|
1
|
|
|
# Copyright 2018-2020 by Christopher C. Little. |
|
2
|
|
|
# This file is part of Abydos. |
|
3
|
|
|
# |
|
4
|
|
|
# Abydos is free software: you can redistribute it and/or modify |
|
5
|
|
|
# it under the terms of the GNU General Public License as published by |
|
6
|
|
|
# the Free Software Foundation, either version 3 of the License, or |
|
7
|
|
|
# (at your option) any later version. |
|
8
|
|
|
# |
|
9
|
|
|
# Abydos is distributed in the hope that it will be useful, |
|
10
|
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of |
|
11
|
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
|
12
|
|
|
# GNU General Public License for more details. |
|
13
|
|
|
# |
|
14
|
|
|
# You should have received a copy of the GNU General Public License |
|
15
|
|
|
# along with Abydos. If not, see <http://www.gnu.org/licenses/>. |
|
16
|
|
|
|
|
17
|
|
|
"""abydos.distance._gilbert. |
|
18
|
|
|
|
|
19
|
1 |
|
Gilbert correlation |
|
20
|
|
|
""" |
|
21
|
|
|
|
|
22
|
|
|
from typing import Any, Counter as TCounter, Optional, Sequence, Set, Union |
|
23
|
|
|
|
|
24
|
1 |
|
from ._token_distance import _TokenDistance |
|
25
|
|
|
from ..tokenizer import _Tokenizer |
|
26
|
|
|
|
|
27
|
|
|
__all__ = ['Gilbert'] |
|
28
|
|
|
|
|
29
|
|
|
|
|
30
|
|
View Code Duplication |
class Gilbert(_TokenDistance): |
|
|
|
|
|
|
31
|
1 |
|
r"""Gilbert correlation. |
|
32
|
|
|
|
|
33
|
1 |
|
For two sets X and Y and a population N, the Gilbert correlation |
|
34
|
|
|
:cite:`Gilbert:1884` is |
|
35
|
|
|
|
|
36
|
1 |
|
.. math:: |
|
37
|
|
|
|
|
38
|
|
|
corr_{Gilbert}(X, Y) = |
|
39
|
|
|
\frac{2(|X \cap Y| \cdot |(N \setminus X) \setminus Y| - |
|
40
|
|
|
|X \setminus Y| \cdot |Y \setminus X|)} |
|
41
|
|
|
{|N|^2 - |X \cap Y|^2 + |X \setminus Y|^2 + |Y \setminus X|^2 - |
|
42
|
|
|
|(N \setminus X) \setminus Y|^2} |
|
43
|
|
|
|
|
44
|
|
|
For lack of access to the original, this formula is based on the concurring |
|
45
|
|
|
formulae presented in :cite:`Peirce:1884` and :cite:`Doolittle:1884`. |
|
46
|
|
|
|
|
47
|
|
|
In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n, |
|
48
|
|
|
this is |
|
49
|
|
|
|
|
50
|
|
|
.. math:: |
|
51
|
|
|
|
|
52
|
|
|
corr_{Gilbert} = |
|
53
|
|
|
\frac{2(ad-cd)}{n^2-a^2+b^2+c^2-d^2} |
|
54
|
|
|
|
|
55
|
|
|
.. versionadded:: 0.4.0 |
|
56
|
|
|
""" |
|
57
|
|
|
|
|
58
|
|
|
def __init__( |
|
59
|
|
|
self, |
|
60
|
|
|
alphabet: Optional[ |
|
61
|
|
|
Union[TCounter[str], Sequence[str], Set[str], int] |
|
62
|
|
|
] = None, |
|
63
|
|
|
tokenizer: Optional[_Tokenizer] = None, |
|
64
|
1 |
|
intersection_type: str = 'crisp', |
|
65
|
|
|
**kwargs: Any |
|
66
|
|
|
) -> None: |
|
67
|
|
|
"""Initialize Gilbert instance. |
|
68
|
|
|
|
|
69
|
|
|
Parameters |
|
70
|
|
|
---------- |
|
71
|
|
|
alphabet : Counter, collection, int, or None |
|
72
|
|
|
This represents the alphabet of possible tokens. |
|
73
|
|
|
See :ref:`alphabet <alphabet>` description in |
|
74
|
|
|
:py:class:`_TokenDistance` for details. |
|
75
|
|
|
tokenizer : _Tokenizer |
|
76
|
|
|
A tokenizer instance from the :py:mod:`abydos.tokenizer` package |
|
77
|
|
|
intersection_type : str |
|
78
|
|
|
Specifies the intersection type, and set type as a result: |
|
79
|
|
|
See :ref:`intersection_type <intersection_type>` description in |
|
80
|
|
|
:py:class:`_TokenDistance` for details. |
|
81
|
|
|
**kwargs |
|
82
|
|
|
Arbitrary keyword arguments |
|
83
|
|
|
|
|
84
|
|
|
Other Parameters |
|
85
|
|
|
---------------- |
|
86
|
|
|
qval : int |
|
87
|
|
|
The length of each q-gram. Using this parameter and tokenizer=None |
|
88
|
|
|
will cause the instance to use the QGram tokenizer with this |
|
89
|
|
|
q value. |
|
90
|
|
|
metric : _Distance |
|
91
|
|
|
A string distance measure class for use in the ``soft`` and |
|
92
|
|
|
``fuzzy`` variants. |
|
93
|
|
|
threshold : float |
|
94
|
|
|
A threshold value, similarities above which are counted as |
|
95
|
|
|
members of the intersection for the ``fuzzy`` variant. |
|
96
|
|
|
|
|
97
|
|
|
|
|
98
|
|
|
.. versionadded:: 0.4.0 |
|
99
|
|
|
|
|
100
|
|
|
""" |
|
101
|
|
|
super(Gilbert, self).__init__( |
|
102
|
|
|
alphabet=alphabet, |
|
103
|
|
|
tokenizer=tokenizer, |
|
104
|
|
|
intersection_type=intersection_type, |
|
105
|
1 |
|
**kwargs |
|
106
|
|
|
) |
|
107
|
|
|
|
|
108
|
|
|
def corr(self, src: str, tar: str) -> float: |
|
109
|
|
|
"""Return the Gilbert correlation of two strings. |
|
110
|
|
|
|
|
111
|
|
|
Parameters |
|
112
|
1 |
|
---------- |
|
113
|
|
|
src : str |
|
114
|
|
|
Source string (or QGrams/Counter objects) for comparison |
|
115
|
|
|
tar : str |
|
116
|
|
|
Target string (or QGrams/Counter objects) for comparison |
|
117
|
|
|
|
|
118
|
|
|
Returns |
|
119
|
|
|
------- |
|
120
|
|
|
float |
|
121
|
|
|
Gilbert correlation |
|
122
|
|
|
|
|
123
|
|
|
Examples |
|
124
|
|
|
-------- |
|
125
|
|
|
>>> cmp = Gilbert() |
|
126
|
|
|
>>> cmp.corr('cat', 'hat') |
|
127
|
|
|
0.3310580204778157 |
|
128
|
|
|
>>> cmp.corr('Niall', 'Neil') |
|
129
|
|
|
0.21890122402504983 |
|
130
|
|
|
>>> cmp.corr('aluminum', 'Catalan') |
|
131
|
|
|
0.057094811018577836 |
|
132
|
|
|
>>> cmp.corr('ATCG', 'TAGC') |
|
133
|
|
|
-0.003198976327575176 |
|
134
|
|
|
|
|
135
|
|
|
|
|
136
|
|
|
.. versionadded:: 0.4.0 |
|
137
|
|
|
|
|
138
|
|
|
""" |
|
139
|
|
|
if src == tar: |
|
140
|
|
|
return 1.0 |
|
141
|
|
|
|
|
142
|
|
|
self._tokenize(src, tar) |
|
143
|
1 |
|
|
|
144
|
1 |
|
a = self._intersection_card() |
|
145
|
|
|
b = self._src_only_card() |
|
146
|
1 |
|
c = self._tar_only_card() |
|
147
|
|
|
n = self._population_unique_card() |
|
148
|
1 |
|
|
|
149
|
1 |
|
num = a * n - (a + b) * (a + c) |
|
150
|
1 |
|
if num: |
|
151
|
1 |
|
return num / (n * (a + b + c) - (a + b) * (a + c)) |
|
152
|
|
|
return 0.0 |
|
153
|
1 |
|
|
|
154
|
1 |
|
def sim(self, src: str, tar: str) -> float: |
|
155
|
1 |
|
"""Return the Gilbert similarity of two strings. |
|
156
|
1 |
|
|
|
157
|
|
|
Parameters |
|
158
|
1 |
|
---------- |
|
159
|
|
|
src : str |
|
160
|
|
|
Source string (or QGrams/Counter objects) for comparison |
|
161
|
|
|
tar : str |
|
162
|
|
|
Target string (or QGrams/Counter objects) for comparison |
|
163
|
|
|
|
|
164
|
|
|
Returns |
|
165
|
|
|
------- |
|
166
|
|
|
float |
|
167
|
|
|
Gilbert similarity |
|
168
|
|
|
|
|
169
|
|
|
Examples |
|
170
|
|
|
-------- |
|
171
|
|
|
>>> cmp = Gilbert() |
|
172
|
|
|
>>> cmp.sim('cat', 'hat') |
|
173
|
|
|
0.6655290102389079 |
|
174
|
|
|
>>> cmp.sim('Niall', 'Neil') |
|
175
|
|
|
0.6094506120125249 |
|
176
|
|
|
>>> cmp.sim('aluminum', 'Catalan') |
|
177
|
|
|
0.5285474055092889 |
|
178
|
|
|
>>> cmp.sim('ATCG', 'TAGC') |
|
179
|
|
|
0.4984005118362124 |
|
180
|
|
|
|
|
181
|
|
|
|
|
182
|
|
|
.. versionadded:: 0.4.0 |
|
183
|
|
|
|
|
184
|
|
|
""" |
|
185
|
|
|
return (1.0 + self.corr(src, tar)) / 2.0 |
|
186
|
|
|
|
|
187
|
|
|
|
|
188
|
|
|
if __name__ == '__main__': |
|
189
|
1 |
|
import doctest |
|
190
|
|
|
|
|
191
|
|
|
doctest.testmod() |
|
192
|
|
|
|
chrislit /
abydos
Loading history...