PLearn 0.1
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00001 // -*- C++ -*- 00002 00003 // BinaryKernelDiscrimination.cc 00004 // 00005 // Copyright (C) 2006 Pierre-Jean L Heureux 00006 // 00007 // Redistribution and use in source and binary forms, with or without 00008 // modification, are permitted provided that the following conditions are met: 00009 // 00010 // 1. Redistributions of source code must retain the above copyright 00011 // notice, this list of conditions and the following disclaimer. 00012 // 00013 // 2. Redistributions in binary form must reproduce the above copyright 00014 // notice, this list of conditions and the following disclaimer in the 00015 // documentation and/or other materials provided with the distribution. 00016 // 00017 // 3. The name of the authors may not be used to endorse or promote 00018 // products derived from this software without specific prior written 00019 // permission. 00020 // 00021 // THIS SOFTWARE IS PROVIDED BY THE AUTHORS ``AS IS'' AND ANY EXPRESS OR 00022 // IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 00023 // OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN 00024 // NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 00025 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED 00026 // TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 00027 // PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 00028 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 00029 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 00030 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 00031 // 00032 // This file is part of the PLearn library. For more information on the PLearn 00033 // library, go to the PLearn Web site at www.plearn.org 00034 00035 /* ******************************************************* 00036 * $Id: .pyskeleton_header 544 2003-09-01 00:05:31Z plearner $ 00037 ******************************************************* */ 00038 00039 // Authors: Pierre-Jean L Heureux 00040 00044 #include "BinaryKernelDiscrimination.h" 00045 00046 namespace PLearn { 00047 using namespace std; 00048 00049 PLEARN_IMPLEMENT_OBJECT( 00050 BinaryKernelDiscrimination, 00051 "Kernel suitable for a binary vector input", 00052 "Based on Harper,et al. J.Chem.Inf.Comput.Sci. 2001,41,p.1295. \nHELP" 00053 ); 00054 00056 // BinaryKernelDiscrimination // 00058 BinaryKernelDiscrimination::BinaryKernelDiscrimination() : 00059 /* ### Initialize all fields to their default value here */ 00060 K(1), 00061 ExpOutput(false) 00062 { 00063 // ... 00064 00065 // ### You may (or not) want to call build_() to finish building the object 00066 // ### (doing so assumes the parent classes' build_() have been called too 00067 // ### in the parent classes' constructors, something that you must ensure) 00068 } 00069 00071 // declareOptions // 00073 void BinaryKernelDiscrimination::declareOptions(OptionList& ol) 00074 { 00075 // ### Declare all of this object's options here 00076 // ### For the "flags" of each option, you should typically specify 00077 // ### one of OptionBase::buildoption, OptionBase::learntoption or 00078 // ### OptionBase::tuningoption. Another possible flag to be combined with 00079 // ### is OptionBase::nosave 00080 00081 // ### ex: 00082 declareOption(ol, "lambda", &BinaryKernelDiscrimination::lambda, OptionBase::buildoption, 00083 "The base of the kernel"); 00084 declareOption(ol, "K", &BinaryKernelDiscrimination::K, OptionBase::buildoption, 00085 "a constant"); 00086 declareOption(ol, "ExpOutput", &BinaryKernelDiscrimination::ExpOutput, OptionBase::buildoption, 00087 "Flag to 1 if you do not want the log of the output. The exponential form will be outputted instead"); 00088 00089 // Now call the parent class' declareOptions 00090 inherited::declareOptions(ol); 00091 } 00092 00094 // build // 00096 void BinaryKernelDiscrimination::build() 00097 { 00098 // ### Nothing to add here, simply calls build_ 00099 inherited::build(); 00100 build_(); 00101 } 00102 00104 // build_ // 00106 void BinaryKernelDiscrimination::build_() 00107 { 00108 // ### This method should do the real building of the object, 00109 // ### according to set 'options', in *any* situation. 00110 // ### Typical situations include: 00111 // ### - Initial building of an object from a few user-specified options 00112 // ### - Building of a "reloaded" object: i.e. from the complete set of all serialised options. 00113 // ### - Updating or "re-building" of an object after a few "tuning" options have been modified. 00114 // ### You should assume that the parent class' build_() has already been called. 00115 } 00116 00118 // evaluate // 00120 real BinaryKernelDiscrimination::evaluate(const Vec& x1, const Vec& x2) const { 00121 // ### Evaluate the kernel on a pair of points. 00122 int i; 00123 00124 if (x1.length() != x2.length()){PLERROR("Vector not of same length");} 00125 int N= x1.length(); 00126 int dij = 0; 00127 00128 for (i=0; i < x1.length();i++) 00129 { 00130 if (x1[i] != x2[i]){dij++;}; 00131 } 00132 if (ExpOutput) 00133 return pow(lambda,(K-((K*dij)/N)))*pow(1-lambda,K*dij/N); 00134 else 00135 return safeflog(pow(lambda,(K-((K*dij)/N)))*pow(1-lambda,K*dij/N)); 00136 } 00137 00138 /* ### This method will very often be overridden. 00140 // evaluate_i_j // 00142 real BinaryKernelDiscrimination::evaluate_i_j(int i, int j) const { 00143 // ### Evaluate the kernel on a pair of training points. 00144 } 00145 */ 00146 00148 // makeDeepCopyFromShallowCopy // 00150 void BinaryKernelDiscrimination::makeDeepCopyFromShallowCopy(CopiesMap& copies) 00151 { 00152 inherited::makeDeepCopyFromShallowCopy(copies); 00153 00154 // ### Call deepCopyField on all "pointer-like" fields 00155 // ### that you wish to be deepCopied rather than 00156 // ### shallow-copied. 00157 // ### ex: 00158 // deepCopyField(trainvec, copies); 00159 00160 // ### Remove this line when you have fully implemented this method. 00161 PLERROR("BinaryKernelDiscrimination::makeDeepCopyFromShallowCopy not fully (correctly) implemented yet!"); 00162 } 00163 00164 /* ### This method will be overridden if computations need to be done, 00165 ### or to forward the call to another object. 00166 ### In this case, be careful that it may be called BEFORE the build_() 00167 ### method has been called, if the 'specify_dataset' option is used. 00169 // setDataForKernelMatrix // 00171 void BinaryKernelDiscrimination::setDataForKernelMatrix(VMat the_data) { 00172 } 00173 */ 00174 00175 } // end of namespace PLearn 00176 00177 00178 /* 00179 Local Variables: 00180 mode:c++ 00181 c-basic-offset:4 00182 c-file-style:"stroustrup" 00183 c-file-offsets:((innamespace . 0)(inline-open . 0)) 00184 indent-tabs-mode:nil 00185 fill-column:79 00186 End: 00187 */ 00188 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :