/usr/include/shogun/kernel/string/SpectrumRBFKernel.h is in libshogun-dev 3.2.0-7.3build4.
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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) 1999-2009 Soeren Sonnenburg
* Written (W) 1999-2008 Gunnar Raetsch
* Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef _SPECTRUMRBFKERNEL_H___
#define _SPECTRUMRBFKERNEL_H___
#include <shogun/lib/common.h>
#include <shogun/lib/Trie.h>
#include <shogun/kernel/string/StringKernel.h>
#include <shogun/features/StringFeatures.h>
#include <shogun/lib/DynamicArray.h>
#include <vector> // profile
#include <string> // profile
namespace shogun
{
/** @brief spectrum rbf kernel */
class CSpectrumRBFKernel: public CStringKernel<char>
{
public:
/** default constructor */
CSpectrumRBFKernel();
/** constructor
* @param size
* @param AA_matrix
* @param degree
* @param width
*/
CSpectrumRBFKernel(int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width);
/** constructor
*
* @param l features of left-hand side
* @param r features of right-hand side
* @param size
* @param AA_matrix
* @param degree
* @param width
*/
CSpectrumRBFKernel(
CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix, int32_t degree, float64_t width);
/** destructor */
virtual ~CSpectrumRBFKernel();
/** initialize kernel
*
* @param l features of left-hand side
* @param r features of right-hand side
* @return if initializing was successful
*/
virtual bool init(CFeatures* l, CFeatures* r);
/** clean up kernel */
virtual void cleanup();
/** get degree
*
* @return degree of the kernel
*/
int32_t get_degree() const
{
return degree;
}
/** return what type of kernel we are
*
* @return kernel type
*/
virtual EKernelType get_kernel_type() { return K_SPECTRUMRBF; }
/** return the kernel's name
*
* @return name
*/
virtual const char* get_name() const { return "SpectrumRBFKernel"; }
/** set degree
*
* @param deg new degree
* @return if setting was successful
*/
inline bool set_degree(int32_t deg) { degree=deg; return true; }
/** get degree
*
* @return degree
*/
inline int32_t get_degree() { return degree; }
/** set AA matrix
* @param AA_matrix_
*/
bool set_AA_matrix(float64_t* AA_matrix_);
protected:
/** AA helper
* @param path
* @param degree
* @param joint_seq
* @param index
*/
float64_t AA_helper(const char* path, const int degree, const char* joint_seq, unsigned int index);
/** read profiles and sequences */
void read_profiles_and_sequences();
/** 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
*/
float64_t compute(int32_t idx_a, int32_t idx_b);
/** register the parameters */
virtual void register_param();
/** register the alphabet */
void register_alphabet();
protected:
/** alphabet of features */
CAlphabet* alphabet;
/** degree */
int32_t degree;
/** maximum mismatch */
int32_t max_mismatch;
/** 128x128 scalar product matrix */
SGMatrix<float64_t> AA_matrix ;
/** width of Gaussian*/
float64_t width;
//int32_t* aa_to_index; // profile
//double background[20]; // profile
/** profiles */
std::vector< std::vector<float64_t> > profiles; //profile
/** sequence labels */
std::vector<std::string> sequence_labels; // profile
/** sequences */
SGString<char>* sequences; // profile
/** string features */
CStringFeatures<char>* string_features;
/** nof sequences */
int32_t nof_sequences;
/** max sequence length */
int32_t max_sequence_length;
/** if kernel is initialized */
bool initialized;
/** kernel matrix */
CDynamicArray<float64_t> kernel_matrix; // 2d
/** target letter 0 */
int32_t target_letter_0;
private:
void init();
};
}
#endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */
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