/usr/include/shogun/kernel/TanimotoKernelNormalizer.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
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* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* Written (W) 2008-2009 Soeren Sonnenburg
* Copyright (C) 2008-2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef _TANIMOTOKERNELNORMALIZER_H___
#define _TANIMOTOKERNELNORMALIZER_H___
#include <shogun/kernel/KernelNormalizer.h>
#include <shogun/kernel/CommWordStringKernel.h>
namespace shogun
{
/** @brief TanimotoKernelNormalizer performs kernel normalization inspired by
* the Tanimoto coefficient (see http://en.wikipedia.org/wiki/Jaccard_index )
*
* \f[
* k'({\bf x},{\bf x'}) = \frac{k({\bf x},{\bf x'})}{k({\bf x},{\bf x})+k({\bf x'},{\bf x'})-k({\bf x},{\bf x'})}
* \f]
*/
class CTanimotoKernelNormalizer : public CKernelNormalizer
{
public:
/** default constructor
* @param use_opt_diag - some kernels support faster diagonal compuation
* via compute_diag(idx), this flag enables this
*/
CTanimotoKernelNormalizer(bool use_opt_diag=false)
: CKernelNormalizer(), diag_lhs(NULL), diag_rhs(NULL),
use_optimized_diagonal_computation(use_opt_diag)
{
}
/** default destructor */
virtual ~CTanimotoKernelNormalizer()
{
SG_FREE(diag_lhs);
SG_FREE(diag_rhs);
}
/** initialization of the normalizer
* @param k kernel */
virtual bool init(CKernel* k)
{
ASSERT(k);
int32_t num_lhs=k->get_num_vec_lhs();
int32_t num_rhs=k->get_num_vec_rhs();
ASSERT(num_lhs>0);
ASSERT(num_rhs>0);
CFeatures* old_lhs=k->lhs;
CFeatures* old_rhs=k->rhs;
k->lhs=old_lhs;
k->rhs=old_lhs;
bool r1=alloc_and_compute_diag(k, diag_lhs, num_lhs);
k->lhs=old_rhs;
k->rhs=old_rhs;
bool r2=alloc_and_compute_diag(k, diag_rhs, num_rhs);
k->lhs=old_lhs;
k->rhs=old_rhs;
return r1 && r2;
}
/** normalize the kernel value
* @param value kernel value
* @param idx_lhs index of left hand side vector
* @param idx_rhs index of right hand side vector
*/
inline virtual float64_t normalize(
float64_t value, int32_t idx_lhs, int32_t idx_rhs)
{
float64_t diag_sum=diag_lhs[idx_lhs]*diag_rhs[idx_rhs];
return value/(diag_sum-value);
}
/** normalize only the left hand side vector
* @param value value of a component of the left hand side feature vector
* @param idx_lhs index of left hand side vector
*/
inline virtual float64_t normalize_lhs(float64_t value, int32_t idx_lhs)
{
SG_ERROR("linadd not supported with Tanimoto normalization.\n");
return 0;
}
/** normalize only the right hand side vector
* @param value value of a component of the right hand side feature vector
* @param idx_rhs index of right hand side vector
*/
inline virtual float64_t normalize_rhs(float64_t value, int32_t idx_rhs)
{
SG_ERROR("linadd not supported with Tanimoto normalization.\n");
return 0;
}
/** Returns the name of the SGSerializable instance. It MUST BE
* the CLASS NAME without the prefixed `C'.
*
* @return name of the SGSerializable
*/
virtual const char* get_name() const {
return "TanimotoKernelNormalizer"; }
public:
/**
* alloc and compute the vector containing the square root of the
* diagonal elements of this kernel.
*/
bool alloc_and_compute_diag(CKernel* k, float64_t* &v, int32_t num)
{
SG_FREE(v);
v=SG_MALLOC(float64_t, num);
for (int32_t i=0; i<num; i++)
{
if (k->get_kernel_type() == K_COMMWORDSTRING)
{
if (use_optimized_diagonal_computation)
v[i]=((CCommWordStringKernel*) k)->compute_diag(i);
else
v[i]=((CCommWordStringKernel*) k)->compute_helper(i,i, true);
}
else
v[i]=k->compute(i,i);
if (v[i]==0.0)
v[i]=1e-16; /* avoid divide by zero exception */
}
return (v!=NULL);
}
protected:
/** diagonal left-hand side */
float64_t* diag_lhs;
/** diagonal right-hand side */
float64_t* diag_rhs;
/** flat if optimized diagonal computation is used */
bool use_optimized_diagonal_computation;
};
}
#endif
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