SpectrumMismatchRBFKernel.h

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00001 /*
00002  * This program is free software; you can redistribute it and/or modify
00003  * it under the terms of the GNU General Public License as published by
00004  * the Free Software Foundation; either version 3 of the License, or
00005  * (at your option) any later version.
00006  *
00007  * Written (W) 1999-2009 Soeren Sonnenburg
00008  * Written (W) 1999-2008 Gunnar Raetsch
00009  * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
00010  */
00011 
00012 #ifndef _SPECTRUMMISMATCHRBFKERNEL_H___
00013 #define _SPECTRUMMISMATCHRBFKERNEL_H___
00014 
00015 #include "lib/common.h"
00016 #include "lib/Trie.h"
00017 #include "kernel/StringKernel.h"
00018 #include "features/StringFeatures.h"
00019 
00020 
00021 #include "lib/Array.h"
00022 #include "lib/Array2.h"
00023 
00024 namespace shogun
00025 {
00026 
00027 struct joint_list_struct
00028 {
00029     unsigned int ex_index ;
00030     unsigned int index ;
00031     unsigned int mismatch ;
00032 } ;
00033 
00034 class CSpectrumMismatchRBFKernel: public CStringKernel<char>
00035 {
00036     public:
00037 
00043         CSpectrumMismatchRBFKernel(int32_t size, float64_t* AA_matrix, int32_t degree, int32_t max_mismatch, float64_t width);
00044 
00051         CSpectrumMismatchRBFKernel(
00052             CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix, int32_t degree, int32_t max_mismatch, float64_t width);
00053 
00054         virtual ~CSpectrumMismatchRBFKernel();
00055 
00062         virtual bool init(CFeatures* l, CFeatures* r);
00063 
00065         virtual void cleanup();
00066 
00071         int32_t get_degree() const
00072         {
00073             return degree;
00074         }
00075 
00080         int32_t get_max_mismatch() const
00081         {
00082             return max_mismatch;
00083         }
00084 
00089         virtual EKernelType get_kernel_type() { return K_SPECTRUMMISMATCHRBF; }
00090 
00095         virtual const char* get_name() const { return "SpectrumMismatchRBF"; }
00096 
00102         bool set_max_mismatch(int32_t max);
00103 
00108         inline int32_t get_max_mismatch() { return max_mismatch; }
00109 
00115         inline bool set_degree(int32_t deg) { degree=deg; return true; }
00116 
00121         inline int32_t get_degree() { return degree; }
00122 
00123 
00124         bool set_AA_matrix(float64_t* AA_matrix_);
00125 
00126     protected:
00127 
00128         float64_t AA_helper(std::string &path, const char* joint_seq, unsigned int index) ;
00129         float64_t compute_helper(const char* joint_seq, 
00130                                  std::vector<unsigned int> joint_index, std::vector<unsigned int> joint_mismatch, 
00131                                  std::string path, unsigned int d, 
00132                                  const int & alen) ;
00133 
00134         
00135         void compute_helper_all(const char* joint_seq, 
00136                                 std::vector<struct joint_list_struct> & joint_list,
00137                                 std::string path, unsigned int d)  ;
00138         void compute_all() ;
00139         
00140 
00149         float64_t compute(int32_t idx_a, int32_t idx_b);
00150 
00152         virtual void remove_lhs();
00153 
00154 
00155     protected:
00157         CAlphabet* alphabet;
00159         int32_t degree;
00161         int32_t max_mismatch;
00163         double* AA_matrix ; 
00165         double width;
00166 
00168         bool initialized;
00169 
00170 
00171         CArray2<float64_t> kernel_matrix ;
00172         int target_letter_0 ;
00173 };
00174 
00175 }
00176 
00177 
00178 
00179 #endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */
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