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 "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 #include "classifier/PluginEstimate.h"
00017 #include "features/StringFeatures.h"
00018 
00027 class CSalzbergWordStringKernel: public CStringKernel<uint16_t>
00028 {
00029     public:
00036         CSalzbergWordStringKernel(int32_t size, CPluginEstimate* pie, CLabels* labels=NULL);
00037 
00045         CSalzbergWordStringKernel(
00046             CStringFeatures<uint16_t>* l, CStringFeatures<uint16_t>* r,
00047             CPluginEstimate *pie, CLabels* labels=NULL);
00048 
00049         virtual ~CSalzbergWordStringKernel();
00050 
00056         void set_prior_probs(float64_t pos_prior_, float64_t neg_prior_)
00057         {
00058             pos_prior=pos_prior_ ;
00059             neg_prior=neg_prior_ ;
00060             if (fabs(pos_prior+neg_prior-1)>1e-6)
00061                 SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
00062         };
00063 
00068         void set_prior_probs_from_labels(CLabels* labels);
00069 
00076         virtual bool init(CFeatures* l, CFeatures* r);
00077 
00079         virtual void cleanup();
00080 
00086         bool load_init(FILE* src);
00087 
00093         bool save_init(FILE* dest);
00094 
00099         virtual EKernelType get_kernel_type() { return K_SALZBERG; }
00100 
00105         virtual const char* get_name() const { return "Salzberg" ; }
00106 
00107     protected:
00116         float64_t compute(int32_t idx_a, int32_t idx_b);
00117         //  float64_t compute_slow(int64_t idx_a, int64_t idx_b);
00118 
00125         inline int32_t compute_index(int32_t position, uint16_t symbol)
00126         {
00127             return position*num_symbols+symbol;
00128         }
00129 
00130     protected:
00132         CPluginEstimate* estimate;
00133 
00135         float64_t* mean;
00137         float64_t* variance;
00138 
00140         float64_t* sqrtdiag_lhs;
00142         float64_t* sqrtdiag_rhs;
00143 
00145         float64_t* ld_mean_lhs;
00147         float64_t* ld_mean_rhs;
00148 
00150         int32_t num_params;
00152         int32_t num_symbols;
00154         float64_t sum_m2_s2;
00156         float64_t pos_prior;
00158         float64_t neg_prior;
00160         bool initialized;
00161 };
00162 
00163 #endif /* _SALZBERGWORDKERNEL_H__ */

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