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) 1999-2008 Fraunhofer Institute FIRST and Max-Planck-Society
00009  */
00010 
00011 #ifndef _SALZBERGWORDSTRINGKERNEL_H___
00012 #define _SALZBERGWORDSTRINGKERNEL_H___
00013 
00014 #include "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 #include "classifier/PluginEstimate.h"
00017 #include "features/StringFeatures.h"
00018 
00025 class CSalzbergWordStringKernel: public CStringKernel<uint16_t>
00026 {
00027     public:
00034         CSalzbergWordStringKernel(int32_t size, CPluginEstimate* pie, CLabels* labels=NULL);
00035 
00043         CSalzbergWordStringKernel(
00044             CStringFeatures<uint16_t>* l, CStringFeatures<uint16_t>* r,
00045             CPluginEstimate *pie, CLabels* labels=NULL);
00046 
00047         virtual ~CSalzbergWordStringKernel();
00048 
00054         void set_prior_probs(float64_t pos_prior_, float64_t neg_prior_)
00055         {
00056             pos_prior=pos_prior_ ;
00057             neg_prior=neg_prior_ ;
00058             if (fabs(pos_prior+neg_prior-1)>1e-6)
00059                 SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
00060         };
00061 
00066         void set_prior_probs_from_labels(CLabels* labels);
00067 
00074         virtual bool init(CFeatures* l, CFeatures* r);
00075 
00077         virtual void cleanup();
00078 
00084         bool load_init(FILE* src);
00085 
00091         bool save_init(FILE* dest);
00092 
00097         virtual EKernelType get_kernel_type() { return K_SALZBERG; }
00098 
00103         virtual const char* get_name() { return "Salzberg" ; }
00104 
00105     protected:
00114         float64_t compute(int32_t idx_a, int32_t idx_b);
00115         //  float64_t compute_slow(int64_t idx_a, int64_t idx_b);
00116 
00123         inline int32_t compute_index(int32_t position, uint16_t symbol)
00124         {
00125             return position*num_symbols+symbol;
00126         }
00127 
00128     protected:
00130         CPluginEstimate* estimate;
00131 
00133         float64_t* mean;
00135         float64_t* variance;
00136 
00138         float64_t* sqrtdiag_lhs;
00140         float64_t* sqrtdiag_rhs;
00141 
00143         float64_t* ld_mean_lhs;
00145         float64_t* ld_mean_rhs;
00146 
00148         int32_t num_params;
00150         int32_t num_symbols;
00152         float64_t sum_m2_s2;
00154         float64_t pos_prior;
00156         float64_t neg_prior;
00158         bool initialized;
00159 };
00160 
00161 #endif /* _SALZBERGWORDKERNEL_H__ */

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