def _get_sampling(self, X, Y):
'''
Initialize population from data.
Parameters
----------
X: np.array
Design variables.
Y: np.array
Performance values.
Returns
-------
sampling: np.array or pymoo.model.sampling.Sampling
Initial population or a sampling method for generating initial population.
'''
if self.pop_init_method == 'lhs':
sampling = LatinHypercubeSampling()
elif self.pop_init_method == 'nds':
sorted_indices = NonDominatedSorting().do(Y)
pop_size = self.algo_kwargs['pop_size']
sampling = X[np.concatenate(sorted_indices)][:pop_size]
# NOTE: use lhs if current samples are not enough
if len(sampling) < pop_size:
rest_sampling = lhs(X.shape[1], pop_size - len(sampling))
sampling = np.vstack([sampling, rest_sampling])
elif self.pop_init_method == 'random':
sampling = FloatRandomSampling()
else:
raise NotImplementedError
return sampling
def __init__(self,
pop_size=100,
sampling=LatinHypercubeSampling(iterations=100,
criterion="maxmin"),
variant="DE/rand/1/bin",
CR=0.5,
F=0.3,
dither="vector",
jitter=False,
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
variant : {{DE/(rand|best)/1/(bin/exp)}}
The different variants of DE to be used. DE/x/y/z where x how to select individuals to be pertubed,
y the number of difference vector to be used and z the crossover type. One of the most common variant
is DE/rand/1/bin.
F : float
The weight to be used during the crossover.
CR : float
The probability the individual exchanges variable values from the donor vector.
dither : {{'no', 'scalar', 'vector'}}
One strategy to introduce adaptive weights (F) during one run. The option allows
the same dither to be used in one iteration ('scalar') or a different one for
each individual ('vector).
jitter : bool
Another strategy for adaptive weights (F). Here, only a very small value is added or
subtracted to the weight used for the crossover for each individual.
"""
_, self.var_selection, self.var_n, self.var_mutation, = variant.split(
"/")
if self.var_mutation == "exp":
mutation = ExponentialCrossover(CR)
elif self.var_mutation == "bin":
mutation = UniformCrossover(CR)
super().__init__(pop_size=pop_size,
sampling=sampling,
selection=RandomSelection(),
crossover=DifferentialEvolutionCrossover(
weight=F, dither=dither, jitter=jitter),
mutation=mutation,
survival=None,
**kwargs)
self.func_display_attrs = disp_single_objective
def _get_sampling(self, X, Y, bound=None, mode=0):
'''
Initialize population from data
'''
if self.pop_init_method == 'lhs':
sampling = LatinHypercubeSampling()
elif self.pop_init_method == 'nds':
sorted_indices = NonDominatedSorting().do(Y)
pop_size = self.algo_kwargs['pop_size']
sampling = X[np.concatenate(sorted_indices)][:pop_size]
# NOTE: use lhs if current samples are not enough
if len(sampling) < pop_size:
if bound is None:
rest_sampling = lhs(X.shape[1], pop_size - len(sampling))
else:
rest_sampling = lhs(X.shape[1], pop_size - len(sampling))
rest_sampling = bound[0] + rest_sampling * (bound[1] - bound[0])
rest_sampling = np.round(rest_sampling)
sampling = np.vstack([sampling, rest_sampling])
elif self.pop_init_method == 'random':
sampling = FloatRandomSampling()
else:
raise NotImplementedError
return sampling
def de(
pop_size=100,
sampling=LatinHypercubeSampling(criterion="maxmin", iterations=100),
variant="DE/rand+best/1/bin",
CR=0.5,
F=0.75,
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
variant : str
CR : float
F : float
Returns
-------
de : :class:`~pymoo.model.algorithm.Algorithm`
Returns an DifferentialEvolution algorithm object.
"""
_, _selection, _n, _mutation, = variant.split("/")
return DifferentialEvolution(pop_size=pop_size,
sampling=sampling,
selection=RandomSelection(),
crossover=DifferentialEvolutionCrossover(weight=F),
mutation=DifferentialEvolutionMutation(_mutation, CR),
**kwargs)
def __init__(self,
n_points_per_iteration=100,
sampling=LatinHypercubeSampling(),
display=SingleObjectiveDisplay(),
**kwargs):
super().__init__(display=display, **kwargs)
self.n_points_per_iteration = n_points_per_iteration
self.sampling = sampling
def de(
pop_size=100,
sampling=LatinHypercubeSampling(iterations=100, criterion="maxmin"),
variant="DE/rand/1/bin",
CR=0.5,
F=0.3,
dither="vector",
jitter=False,
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
variant : {{DE/(rand|best)/1/(bin/exp)}}
The different variants of DE to be used. DE/x/y/z where x how to select individuals to be pertubed,
y the number of difference vector to be used and z the crossover type. One of the most common variant
is DE/rand/1/bin.
F : float
The weight to be used during the crossover.
CR : float
The probability the individual exchanges variable values from the donor vector.
dither : {{'no', 'scalar', 'vector'}}
One strategy to introduce adaptive weights (F) during one run. The option allows
the same dither to be used in one iteration ('scalar') or a different one for
each individual ('vector).
jitter : bool
Another strategy for adaptive weights (F). Here, only a very small value is added or
substracted to the weight used for the crossover for each individual.
Returns
-------
de : :class:`~pymoo.model.algorithm.Algorithm`
Returns an DifferentialEvolution algorithm object.
"""
_, _selection, _n, _mutation, = variant.split("/")
return DifferentialEvolution(
variant,
CR,
F,
dither,
jitter,
pop_size=pop_size,
sampling=sampling,
**kwargs)
def __init__(self, n_initial_samples=50, n_parallel_searches=5, **kwargs):
super().__init__(**kwargs)
# the algorithm to be used for optimization
self.n_parallel_searches = n_parallel_searches
# the initial sampling to be used
self.sampling = LatinHypercubeSampling(iterations=100)
self.n_initial_samples = n_initial_samples
# create a global evaluator that keeps track if the inner algorithms as well
self.evaluator = GlobalEvaluator()
# objects used during the optimization
self.algorithms = []
# display the single-objective metrics
self.func_display_attrs = disp_single_objective
def __init__(self,
x0=None,
sampling=LatinHypercubeSampling(),
n_sample_points="auto",
**kwargs):
super().__init__(**kwargs)
self.x0 = x0
self.sampling = sampling
self.n_sample_points = n_sample_points
def __init__(self,
pop_size=100,
sampling=LatinHypercubeSampling(),
variant="DE/rand/1/bin",
CR=0.5,
F=0.3,
dither="vector",
jitter=False,
display=SingleObjectiveDisplay(),
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
variant : {{DE/(rand|best)/1/(bin/exp)}}
The different variants of DE to be used. DE/x/y/z where x how to select individuals to be pertubed,
y the number of difference vector to be used and z the crossover type. One of the most common variant
is DE/rand/1/bin.
F : float
The weight to be used during the crossover.
CR : float
The probability the individual exchanges variable values from the donor vector.
dither : {{'no', 'scalar', 'vector'}}
One strategy to introduce adaptive weights (F) during one run. The option allows
the same dither to be used in one iteration ('scalar') or a different one for
each individual ('vector).
jitter : bool
Another strategy for adaptive weights (F). Here, only a very small value is added or
subtracted to the weight used for the crossover for each individual.
"""
mating = DifferentialEvolutionMating(variant=variant,
CR=CR,
F=F,
dither=dither,
jitter=jitter)
super().__init__(pop_size=pop_size,
sampling=sampling,
mating=mating,
survival=None,
display=display,
**kwargs)
self.default_termination = SingleObjectiveDefaultTermination()
def __init__(self,
pop_size=200,
n_parallel=10,
sampling=LatinHypercubeSampling(),
display=SingleObjectiveDisplay(),
repair=None,
individual=Individual(),
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
selection : {selection}
crossover : {crossover}
mutation : {mutation}
eliminate_duplicates : {eliminate_duplicates}
n_offsprings : {n_offsprings}
"""
super().__init__(display=display, **kwargs)
self.initialization = Initialization(sampling,
individual=individual,
repair=repair)
self.pop_size = pop_size
self.n_parallel = n_parallel
self.each_pop_size = pop_size // n_parallel
self.solvers = None
self.niches = []
def cmaes(problem, x):
solver = CMAES(x0=x, tolfun=1e-11, tolx=1e-3, restarts=0)
solver.initialize(problem)
solver.next()
return solver
def nelder_mead(problem, x):
solver = NelderMead(X=x)
solver.initialize(problem)
solver._initialize()
solver.n_gen = 1
solver.next()
return solver
self.func_create_solver = nelder_mead
self.default_termination = SingleObjectiveDefaultTermination()
def __init__(self,
variant="DE/rand+best/1/bin",
CR=0.5,
F=0.75,
n_replace=None,
**kwargs):
_, self.var_selection, self.var_n, self.var_mutation, = variant.split("/")
set_if_none(kwargs, 'pop_size', 200)
set_if_none(kwargs, 'sampling', LatinHypercubeSampling(criterion="maxmin", iterations=100))
set_if_none(kwargs, 'crossover', DifferentialEvolutionCrossover(weight=F))
set_if_none(kwargs, 'selection', RandomSelection())
set_if_none(kwargs, 'mutation', DifferentialEvolutionMutation(self.var_mutation, CR))
set_if_none(kwargs, 'survival', None)
super().__init__(**kwargs)
self.n_replace = n_replace
self.func_display_attrs = disp_single_objective
def __init__(self,
variant,
CR,
F,
dither,
jitter,
**kwargs):
_, self.var_selection, self.var_n, self.var_mutation, = variant.split("/")
set_if_none(kwargs, 'pop_size', 200)
set_if_none(kwargs, 'sampling', LatinHypercubeSampling(criterion="maxmin", iterations=100))
set_if_none(kwargs, 'crossover', DifferentialEvolutionCrossover(weight=F, dither=dither, jitter=jitter))
set_if_none(kwargs, 'selection', RandomSelection())
if self.var_mutation == "exp":
set_if_none(kwargs, 'mutation', ExponentialCrossover(CR))
elif self.var_mutation == "bin":
set_if_none(kwargs, 'mutation', UniformCrossover(CR))
set_if_none(kwargs, 'survival', None)
super().__init__(**kwargs)
self.func_display_attrs = disp_single_objective
def __init__(self,
pop_size=20,
w=0.9,
c1=2.0,
c2=2.0,
sampling=LatinHypercubeSampling(),
adaptive=True,
pertube_best=True,
display=PSODisplay(),
repair=None,
individual=Individual(),
**kwargs):
"""
Parameters
----------
pop_size : {pop_size}
sampling : {sampling}
"""
super().__init__(display=display, **kwargs)
self.initialization = Initialization(sampling,
individual=individual,
repair=repair)
self.pop_size = pop_size
self.adaptive = adaptive
self.pertube_best = pertube_best
self.default_termination = SingleObjectiveDefaultTermination()
self.V_max = None
self.w = w
self.c1 = c1
self.c2 = c2
def main():
# get argument values
args = get_args()
# get reference point
if args.ref_point is None:
args.ref_point = get_ref_point(args.problem, args.n_var, args.n_obj,
args.n_init_sample)
t0 = time()
# set seed
np.random.seed(args.seed)
# build problem, get initial samples
problem, true_pfront, X_init, Y_init = build_problem(
args.problem, args.n_var, args.n_obj, args.n_init_sample,
args.n_process)
args.n_var, args.n_obj, args.algo = problem.n_var, problem.n_obj, 'nsga2'
# save arguments and setup logger
save_args(args)
logger = setup_logger(args)
print(problem)
# initialize data exporter
exporter = DataExport(X_init, Y_init, args)
# initialize population
if args.pop_init_method == 'lhs':
sampling = LatinHypercubeSampling()
elif args.pop_init_method == 'nds':
sorted_indices = NonDominatedSorting().do(Y_init)
sampling = X_init[np.concatenate(sorted_indices)][:args.batch_size]
if len(sampling) < args.batch_size:
rest_sampling = lhs(X_init.shape[1],
args.batch_size - len(sampling))
sampling = np.vstack([sampling, rest_sampling])
elif args.pop_init_method == 'random':
sampling = FloatRandomSampling()
else:
raise NotImplementedError
# initialize evolutionary algorithm
ea_algorithm = NSGA2(pop_size=args.batch_size, sampling=sampling)
# find Pareto front
res = minimize(problem,
ea_algorithm, ('n_gen', args.n_iter),
save_history=True)
X_history = np.array([algo.pop.get('X') for algo in res.history])
Y_history = np.array([algo.pop.get('F') for algo in res.history])
# update data exporter
for X_next, Y_next in zip(X_history, Y_history):
exporter.update(X_next, Y_next)
# export all result to csv
exporter.write_csvs()
if true_pfront is not None:
exporter.write_truefront_csv(true_pfront)
# statistics
final_hv = calc_hypervolume(exporter.Y, exporter.ref_point)
print('========== Result ==========')
print('Total runtime: %.2fs' % (time() - t0))
print('Total evaluations: %d, hypervolume: %.4f\n' %
(args.batch_size * args.n_iter, final_hv))
# close logger
if logger is not None:
logger.close()
def _do(self):
x = sample(LatinHypercubeSampling(), self.n_points - self.n_dim,
self.n_dim)
x = map_onto_unit_simplex(x, "kraemer")
x = np.row_stack([x, np.eye(self.n_dim)])
return x
from pymoo.algorithms.so_de import DE
from pymoo.factory import get_problem
from pymoo.operators.sampling.latin_hypercube_sampling import LatinHypercubeSampling
from pymoo.optimize import minimize
problem = get_problem("ackley", n_var=10)
algorithm = DE(pop_size=100,
sampling=LatinHypercubeSampling(iterations=100,
criterion="maxmin"),
variant="DE/rand/1/bin",
CR=0.5,
F=0.3,
dither="vector",
jitter=False)
res = minimize(problem, algorithm, seed=1, verbose=True)
print("Best solution found: \nX = %s\nF = %s" % (res.X, res.F))
def main():
# get argument values
args = get_args()
# get reference point
if args.ref_point is None:
args.ref_point = get_ref_point(args.problem, args.n_var, args.n_obj,
args.n_init_sample)
t0 = time()
# set seed
np.random.seed(args.seed)
# build problem, get initial samples
jsonFile = "/home/picarib/Desktop/cdnet/config/json/sbd_custom.json"
configDirPath = "/home/picarib/Desktop/cdnet/config/sbd_custom/"
dataPath = "/home/picarib/Desktop/cdnet/data/"
config = loadJSON(jsonFile)
interval = 1 if "custom" not in config["RequestModels"] else config[
"RequestModels"]["custom"]["interval"]
isLoadRTable = config["isLoadRTable"]
isLoadSeparatorRank = config["isLoadSeparatorRank"]
mode = config["RoutingMode"] # [no-cache, no-color, tag-color, full-color]
fileSize = config["FileSize"]
runReqNums = config["RunReqNums"] if "RunReqNums" in config else -1
warmUpReqNums = config["WarmUpReqNums"] if "WarmUpReqNums" in config else -1
colorNums = config["colorNums"]
separatorRankIncrement = config["separatorRankIncrement"]
colorList = [
''.join(random.choices(string.ascii_uppercase + string.digits, k=6))
for i in range(colorNums)
]
topo = NetTopology(config, configDirPath, mode, warmUpReqNums, fileSize,
colorList)
topo.build()
extra_params = (topo, fileSize, mode, colorList, runReqNums, warmUpReqNums,
separatorRankIncrement)
problem, X_init, Y_init = build_problem(args.problem,
args.n_var,
args.n_obj,
args.n_init_sample,
args.n_process,
extra_params=extra_params)
args.n_var, args.n_obj, args.algo = problem.n_var, problem.n_obj, 'moeda'
# save arguments and setup logger
save_args(args)
logger = setup_logger(args)
print(problem)
# initialize evolutionary algorithm
ref_dir = get_reference_directions("das-dennis", 2, n_partitions=15)
args.batch_size = min(len(ref_dir), args.batch_size)
# initialize population
if args.pop_init_method == 'lhs':
sampling = LatinHypercubeSampling()
elif args.pop_init_method == 'nds':
sorted_indices = NonDominatedSorting().do(Y_init)
sampling = X_init[np.concatenate(sorted_indices)][:args.batch_size]
if len(sampling) < args.batch_size:
rest_sampling = lhs(X_init.shape[1],
args.batch_size - len(sampling))
sampling = np.vstack([sampling, rest_sampling])
elif args.pop_init_method == 'random':
sampling = FloatRandomSampling()
else:
raise NotImplementedError
ea_algorithm = MOEAD(ref_dir,
n_neighbors=args.batch_size,
sampling=sampling,
crossover=get_crossover("int_one_point"),
mutation=get_mutation("int_pm", prob=1.0 / 13),
decomposition="pbi",
seed=1)
# initialize data exporter
exporter = DataExport(X_init, Y_init, args)
# find Pareto front
res = minimize(problem,
ea_algorithm, ('n_gen', args.n_iter),
save_history=True)
X_history = np.array([algo.pop.get('X') for algo in res.history])
Y_history = np.array([algo.pop.get('F') for algo in res.history])
# update data exporter
for X_next, Y_next in zip(X_history, Y_history):
exporter.update(X_next, Y_next)
# export all result to csv
exporter.write_csvs()
# statistics
final_hv = calc_hypervolume(exporter.Y, exporter.ref_point)
print('========== Result ==========')
print('Total runtime: %.2fs' % (time() - t0))
print('Total evaluations: %d, hypervolume: %.4f\n' %
(args.batch_size * args.n_iter, final_hv))
# close logger
if logger is not None:
logger.close()
class SingleObjectiveGlobalOptimization(Algorithm):
def __init__(self, n_initial_samples=50, n_parallel_searches=5, **kwargs):
super().__init__(**kwargs)
# the algorithm to be used for optimization
self.n_parallel_searches = n_parallel_searches
# the initial sampling to be used
self.sampling = LatinHypercubeSampling(iterations=100)
self.n_initial_samples = n_initial_samples
# create a global evaluator that keeps track if the inner algorithms as well
self.evaluator = GlobalEvaluator()
# objects used during the optimization
self.algorithms = []
# display the single-objective metrics
self.func_display_attrs = disp_single_objective
def _initialize(self):
pop = pop_from_sampling(self.problem, self.sampling,
self.n_initial_samples)
evaluate_if_not_done_yet(self.evaluator,
self.problem,
pop,
algorithm=self)
for i in np.argsort(pop.get("F")[:, 0]):
algorithm = get_algorithm("nelder-mead",
problem=self.problem,
x0=pop[i],
termination=NelderAndMeadTermination(
xtol=1e-3, ftol=1e-3),
evaluator=self.evaluator)
algorithm.initialize()
self.algorithms.append(algorithm)
self.pop = pop
def _next(self):
# all place visited so far
_X, _F, _evaluated_by_algorithm = self.evaluator.history.get(
"X", "F", "algorithm")
# collect attributes from each algorithm and determine whether it has to be replaced or not
pop, F, n_evals = [], [], []
for k, algorithm in enumerate(self.algorithms):
# collect some data from the current algorithms
_pop = algorithm.pop
# if the algorithm has terminated or not
has_finished = algorithm.termination.has_finished(algorithm)
# if the area was already explored before
closest_dist_to_others = vectorized_cdist(
_pop.get("X"),
_X[_evaluated_by_algorithm != algorithm],
func_dist=norm_euclidean_distance(self.problem))
too_close_to_others = (closest_dist_to_others.min(axis=1) <
1e-3).all()
# whether the algorithm is the current best - if yes it will not be replaced
current_best = self.evaluator.opt.get("F") == _pop.get("F").min()
# algorithm not really useful anymore
if not current_best and (has_finished or too_close_to_others):
# find a suitable x0 which is far from other or has good expectations
self.sampling.criterion = lambda X: vectorized_cdist(X, _X
).min()
X = self.sampling.do(self.problem,
self.n_initial_samples).get("X")
# distance in x space to other existing points
x_dist = vectorized_cdist(X,
_X,
func_dist=norm_euclidean_distance(
self.problem)).min(axis=1)
f_pred, f_uncert = predict_by_nearest_neighbors(
_X, _F, X, 5, self.problem)
fronts = NonDominatedSorting().do(
np.column_stack([-x_dist, f_pred, f_uncert]))
I = np.random.choice(fronts[0])
# I = vectorized_cdist(X, _X, func_dist=norm_euclidean_distance(self.problem)).min(axis=1).argmax()
# choose the one with the largest distance to current solutions
x0 = X[[I]]
# replace the current algorithm
algorithm = get_algorithm(
"nelder-mead",
problem=self.problem,
x0=x0,
termination=NelderAndMeadTermination(xtol=1e-3, ftol=1e-3),
evaluator=self.evaluator,
)
algorithm.initialize()
self.algorithms[k] = algorithm
pop.append(algorithm.pop)
F.append(algorithm.pop.get("F"))
n_evals.append(self.evaluator.algorithms[algorithm])
# get the values of all algorithms as arrays
F, n_evals = np.array(F), np.array(n_evals)
rewards = 1 - normalize(F.min(axis=1))[:, 0]
n_evals_total = self.evaluator.n_eval - self.evaluator.algorithms[self]
# calculate the upper confidence bound
ucb = rewards + 0.95 * np.sqrt(np.log(n_evals_total) / n_evals)
I = ucb.argmax()
self.algorithms[I].next()
# create the population object with all algorithms
self.pop = Population.create(*pop)
# update the current optimum
self.opt = self.evaluator.opt
def __init__(self,
pop_size=25,
sampling=LatinHypercubeSampling(),
w=0.9,
c1=2.0,
c2=2.0,
adaptive=True,
initial_velocity="random",
max_velocity_rate=0.20,
pertube_best=True,
display=PSODisplay(),
**kwargs):
"""
Parameters
----------
pop_size : The size of the swarm being used.
sampling : {sampling}
adaptive : bool
Whether w, c1, and c2 are changed dynamically over time. The update uses the spread from the global
optimum to determine suitable values.
w : float
The inertia weight to be used in each iteration for the velocity update. This can be interpreted
as the momentum term regarding the velocity. If `adaptive=True` this is only the
initially used value.
c1 : float
The cognitive impact (personal best) during the velocity update. If `adaptive=True` this is only the
initially used value.
c2 : float
The social impact (global best) during the velocity update. If `adaptive=True` this is only the
initially used value.
initial_velocity : str - ('random', or 'zero')
How the initial velocity of each particle should be assigned. Either 'random' which creates a
random velocity vector or 'zero' which makes the particles start to find the direction through the
velocity update equation.
max_velocity_rate : float
The maximum velocity rate. It is determined variable (and not vector) wise. We consider the rate here
since the value is normalized regarding the `xl` and `xu` defined in the problem.
pertube_best : bool
Some studies have proposed to mutate the global best because it has been found to converge better.
Which means the population size is reduced by one particle and one function evaluation is spend
additionally to permute the best found solution so far.
"""
super().__init__(display=display, **kwargs)
self.initialization = Initialization(sampling)
self.pop_size = pop_size
self.adaptive = adaptive
self.pertube_best = pertube_best
self.default_termination = SingleObjectiveDefaultTermination()
self.V_max = None
self.initial_velocity = initial_velocity
self.max_velocity_rate = max_velocity_rate
self.w = w
self.c1 = c1
self.c2 = c2
from pymoo.algorithms.so_random_search import RandomSearch
from pymoo.factory import get_problem
from pymoo.operators.sampling.latin_hypercube_sampling import LatinHypercubeSampling
from pymoo.optimize import minimize
problem = get_problem("ackley")
algorithm = RandomSearch(n_points_per_iteration=100,
sampling=LatinHypercubeSampling())
res = minimize(problem, algorithm, ("n_gen", 5), seed=1, verbose=False)
print("Best solution found: \nX = %s\nF = %s" % (res.X, res.F))
