# Copyright 2014-2020 by Christopher C. Little.
# This file is part of Abydos.
#
# Abydos 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.
#
# Abydos is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Abydos. If not, see <http://www.gnu.org/licenses/>.
"""abydos.distance._cosine.
Cosine similarity & distance
"""
from math import sqrt
from deprecation import deprecated
from ._token_distance import _TokenDistance
from .. import __version__
__all__ = ['Cosine', 'dist_cosine', 'sim_cosine']
[docs]class Cosine(_TokenDistance):
r"""Cosine similarity.
For two sets X and Y, the cosine similarity, Otsuka-Ochiai coefficient, or
Ochiai coefficient :cite:`Otsuka:1936,Ochiai:1957` is
.. math::
sim_{cosine}(X, Y) = \frac{|X \cap Y|}{\sqrt{|X| \cdot |Y|}}
In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n,
this is
.. math::
sim_{cosine} =
\frac{a}{\sqrt{(a+b)(a+c)}}
Notes
-----
This measure is also known as the Fowlkes-Mallows index
:cite:`Fowlkes:1983` for two classes and G-measure, the geometric mean of
precision & recall.
.. versionadded:: 0.3.6
"""
def __init__(self, tokenizer=None, intersection_type='crisp', **kwargs):
"""Initialize Cosine instance.
Parameters
----------
tokenizer : _Tokenizer
A tokenizer instance from the :py:mod:`abydos.tokenizer` package
intersection_type : str
Specifies the intersection type, and set type as a result:
See :ref:`intersection_type <intersection_type>` description in
:py:class:`_TokenDistance` for details.
**kwargs
Arbitrary keyword arguments
Other Parameters
----------------
qval : int
The length of each q-gram. Using this parameter and tokenizer=None
will cause the instance to use the QGram tokenizer with this
q value.
metric : _Distance
A string distance measure class for use in the ``soft`` and
``fuzzy`` variants.
threshold : float
A threshold value, similarities above which are counted as
members of the intersection for the ``fuzzy`` variant.
.. versionadded:: 0.4.0
"""
super(Cosine, self).__init__(
tokenizer=tokenizer, intersection_type=intersection_type, **kwargs
)
[docs] def sim(self, src, tar):
r"""Return the cosine similarity of two strings.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
Returns
-------
float
Cosine similarity
Examples
--------
>>> cmp = Cosine()
>>> cmp.sim('cat', 'hat')
0.5
>>> cmp.sim('Niall', 'Neil')
0.3651483716701107
>>> cmp.sim('aluminum', 'Catalan')
0.11785113019775793
>>> cmp.sim('ATCG', 'TAGC')
0.0
.. versionadded:: 0.1.0
.. versionchanged:: 0.3.6
Encapsulated in class
"""
if src == tar:
return 1.0
if not src or not tar:
return 0.0
self._tokenize(src, tar)
num = self._intersection_card()
if num:
return num / sqrt(self._src_card() * self._tar_card())
return 0.0
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the Cosine.sim method instead.',
)
def sim_cosine(src, tar, qval=2):
r"""Return the cosine similarity of two strings.
This is a wrapper for :py:meth:`Cosine.sim`.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
qval : int
The length of each q-gram
Returns
-------
float
Cosine similarity
Examples
--------
>>> sim_cosine('cat', 'hat')
0.5
>>> sim_cosine('Niall', 'Neil')
0.3651483716701107
>>> sim_cosine('aluminum', 'Catalan')
0.11785113019775793
>>> sim_cosine('ATCG', 'TAGC')
0.0
.. versionadded:: 0.1.0
"""
return Cosine(qval=qval).sim(src, tar)
[docs]@deprecated(
deprecated_in='0.4.0',
removed_in='0.6.0',
current_version=__version__,
details='Use the Cosine.dist method instead.',
)
def dist_cosine(src, tar, qval=2):
"""Return the cosine distance between two strings.
This is a wrapper for :py:meth:`Cosine.dist`.
Parameters
----------
src : str
Source string (or QGrams/Counter objects) for comparison
tar : str
Target string (or QGrams/Counter objects) for comparison
qval : int
The length of each q-gram
Returns
-------
float
Cosine distance
Examples
--------
>>> dist_cosine('cat', 'hat')
0.5
>>> dist_cosine('Niall', 'Neil')
0.6348516283298893
>>> dist_cosine('aluminum', 'Catalan')
0.882148869802242
>>> dist_cosine('ATCG', 'TAGC')
1.0
.. versionadded:: 0.1.0
"""
return Cosine(qval=qval).dist(src, tar)
if __name__ == '__main__':
import doctest
doctest.testmod()