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 
00019 namespace shogun
00020 {
00029 class CSalzbergWordStringKernel: public CStringKernel<uint16_t>
00030 {
00031     public:
00038         CSalzbergWordStringKernel(int32_t size, CPluginEstimate* pie, CLabels* labels=NULL);
00039 
00047         CSalzbergWordStringKernel(
00048             CStringFeatures<uint16_t>* l, CStringFeatures<uint16_t>* r,
00049             CPluginEstimate *pie, CLabels* labels=NULL);
00050 
00051         virtual ~CSalzbergWordStringKernel();
00052 
00058         void set_prior_probs(float64_t pos_prior_, float64_t neg_prior_)
00059         {
00060             pos_prior=pos_prior_ ;
00061             neg_prior=neg_prior_ ;
00062             if (fabs(pos_prior+neg_prior-1)>1e-6)
00063                 SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
00064         };
00065 
00070         void set_prior_probs_from_labels(CLabels* labels);
00071 
00078         virtual bool init(CFeatures* l, CFeatures* r);
00079 
00081         virtual void cleanup();
00082 
00087         virtual EKernelType get_kernel_type() { return K_SALZBERG; }
00088 
00093         virtual const char* get_name() const { return "Salzberg" ; }
00094 
00095     protected:
00104         float64_t compute(int32_t idx_a, int32_t idx_b);
00105         //  float64_t compute_slow(int64_t idx_a, int64_t idx_b);
00106 
00113         inline int32_t compute_index(int32_t position, uint16_t symbol)
00114         {
00115             return position*num_symbols+symbol;
00116         }
00117 
00118     protected:
00120         CPluginEstimate* estimate;
00121 
00123         float64_t* mean;
00125         float64_t* variance;
00126 
00128         float64_t* sqrtdiag_lhs;
00130         float64_t* sqrtdiag_rhs;
00131 
00133         float64_t* ld_mean_lhs;
00135         float64_t* ld_mean_rhs;
00136 
00138         int32_t num_params;
00140         int32_t num_symbols;
00142         float64_t sum_m2_s2;
00144         float64_t pos_prior;
00146         float64_t neg_prior;
00148         bool initialized;
00149 };
00150 }
00151 #endif /* _SALZBERGWORDKERNEL_H__ */

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