SHOGUN v0.9.0
|
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 #include <string> 00024 00025 namespace shogun 00026 { 00027 00028 struct joint_list_struct 00029 { 00030 unsigned int ex_index ; 00031 unsigned int index ; 00032 unsigned int mismatch ; 00033 } ; 00034 00035 class CSpectrumMismatchRBFKernel: public CStringKernel<char> 00036 { 00037 public: 00039 CSpectrumMismatchRBFKernel(void); 00040 00046 CSpectrumMismatchRBFKernel(int32_t size, float64_t* AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width); 00047 00054 CSpectrumMismatchRBFKernel( 00055 CStringFeatures<char>* l, CStringFeatures<char>* r, int32_t size, float64_t* AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width); 00056 00057 virtual ~CSpectrumMismatchRBFKernel(); 00058 00065 virtual bool init(CFeatures* l, CFeatures* r); 00066 00068 virtual void cleanup(); 00069 00074 int32_t get_degree() const 00075 { 00076 return degree; 00077 } 00078 00083 int32_t get_max_mismatch() const 00084 { 00085 return max_mismatch; 00086 } 00087 00092 virtual EKernelType get_kernel_type() { return K_SPECTRUMMISMATCHRBF; } 00093 00098 virtual const char* get_name() const { return "SpectrumMismatchRBF"; } 00099 00105 bool set_max_mismatch(int32_t max); 00106 00111 inline int32_t get_max_mismatch() { return max_mismatch; } 00112 00118 inline bool set_degree(int32_t deg) { degree=deg; return true; } 00119 00124 inline int32_t get_degree() { return degree; } 00125 00126 00127 bool set_AA_matrix(float64_t* AA_matrix_=NULL, int32_t nr=128, int32_t nc=128); 00128 00129 protected: 00130 00131 float64_t AA_helper(std::string &path, const char* joint_seq, unsigned int index) ; 00132 float64_t compute_helper(const char* joint_seq, 00133 std::vector<unsigned int> joint_index, std::vector<unsigned int> joint_mismatch, 00134 std::string path, unsigned int d, 00135 const int & alen) ; 00136 00137 00138 void compute_helper_all(const char* joint_seq, 00139 std::vector<struct joint_list_struct> & joint_list, 00140 std::string path, unsigned int d) ; 00141 void compute_all() ; 00142 00143 00152 float64_t compute(int32_t idx_a, int32_t idx_b); 00153 00155 virtual void remove_lhs(); 00156 00157 00158 protected: 00160 CAlphabet* alphabet; 00162 int32_t degree; 00164 int32_t max_mismatch; 00166 float64_t* AA_matrix; 00168 float64_t width; 00169 00171 bool initialized; 00172 00173 00174 CArray2<float64_t> kernel_matrix ; 00175 int32_t target_letter_0 ; 00176 }; 00177 00178 } 00179 00180 #endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */