SalzbergWordStringKernel.h

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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) 1999-2008 Gunnar Raetsch
00008  * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
00009  */
00010 
00011 #ifndef _SALZBERGWORDSTRINGKERNEL_H___
00012 #define _SALZBERGWORDSTRINGKERNEL_H___
00013 
00014 #include <shogun/lib/common.h>
00015 #include <shogun/kernel/StringKernel.h>
00016 #include <shogun/classifier/PluginEstimate.h>
00017 #include <shogun/features/StringFeatures.h>
00018 
00019 namespace shogun
00020 {
00029 class CSalzbergWordStringKernel: public CStringKernel<uint16_t>
00030 {
00031     public:
00033         CSalzbergWordStringKernel();
00034 
00041         CSalzbergWordStringKernel(int32_t size, CPluginEstimate* pie, CLabels* labels=NULL);
00042 
00050         CSalzbergWordStringKernel(
00051             CStringFeatures<uint16_t>* l, CStringFeatures<uint16_t>* r,
00052             CPluginEstimate *pie, CLabels* labels=NULL);
00053 
00054         virtual ~CSalzbergWordStringKernel();
00055 
00061         void set_prior_probs(float64_t pos_prior_, float64_t neg_prior_)
00062         {
00063             pos_prior=pos_prior_ ;
00064             neg_prior=neg_prior_ ;
00065             if (fabs(pos_prior+neg_prior-1)>1e-6)
00066                 SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
00067         };
00068 
00073         void set_prior_probs_from_labels(CLabels* labels);
00074 
00081         virtual bool init(CFeatures* l, CFeatures* r);
00082 
00084         virtual void cleanup();
00085 
00090         virtual EKernelType get_kernel_type() { return K_SALZBERG; }
00091 
00096         virtual const char* get_name() const { return "SalzbergWordStringKernel" ; }
00097 
00098     protected:
00107         float64_t compute(int32_t idx_a, int32_t idx_b);
00108         //  float64_t compute_slow(int64_t idx_a, int64_t idx_b);
00109 
00116         inline int32_t compute_index(int32_t position, uint16_t symbol)
00117         {
00118             return position*num_symbols+symbol;
00119         }
00120     private:
00121         void init();
00122 
00123     protected:
00125         CPluginEstimate* estimate;
00126 
00128         float64_t* mean;
00130         float64_t* variance;
00131 
00133         float64_t* sqrtdiag_lhs;
00135         float64_t* sqrtdiag_rhs;
00136 
00138         float64_t* ld_mean_lhs;
00140         float64_t* ld_mean_rhs;
00141 
00143         int32_t num_params;
00145         int32_t num_symbols;
00147         float64_t sum_m2_s2;
00149         float64_t pos_prior;
00151         float64_t neg_prior;
00153         bool initialized;
00154 };
00155 }
00156 #endif /* _SALZBERGWORDKERNEL_H__ */
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