/usr/include/shogun/structure/SegmentLoss.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 | /*
* 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) 2009 Jonas Behr
* Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef __SEGMENT_LOSS__
#define __SEGMENT_LOSS__
#include <shogun/lib/common.h>
#include <shogun/base/SGObject.h>
#include <shogun/lib/Array.h>
#include <shogun/lib/Array2.h>
#include <shogun/lib/Array3.h>
namespace shogun
{
template <class T> class CArray;
template <class T> class CArray2;
template <class T> class CArray3;
/** @brief class IntronList */
class CSegmentLoss : public CSGObject
{
public:
/** constructor
*/
CSegmentLoss();
virtual ~CSegmentLoss();
/** get segment loss for a given range
*
* @param from_pos start position
* @param to_pos end position
* @param segment_id type of the segment
*/
float32_t get_segment_loss(int32_t from_pos, int32_t to_pos, int32_t segment_id);
/** get segment loss for a given range
*
* @param from_pos start position
* @param to_pos end position
* @param segment_id type of the segment
*/
float32_t get_segment_loss_extend(int32_t from_pos, int32_t to_pos, int32_t segment_id);
/** set best path segment loss
*
* @param segment_loss segment loss
* @param m number of segment id1
* @param n number of segment id2
*/
void set_segment_loss(float64_t* segment_loss, int32_t m, int32_t n);
/** set best path segmend ids
*
* @param segment_ids segment ids
*/
void set_segment_ids(CArray<int32_t>* segment_ids);
/** mask parts of the sequence such that there is no
* loss incured there; this is used if there is uncertainty
* in the label
*
* @param segment_mask mask
*/
void set_segment_mask(CArray<float64_t>* segment_mask);
/** set num segment types
*
* @param num_segment_types num segment types
*/
void set_num_segment_types(int32_t num_segment_types)
{
m_num_segment_types = num_segment_types;
}
/** compute loss
*
* @param all_pos all candidate positions
* @param len number of positions
*/
void compute_loss(int32_t* all_pos, int32_t len);
/**
* @return object name
*/
inline virtual const char* get_name() const { return "SegmentLoss"; }
protected:
/** segment loss matrix*/
CArray2<float32_t> m_segment_loss_matrix;
/** segment loss
* two square matrices:
* one for segment based loss and
* one for length contribution*/
CArray3<float64_t> m_segment_loss;
/** segment IDs */
CArray<int32_t>* m_segment_ids;
/** segment mask */
CArray<float64_t>* m_segment_mask;
/** number of different segment types (former: max_a_id)*/
int32_t m_num_segment_types;
};
inline float32_t CSegmentLoss::get_segment_loss(int32_t from_pos, int32_t to_pos, int32_t segment_id)
{
/* int32_t from_pos_shift = from_pos ;
if (print)
SG_PRINT("# pos=%i,%i segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
from_pos_shift, to_pos, segment_id,
m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;
while(1)
{
while (m_segment_ids->element(from_pos_shift)==m_segment_ids->element(from_pos_shift+1) && from_pos_shift<to_pos)
from_pos_shift++ ;
if (print)
SG_PRINT("# pos=%i,%i segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
from_pos_shift, to_pos, segment_id,
m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;
if (from_pos_shift>=to_pos)
{
//SG_PRINT("break") ;
break ;
}
else from_pos_shift++ ;
}
if (print)
SG_PRINT("break\n") ; */
float32_t diff_contrib = m_segment_loss_matrix.element(segment_id, from_pos)-m_segment_loss_matrix.element(segment_id, to_pos);
diff_contrib += m_segment_mask->element(to_pos-1)*m_segment_loss.element(segment_id, m_segment_ids->element(to_pos-1), 0);
return diff_contrib;
}
inline float32_t CSegmentLoss::get_segment_loss_extend(int32_t from_pos, int32_t to_pos, int32_t segment_id)
{
int32_t from_pos_shift = from_pos ;
/*SG_PRINT("segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
segment_id,
m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;*/
while (from_pos_shift<to_pos && m_segment_ids->element(from_pos_shift)==m_segment_ids->element(from_pos_shift+1))
from_pos_shift++ ;
/*SG_PRINT("segment_id=%i, m_segment_ids[from-2]=%i (%1.1f), m_segment_ids[from-1]=%i (%1.1f), m_segment_ids[from]=%i (%1.1f), m_segment_ids[from+1]=%i (%1.1f), \n",
segment_id,
m_segment_ids->element(from_pos_shift-2), m_segment_loss_matrix.element(segment_id, from_pos_shift-2)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift-1), m_segment_loss_matrix.element(segment_id, from_pos_shift-1)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift), m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos),
m_segment_ids->element(from_pos_shift+1), m_segment_loss_matrix.element(segment_id, from_pos_shift+1)-m_segment_loss_matrix.element(segment_id, to_pos)) ;*/
float32_t diff_contrib = m_segment_loss_matrix.element(segment_id, from_pos_shift)-m_segment_loss_matrix.element(segment_id, to_pos);
//diff_contrib += m_segment_mask->element(to_pos)*m_segment_loss.element(segment_id, m_segment_ids->element(to_pos), 0);
//if (from_pos_shift!=from_pos)
// SG_PRINT("shifting from %i to %i, to_pos=%i, loss=%1.1f\n", from_pos, from_pos_shift, to_pos, diff_contrib) ;
return diff_contrib;
}
}
#endif
|