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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
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