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from __future__ import division
import random
import numpy as np
from functools import partial
from operator import attrgetter
######################################
# Selections #
######################################
def selRandom(individuals, k):
"""Select *k* individuals at random from the input *individuals* with
replacement. The list returned contains references to the input
*individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
This function uses the :func:`~random.choice` function from the
python base :mod:`random` module.
"""
return [random.choice(individuals) for i in xrange(k)]
def selBest(individuals, k, fit_attr="fitness"):
"""Select the *k* best individuals among the input *individuals*. The
list returned contains references to the input *individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param fit_attr: The attribute of individuals to use as selection criterion
:returns: A list containing the k best individuals.
"""
return sorted(individuals, key=attrgetter(fit_attr), reverse=True)[:k]
def selWorst(individuals, k, fit_attr="fitness"):
"""Select the *k* worst individuals among the input *individuals*. The
list returned contains references to the input *individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param fit_attr: The attribute of individuals to use as selection criterion
:returns: A list containing the k worst individuals.
"""
return sorted(individuals, key=attrgetter(fit_attr))[:k]
def selTournament(individuals, k, tournsize, fit_attr="fitness"):
"""Select the best individual among *tournsize* randomly chosen
individuals, *k* times. The list returned contains
references to the input *individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param tournsize: The number of individuals participating in each tournament.
:param fit_attr: The attribute of individuals to use as selection criterion
:returns: A list of selected individuals.
This function uses the :func:`~random.choice` function from the python base
:mod:`random` module.
"""
chosen = []
for i in xrange(k):
aspirants = selRandom(individuals, tournsize)
chosen.append(max(aspirants, key=attrgetter(fit_attr)))
return chosen
def selRoulette(individuals, k, fit_attr="fitness"):
"""Select *k* individuals from the input *individuals* using *k*
spins of a roulette. The selection is made by looking only at the first
objective of each individual. The list returned contains references to
the input *individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param fit_attr: The attribute of individuals to use as selection criterion
:returns: A list of selected individuals.
This function uses the :func:`~random.random` function from the python base
:mod:`random` module.
.. warning::
The roulette selection by definition cannot be used for minimization
or when the fitness can be smaller or equal to 0.
"""
s_inds = sorted(individuals, key=attrgetter(fit_attr), reverse=True)
sum_fits = sum(getattr(ind, fit_attr).values[0] for ind in individuals)
chosen = []
for i in xrange(k):
u = random.random() * sum_fits
sum_ = 0
for ind in s_inds:
sum_ += getattr(ind, fit_attr).values[0]
if sum_ > u:
chosen.append(ind)
break
return chosen
def selDoubleTournament(individuals, k, fitness_size, parsimony_size, fitness_first, fit_attr="fitness"):
"""Tournament selection which use the size of the individuals in order
to discriminate good solutions. This kind of tournament is obviously
useless with fixed-length representation, but has been shown to
significantly reduce excessive growth of individuals, especially in GP,
where it can be used as a bloat control technique (see
[Luke2002fighting]_). This selection operator implements the double
tournament technique presented in this paper.
The core principle is to use a normal tournament selection, but using a
special sample function to select aspirants, which is another tournament
based on the size of the individuals. To ensure that the selection
pressure is not too high, the size of the size tournament (the number
of candidates evaluated) can be a real number between 1 and 2. In this
case, the smaller individual among two will be selected with a probability
*size_tourn_size*/2. For instance, if *size_tourn_size* is set to 1.4,
then the smaller individual will have a 0.7 probability to be selected.
.. note::
In GP, it has been shown that this operator produces better results
when it is combined with some kind of a depth limit.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param fitness_size: The number of individuals participating in each \
fitness tournament
:param parsimony_size: The number of individuals participating in each \
size tournament. This value has to be a real number\
in the range [1,2], see above for details.
:param fitness_first: Set this to True if the first tournament done should \
be the fitness one (i.e. the fitness tournament producing aspirants for \
the size tournament). Setting it to False will behaves as the opposite \
(size tournament feeding fitness tournaments with candidates). It has been \
shown that this parameter does not have a significant effect in most cases\
(see [Luke2002fighting]_).
:param fit_attr: The attribute of individuals to use as selection criterion
:returns: A list of selected individuals.
.. [Luke2002fighting] Luke and Panait, 2002, Fighting bloat with
nonparametric parsimony pressure
"""
assert (1 <= parsimony_size <= 2), "Parsimony tournament size has to be in the range [1, 2]."
def _sizeTournament(individuals, k, select):
chosen = []
for i in xrange(k):
# Select two individuals from the population
# The first individual has to be the shortest
prob = parsimony_size / 2.
ind1, ind2 = select(individuals, k=2)
if len(ind1) > len(ind2):
ind1, ind2 = ind2, ind1
elif len(ind1) == len(ind2):
# random selection in case of a tie
prob = 0.5
# Since size1 <= size2 then ind1 is selected
# with a probability prob
chosen.append(ind1 if random.random() < prob else ind2)
return chosen
def _fitTournament(individuals, k, select):
chosen = []
for i in xrange(k):
aspirants = select(individuals, k=fitness_size)
chosen.append(max(aspirants, key=attrgetter(fit_attr)))
return chosen
if fitness_first:
tfit = partial(_fitTournament, select=selRandom)
return _sizeTournament(individuals, k, tfit)
else:
tsize = partial(_sizeTournament, select=selRandom)
return _fitTournament(individuals, k, tsize)
def selStochasticUniversalSampling(individuals, k, fit_attr="fitness"):
"""Select the *k* individuals among the input *individuals*.
The selection is made by using a single random value to sample all of the
individuals by choosing them at evenly spaced intervals. The list returned
contains references to the input *individuals*.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:param fit_attr: The attribute of individuals to use as selection criterion
:return: A list of selected individuals.
This function uses the :func:`~random.uniform` function from the python base
:mod:`random` module.
"""
s_inds = sorted(individuals, key=attrgetter(fit_attr), reverse=True)
sum_fits = sum(getattr(ind, fit_attr).values[0] for ind in individuals)
distance = sum_fits / float(k)
start = random.uniform(0, distance)
points = [start + i*distance for i in xrange(k)]
chosen = []
for p in points:
i = 0
sum_ = getattr(s_inds[i], fit_attr).values[0]
while sum_ < p:
i += 1
sum_ += getattr(s_inds[i], fit_attr).values[0]
chosen.append(s_inds[i])
return chosen
def selLexicase(individuals, k):
"""Returns an individual that does the best on the fitness cases when
considered one at a time in random order.
http://faculty.hampshire.edu/lspector/pubs/lexicase-IEEE-TEC.pdf
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
"""
selected_individuals = []
for i in range(k):
fit_weights = individuals[0].fitness.weights
candidates = individuals
cases = list(range(len(individuals[0].fitness.values)))
random.shuffle(cases)
while len(cases) > 0 and len(candidates) > 1:
f = min
if fit_weights[cases[0]] > 0:
f = max
best_val_for_case = f(map(lambda x: x.fitness.values[cases[0]], candidates))
candidates = list(filter(lambda x: x.fitness.values[cases[0]] == best_val_for_case, candidates))
cases.pop(0)
selected_individuals.append(random.choice(candidates))
return selected_individuals
def selEpsilonLexicase(individuals, k, epsilon):
"""
Returns an individual that does the best on the fitness cases when
considered one at a time in random order. Requires a epsilon parameter.
https://push-language.hampshire.edu/uploads/default/original/1X/35c30e47ef6323a0a949402914453f277fb1b5b0.pdf
Implemented epsilon_y implementation.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
"""
selected_individuals = []
for i in range(k):
fit_weights = individuals[0].fitness.weights
candidates = individuals
cases = list(range(len(individuals[0].fitness.values)))
random.shuffle(cases)
while len(cases) > 0 and len(candidates) > 1:
if fit_weights[cases[0]] > 0:
best_val_for_case = max(map(lambda x: x.fitness.values[cases[0]], candidates))
min_val_to_survive_case = best_val_for_case - epsilon
candidates = list(filter(lambda x: x.fitness.values[cases[0]] >= min_val_to_survive_case, candidates))
else :
best_val_for_case = min(map(lambda x: x.fitness.values[cases[0]], candidates))
max_val_to_survive_case = best_val_for_case + epsilon
candidates = list(filter(lambda x: x.fitness.values[cases[0]] <= max_val_to_survive_case, candidates))
cases.pop(0)
selected_individuals.append(random.choice(candidates))
return selected_individuals
def selAutomaticEpsilonLexicase(individuals, k):
"""
Returns an individual that does the best on the fitness cases when considered one at a
time in random order.
https://push-language.hampshire.edu/uploads/default/original/1X/35c30e47ef6323a0a949402914453f277fb1b5b0.pdf
Implemented lambda_epsilon_y implementation.
:param individuals: A list of individuals to select from.
:param k: The number of individuals to select.
:returns: A list of selected individuals.
"""
selected_individuals = []
for i in range(k):
fit_weights = individuals[0].fitness.weights
candidates = individuals
cases = list(range(len(individuals[0].fitness.values)))
random.shuffle(cases)
while len(cases) > 0 and len(candidates) > 1:
errors_for_this_case = [x.fitness.values[cases[0]] for x in candidates]
median_val = np.median(errors_for_this_case)
median_absolute_deviation = np.median([abs(x - median_val) for x in errors_for_this_case])
if fit_weights[cases[0]] > 0:
best_val_for_case = max(errors_for_this_case)
min_val_to_survive = best_val_for_case - median_absolute_deviation
candidates = list(filter(lambda x: x.fitness.values[cases[0]] >= min_val_to_survive, candidates))
else :
best_val_for_case = min(errors_for_this_case)
max_val_to_survive = best_val_for_case + median_absolute_deviation
candidates = list(filter(lambda x: x.fitness.values[cases[0]] <= max_val_to_survive, candidates))
cases.pop(0)
selected_individuals.append(random.choice(candidates))
return selected_individuals
__all__ = ['selRandom', 'selBest', 'selWorst', 'selRoulette',
'selTournament', 'selDoubleTournament', 'selStochasticUniversalSampling',
'selLexicase', 'selEpsilonLexicase', 'selAutomaticEpsilonLexicase']