PLearn 0.1
KernelPCA.cc
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00001 // -*- C++ -*-
00002 
00003 // KernelPCA.cc
00004 //
00005 // Copyright (C) 2004 Olivier Delalleau 
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: KernelPCA.cc 3994 2005-08-25 13:35:03Z chapados $ 
00037  ******************************************************* */
00038 
00039 // Authors: Olivier Delalleau
00040 
00043 #include <plearn/ker/AdditiveNormalizationKernel.h>
00044 #include "KernelPCA.h"
00045 
00046 namespace PLearn {
00047 using namespace std;
00048 
00050 // KernelPCA //
00052 KernelPCA::KernelPCA() 
00053     : kernel_is_distance(false),
00054       remove_bias(false),
00055       remove_bias_in_evaluate(false)
00056 {
00057     // Usually, one will want only positive eigenvalues.
00058     min_eigenvalue = 0;
00059 }
00060 
00061 PLEARN_IMPLEMENT_OBJECT(KernelPCA,
00062                         "Kernel Principal Component Analysis",
00063                         "Perform PCA in a feature space phi(x), defined by a kernel K such that\n"
00064                         " K(x,y) = < phi(x), phi(y) >\n"
00065     );
00066 
00068 // declareOptions //
00070 void KernelPCA::declareOptions(OptionList& ol)
00071 {
00072     declareOption(ol, "kernel_is_distance", &KernelPCA::kernel_is_distance, OptionBase::buildoption,
00073                   "If set to 1, then the kernel will be considered as a squared distance instead of\n"
00074                   "a dot product (i.e. the double-centering formula will be applied).");
00075 
00076     declareOption(ol, "remove_bias", &KernelPCA::remove_bias, OptionBase::buildoption,
00077                   "If set to 1, the (additively) normalized kernel will not take into account terms\n"
00078                   "of the form K(x_i,x_i), in order to remove bias induced by those terms.");
00079 
00080     declareOption(ol, "remove_bias_in_evaluate", &KernelPCA::remove_bias_in_evaluate, OptionBase::buildoption,
00081                   "If set to 1, the (additively) normalized kernel will not take into account terms\n"
00082                   "of the form K(x_i,x_i), but only when evaluated on test points.");
00083 
00084     // Now call the parent class' declareOptions
00085     inherited::declareOptions(ol);
00086 
00087     // Redirect the 'kernel' option toward kpca_kernel.
00088     redeclareOption(ol, "kernel", &KernelPCA::kpca_kernel, OptionBase::buildoption,
00089                     "The kernel used to (implicitly) project the data in feature space.");
00090   
00091     redeclareOption(ol, "ignore_n_first", &KernelPCA::ignore_n_first, OptionBase::nosave,
00092                     "In KernelPCA, no eigenvector is ignored.");
00093 
00094     // And declare the normalized kernel so that it can be saved.
00095     declareOption(ol, "normalized_kernel", &KernelProjection::kernel, OptionBase::learntoption,
00096                   "The normalized kernel.");
00097 
00098 }
00099 
00101 // build //
00103 void KernelPCA::build()
00104 {
00105     inherited::build();
00106     build_();
00107 }
00108 
00110 // build_ //
00112 void KernelPCA::build_()
00113 {
00114     // Obtain the "real" kernel by additive normalization of 'kpca_kernel'.
00115     // We have to do this iff:
00116     // 1. A 'kpca_kernel' is provided, and
00117     // 2. either:
00118     //    2.a. the 'kernel' option is not set, or
00119     //    2.b. the 'kernel' option is not an AdditiveNormalization acting on 'kpca_kernel'.
00120     // This is to ensure that a loaded 'kernel' won't be overwritten.
00121     if (kpca_kernel &&
00122         (!kernel ||
00123          (dynamic_cast<AdditiveNormalizationKernel*>((Kernel*) kernel))->source_kernel != kpca_kernel)) {
00124         this->kernel = new AdditiveNormalizationKernel
00125             (kpca_kernel, remove_bias, remove_bias_in_evaluate, kernel_is_distance);
00126     }
00127 }
00128 
00130 // forget //
00132 void KernelPCA::forget()
00133 {
00134     inherited::forget();
00135 }
00136     
00138 // makeDeepCopyFromShallowCopy //
00140 void KernelPCA::makeDeepCopyFromShallowCopy(CopiesMap& copies)
00141 {
00142     inherited::makeDeepCopyFromShallowCopy(copies);
00143     deepCopyField(kpca_kernel, copies);
00144 }
00145 
00146 } // end of namespace PLearn
00147 
00148 
00149 /*
00150   Local Variables:
00151   mode:c++
00152   c-basic-offset:4
00153   c-file-style:"stroustrup"
00154   c-file-offsets:((innamespace . 0)(inline-open . 0))
00155   indent-tabs-mode:nil
00156   fill-column:79
00157   End:
00158 */
00159 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :
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