BALL
1.4.1
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00001 /* kernel.h 00002 * 00003 * Copyright (C) 2009 Marcel Schumann 00004 * 00005 * This file is part of QuEasy -- A Toolbox for Automated QSAR Model 00006 * Construction and Validation. 00007 * QuEasy is free software; you can redistribute it and/or modify 00008 * it under the terms of the GNU General Public License as published by 00009 * the Free Software Foundation; either version 3 of the License, or (at 00010 * your option) any later version. 00011 * 00012 * QuEasy is distributed in the hope that it will be useful, but 00013 * WITHOUT ANY WARRANTY; without even the implied warranty of 00014 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 00015 * General Public License for more details. 00016 * 00017 * You should have received a copy of the GNU General Public License 00018 * along with this program; if not, see <http://www.gnu.org/licenses/>. 00019 */ 00020 00021 // -*- Mode: C++; tab-width: 2; -*- 00022 // vi: set ts=2: 00023 // 00024 // 00025 00026 #ifndef KERNEL 00027 #define KERNEL 00028 00029 #ifndef LMODEL 00030 #include <BALL/QSAR/linearModel.h> 00031 #endif 00032 00033 #ifndef MODEL 00034 #include <BALL/QSAR/Model.h> 00035 #endif 00036 00037 #ifndef QSAR_EXCEPTION 00038 #include <BALL/QSAR/exception.h> 00039 #endif 00040 00041 #ifndef REGRESSION 00042 #include <BALL/QSAR/regressionModel.h> 00043 #endif 00044 00045 #include <cmath> 00046 #include <sstream> 00047 00048 00049 namespace BALL 00050 { 00051 namespace QSAR 00052 { 00053 class BALL_EXPORT Kernel 00054 { 00055 00056 00057 public: 00061 Kernel(Model* m, int k_type, double p1, double p2=-1); 00062 00063 Kernel(Model* m, String f, String g); 00064 00065 Kernel(Model* m, Vector<double>& w); 00066 00069 Kernel(Model* m, const LinearModel& lm, int column); 00070 00071 ~Kernel(); 00073 00074 00082 void calculateKernelMatrix(Matrix<double>& input, Matrix<double>& output); 00083 00088 void calculateKernelMatrix(Matrix<double>& K, Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00089 00090 00092 void calculateKernelVector(Matrix<double>& K,Vector<double>& m1, Matrix<double>& m2, Vector<double>& output); 00093 00100 void gridSearch(double step_width, int steps, int recursions, int k, bool opt=0); 00102 00103 00113 int type; 00114 00116 double par1, par2; 00117 00121 String equation1; 00122 00126 String equation2; 00128 00129 00130 protected: 00134 00135 void gridSearch(double step_width, int steps, bool first_rec, int k, double par1_start, double par2_start, bool opt); 00136 00139 void calculateWeightedKernelMatrix(Matrix<double>& input, Matrix<double>& output); 00140 00141 00144 void calculateWeightedKernelMatrix(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00145 00146 00147 void calculateKernelMatrix1(Matrix<double>& input, Matrix<double>& output); 00148 00149 void calculateKernelMatrix2(Matrix<double>& input, Matrix<double>& output); 00150 00151 void calculateKernelMatrix3(Matrix<double>& input, Matrix<double>& output); 00152 00153 void calculateKernelMatrix4(Matrix<double>& input, Matrix<double>& output); 00154 00155 00156 void calculateKernelMatrix1(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00157 00158 void calculateKernelMatrix2(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00159 00160 void calculateKernelMatrix3(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00161 00162 void calculateKernelMatrix4(Matrix<double>& m1, Matrix<double>& m2, Matrix<double>& output); 00164 00165 00170 Model* model_; 00171 00172 Vector<double> weights_; 00174 00175 00176 friend class FeatureSelection; 00177 00178 }; 00179 } 00180 } 00181 00182 #endif // KERNEL