TanimotoKernelNormalizer.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) 2008 Soeren Sonnenburg
00008  * Copyright (C) 2008 Fraunhofer Institute FIRST and Max-Planck-Society
00009  */
00010 
00011 #ifndef _TANIMOTOKERNELNORMALIZER_H___
00012 #define _TANIMOTOKERNELNORMALIZER_H___
00013 
00014 #include "kernel/KernelNormalizer.h"
00015 #include "kernel/CommWordStringKernel.h"
00016 
00025 class CTanimotoKernelNormalizer : public CKernelNormalizer
00026 {
00027     public:
00032         CTanimotoKernelNormalizer(bool use_opt_diag=false) : diag_lhs(NULL),
00033             diag_rhs(NULL), use_optimized_diagonal_computation(use_opt_diag)
00034         {
00035         }
00036 
00038         virtual ~CTanimotoKernelNormalizer()
00039         {
00040             delete[] diag_lhs;
00041             delete[] diag_rhs;
00042         }
00043 
00046         virtual bool init(CKernel* k)
00047         {
00048             ASSERT(k);
00049             int32_t num_lhs=k->get_num_vec_lhs();
00050             int32_t num_rhs=k->get_num_vec_rhs();
00051             ASSERT(num_lhs>0);
00052             ASSERT(num_rhs>0);
00053 
00054             CFeatures* old_lhs=k->lhs;
00055             CFeatures* old_rhs=k->rhs;
00056 
00057             k->lhs=old_lhs;
00058             k->rhs=old_lhs;
00059             bool r1=alloc_and_compute_diag(k, diag_lhs, num_lhs);
00060 
00061             k->lhs=old_rhs;
00062             k->rhs=old_rhs;
00063             bool r2=alloc_and_compute_diag(k, diag_rhs, num_rhs);
00064 
00065             k->lhs=old_lhs;
00066             k->rhs=old_rhs;
00067 
00068             return r1 && r2;
00069         }
00070 
00076         inline virtual float64_t normalize(
00077             float64_t value, int32_t idx_lhs, int32_t idx_rhs)
00078         {
00079             float64_t diag_sum=diag_lhs[idx_lhs]*diag_rhs[idx_rhs];
00080             return value/(diag_sum-value);
00081         }
00082 
00087         inline virtual float64_t normalize_lhs(float64_t value, int32_t idx_lhs)
00088         {
00089             SG_ERROR("linadd not supported with Tanimoto normalization.\n");
00090             return 0;
00091         }
00092 
00097         inline virtual float64_t normalize_rhs(float64_t value, int32_t idx_rhs)
00098         {
00099             SG_ERROR("linadd not supported with Tanimoto normalization.\n");
00100             return 0;
00101         }
00102 
00103     public:
00108         bool alloc_and_compute_diag(CKernel* k, float64_t* &v, int32_t num)
00109         {
00110             delete[] v;
00111             v=new float64_t[num];
00112 
00113             for (int32_t i=0; i<num; i++)
00114             {
00115                 if (k->get_kernel_type() == K_COMMWORDSTRING)
00116                 {
00117                     if (use_optimized_diagonal_computation)
00118                         v[i]=((CCommWordStringKernel*) k)->compute_diag(i);
00119                     else
00120                         v[i]=((CCommWordStringKernel*) k)->compute_helper(i,i, true);
00121                 }
00122                 else
00123                     v[i]=k->compute(i,i);
00124 
00125                 if (v[i]==0.0)
00126                     v[i]=1e-16; /* avoid divide by zero exception */
00127             }
00128 
00129             return (v!=NULL);
00130         }
00131 
00132     protected:
00134         float64_t* diag_lhs;
00136         float64_t* diag_rhs;
00138         bool use_optimized_diagonal_computation;
00139 };
00140 
00141 #endif

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