SalzbergWordKernel.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 _SALZBERGWORDKERNEL_H___
00012 #define _SALZBERGWORDKERNEL_H___
00013 
00014 #include "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 #include "classifier/PluginEstimate.h"
00017 #include "features/StringFeatures.h"
00018 
00020 class CSalzbergWordKernel: public CStringKernel<WORD>
00021 {
00022     public:
00028         CSalzbergWordKernel(INT size, CPluginEstimate* pie);
00029 
00036         CSalzbergWordKernel(
00037             CStringFeatures<WORD>* l, CStringFeatures<WORD>* r,
00038             CPluginEstimate *pie);
00039 
00040         virtual ~CSalzbergWordKernel();
00041 
00047         void set_prior_probs(DREAL pos_prior_, DREAL neg_prior_)
00048         {
00049             pos_prior=pos_prior_ ;
00050             neg_prior=neg_prior_ ;
00051             if (fabs(pos_prior+neg_prior-1)>1e-6)
00052                 SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
00053         };
00054 
00061         virtual bool init(CFeatures* l, CFeatures* r);
00062 
00064         virtual void cleanup();
00065 
00071         bool load_init(FILE* src);
00072 
00078         bool save_init(FILE* dest);
00079 
00084         virtual EKernelType get_kernel_type() { return K_SALZBERG; }
00085 
00090         virtual const CHAR* get_name() { return "Salzberg" ; }
00091 
00092     protected:
00101         DREAL compute(INT idx_a, INT idx_b);
00102         //  DREAL compute_slow(LONG idx_a, LONG idx_b);
00103 
00110         inline INT compute_index(INT position, WORD symbol)
00111         {
00112             return position*num_symbols+symbol;
00113         }
00114 
00115     protected:
00117         CPluginEstimate* estimate;
00118 
00120         DREAL* mean;
00122         DREAL* variance;
00123 
00125         DREAL* sqrtdiag_lhs;
00127         DREAL* sqrtdiag_rhs;
00128 
00130         DREAL* ld_mean_lhs;
00132         DREAL* ld_mean_rhs;
00133 
00135         INT num_params;
00137         INT num_symbols;
00139         DREAL sum_m2_s2;
00141         DREAL pos_prior;
00143         DREAL neg_prior;
00145         bool initialized;
00146 };
00147 
00148 #endif /* _SALZBERGWORDKERNEL_H__ */

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