Source code for abydos.distance._ample

# Copyright 2018-2020 by Christopher C. Little.
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AMPLE similarity

from ._token_distance import _TokenDistance

__all__ = ['AMPLE']

[docs]class AMPLE(_TokenDistance): r"""AMPLE similarity. The AMPLE similarity :cite:`Dallmeier:2005,Abreu:2007` is defined in getAverageSequenceWeight() in the file of AMPLE's source code. For two sets X and Y and a population N, it is .. math:: sim_{AMPLE}(X, Y) = \big|\frac{|X \cap Y|}{|X|} - \frac{|Y \setminus X|}{|N \setminus X|}\big| In :ref:`2x2 confusion table terms <confusion_table>`, where a+b+c+d=n, this is .. math:: sim_{AMPLE} = \big|\frac{a}{a+b}-\frac{c}{c+d}\big| Notes ----- This measure is asymmetric. The first ratio considers how similar the two strings are, while the second considers how dissimilar the second string is. As a result, both very similar and very dissimilar strings will score high on this measure, provided the unique aspects are present chiefly in the latter string. .. versionadded:: 0.4.0 """ def __init__( self, alphabet=None, tokenizer=None, intersection_type='crisp', **kwargs ): """Initialize AMPLE instance. Parameters ---------- alphabet : Counter, collection, int, or None This represents the alphabet of possible tokens. See :ref:`alphabet <alphabet>` description in :py:class:`_TokenDistance` for details. 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(AMPLE, self).__init__( alphabet=alphabet, tokenizer=tokenizer, intersection_type=intersection_type, **kwargs )
[docs] def sim(self, src, tar): """Return the AMPLE 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 AMPLE similarity Examples -------- >>> cmp = AMPLE() >>> cmp.sim('cat', 'hat') 0.49743589743589745 >>> cmp.sim('Niall', 'Neil') 0.32947729220222793 >>> cmp.sim('aluminum', 'Catalan') 0.10209049255441008 >>> cmp.sim('ATCG', 'TAGC') 0.006418485237483954 .. versionadded:: 0.4.0 """ if src == tar: return 1.0 self._tokenize(src, tar) a = self._intersection_card() b = self._src_only_card() c = self._tar_only_card() d = self._total_complement_card() # If the denominators are 0, set them to 1. # This is a deviation from the formula, but prevents division by zero # while retaining the contribution of the other ratio. if a + b == 0: b = 1 if c + d == 0: d = 1 return abs((a / (a + b)) - (c / (c + d)))
if __name__ == '__main__': import doctest doctest.testmod()