(CStringFeatures<char>* l, CStringFeatures<char>* r,
int32_t size, int32_t delta, int32_t theta);
/** initialize kernel with features
*
* @param l features of left-side
* @param r features of right-side
* @return true if successful
*/
virtual bool init(CFeatures* l, CFeatures* r);
/**
* @return kernel type
*/
virtual EKernelType get_kernel_type()
{
return K_DISTANTSEGMENTS;
}
/**
* @return name of kernel
*/
virtual const char* get_name() const
{
return "DistantSegmentsKernel";
}
protected:
/**
* compute kernel function for features a and b
* idx_{a,b} denote the index of the feature vectors
* in the corresponding feature object
*
* @param idx_a index a
* @param idx_b index b
* @return computed kernel function at indices a,b
*/
virtual float64_t compute(int32_t idx_a, int32_t idx_b);
private:
/** initializes kernel parameters and registers them */
void init();
/**
* helper function taken from
* http://www.retrovirology.com/content/5/1/110/
* */
int32_t bin(int32_t j, int32_t i);
/**
* Computes the DS-kernel for the given strings and parameters.
* Taken from http://www.retrovirology.com/content/5/1/110/
* with little adjustments.
*
* @param s first string for kernel computation
* @param sLength length of that string
* @param b second string for kernel computation
* @param bLength length of that string
* @param delta_m delta parameter
* @param theta_m theta parameter
* @return computed kernel function of the given strings and parameters
*/
int32_t compute(char* s, int32_t sLength, char* b, int32_t bLength,
int32_t delta_m, int32_t theta_m);
protected:
/** delta parameter of DS-kernel */
int32_t m_delta;
/** theta parameter of DS-kernel */
int32_t m_theta;
};
}
#endif /* DISTANTSEGMENTSKERNEL_H_ */
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