293 lines
14 KiB
Python
293 lines
14 KiB
Python
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# This file is part of DEAP.
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#
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# DEAP is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License as
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# published by the Free Software Foundation, either version 3 of
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# the License, or (at your option) any later version.
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#
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# DEAP is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with DEAP. If not, see <http://www.gnu.org/licenses/>.
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# Special thanks to Nikolaus Hansen for providing major part of
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# this code. The CMA-ES algorithm is provided in many other languages
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# and advanced versions at http://www.lri.fr/~hansen/cmaesintro.html.
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"""A module that provides support for the Covariance Matrix Adaptation
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Evolution Strategy.
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"""
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import numpy
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import copy
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from math import sqrt, log, exp
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class Strategy(object):
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"""
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A strategy that will keep track of the basic parameters of the CMA-ES
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algorithm.
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:param centroid: An iterable object that indicates where to start the
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evolution.
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:param sigma: The initial standard deviation of the distribution.
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:param parameter: One or more parameter to pass to the strategy as
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described in the following table, optional.
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+----------------+---------------------------+----------------------------+
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| Parameter | Default | Details |
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+================+===========================+============================+
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| ``lambda_`` | ``int(4 + 3 * log(N))`` | Number of children to |
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| | | produce at each generation,|
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| | | ``N`` is the individual's |
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| | | size (integer). |
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+----------------+---------------------------+----------------------------+
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| ``mu`` | ``int(lambda_ / 2)`` | The number of parents to |
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| | | keep from the |
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| | | lambda children (integer). |
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+----------------+---------------------------+----------------------------+
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| ``cmatrix`` | ``identity(N)`` | The initial covariance |
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| | | matrix of the distribution |
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| | | that will be sampled. |
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+----------------+---------------------------+----------------------------+
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| ``weights`` | ``"superlinear"`` | Decrease speed, can be |
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| | | ``"superlinear"``, |
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| | | ``"linear"`` or |
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| | | ``"equal"``. |
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+----------------+---------------------------+----------------------------+
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| ``cs`` | ``(mueff + 2) / | Cumulation constant for |
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| | (N + mueff + 3)`` | step-size. |
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+----------------+---------------------------+----------------------------+
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| ``damps`` | ``1 + 2 * max(0, sqrt(( | Damping for step-size. |
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| | mueff - 1) / (N + 1)) - 1)| |
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| | + cs`` | |
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+----------------+---------------------------+----------------------------+
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| ``ccum`` | ``4 / (N + 4)`` | Cumulation constant for |
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| | | covariance matrix. |
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+----------------+---------------------------+----------------------------+
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| ``ccov1`` | ``2 / ((N + 1.3)^2 + | Learning rate for rank-one |
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| | mueff)`` | update. |
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+----------------+---------------------------+----------------------------+
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| ``ccovmu`` | ``2 * (mueff - 2 + 1 / | Learning rate for rank-mu |
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| | mueff) / ((N + 2)^2 + | update. |
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| | mueff)`` | |
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+----------------+---------------------------+----------------------------+
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"""
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def __init__(self, centroid, sigma, **kargs):
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self.params = kargs
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# Create a centroid as a numpy array
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self.centroid = numpy.array(centroid)
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self.dim = len(self.centroid)
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self.sigma = sigma
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self.pc = numpy.zeros(self.dim)
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self.ps = numpy.zeros(self.dim)
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self.chiN = sqrt(self.dim) * (1 - 1. / (4. * self.dim) + \
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1. / (21. * self.dim**2))
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self.C = self.params.get("cmatrix", numpy.identity(self.dim))
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self.diagD, self.B = numpy.linalg.eigh(self.C)
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indx = numpy.argsort(self.diagD)
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self.diagD = self.diagD[indx]**0.5
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self.B = self.B[:, indx]
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self.BD = self.B * self.diagD
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self.cond = self.diagD[indx[-1]]/self.diagD[indx[0]]
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self.lambda_ = self.params.get("lambda_", int(4 + 3 * log(self.dim)))
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self.update_count = 0
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self.computeParams(self.params)
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def generate(self, ind_init):
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"""Generate a population of :math:`\lambda` individuals of type
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*ind_init* from the current strategy.
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:param ind_init: A function object that is able to initialize an
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individual from a list.
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:returns: A list of individuals.
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"""
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arz = numpy.random.standard_normal((self.lambda_, self.dim))
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arz = self.centroid + self.sigma * numpy.dot(arz, self.BD.T)
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return map(ind_init, arz)
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def update(self, population):
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"""Update the current covariance matrix strategy from the
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*population*.
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:param population: A list of individuals from which to update the
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parameters.
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"""
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population.sort(key=lambda ind: ind.fitness, reverse=True)
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old_centroid = self.centroid
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self.centroid = numpy.dot(self.weights, population[0:self.mu])
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c_diff = self.centroid - old_centroid
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# Cumulation : update evolution path
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self.ps = (1 - self.cs) * self.ps \
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+ sqrt(self.cs * (2 - self.cs) * self.mueff) / self.sigma \
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* numpy.dot(self.B, (1. / self.diagD) \
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* numpy.dot(self.B.T, c_diff))
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hsig = float((numpy.linalg.norm(self.ps) /
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sqrt(1. - (1. - self.cs)**(2. * (self.update_count + 1.))) / self.chiN
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< (1.4 + 2. / (self.dim + 1.))))
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self.update_count += 1
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self.pc = (1 - self.cc) * self.pc + hsig \
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* sqrt(self.cc * (2 - self.cc) * self.mueff) / self.sigma \
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* c_diff
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# Update covariance matrix
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artmp = population[0:self.mu] - old_centroid
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self.C = (1 - self.ccov1 - self.ccovmu + (1 - hsig) \
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* self.ccov1 * self.cc * (2 - self.cc)) * self.C \
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+ self.ccov1 * numpy.outer(self.pc, self.pc) \
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+ self.ccovmu * numpy.dot((self.weights * artmp.T), artmp) \
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/ self.sigma**2
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self.sigma *= numpy.exp((numpy.linalg.norm(self.ps) / self.chiN - 1.) \
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* self.cs / self.damps)
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self.diagD, self.B = numpy.linalg.eigh(self.C)
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indx = numpy.argsort(self.diagD)
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self.cond = self.diagD[indx[-1]]/self.diagD[indx[0]]
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self.diagD = self.diagD[indx]**0.5
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self.B = self.B[:, indx]
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self.BD = self.B * self.diagD
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def computeParams(self, params):
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"""Computes the parameters depending on :math:`\lambda`. It needs to
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be called again if :math:`\lambda` changes during evolution.
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:param params: A dictionary of the manually set parameters.
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"""
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self.mu = params.get("mu", int(self.lambda_ / 2))
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rweights = params.get("weights", "superlinear")
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if rweights == "superlinear":
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self.weights = log(self.mu + 0.5) - \
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numpy.log(numpy.arange(1, self.mu + 1))
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elif rweights == "linear":
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self.weights = self.mu + 0.5 - numpy.arange(1, self.mu + 1)
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elif rweights == "equal":
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self.weights = numpy.ones(self.mu)
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else:
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raise RuntimeError("Unknown weights : %s" % rweights)
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self.weights /= sum(self.weights)
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self.mueff = 1. / sum(self.weights**2)
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self.cc = params.get("ccum", 4. / (self.dim + 4.))
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self.cs = params.get("cs", (self.mueff + 2.) /
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(self.dim + self.mueff + 3.))
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self.ccov1 = params.get("ccov1", 2. / ((self.dim + 1.3)**2 + \
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self.mueff))
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self.ccovmu = params.get("ccovmu", 2. * (self.mueff - 2. + \
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1. / self.mueff) / \
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((self.dim + 2.)**2 + self.mueff))
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self.ccovmu = min(1 - self.ccov1, self.ccovmu)
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self.damps = 1. + 2. * max(0, sqrt((self.mueff - 1.) / \
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(self.dim + 1.)) - 1.) + self.cs
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self.damps = params.get("damps", self.damps)
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class StrategyOnePlusLambda(object):
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"""
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A CMA-ES strategy that uses the :math:`1 + \lambda` paradigme.
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:param parent: An iterable object that indicates where to start the
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evolution. The parent requires a fitness attribute.
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:param sigma: The initial standard deviation of the distribution.
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:param parameter: One or more parameter to pass to the strategy as
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described in the following table, optional.
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"""
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def __init__(self, parent, sigma, **kargs):
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self.parent = parent
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self.sigma = sigma
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self.dim = len(self.parent)
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self.C = numpy.identity(self.dim)
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self.A = numpy.identity(self.dim)
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self.pc = numpy.zeros(self.dim)
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self.computeParams(kargs)
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self.psucc = self.ptarg
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def computeParams(self, params):
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"""Computes the parameters depending on :math:`\lambda`. It needs to
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be called again if :math:`\lambda` changes during evolution.
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:param params: A dictionary of the manually set parameters.
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"""
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# Selection :
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self.lambda_ = params.get("lambda_", 1)
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# Step size control :
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self.d = params.get("d", 1.0 + self.dim/(2.0*self.lambda_))
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self.ptarg = params.get("ptarg", 1.0/(5+sqrt(self.lambda_)/2.0))
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self.cp = params.get("cp", self.ptarg*self.lambda_/(2+self.ptarg*self.lambda_))
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# Covariance matrix adaptation
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self.cc = params.get("cc", 2.0/(self.dim+2.0))
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self.ccov = params.get("ccov", 2.0/(self.dim**2 + 6.0))
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self.pthresh = params.get("pthresh", 0.44)
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def generate(self, ind_init):
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"""Generate a population of :math:`\lambda` individuals of type
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*ind_init* from the current strategy.
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:param ind_init: A function object that is able to initialize an
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individual from a list.
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:returns: A list of individuals.
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"""
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# self.y = numpy.dot(self.A, numpy.random.standard_normal(self.dim))
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arz = numpy.random.standard_normal((self.lambda_, self.dim))
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arz = self.parent + self.sigma * numpy.dot(arz, self.A.T)
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return map(ind_init, arz)
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def update(self, population):
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"""Update the current covariance matrix strategy from the
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*population*.
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:param population: A list of individuals from which to update the
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parameters.
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"""
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population.sort(key=lambda ind: ind.fitness, reverse=True)
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lambda_succ = sum(self.parent.fitness <= ind.fitness for ind in population)
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p_succ = float(lambda_succ) / self.lambda_
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self.psucc = (1-self.cp)*self.psucc + self.cp*p_succ
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if self.parent.fitness <= population[0].fitness:
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x_step = (population[0] - numpy.array(self.parent)) / self.sigma
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self.parent = copy.deepcopy(population[0])
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if self.psucc < self.pthresh:
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self.pc = (1 - self.cc)*self.pc + sqrt(self.cc * (2 - self.cc)) * x_step
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self.C = (1-self.ccov)*self.C + self.ccov * numpy.outer(self.pc, self.pc)
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else:
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self.pc = (1 - self.cc)*self.pc
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self.C = (1-self.ccov)*self.C + self.ccov * (numpy.outer(self.pc, self.pc) + self.cc*(2-self.cc)*self.C)
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self.sigma = self.sigma * exp(1.0/self.d * (self.psucc - self.ptarg)/(1.0-self.ptarg))
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# We use Cholesky since for now we have no use of eigen decomposition
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# Basically, Cholesky returns a matrix A as C = A*A.T
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# Eigen decomposition returns two matrix B and D^2 as C = B*D^2*B.T = B*D*D*B.T
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# So A == B*D
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# To compute the new individual we need to multiply each vector z by A
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# as y = centroid + sigma * A*z
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# So the Cholesky is more straightforward as we don't need to compute
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# the squareroot of D^2, and multiply B and D in order to get A, we directly get A.
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# This can't be done (without cost) with the standard CMA-ES as the eigen decomposition is used
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# to compute covariance matrix inverse in the step-size evolutionary path computation.
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self.A = numpy.linalg.cholesky(self.C)
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