/usr/include/shogun/kernel/SalzbergWordStringKernel.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | /*
* 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) 1999-2008 Gunnar Raetsch
* Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef _SALZBERGWORDSTRINGKERNEL_H___
#define _SALZBERGWORDSTRINGKERNEL_H___
#include <shogun/lib/common.h>
#include <shogun/kernel/StringKernel.h>
#include <shogun/classifier/PluginEstimate.h>
#include <shogun/features/StringFeatures.h>
namespace shogun
{
/** @brief The SalzbergWordString kernel implements the Salzberg kernel.
*
* It is described in
*
* Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites
* A. Zien, G.Raetsch, S. Mika, B. Schoelkopf, T. Lengauer, K.-R. Mueller
*
*/
class CSalzbergWordStringKernel: public CStringKernel<uint16_t>
{
public:
/** default constructor */
CSalzbergWordStringKernel();
/** constructor
*
* @param size cache size
* @param pie the plugin estimate
* @param labels optional labels to set prior from
*/
CSalzbergWordStringKernel(int32_t size, CPluginEstimate* pie, CLabels* labels=NULL);
/** constructor
*
* @param l features of left-hand side
* @param r features of right-hand side
* @param pie the plugin estimate
* @param labels optional labels to set prior from
*/
CSalzbergWordStringKernel(
CStringFeatures<uint16_t>* l, CStringFeatures<uint16_t>* r,
CPluginEstimate *pie, CLabels* labels=NULL);
virtual ~CSalzbergWordStringKernel();
/** set prior probs
*
* @param pos_prior_ positive prior
* @param neg_prior_ negative prior
*/
void set_prior_probs(float64_t pos_prior_, float64_t neg_prior_)
{
pos_prior=pos_prior_ ;
neg_prior=neg_prior_ ;
if (fabs(pos_prior+neg_prior-1)>1e-6)
SG_WARNING( "priors don't sum to 1: %f+%f-1=%f\n", pos_prior, neg_prior, pos_prior+neg_prior-1) ;
};
/** set prior probs from labels
*
* @param labels labels to set prior probabilites from
*/
void set_prior_probs_from_labels(CLabels* labels);
/** initialize kernel
*
* @param l features of left-hand side
* @param r features of right-hand side
* @return if initializing was successful
*/
virtual bool init(CFeatures* l, CFeatures* r);
/** clean up kernel */
virtual void cleanup();
/** return what type of kernel we are
*
* @return kernel type SALZBERG
*/
virtual EKernelType get_kernel_type() { return K_SALZBERG; }
/** return the kernel's name
*
* @return name Salzberg
*/
virtual const char* get_name() const { return "SalzbergWordStringKernel" ; }
protected:
/** compute kernel function for features a and b
* idx_{a,b} denote the index of the feature vectors
* in the corresponding feature object
*
* @param idx_a index a
* @param idx_b index b
* @return computed kernel function at indices a,b
*/
float64_t compute(int32_t idx_a, int32_t idx_b);
// float64_t compute_slow(int64_t idx_a, int64_t idx_b);
/** compute index of given symbol at given position
*
* @param position position
* @param symbol symbol
* @return index
*/
inline int32_t compute_index(int32_t position, uint16_t symbol)
{
return position*num_symbols+symbol;
}
private:
void init();
protected:
/** the plugin estimate */
CPluginEstimate* estimate;
/** mean */
float64_t* mean;
/** variance */
float64_t* variance;
/** sqrt diagonal of left-hand side */
float64_t* sqrtdiag_lhs;
/** sqrt diagonal of right-hand side */
float64_t* sqrtdiag_rhs;
/** ld mean left-hand side */
float64_t* ld_mean_lhs;
/** ld mean right-hand side */
float64_t* ld_mean_rhs;
/** number of params */
int32_t num_params;
/** number of symbols */
int32_t num_symbols;
/** sum m2 s2 */
float64_t sum_m2_s2;
/** positive prior */
float64_t pos_prior;
/** negative prior */
float64_t neg_prior;
/** if kernel is initialized */
bool initialized;
};
}
#endif /* _SALZBERGWORDKERNEL_H__ */
|