PLearn 0.1
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00001 // -*- C++ -*- 00002 00003 // ScoreLayerVariable.h 00004 // 00005 // Copyright (C) 2006 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 // Authors: Olivier Delalleau 00036 00040 #ifndef ScoreLayerVariable_INC 00041 #define ScoreLayerVariable_INC 00042 00043 #include "ChemicalICP.h" 00044 #include "Molecule.h" 00045 #include "RunICPVariable.h" 00046 #include <plearn/math/PRandom.h> 00047 #include <plearn/var/NaryVariable.h> 00048 00049 namespace PLearn { 00050 using namespace std; 00051 00064 class ScoreLayerVariable : public NaryVariable 00065 { 00066 typedef NaryVariable inherited; 00067 00068 public: 00069 00071 PP<RunICPVariable> run_icp_var; 00072 00073 //##### Public Build Options ############################################ 00074 00077 00078 PP<ChemicalICP> icp_aligner_template; 00079 int n_active_templates; 00080 int n_inactive_templates; 00081 bool normalize_by_n_features; 00082 int32_t seed_; 00083 bool simple_mixture; 00084 VMat templates_source; 00085 00086 public: 00087 00088 //##### Public Member Functions ######################################### 00089 00091 ScoreLayerVariable(); 00092 00095 PP<MoleculeTemplate> getMoleculeTemplate(real molecule_id, 00096 real activity = -1); 00097 00102 PP<Molecule> getMolecule(real molecule_id); 00103 00105 void setMappingsSource(const VMat& source_vmat); 00106 00108 void setScalingCoefficient(int i, real coeff); 00109 00110 //##### PLearn::Variable methods ######################################### 00111 virtual void recomputeSize(int& l, int& w) const; 00112 virtual void fprop(); 00113 virtual void bprop(); 00114 00115 // ### These ones are not always implemented 00116 // virtual void bbprop(); 00117 // virtual void symbolicBprop(); 00118 // virtual void rfprop(); 00119 00120 //##### PLearn::Object Protocol ######################################### 00121 00122 // Declares other standard object methods. 00123 PLEARN_DECLARE_OBJECT(ScoreLayerVariable); 00124 00125 // Simply calls inherited::build() then build_() 00126 virtual void build(); 00127 00129 virtual void makeDeepCopyFromShallowCopy(CopiesMap& copies); 00130 00131 protected: 00132 00134 VMat mappings_source; 00135 00137 PP<PRandom> random_gen; 00138 00142 VarArray outputs; 00143 00146 Var final_output; 00147 00149 hash_map< string, PP<MoleculeTemplate> > molecule_templates; 00150 00152 hash_map< string, PP<Molecule> > molecules; 00153 00155 int n_active_in_source; 00156 00158 int n_inactive_in_source; 00159 00167 VarArray scaling_coeffs; 00168 00169 //##### Protected Options ############################################### 00170 00171 protected: 00172 //##### Protected Member Functions ###################################### 00173 00177 int getNActiveTemplates(); 00178 00182 int getNInactiveTemplates(); 00183 00185 // (PLEASE IMPLEMENT IN .cc) 00186 static void declareOptions(OptionList& ol); 00187 00188 private: 00189 //##### Private Member Functions ######################################## 00190 00192 // (PLEASE IMPLEMENT IN .cc) 00193 void build_(); 00194 00195 private: 00196 //##### Private Data Members ############################################ 00197 00198 // The rest of the private stuff goes here 00199 }; 00200 00201 // Declares a few other classes and functions related to this class 00202 DECLARE_OBJECT_PTR(ScoreLayerVariable); 00203 00204 // ### Put here a convenient method for building your variable from other 00205 // ### existing ones, or a VarArray. 00206 // ### e.g., if your class is TotoVariable, with two parameters foo_type foo 00207 // ### and bar_type bar, you could write, depending on your constructor: 00208 // inline Var toto(Var v1, Var v2, Var v3, 00209 // foo_type foo=default_foo, bar_type bar=default_bar) 00210 // { return new TotoVariable(v1, v2, v3, foo, bar); } 00211 // ### or: 00212 // inline Var toto(Var v1, Var v2, v3 00213 // foo_type foo=default_foo, bar_type bar=default_bar) 00214 // { return new TotoVariable(v1 & v2 & v3, foo, bar); } 00215 // ### or: 00216 // inline Var toto(const VarArray& varray, foo_type foo=default_foo, 00217 // bar_type bar=default_bar) 00218 // { return new TotoVariable( varray, foo, bar); } 00219 00220 } // end of namespace PLearn 00221 00222 #endif 00223 00224 00225 /* 00226 Local Variables: 00227 mode:c++ 00228 c-basic-offset:4 00229 c-file-style:"stroustrup" 00230 c-file-offsets:((innamespace . 0)(inline-open . 0)) 00231 indent-tabs-mode:nil 00232 fill-column:79 00233 End: 00234 */ 00235 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :