def newton_method(fun,
x0,
fprime,
args,
tol=1.0e-4,
maxiter=1000,
callback=None):
'''ニュートン法 ステップサイズにArmijo条件
'''
x = numpy.array(x0)
A, b = args
for itr in xrange(maxiter):
direction = -1 * numpy.linalg.solve(A, fprime(x, *args))
alpha, obj_current, obj_next = armijo_stepsize(fun,
x,
fprime,
direction,
args=args)
if numpy.linalg.norm(obj_current - obj_next) < tol:
break
x = x + alpha * direction
if callback is not None:
callback(x)
result = OptimizeResult()
result.x = x
result.fun = fun(x, *args)
result.nit = itr
return result
def steepest_decent(fun,
x0,
fprime,
args,
tol=1.0e-4,
maxiter=1000,
callback=None):
'''最急降下法
'''
x = numpy.array(x0)
for itr in xrange(maxiter):
direction = -1 * fprime(x, *args)
alpha, obj_current, obj_next = armijo_stepsize(fun,
x,
fprime,
direction,
args=args)
if numpy.linalg.norm(obj_current - obj_next) < tol:
break
x = x + alpha * direction
if callback is not None:
callback(x)
result = OptimizeResult()
result.x = x
result.fun = fun(x, *args)
result.nit = itr
return result
def get_optimization_results(
t,
population,
factorial_cost,
scalar_fitness,
skill_factor,
pairs=None,
tasks=None):
K = len(set(skill_factor))
N = len(population) // 2
results = []
for k in range(K):
result = OptimizeResult()
x, fun = get_best_individual(
population, factorial_cost, scalar_fitness, skill_factor, k)
result.x = x
result.fun = fun
result.nit = t
result.nfev = (t + 1) * N
if pairs is not None:
result.pair = pairs[k, :]
else:
result.pair = None
if tasks is not None:
result.ucb_value = tasks[k].ucb_solver.value
else:
result.ucb_value = None
results.append(result)
return results
def result(self):
""" The OptimizeResult """
res = OptimizeResult()
res.x = self._xmin
res.fun = self._fvalue
res.message = self._message
res.nit = self._step_record
return res
def result(self):
""" The OptimizeResult """
res = OptimizeResult()
res.x = self.es.xbest
res.fun = self.es.ebest
res.nit = self._iter
res.ncall = self.owf.nb_fun_call
return res
def result(self):
""" The OptimizeResult """
res = OptimizeResult()
res.x = self._xmin
res.fun = self._fvalue
res.message = self._message
res.nit = self._step_record
return res
def result(self):
""" The OptimizeResult """
res = OptimizeResult()
res.x = self.es.xbest
res.fun = self.es.ebest
res.nit = self._iter
res.ncall = self.owf.nb_fun_call
return res
def get_optimization_results(t, N, factors, taskset):
K = len(factors)
results = []
for k in range(K):
factor = factors[k]
result = OptimizeResult()
result.x = deepcopy(factor.theta)
result.fun = factor.f_opt
result.nit = t
result.nfev = (t + 1) * 2 * N
result.message = deepcopy(taskset.normalizers)
results.append(result)
return results
def get_results(self, t):
K = self.K
N = self.args.pop_size
results = []
for k in range(K):
result = OptimizeResult()
x, fun = self.stos[k].population[0], self.stos[k].fitness[0]
result.x = x
result.fun = fun
result.nit = t
result.nfev = (t + 1) * N
result.pair = self.stos[k].pair
result.ucb_value = self.stos[k].ucb.value
results.append(result)
return results
def get_optimization_results(t, population, factorial_cost, scalar_fitness,
skill_factor, message):
K = len(set(skill_factor))
N = len(population) // 2
results = []
for k in range(K):
result = OptimizeResult()
x, fun = get_best_individual(population, factorial_cost,
scalar_fitness, skill_factor, k)
result.x = x
result.fun = fun
result.message = message
result.nit = t
result.nfev = (t + 1) * N
mean, std = get_statistics(factorial_cost, skill_factor, k)
result.mean = mean
result.std = std
results.append(result)
return results
def steepest_decent(fun, x0, fprime, args, tol=1.0e-4, maxiter=1000,
callback=None):
'''最急降下法
'''
x = numpy.array(x0)
for itr in xrange(maxiter):
direction = -1 * fprime(x, *args)
alpha, obj_current, obj_next = armijo_stepsize(fun, x, fprime, direction, args=args)
if numpy.linalg.norm(obj_current - obj_next) < tol:
break
x = x + alpha * direction
if callback is not None:
callback(x)
result = OptimizeResult()
result.x = x
result.fun = fun(x, *args)
result.nit = itr
return result
def newton_method(fun, x0, fprime, args, tol=1.0e-4, maxiter=1000,
callback=None):
'''ニュートン法 ステップサイズにArmijo条件
'''
x = numpy.array(x0)
A, b = args
for itr in xrange(maxiter):
direction = -1 * numpy.linalg.solve(A, fprime(x, *args))
alpha, obj_current, obj_next = armijo_stepsize(fun, x, fprime, direction, args=args)
if numpy.linalg.norm(obj_current - obj_next) < tol:
break
x = x + alpha * direction
if callback is not None:
callback(x)
result = OptimizeResult()
result.x = x
result.fun = fun(x, *args)
result.nit = itr
return result
def model_policy_gradient(
f: Callable[..., float],
x0: np.ndarray,
*,
args=(),
learning_rate: float = 1e-2,
decay_rate: float = 0.96,
decay_steps: int = 5,
log_sigma_init: float = -5.0,
max_iterations: int = 1000,
batch_size: int = 10,
radius_coeff: float = 3.0,
warmup_steps: int = 10,
batch_size_model: int = 65536,
save_func_vals: bool = False,
random_state: "cirq.RANDOM_STATE_OR_SEED_LIKE" = None,
known_values: Optional[Tuple[List[np.ndarray], List[float]]] = None,
max_evaluations: Optional[int] = None
) -> scipy.optimize.OptimizeResult:
"""Model policy gradient algorithm for black-box optimization.
The idea of this algorithm is to perform policy gradient, but estimate
the function values using a surrogate model.
The surrogate model is a least-squared quadratic
fit to points sampled from the vicinity of the current iterate.
Args:
f: The function to minimize.
x0: An initial guess.
args: Additional arguments to pass to the function.
learning_rate: The learning rate for the policy gradient.
decay_rate: the learning decay rate for the Adam optimizer.
decay_steps: the learning decay steps for the Adam optimizer.
log_sigma_init: the intial value for the sigma of the policy
in the log scale.
max_iterations: The maximum number of iterations to allow before
termination.
batch_size: The number of points to sample in each iteration. The cost
of evaluation of these samples are computed through the
quantum computer cost model.
radius_coeff: The ratio determining the size of the radius around
the current iterate to sample points from to build the quadratic model.
The ratio is with respect to the maximal ratio of the samples
from the current policy.
warmup_steps: The number of steps before the model policy gradient is performed.
before these steps, we use the policy gradient without the model.
batch_size_model: The model sample batch size.
After we fit the quadratic model, we use the model to evaluate
on big enough batch of samples.
save_func_vals: whether to compute and save the function values for
the current value of parameter.
random_state: A seed (int) or `np.random.RandomState` class to use when
generating random values. If not set, defaults to using the module
methods in `np.random`.
known_values: Any prior known values of the objective function.
This is given as a tuple where the first element is a list
of points and the second element is a list of the function values
at those points.
max_evaluations: The maximum number of function evaluations to allow
before termination.
Returns:
Scipy OptimizeResult
"""
random_state = value.parse_random_state(random_state)
if known_values is not None:
known_xs, known_ys = known_values
known_xs = [np.copy(x) for x in known_xs]
known_ys = [np.copy(y) for y in known_ys]
else:
known_xs, known_ys = [], []
if max_evaluations is None:
max_evaluations = np.inf
n = len(x0)
log_sigma = np.ones(n) * log_sigma_init
sigma = np.exp(log_sigma)
# set up the first and second moment estimate
m_mean = np.zeros(n)
v_mean = np.zeros(n)
m_log_sigma = np.zeros(n)
v_log_sigma = np.zeros(n)
# set up lr schedule and optimizer
lr_schedule1 = _ExponentialSchedule(learning_rate,
decay_steps=decay_steps,
decay_rate=decay_rate,
staircase=True)
lr_schedule2 = _ExponentialSchedule(learning_rate,
decay_steps=decay_steps,
decay_rate=decay_rate,
staircase=True)
_, f = wrap_function(f, args)
res = OptimizeResult()
current_x = np.copy(x0)
res.x_iters = [] # initializes as lists
res.xs_iters = []
res.ys_iters = []
res.func_vals = []
res.fun = 0
total_evals = 0
num_iter = 0
message = None
# stats
history_max = -np.inf
while num_iter < max_iterations:
# get samples from the current policy to evaluate
z = random_state.randn(batch_size, n)
new_xs = sigma * z + current_x
if total_evals + batch_size > max_evaluations:
message = "Reached maximum number of evaluations."
break
# Evaluate points
res.xs_iters.append(new_xs)
new_ys = [f(x) for x in new_xs]
res.ys_iters.append(new_ys)
total_evals += batch_size
known_xs.extend(new_xs)
known_ys.extend(new_ys)
# Save function value
if save_func_vals:
res.func_vals.append(f(current_x))
res.x_iters.append(np.copy(current_x))
res.fun = res.func_vals[-1]
# current sampling radius (maximal)
max_radius = 0
for x in new_xs:
if np.linalg.norm(x - current_x) > max_radius:
max_radius = np.linalg.norm(x - current_x)
reward = [-y for y in new_ys]
# warmup steps control whether to use the model to estimate the f
if num_iter >= warmup_steps:
# Determine points to use to build model
model_xs = []
model_ys = []
for x, y in zip(known_xs, known_ys):
if np.linalg.norm(x - current_x) < radius_coeff * max_radius:
model_xs.append(x)
model_ys.append(y)
# safer way without the `SVD` not converging
try:
model = _get_quadratic_model(model_xs, model_ys, x)
use_model = True
except ValueError:
use_model = False
if use_model:
# get samples (from model)
z = random_state.randn(batch_size_model, n)
new_xs = sigma * z + current_x
# use the model for prediction
new_ys = model.predict(new_xs - current_x)
reward = [-y for y in new_ys]
reward = np.array(reward)
# stats
reward_mean = np.mean(reward)
reward_max = np.max(reward)
if reward_max > history_max:
history_max = reward_max
# subtract baseline
reward = reward - reward_mean
# analytic derivatives (natural gradient policy gradient)
delta_mean = np.dot(z.T, reward) * sigma
delta_log_sigma = np.dot(z.T**2, reward) / np.sqrt(2)
delta_mean_norm = np.linalg.norm(np.dot(z.T, reward))
delta_log_sigma_norm = np.linalg.norm(np.dot(z.T**2, reward))
delta_mean = delta_mean / delta_mean_norm
delta_log_sigma = delta_log_sigma / delta_log_sigma_norm
# gradient ascend to update the parameters
current_x, m_mean, v_mean = _adam_update(delta_mean,
current_x,
num_iter,
m_mean,
v_mean,
lr_schedule=lr_schedule1)
log_sigma, m_log_sigma, v_log_sigma = _adam_update(
delta_log_sigma,
log_sigma,
num_iter,
m_log_sigma,
v_log_sigma,
lr_schedule=lr_schedule2,
)
log_sigma = np.clip(log_sigma, -20.0, 2.0)
sigma = np.exp(log_sigma)
num_iter += 1
final_val = f(current_x)
res.func_vals.append(final_val)
if message is None:
message = "Reached maximum number of iterations."
res.x_iters.append(current_x)
total_evals += 1
res.x = current_x
res.fun = final_val
res.nit = num_iter
res.nfev = total_evals
res.message = message
return res
def _sequential_random_embeddings(f,
x0,
bounds,
n_reduced_dims_eff=3,
n_embeddings=10,
verbosity=1,
**optimizer_kwargs):
"""
Implementation of the Sequential Random Embeddings algorithm described in
+++++
H. Qian, Y.-Q. Hu, and Y. Yu, Derivative-Free Optimization of High-Dimensional Non-Convex
Functions by Sequential Random Embeddings, Proceedings of the Twenty-Fifth International Joint
Conference on Artificial Intelligence, AAAI Press (2016).
+++++
The idea is basically to reduce high-dimensional problems to low-dimensional ones by embedding
the original, high-dimensional search space ℝ^h into a low dimensional one, ℝ^l, by
sequentially applying the random linear transformation
x(n+1) = α(n+1)x(n) + A•y(n+1), x ∈ ℝ^h, y ∈ ℝ^l, A ∈ N(0, 1)^(h×l), α ∈ ℝ
and minimizing the objective function f(αx + A•y) w.r.t. (α, y).
:param f: [callable] Objective function. Must accept its argument x as numpy array
:param x0: [np.array] Initial values for the bacteria population in the original,
high-dimensional space ℝ^h
:param bounds: [callable] Bounds projection, see description of parameter
``projection_callback`` in :func:`local_search.bfgs_b`
:param n_reduced_dims_eff: [int] Effective dimension of the embedded problem, ℝ^(l+1)
:param n_embeddings: [int] Number of embedding iterations
:param verbosity: [int] Output verbosity. Must be 0, 1, or 2
:param optimizer_args: [dict] Arguments to pass to the actual optimization routine
:return: Best minimum of f found [scipy.optimize.OptimizeResult]
"""
assert verbosity in [0, 1, 2], 'verbosity must be 0, 1, or 2.'
orig_dim = x0.shape[1]
x = np.zeros(orig_dim)
x_best = x.copy()
f_best = np.inf
nfev = nit = 0
success_best = False
for i in range(n_embeddings):
A = np.random.normal(size=(orig_dim, n_reduced_dims_eff - 1))
# Normalize rows of A
normalization_sum = A.sum(axis=1)
normalization_sum = np.where(normalization_sum == 0, 1,
normalization_sum)
A = A / normalization_sum[:, np.newaxis]
def f_embedded(arg):
return f(bounds(arg[0] * x + A.dot(arg[1:]))[0])
# Set up bounds callback
def bounds_embedded(arg):
bounds_hit = np.zeros(len(arg), dtype=bool)
x_proj, bounds_hit_orig = bounds(arg[0] * x + A.dot(arg[1:]))
if bounds_hit_orig.any(
): # Boundary hit in original, non-embedded variable
arg[1:] = np.linalg.lstsq(A, x_proj - arg[0] * x,
rcond=None)[0]
bounds_hit[1:] = (A[bounds_hit_orig] != 0).any(axis=0)
return arg, bounds_hit
# Set up y0
y0 = np.zeros((x0.shape[0], n_reduced_dims_eff))
y0[:, 0] = 1
y0[:, 1:] = np.array(
[np.linalg.lstsq(A, x_orig - x, rcond=None)[0] for x_orig in x0])
if verbosity > 0:
infoMsg = f'\nEmbedding iteration {i}'
print(infoMsg)
print('-' * len(infoMsg))
optimizer_kwargs['verbosity'] = verbosity
with warnings.catch_warnings():
warnings.filterwarnings(
'ignore',
message=
'Found initial conditions outside the defined search domain.')
res_embedded = optimize(f_embedded,
x0=y0,
bounds=bounds_embedded,
**optimizer_kwargs)
y = res_embedded.x
f_val = res_embedded.fun
nfev += res_embedded.nfev
nit += res_embedded.nit
x = bounds(y[0] * x + A.dot(y[1:]))[0]
if verbosity > 0:
print(f'Random embedding gave x = {x}.')
if f_val < f_best:
f_best = f_val
x_best = x.copy()
success_best = res_embedded.success
result = OptimizeResult()
result.success = success_best
result.x = x_best
result.fun = f_best
result.nfev = nfev
result.nit = nit
result.trace = None
return result
def model_gradient_descent(
f: Callable[..., float],
x0: np.ndarray,
*,
args=(),
rate: float = 1e-1,
sample_radius: float = 1e-1,
n_sample_points: int = 100,
n_sample_points_ratio: Optional[float] = None,
rate_decay_exponent: float = 0.0,
stability_constant: float = 0.0,
sample_radius_decay_exponent: float = 0.0,
tol: float = 1e-8,
known_values: Optional[Tuple[List[np.ndarray], List[float]]] = None,
max_iterations: Optional[int] = None,
max_evaluations: Optional[int] = None) -> scipy.optimize.OptimizeResult:
"""Model gradient descent algorithm for black-box optimization.
The idea of this algorithm is to perform gradient descent, but estimate
the gradient using a surrogate model instead of, say, by
finite-differencing. The surrogate model is a least-squared quadratic
fit to points sampled from the vicinity of the current iterate.
This algorithm works well when you have an initial guess which is in the
convex neighborhood of a local optimum and you want to converge to that
local optimum. It's meant to be used when the function is stochastic.
Args:
f: The function to minimize.
x0: An initial guess.
args: Additional arguments to pass to the function.
rate: The learning rate for the gradient descent.
sample_radius: The radius around the current iterate to sample
points from to build the quadratic model.
n_sample_points: The number of points to sample in each iteration.
n_sample_points_ratio: This specifies the number of points to sample
in each iteration as a coefficient of the number of points
required to exactly determine a quadratic model. The number
of sample points will be this coefficient times (n+1)(n+2)/2,
rounded up, where n is the number of parameters.
Setting this overrides n_sample_points.
rate_decay_exponent: Controls decay of learning rate.
In each iteration, the learning rate is changed to the
base learning rate divided by (i + 1 + S)**a, where S
is the stability constant and a is the rate decay exponent
(this parameter).
stability_constant: Affects decay of learning rate.
In each iteration, the learning rate is changed to the
base learning rate divided by (i + 1 + S)**a, where S
is the stability constant (this parameter) and a is the rate decay
exponent.
sample_radius_decay_exponent: Controls decay of sample radius.
tol: The algorithm terminates when the difference between the current
iterate and the next suggested iterate is smaller than this value.
known_values: Any prior known values of the objective function.
This is given as a tuple where the first element is a list
of points and the second element is a list of the function values
at those points.
max_iterations: The maximum number of iterations to allow before
termination.
max_evaluations: The maximum number of function evaluations to allow
before termination.
Returns:
Scipy OptimizeResult
"""
if known_values is not None:
known_xs, known_ys = known_values
known_xs = [np.copy(x) for x in known_xs]
known_ys = [np.copy(y) for y in known_ys]
else:
known_xs, known_ys = [], []
if max_iterations is None:
max_iterations = np.inf
if max_evaluations is None:
max_evaluations = np.inf
n = len(x0)
if n_sample_points_ratio is not None:
n_sample_points = int(
np.ceil(n_sample_points_ratio * (n + 1) * (n + 2) / 2))
_, f = wrap_function(f, args)
res = OptimizeResult()
current_x = np.copy(x0)
res.x_iters = [] # initializes as lists
res.xs_iters = []
res.ys_iters = []
res.func_vals = []
res.model_vals = [None]
res.fun = 0
total_evals = 0
num_iter = 0
converged = False
message = None
while num_iter < max_iterations:
current_sample_radius = (sample_radius /
(num_iter + 1)**sample_radius_decay_exponent)
# Determine points to evaluate
# in ball around current point
new_xs = [np.copy(current_x)] + [
current_x + _random_point_in_ball(n, current_sample_radius)
for _ in range(n_sample_points)
]
if total_evals + len(new_xs) > max_evaluations:
message = 'Reached maximum number of evaluations.'
break
# Evaluate points
res.xs_iters.append(new_xs)
new_ys = [f(x) for x in new_xs]
res.ys_iters.append(new_ys)
total_evals += len(new_ys)
known_xs.extend(new_xs)
known_ys.extend(new_ys)
# Save function value
res.func_vals.append(new_ys[0])
res.x_iters.append(np.copy(current_x))
res.fun = res.func_vals[-1]
# Determine points to use to build model
model_xs = []
model_ys = []
for x, y in zip(known_xs, known_ys):
if np.linalg.norm(x - current_x) < current_sample_radius:
model_xs.append(x)
model_ys.append(y)
# Build and solve model
model_gradient, model = _get_least_squares_model_gradient(
model_xs, model_ys, current_x)
# calculate the gradient and update the current point
gradient_norm = np.linalg.norm(model_gradient)
decayed_rate = (
rate / (num_iter + 1 + stability_constant)**rate_decay_exponent)
# Convergence criteria
if decayed_rate * gradient_norm < tol:
converged = True
message = 'Optimization converged successfully.'
break
# Update
current_x -= decayed_rate * model_gradient
res.model_vals.append(
model.predict([-decayed_rate * model_gradient])[0])
num_iter += 1
if converged:
final_val = res.func_vals[-1]
else:
final_val = f(current_x)
res.func_vals.append(final_val)
if message is None:
message = 'Reached maximum number of iterations.'
res.x_iters.append(current_x)
total_evals += 1
res.x = current_x
res.fun = final_val
res.nit = num_iter
res.nfev = total_evals
res.message = message
return res
def optimize_minimize_mhmcmc_cluster(objective,
bounds,
args=(),
x0=None,
T=1,
N=3,
burnin=100000,
maxiter=1000000,
target_ar=0.4,
ar_tolerance=0.05,
cluster_eps=DEFAULT_CLUSTER_EPS,
rnd_seed=None,
collect_samples=None,
logger=None):
"""
Minimize objective function and return up to N local minima solutions.
:param objective: Objective function to minimize. Takes unpacked args as function call arguments and returns
a float.
:type objective: Callable(\*args) -> float
:param bounds: Bounds of the parameter space.
:type bounds: scipy.optimize.Bounds
:param args: Any additional fixed parameters needed to completely specify the objective function.
:type args: tuple or list
:param x0: Initial guess. If None, will be selected randomly and uniformly within the parameter bounds.
:type x0: numpy.array with same shape as elements of bounds
:param T: The "temperature" parameter for the accept or reject criterion. To sample the domain well,
should be in the order of the typical difference in local minima objective valuations.
:type T: float
:param N: Maximum number of minima to return
:type N: int
:param burnin: Number of random steps to discard before starting to accumulate statistics.
:type burnin: int
:param maxiter: Maximum number of steps to take (including burnin).
:type maxiter: int
:param target_ar: Target acceptance rate of point samples generated by stepping.
:type target_ar: float between 0 and 1
:param ar_tolerance: Tolerance on the acceptance rate before actively adapting the step size.
:type ar_tolerance: float
:param cluster_eps: Point proximity tolerance for DBSCAN clustering, in normalized bounds coordinates.
:type cluster_eps: float
:param rnd_seed: Random seed to force deterministic behaviour
:type rnd_seed: int
:param collect_samples: If not None and integral type, collect collect_samples at regular intervals
and return as part of solution.
:type collect_samples: int or NoneType
:param logger: Logger instance for outputting log messages.
:return: OptimizeResult containing solution(s) and solver data.
:rtype: scipy.optimize.OptimizeResult with additional attributes
"""
@call_counter
def obj_counted(*args):
return objective(*args)
# end func
assert maxiter >= 2 * burnin, "maxiter {} should be at least twice burnin steps {}".format(
maxiter, burnin)
main_iter = maxiter - burnin
if collect_samples is not None:
assert isinstance(collect_samples,
int), "collect_samples expected to be integral type"
assert collect_samples > 0, "collect_samples expected to be positive"
# end if
beta = 1.0 / T
if rnd_seed is None:
rnd_seed = int(time.time() * 1000) % (1 << 31)
# end if
np.random.seed(rnd_seed)
if logger:
logger.info('Using random seed {}'.format(rnd_seed))
# end
if x0 is None:
x0 = np.random.uniform(bounds.lb, bounds.ub)
# end if
assert np.all((x0 >= bounds.lb) & (x0 <= bounds.ub))
x = x0.copy()
funval = obj_counted(x, *args)
# Set up stepper with adaptive acceptance rate
stepper = BoundedRandNStepper(bounds)
stepper = AdaptiveStepsize(stepper,
accept_rate=target_ar,
ar_tolerance=ar_tolerance,
interval=50)
# -------------------------------
# DO BURN-IN
rejected_randomly = 0
accepted_burnin = 0
tracked_range = tqdm(range(burnin), total=burnin, desc='BURN-IN')
if logger:
stepper.logger = lambda msg: tracked_range.write(logger.name + ':' +
msg)
else:
stepper.logger = tracked_range.write
# end if
for _ in tracked_range:
x_new = stepper(x)
funval_new = obj_counted(x_new, *args)
log_alpha = -(funval_new - funval) * beta
if log_alpha > 0 or np.log(np.random.rand()) <= log_alpha:
x = x_new
funval = funval_new
stepper.notify_accept()
accepted_burnin += 1
elif log_alpha <= 0:
rejected_randomly += 1
# end if
# end for
ar = float(accepted_burnin) / burnin
if logger:
logger.info("Burn-in acceptance rate: {}".format(ar))
# end if
# -------------------------------
# DO MAIN LOOP
if collect_samples is not None:
nsamples = min(collect_samples, main_iter)
sample_cadence = main_iter / nsamples
samples = np.zeros((nsamples, len(x)))
samples_fval = np.zeros(nsamples)
# end if
accepted = 0
rejected_randomly = 0
minima_sorted = SortedList(
key=lambda rec: rec[1]) # Sort by objective function value
hist = HistogramIncremental(bounds, nbins=100)
# Cached a lot of potential minimum values, as these need to be clustered before return N results
N_cached = int(np.ceil(N * main_iter / 500))
next_sample = 0.0
sample_count = 0
tracked_range = tqdm(range(main_iter), total=main_iter, desc='MAIN')
if logger:
stepper.logger = lambda msg: tracked_range.write(logger.name + ':' +
msg)
else:
stepper.logger = tracked_range.write
# end if
for i in tracked_range:
if collect_samples and i >= next_sample:
assert sample_count < collect_samples
samples[sample_count] = x
samples_fval[sample_count] = funval
sample_count += 1
next_sample += sample_cadence
# end if
x_new = stepper(x)
funval_new = obj_counted(x_new, *args)
log_alpha = -(funval_new - funval) * beta
if log_alpha > 0 or np.log(np.random.rand()) <= log_alpha:
x = x_new
funval = funval_new
minima_sorted.add((x, funval))
if len(minima_sorted) > N_cached:
minima_sorted.pop()
# end if
stepper.notify_accept()
hist += x
accepted += 1
elif log_alpha <= 0:
rejected_randomly += 1
# end if
# end for
stepper.logger = None
ar = float(accepted) / main_iter
if logger:
logger.info("Acceptance rate: {}".format(ar))
logger.info("Best minima (before clustering):\n{}".format(
np.array([_mx[0] for _mx in minima_sorted[:10]])))
# end if
# -------------------------------
# Cluster minima and associate each cluster with a local minimum.
# Using a normalized coordinate space for cluster detection.
x_range = bounds.ub - bounds.lb
pts = np.array([x[0] for x in minima_sorted])
fvals = np.array([x[1] for x in minima_sorted])
pts_norm = (pts - bounds.lb) / x_range
_, labels = dbscan(pts_norm, eps=cluster_eps, min_samples=21, n_jobs=-1)
# Compute mean of each cluster and evaluate objective function at cluster mean locations.
minima_candidates = []
for grp in range(max(labels) + 1):
mask = (labels == grp)
mean_loc = np.mean(pts[mask, :], axis=0)
# Evaluate objective function precisely at the mean location of each cluster
fval = obj_counted(mean_loc, *args)
minima_candidates.append((mean_loc, grp, fval))
# end for
# Rank minima locations by objective function.
minima_candidates.sort(key=lambda c: c[2])
# Pick up to N solutions
solutions = minima_candidates[:N]
# Put results into OptimizeResult container.
# Add histograms to output result (in form of scipy.stats.rv_histogram)
solution = OptimizeResult()
solution.x = np.array([s[0] for s in solutions])
solution.clusters = [pts[(labels == s[1])] for s in solutions]
solution.cluster_funvals = [fvals[(labels == s[1])] for s in solutions]
solution.bins = hist.bins
solution.distribution = hist.histograms
solution.acceptance_rate = ar
solution.success = True
solution.status = 0
if len(solutions) > 0:
solution.message = 'SUCCESS: Found {} local minima'.format(
len(solutions))
else:
solution.message = 'WARNING: Found no clusters within tolerance {}'.format(
cluster_eps)
# end if
solution.fun = np.array([s[2] for s in solutions])
solution.jac = None
solution.nfev = obj_counted.counter
solution.njev = 0
solution.nit = main_iter
solution.maxcv = None
solution.samples = samples if collect_samples else None
solution.sample_funvals = samples_fval if collect_samples else None
solution.bounds = bounds
solution.version = 's0.3' # Solution version for future traceability
solution.rnd_seed = rnd_seed
return solution
def dual_annealing(func, x0, bounds, args=(), maxiter=1000,
local_search_options={}, initial_temp=5230.,
restart_temp_ratio=2.e-5, visit=2.62, accept=-5.0,
maxfun=1e7, seed=None, no_local_search=False,
callback=None):
"""
Find the global minimum of a function using Dual Annealing.
Parameters
----------
func : callable
The objective function to be minimized. Must be in the form
``f(x, *args)``, where ``x`` is the argument in the form of a 1-D array
and ``args`` is a tuple of any additional fixed parameters needed to
completely specify the function.
x0 : ndarray, shape(n,)
A single initial starting point coordinates. If ``None`` is provided,
initial coordinates are automatically generated (using the ``reset``
method from the internal ``EnergyState`` class).
bounds : sequence, shape (n, 2)
Bounds for variables. ``(min, max)`` pairs for each element in ``x``,
defining bounds for the objective function parameter.
args : tuple, optional
Any additional fixed parameters needed to completely specify the
objective function.
maxiter : int, optional
The maximum number of global search iterations. Default value is 1000.
local_search_options : dict, optional
Extra keyword arguments to be passed to the local minimizer
(`minimize`). Some important options could be:
``method`` for the minimizer method to use and ``args`` for
objective function additional arguments.
initial_temp : float, optional
The initial temperature, use higher values to facilitates a wider
search of the energy landscape, allowing dual_annealing to escape
local minima that it is trapped in. Default value is 5230. Range is
(0.01, 5.e4].
restart_temp_ratio : float, optional
During the annealing process, temperature is decreasing, when it
reaches ``initial_temp * restart_temp_ratio``, the reannealing process
is triggered. Default value of the ratio is 2e-5. Range is (0, 1).
visit : float, optional
Parameter for visiting distribution. Default value is 2.62. Higher
values give the visiting distribution a heavier tail, this makes
the algorithm jump to a more distant region. The value range is (0, 3].
accept : float, optional
Parameter for acceptance distribution. It is used to control the
probability of acceptance. The lower the acceptance parameter, the
smaller the probability of acceptance. Default value is -5.0 with
a range (-1e4, -5].
maxfun : int, optional
Soft limit for the number of objective function calls. If the
algorithm is in the middle of a local search, this number will be
exceeded, the algorithm will stop just after the local search is
done. Default value is 1e7.
seed : {int or `numpy.random.RandomState` instance}, optional
If `seed` is not specified the `numpy.random.RandomState` singleton is
used.
If `seed` is an int, a new ``RandomState`` instance is used,
seeded with `seed`.
If `seed` is already a ``RandomState`` instance, then that
instance is used.
Specify `seed` for repeatable minimizations. The random numbers
generated with this seed only affect the visiting distribution
function and new coordinates generation.
no_local_search : bool, optional
If `no_local_search` is set to True, a traditional Generalized
Simulated Annealing will be performed with no local search
strategy applied.
callback : callable, optional
A callback function with signature ``callback(x, f, context)``,
which will be called for all minima found.
``x`` and ``f`` are the coordinates and function value of the
latest minimum found, and ``context`` has value in [0, 1, 2], with the
following meaning:
- 0: minimum detected in the annealing process.
- 1: detection occured in the local search process.
- 2: detection done in the dual annealing process.
If the callback implementation returns True, the algorithm will stop.
Returns
-------
res : OptimizeResult
The optimization result represented as a `OptimizeResult` object.
Important attributes are: ``x`` the solution array, ``fun`` the value
of the function at the solution, and ``message`` which describes the
cause of the termination.
See `OptimizeResult` for a description of other attributes.
Notes
-----
This function implements the Dual Annealing optimization. This stochastic
approach derived from [3]_ combines the generalization of CSA (Classical
Simulated Annealing) and FSA (Fast Simulated Annealing) [1]_ [2]_ coupled
to a strategy for applying a local search on accepted locations [4]_.
An alternative implementation of this same algorithm is described in [5]_
and benchmarks are presented in [6]_. This approach introduces an advanced
method to refine the solution found by the generalized annealing
process. This algorithm uses a distorted Cauchy-Lorentz visiting
distribution, with its shape controlled by the parameter :math:`q_{v}`
.. math::
g_{q_{v}}(\\Delta x(t)) \\propto \\frac{ \\
\\left[T_{q_{v}}(t) \\right]^{-\\frac{D}{3-q_{v}}}}{ \\
\\left[{1+(q_{v}-1)\\frac{(\\Delta x(t))^{2}} { \\
\\left[T_{q_{v}}(t)\\right]^{\\frac{2}{3-q_{v}}}}}\\right]^{ \\
\\frac{1}{q_{v}-1}+\\frac{D-1}{2}}}
Where :math:`t` is the artificial time. This visiting distribution is used
to generate a trial jump distance :math:`\\Delta x(t)` of variable
:math:`x(t)` under artificial temperature :math:`T_{q_{v}}(t)`.
From the starting point, after calling the visiting distribution
function, the acceptance probability is computed as follows:
.. math::
p_{q_{a}} = \\min{\\{1,\\left[1-(1-q_{a}) \\beta \\Delta E \\right]^{ \\
\\frac{1}{1-q_{a}}}\\}}
Where :math:`q_{a}` is a acceptance parameter. For :math:`q_{a}<1`, zero
acceptance probability is assigned to the cases where
.. math::
[1-(1-q_{a}) \\beta \\Delta E] < 0
The artificial temperature :math:`T_{q_{v}}(t)` is decreased according to
.. math::
T_{q_{v}}(t) = T_{q_{v}}(1) \\frac{2^{q_{v}-1}-1}{\\left( \\
1 + t\\right)^{q_{v}-1}-1}
Where :math:`q_{v}` is the visiting parameter.
.. versionadded:: 1.2.0
References
----------
.. [1] Tsallis C. Possible generalization of Boltzmann-Gibbs
statistics. Journal of Statistical Physics, 52, 479-487 (1998).
.. [2] Tsallis C, Stariolo DA. Generalized Simulated Annealing.
Physica A, 233, 395-406 (1996).
.. [3] Xiang Y, Sun DY, Fan W, Gong XG. Generalized Simulated
Annealing Algorithm and Its Application to the Thomson Model.
Physics Letters A, 233, 216-220 (1997).
.. [4] Xiang Y, Gong XG. Efficiency of Generalized Simulated
Annealing. Physical Review E, 62, 4473 (2000).
.. [5] Xiang Y, Gubian S, Suomela B, Hoeng J. Generalized
Simulated Annealing for Efficient Global Optimization: the GenSA
Package for R. The R Journal, Volume 5/1 (2013).
.. [6] Mullen, K. Continuous Global Optimization in R. Journal of
Statistical Software, 60(6), 1 - 45, (2014). DOI:10.18637/jss.v060.i06
Examples
--------
The following example is a 10-dimensional problem, with many local minima.
The function involved is called Rastrigin
(https://en.wikipedia.org/wiki/Rastrigin_function)
>>> from scipy.optimize import dual_annealing
>>> func = lambda x: np.sum(x*x - 10*np.cos(2*np.pi*x)) + 10*np.size(x)
>>> lw = [-5.12] * 10
>>> up = [5.12] * 10
>>> ret = dual_annealing(func, None, bounds=list(zip(lw, up)), seed=1234)
>>> print("global minimum: xmin = {0}, f(xmin) = {1:.6f}".format(
... ret.x, ret.fun))
global minimum: xmin = [-4.26437714e-09 -3.91699361e-09 -1.86149218e-09 -3.97165720e-09
-6.29151648e-09 -6.53145322e-09 -3.93616815e-09 -6.55623025e-09
-6.05775280e-09 -5.00668935e-09], f(xmin) = 0.000000
"""
if x0 is not None and not len(x0) == len(bounds):
raise ValueError('Bounds size does not match x0')
lu = list(zip(*bounds))
lower = np.array(lu[0])
upper = np.array(lu[1])
# Check that restart temperature ratio is correct
if restart_temp_ratio <= 0. or restart_temp_ratio >= 1.:
raise ValueError('Restart temperature ratio has to be in range (0, 1)')
# Checking bounds are valid
if (np.any(np.isinf(lower)) or np.any(np.isinf(upper)) or np.any(
np.isnan(lower)) or np.any(np.isnan(upper))):
raise ValueError('Some bounds values are inf values or nan values')
# Checking that bounds are consistent
if not np.all(lower < upper):
raise ValueError('Bounds are note consistent min < max')
# Wrapper for the objective function
func_wrapper = ObjectiveFunWrapper(func, maxfun, *args)
# Wrapper fot the minimizer
minimizer_wrapper = LocalSearchWrapper(
bounds, func_wrapper, **local_search_options)
# Initialization of RandomState for reproducible runs if seed provided
rand_state = check_random_state(seed)
# Initialization of the energy state
energy_state = EnergyState(lower, upper, callback)
energy_state.reset(func_wrapper, rand_state, x0)
# Minimum value of annealing temperature reached to perform
# re-annealing
temperature_restart = initial_temp * restart_temp_ratio
# VisitingDistribution instance
visit_dist = VisitingDistribution(lower, upper, visit, rand_state)
# Strategy chain instance
strategy_chain = StrategyChain(accept, visit_dist, func_wrapper,
minimizer_wrapper, rand_state, energy_state)
# Run the search loop
need_to_stop = False
iteration = 0
message = []
t1 = np.exp((visit - 1) * np.log(2.0)) - 1.0
while(not need_to_stop):
for i in range(maxiter):
# Compute temperature for this step
s = float(i) + 2.0
t2 = np.exp((visit - 1) * np.log(s)) - 1.0
temperature = initial_temp * t1 / t2
iteration += 1
if iteration >= maxiter:
message.append("Maximum number of iteration reached")
need_to_stop = True
break
# Need a re-annealing process?
if temperature < temperature_restart:
energy_state.reset(func_wrapper, rand_state)
break
# starting strategy chain
val = strategy_chain.run(i, temperature)
if val is not None:
message.append(val)
need_to_stop = True
break
# Possible local search at the end of the strategy chain
if not no_local_search:
val = strategy_chain.local_search()
if val is not None:
message.append(val)
need_to_stop = True
break
# Return the OptimizeResult
res = OptimizeResult()
res.x = energy_state.xbest
res.fun = energy_state.ebest
res.nit = iteration
res.nfev = func_wrapper.nfev
res.njev = func_wrapper.ngev
res.message = message
return res
def optimize_stiefel(func, X0, args=(), tau_max=.5, max_it=1, tol=1e-6,
disp=False, tau_find_freq=100):
"""
Optimize a function over a Stiefel manifold.
:param func: Function to be optimized
:param X0: Initial point for line search
:param tau_max: Maximum step size
:param max_it: Maximum number of iterations
:param tol: Tolerance criteria to terminate line search
:param disp: Choose whether to display output
:param args: Extra arguments passed to the function
"""
tol = float(tol)
assert tol > 0, 'Tolerance must be positive'
max_it = int(max_it)
assert max_it > 0, 'The maximum number of iterations must be a positive '\
+ 'integer'
tau_max = float(tau_max)
assert tau_max > 0, 'The parameter `tau_max` must be positive.'
k = 0
X = X0.copy()
nit = 0
nfev = 0
success = False
if disp:
print 'Stiefel Optimization'.center(80)
print '{0:4s} {1:11s} {2:5s}'.format('It', 'F', '(F - F_old) / F_old')
print '-' * 30
ls_func = LSFunc()
ls_func.func = func
decrease_tau = False
tau_max0 = tau_max
while nit <= max_it:
nit += 1
F, G = func(X, *args)
F_old = F
nfev += 1
A = compute_A(G, X)
ls_func.A = A
ls_func.X = X
ls_func.func_args = args
ls_func.tau_max = tau_max
increased_tau = False
if nit == 1 or decrease_tau or nit % tau_find_freq == 0:
# Need to minimize ls_func with respect to each argument
tau_init = np.linspace(-10, 0., 3)[:, None]
tau_d = np.linspace(-10, 0., 50)[:, None]
tau_all, F_all = pybgo.minimize(ls_func, tau_init, tau_d, fixed_noise=1e-16,
add_at_least=1, tol=1e-2, scale=True,
train_every=1)[:2]
nfev += tau_all.shape[0]
idx = np.argmin(F_all)
tau = np.exp(tau_all[idx, 0]) * tau_max
if tau_max - tau <= 1e-6:
tau_max = 1.2 * tau_max
if disp:
print 'increasing tau_max to {0:1.5e}'.format(tau_max)
increased_tau = True
if decrease_tau:
tau_max = .8 * tau_max
if disp:
print 'decreasing max_tau to {0:1.5e}'.format(tau_max)
decrease_tau = False
F = F_all[idx, 0]
else:
F = ls_func([np.log(tau / tau_max)])
delta_F = (F_old - F) / np.abs(F_old)
if delta_F < 0:
if disp:
print '*** backtracking'
nit -= 1
decrease_tau = True
continue
X_old = X
X = Y_func(tau, X, A)
if disp:
print '{0:4s} {1:1.5e} {2:5e} tau = {3:1.3e}, tau_max = {4:1.3e}'.format(
str(nit).zfill(4), F, delta_F, tau, tau_max)
if delta_F <= tol:
if disp:
print '*** Converged ***'
success = True
break
res = OptimizeResult()
res.tau_max = tau_max
res.X = X
res.nfev = nfev
res.nit = nit
res.fun = F
res.success = success
return res
def optimize(f,
x0=None,
bounds=None,
domain_scale=None,
init='uniform',
stepsize_start=None,
stepsize_decay_fac=1e-3,
base_tumble_rate=0.1,
niter_rt=400,
n_bacteria_per_dim=3,
stationarity_window=20,
eps_stat=1e-3,
attraction=False,
attraction_window=10,
attraction_sigma=None,
attraction_strength=0.5,
bounds_reflection=False,
n_best_selection=3,
c_gd=1e-6,
a_gd=None,
n_linesearch_gd=20,
alpha_linesearch_gd=0.5,
beta_linesearch_gd=0.33,
eps_abs_gd=1e-9,
eps_rel_gd=1e-6,
niter_gd=100,
n_embeddings=5,
max_dims=3,
n_reduced_dims=2,
verbosity=0):
"""
Metaheuristic global optimization algorithm combining a bacterial run-and-tumble chemotactic
search with a local, gradient-based search around the best minimum candidate points.
The algorithm's goal is to find
min f(x), x ∈ Ω,
where f: Ω ⊂ ℝ^n → ℝ.
Since the chemotactic search becomes more and more ineffective with increasing problem
dimensionality, Sequential Random Embeddings are used to solve the optimization problem once its
dimensionality exceeds a given threshold.
:param f: [callable] Objective function. Must accept its argument x as numpy array
:param x0: [array-like object] Optional initial conditions object. Must have the shape
(n_bacteria, n_dims) or (n_dims,). If x0 == None, initial conditions are sampled randomly
or uniformly-spaced from Ω. Note that this only works if Ω is a rectangular box, i.e., if
no or non-rectangular bounds are imposed, x0 must not be None
:param bounds: [callable or array-like object] Defines the bounded domain Ω. If provided, must
be one of the following:
- Bounds projection callback, as defined in description of parameter
``projection_callback`` in :func:`local_search.bfgs_b`
- Rectangular box constraints. For each component x_i of x,
bounds[i, 0] <= x_i <= bounds[i, 1], that is, bounds must have shape (n_dims, 2)
:param domain_scale: [float] Scale of the optimization problem. If not provided, the algorithm
tries to guess the scale from any provided rectangular box constraints. Used for
auto-scaling algorithm stepsizes
:param init: [string] Determines how initial bacteria positions are sampled from Ω if
x0 == None, see description of parameter ``x0``. Currently supported: 'random' and
'uniform'
:param stepsize_start: [float] See description of parameter ``stepsize_start`` in
:func:`global_search.run_and_tumble`. If not provided, the algorithm tries to auto-scale
this length to the problem's scale
:param stepsize_decay_fac: [float] Factor by which the run-and-tumble stepsize has decayed in
the last run-and-tumble iteration compared to its initial value
:param base_tumble_rate: [float] See description of parameter ``base_tumble_rate`` in
:func:`global_search.run_and_tumble`
:param niter_rt: [int] Maximum number of run-and-tumble iterations
:param n_bacteria_per_dim: [int] How many bacteria to spawn in each dimension. Note that the
total number of bacteria is
i) n_bacteria = n_bacteria_per_dim ** n_dims if n_dims <= max_dims or
ii) n_bacteria = n_bacteria_per_dim ** (n_reduced_dims + 1) if n_dims > max_dims.
If x0 is provided with shape (n_bacteria, n_dims), n_bacteria should agree with this
relation.
:param stationarity_window: [int] See description of parameter ``stationarity_window`` in
:func:`global_search.run_and_tumble`
:param eps_stat: [float] See description of parameter ``stationarity_window`` in
:func:`global_search.run_and_tumble`
:param attraction: [bool] See description of parameter ``attraction`` in
:func:`global_search.run_and_tumble`
:param attraction_window: [int] See description of parameter ``attraction_window`` in
:func:`global_search.run_and_tumble`
:param attraction_sigma: [float] See description of parameter ``attraction_sigma`` in
:func:`global_search.run_and_tumble`. If not provided, the algorithm tries to auto-scale
this length to the problem's scale
:param attraction_strength: [float] See description of parameter ``attraction_strength`` in
:func:`global_search.run_and_tumble`
:param bounds_reflection: [bool] See description of parameter ``bounds_reflection`` in
:func:`global_search.run_and_tumble`
:param n_best_selection: [int] At the end of the run-and-tumble exploration stage, a local
gradient-based search is performed, starting from the best positions found thus far by
the n_best_selection best bacteria
:param c_gd: [float] See description of parameter ``c`` in :func:`local_search.bfgs_b`
:param a_gd: [float] See description of parameter ``a`` in :func:`local_search.bfgs_b`. If not
provided, the algorithm tries to auto-scale this length to the problem's scale
:param n_linesearch_gd: [int] See description of parameter ``n_linesearch`` in
:func:`local_search.bfgs_b`
:param alpha_linesearch_gd: [float] See description of parameter ``alpha_linesearch`` in
:func:`local_search.bfgs_b`
:param beta_linesearch_gd: [float] See description of parameter ``beta_linesearch`` in
:func:`local_search.bfgs_b`
:param eps_abs_gd: [float] See description of parameter ``eps_abs`` in
:func:`local_search.bfgs_b`
:param eps_rel_gd: [float] See description of parameter ``eps_rel`` in
:func:`local_search.bfgs_b`
:param niter_gd: [int] Maximum number of local, gradient-based search iterations
:param n_embeddings: [int] Number of embedding iterations when using Sequential Random
Embeddings. Only has an effect if n_dims > max_dims
:param max_dims: [int] Maximum dimension of problems to be solved without using Sequential
Random Embeddings
:param n_reduced_dims: [int] Dimension of the embedded problem. Only has an effect if
n_dims > max_dims
:param verbosity: [int] Output verbosity. Must be 0, 1, or 2
:return: Best minimum of f found [scipy.optimize.OptimizeResult]
"""
assert verbosity in [0, 1, 2], 'verbosity must be 0, 1, or 2.'
assert n_reduced_dims >= 2, 'n_reduced_dims must not be less than 2.'
n_reduced_dims_eff = n_reduced_dims + 1
if bounds is None or callable(bounds):
assert x0 is not None, (
'If no box constraints are provided for bounds, x0 must not be ' +
'None.')
x0_population = _prepare_x0(x0, n_bacteria_per_dim, max_dims,
n_reduced_dims_eff)
n_bacteria, n_dims = x0_population.shape
if bounds is None:
bound_lower, bound_upper = _prepare_bounds(bounds, n_dims)
def projection_callback(x):
x = np.clip(x, bound_lower, bound_upper)
bounds_hit = np.where(
((x == bound_lower) | (x == bound_upper)), True, False)
return x, bounds_hit
def projection_callback_population(x):
return projection_callback(x)
else:
def projection_callback(x):
return bounds(x)
def projection_callback_population(x):
out = np.array(
[projection_callback(x_single) for x_single in x])
return out[:, 0], out[:, 1]
elif isinstance(bounds, (list, np.ndarray)):
if x0 is not None:
x0_population = _prepare_x0(x0, n_bacteria_per_dim, max_dims,
n_reduced_dims_eff)
n_bacteria, n_dims = x0_population.shape
bound_lower, bound_upper = _prepare_bounds(bounds, n_dims)
else:
bound_lower, bound_upper = _prepare_bounds(bounds, None)
n_dims = len(bound_lower)
n_bacteria = (n_bacteria_per_dim**n_dims if n_dims <= max_dims else
n_bacteria_per_dim**n_reduced_dims_eff)
if init == 'uniform' and n_dims > max_dims:
init = 'random'
if verbosity > 0:
warnings.warn(
'The option init="uniform" is only available for problems with '
+
'dimensionality less than or equal to max_dims, which was '
+
f'set to {max_dims}. Since the current problem has ' +
f'dimensionality {n_dims}, init was automatically set to '
+ f'"random".')
if init == 'random':
x0_population = np.random.uniform(bound_lower,
bound_upper,
size=(n_bacteria, n_dims))
elif init == 'uniform':
init_points = []
for i in range(n_dims):
init_points.append(
np.linspace(bound_lower[i], bound_upper[i],
n_bacteria_per_dim))
x0_population = np.array(np.meshgrid(*init_points)).reshape(
n_dims, -1).T
else:
raise ValueError('init must either be "random" or "uniform".')
def projection_callback(x):
x = np.clip(x, bound_lower, bound_upper)
bounds_hit = np.where(((x == bound_lower) | (x == bound_upper)),
True, False)
return x, bounds_hit
def projection_callback_population(x):
return projection_callback(x)
else:
raise ValueError(
'bounds must either be None, an array or corresponding nested list of '
+
'shape (n_dims, 2), or a custom callback function. See the docstring '
+ 'for details.')
assert niter_rt > stationarity_window, 'niter_rt must be larger than stationarity_window.'
assert n_best_selection <= n_bacteria, 'n_best_selection must not be larger than n_bacteria.'
if stepsize_start is not None:
auto_scale_stepsize = False
else:
auto_scale_stepsize = True
stepsize_start = 1e-1
stepsize_end = stepsize_decay_fac * stepsize_start
if attraction_sigma is not None:
auto_scale_attraction_sigma = False
else:
auto_scale_attraction_sigma = True
attraction_sigma = 1
if a_gd is not None:
auto_scale_a_gd = False
else:
auto_scale_a_gd = True
a_gd = 1e-2
x0_population_orig = x0_population.copy()
x0_population, _ = projection_callback_population(x0_population)
if not np.array_equal(x0_population, x0_population_orig):
warnings.warn(
'Found initial conditions outside the defined search domain.')
max_scale = None
if domain_scale is not None:
max_scale = domain_scale
elif isinstance(bounds, (list, np.ndarray)):
# noinspection PyUnboundLocalVariable
domain_range = bound_upper - bound_lower
max_scale = np.max(np.where(np.isinf(domain_range), 0, domain_range))
if max_scale is not None and max_scale > 0:
if auto_scale_stepsize:
stepsize_start = stepsize_start * max_scale
stepsize_end = stepsize_end * max_scale
if auto_scale_attraction_sigma:
attraction_sigma = attraction_sigma * max_scale
if auto_scale_a_gd:
a_gd = a_gd * max_scale
if n_dims > max_dims:
if verbosity > 0:
print(
f'Using sequential random embeddings in {n_reduced_dims} + 1 dimensions.'
)
return _sequential_random_embeddings(
f,
x0_population,
projection_callback,
n_reduced_dims_eff=n_reduced_dims_eff,
n_embeddings=n_embeddings,
verbosity=verbosity,
domain_scale=max_scale,
init=init,
stepsize_start=stepsize_start,
stepsize_decay_fac=stepsize_decay_fac,
base_tumble_rate=base_tumble_rate,
niter_rt=niter_rt,
n_bacteria_per_dim=n_bacteria_per_dim,
stationarity_window=stationarity_window,
eps_stat=eps_stat,
attraction=attraction,
attraction_window=attraction_window,
attraction_sigma=attraction_sigma,
attraction_strength=attraction_strength,
bounds_reflection=bounds_reflection,
n_best_selection=n_best_selection,
c_gd=c_gd,
a_gd=a_gd,
n_linesearch_gd=n_linesearch_gd,
alpha_linesearch_gd=alpha_linesearch_gd,
beta_linesearch_gd=beta_linesearch_gd,
eps_abs_gd=eps_abs_gd,
eps_rel_gd=eps_rel_gd,
niter_gd=niter_gd,
max_dims=n_reduced_dims_eff)
else:
x_best, f_best, nfev, nit, trace = run_and_tumble(
f,
x0_population,
projection_callback_population,
niter_rt,
stepsize_start,
stepsize_end,
base_tumble_rate=base_tumble_rate,
stationarity_window=stationarity_window,
eps_stat=eps_stat,
attraction=attraction,
attraction_window=attraction_window,
attraction_sigma=attraction_sigma,
attraction_strength=attraction_strength,
bounds_reflection=bounds_reflection,
verbosity=verbosity)
if verbosity == 2:
print(
'==============================================================================='
)
if verbosity > 0:
print(
f'Best result after run-and-tumble stage is x = {x_best[np.argmin(f_best)]}, '
+
f'f(x) = {np.min(f_best)}. Starting local, gradient-based optimization for the '
+ f'{n_best_selection} best bacteria.')
sortIdx = f_best.argsort()
x_best_selection = x_best[sortIdx[:n_best_selection]]
x_best_gd = np.empty(x_best_selection.shape)
f_min_gd = np.empty(n_best_selection)
nfev_gd = 0
nit_gd = 0
success_gd = np.empty(n_best_selection)
trace_gd = np.empty((niter_gd, n_bacteria, n_dims))
trace_gd[:, sortIdx[n_best_selection:], :] = trace[
-1, sortIdx[n_best_selection:], :]
nit_gd_arr = np.empty(n_best_selection)
visited_points = trace.reshape(-1, n_dims)
for n, x_start in enumerate(x_best_selection):
if verbosity == 2:
print(f'Performing gradient descent for bacterium {n}.')
# Calculate quadratic function approximation around x_start
num_sampling_points = 2 * int(special.binom(n_dims + 2, 2))
# noinspection PyArgumentList,PyUnresolvedReferences
sampling_points = visited_points[spatial.cKDTree(
visited_points).query(x_start, num_sampling_points)[1]]
func_values = np.array([f(point) for point in sampling_points])
nfev += num_sampling_points
polynomial_powers = list(
itertools.filterfalse(
lambda prod: sum(list(prod)) > 2,
itertools.product((0, 1, 2), repeat=n_dims)))
sampling_matrix = np.stack([
np.prod(sampling_points**d, axis=1) for d in polynomial_powers
],
axis=-1)
coeffs = np.linalg.lstsq(sampling_matrix, func_values, 2)[0]
# Calculate Hessian matrix from the quadratic approximation
H = np.ones((n_dims, n_dims))
square_powers = list(
itertools.filterfalse(
lambda zipped_item: sum(list(zipped_item[0])) != 2,
zip(polynomial_powers, coeffs)))
for square_power, coeff in square_powers:
idcs_to_consider = np.argwhere(np.array(square_power) != 0)
if len(idcs_to_consider) == 1: # Diagonal
H[idcs_to_consider[0], idcs_to_consider[0]] = 0.5 * coeff
elif len(idcs_to_consider) == 2: # Mixed derivatives
H[idcs_to_consider[0], idcs_to_consider[1]] = coeff
H[idcs_to_consider[1], idcs_to_consider[0]] = coeff
else:
raise RuntimeError(
"Polynomial function approximation seems to be of higher "
"order than two. This shouldn't happen.")
local_optimization_result = bfgs_b(
f,
x_start,
projection_callback,
H_start=H,
a=a_gd,
c=c_gd,
niter=niter_gd,
n_linesearch=n_linesearch_gd,
alpha_linesearch=alpha_linesearch_gd,
beta_linesearch=beta_linesearch_gd,
eps_abs=eps_abs_gd,
eps_rel=eps_rel_gd,
verbosity=verbosity)
x_best_gd[n] = local_optimization_result.x
f_min_gd[n] = local_optimization_result.f
nfev_gd += local_optimization_result.nfev
nit_gd += local_optimization_result.nit
nit_gd_arr[n] = local_optimization_result.nit
success_gd[n] = local_optimization_result.success
trace_gd[:, sortIdx[n], :] = _pad_trace(
local_optimization_result.trace, niter_gd)
result = OptimizeResult()
result.success = success_gd.any()
result.x = x_best_gd[np.argmin(f_min_gd)]
result.fun = np.min(f_min_gd)
result.nfev = nfev + nfev_gd
result.nit = nit + nit_gd
trace_gd = trace_gd[:np.max(nit_gd_arr).astype(int)]
result.trace = np.concatenate((trace, trace_gd))
return result
def glpk(
c,
A_ub=None,
b_ub=None,
A_eq=None,
b_eq=None,
bounds=None,
solver='simplex',
sense=GLPK.GLP_MIN,
scale=True,
maxit=GLPK.INT_MAX,
timeout=GLPK.INT_MAX,
basis_fac='luf+ft',
message_level=GLPK.GLP_MSG_ERR,
disp=False,
simplex_options=None,
ip_options=None,
mip_options=None,
):
'''GLPK ctypes interface.
Parameters
----------
c : 1-D array (n,)
Array of objective coefficients.
A_ub : 2-D array (m, n)
scipy.sparse.coo_matrix
b_ub : 1-D array (m,)
A_eq : 2-D array (k, n)
scipy.sparse.coo_matrix
b_eq : 1-D array (k,)
bounds : None or list (n,) of tuple (2,) or tuple (2,)
The jth entry in the list corresponds to the jth objective coefficient.
Each entry is made up of a tuple describing the bounds.
Use None to indicate that there is no bound. By default, bounds are
(0, None) (all decision variables are non-negative). If a single tuple
(min, max) is provided, then min and max will serve as bounds for all
decision variables.
solver : { 'simplex', 'interior', 'mip' }
Use simplex (LP/MIP) or interior point method (LP only).
Default is ``simplex``.
sense : { 'GLP_MIN', 'GLP_MAX' }
Minimization or maximization problem.
Default is ``GLP_MIN``.
scale : bool
Scale the problem. Default is ``True``.
maxit : int
Maximum number of iterations. Default is ``INT_MAX``.
timout : int
Limit solution time to ``timeout`` seconds.
Default is ``INT_MAX``.
basis_fac : { 'luf+ft', 'luf+cbg', 'luf+cgr', 'btf+cbg', 'btf+cgr' }
LP basis factorization strategy. Default is ``luf+ft``.
These are combinations of the following strategies:
- ``luf`` : plain LU-factorization
- ``btf`` : block triangular LU-factorization
- ``ft`` : Forrest-Tomlin update
- ``cbg`` : Schur complement + Bartels-Golub update
- ``cgr`` : Schur complement + Givens rotation update
message_level : { GLP_MSG_OFF, GLP_MSG_ERR, GLP_MSG_ON, GLP_MSG_ON, GLP_MSG_ALL, GLP_MSG_DBG }
Verbosity level of logging to stdout.
Only applied when ``disp=True``. Default is ``GLP_MSG_ERR``.
One of the following:
``GLP_MSG_OFF`` : no output
``GLP_MSG_ERR`` : warning and error messages only
``GLP_MSG_ON`` : normal output
``GLP_MSG_ALL`` : full output
``GLP_MSG_DBG`` : debug output
disp : bool
Display output to stdout. Default is ``False``.
simplex_options : dict
Options specific to simplex solver. The dictionary consists of
the following fields:
- primal : { 'primal', 'dual', 'dualp' }
Primal or two-phase dual simplex.
Default is ``primal``. One of the following:
- ``primal`` : use two-phase primal simplex
- ``dual`` : use two-phase dual simplex
- ``dualp`` : use two-phase dual simplex, and if it fails,
switch to the primal simplex
- init_basis : { 'std', 'adv', 'bib' }
Choice of initial basis. Default is 'adv'.
One of the following:
- ``std`` : standard initial basis of all slacks
- ``adv`` : advanced initial basis
- ``bib`` : Bixby's initial basis
- steep : bool
Use steepest edge technique or standard "textbook"
pricing. Default is ``True`` (steepest edge).
- ratio : { 'relax', 'norelax', 'flip' }
Ratio test strategy. Default is ``relax``.
One of the following:
- ``relax`` : Harris' two-pass ratio test
- ``norelax`` : standard "textbook" ratio test
- ``flip`` : long-step ratio test
- tol_bnd : double
Tolerance used to check if the basic solution is primal
feasible. (Default: 1e-7).
- tol_dj : double
Tolerance used to check if the basic solution is dual
feasible. (Default: 1e-7).
- tol_piv : double
Tolerance used to choose eligble pivotal elements of
the simplex table. (Default: 1e-10).
- obj_ll : double
Lower limit of the objective function. If the objective
function reaches this limit and continues decreasing,
the solver terminates the search. Used in the dual simplex
only. (Default: -DBL_MAX -- the largest finite float64).
- obj_ul : double
Upper limit of the objective function. If the objective
function reaches this limit and continues increasing,
the solver terminates the search. Used in the dual simplex
only. (Default: +DBL_MAX -- the largest finite float64).
- presolve : bool
Use presolver (assumes ``scale=True`` and
``init_basis='adv'``. Default is ``True``.
- exact : bool
Use simplex method based on exact arithmetic.
Default is ``False``. If ``True``, all other
``simplex_option`` fields are ignored.
ip_options : dict
Options specific to interior-pooint solver.
The dictionary consists of the following fields:
- ordering : { 'nord', 'qmd', 'amd', 'symamd' }
Ordering algorithm used before Cholesky factorizaiton.
Default is ``amd``. One of the following:
- ``nord`` : natural (original) ordering
- ``qmd`` : quotient minimum degree ordering
- ``amd`` : approximate minimum degree ordering
- ``symamd`` : approximate minimum degree ordering
algorithm for Cholesky factorization of symmetric
matrices.
mip_options : dict
Options specific to MIP solver.
The dictionary consists of the following fields:
- intcon : 1-D array
Array of integer contraints, specified as the 0-based
indices of the solution. Default is an empty array.
- bincon : 1-D array
Array of binary constraints, specified as the 0-based
indices of the solution. If any indices are duplicated
between ``bincon`` and ``intcon``, they will be
considered as binary constraints. Default is an empty
array.
- nomip : bool
consider all integer variables as continuous
(allows solving MIP as pure LP). Default is ``False``.
- branch : { 'first', 'last', 'mostf', 'drtom', 'pcost' }
Branching rule. Default is ``drtom``.
One of the following:
- ``first`` : branch on first integer variable
- ``last`` : branch on last integer variable
- ``mostf`` : branch on most fractional variable
- ``drtom`` : branch using heuristic by Driebeck and Tomlin
- ``pcost`` : branch using hybrid pseudocost heuristic
(may be useful for hard instances)
- backtrack : { 'dfs', 'bfs', 'bestp', 'bestb' }
Backtracking rule. Default is ``bestb``.
One of the following:
- ``dfs`` : backtrack using depth first search
- ``bfs`` : backtrack using breadth first search
- ``bestp`` : backtrack using the best projection heuristic
- ``bestb`` : backtrack using node with best local bound
- preprocess : { 'none', 'root', 'all' }
Preprocessing technique. Default is ``GLP_PP_ALL``.
One of the following:
- ``none`` : disable preprocessing
- ``root`` : perform preprocessing only on the root level
- ``all`` : perform preprocessing on all levels
- round : bool
Simple rounding heuristic. Default is ``True``.
- presolve : bool
Use MIP presolver. Default is ``True``.
- binarize : bool
replace general integer variables by binary ones
(only used if ``presolve=True``). Default is ``False``.
- fpump : bool
Apply feasibility pump heuristic. Default is ``False``.
- proxy : int
Apply proximity search heuristic (in seconds). Default is 60.
- cuts : list of { 'gomory', 'mir', 'cover', 'clique', 'all' }
Cuts to generate. Default is no cuts. List of the following:
- ``gomory`` : Gomory's mixed integer cuts
- ``mir`` : MIR (mixed integer rounding) cuts
- ``cover`` : mixed cover cuts
- ``clique`` : clique cuts
- ``all`` : generate all cuts above
- tol_int : float
Absolute tolerance used to check if optimal solution to the
current LP relaxation is integer feasible.
(Default: 1e-5).
- tol_obj : float
Relative tolerance used to check if the objective value in
optimal solution to the current LP relaxation is not better
than in the best known integer feasible solution.
(Default: 1e-7).
- mip_gap : float
Relative mip gap tolerance. If the relative mip gap for
currently known best integer feasiblesolution falls below
this tolerance, the solver terminates the search. This allows
obtaining suboptimal integer feasible solutions if solving the
problem to optimality takes too long time.
(Default: 0.0).
- bound : float
add inequality obj <= bound (minimization) or
obj >= bound (maximization) to integer feasibility
problem (assumes ``minisat=True``).
Notes
-----
In general, don't change tolerances without a detailed understanding
of their purposes.
'''
# Housekeeping
if simplex_options is None:
simplex_options = {}
if ip_options is None:
ip_options = {}
if mip_options is None:
mip_options = {}
# Create and fill the GLPK problem struct
prob, lp = _fill_prob(c, A_ub, b_ub, A_eq, b_eq, bounds, sense, 'problem-name')
c, A_ub, b_ub, A_eq, b_eq, bounds, _x0 = lp
# Get the library
_lib = GLPK()._lib
# Scale the problem
no_need_explict_scale = (solver == "simplex" and
simplex_options.get("presolve"))
if not no_need_explict_scale and scale:
_lib.glp_scale_prob(prob, GLPK.GLP_SF_AUTO) # do auto scaling for now
# Select basis factorization method
bfcp = glp_bfcp()
_lib.glp_get_bfcp(prob, ctypes.byref(bfcp))
bfcp.type = {
'luf+ft': GLPK.GLP_BF_LUF + GLPK.GLP_BF_FT,
'luf+cbg': GLPK.GLP_BF_LUF + GLPK.GLP_BF_BG,
'luf+cgr': GLPK.GLP_BF_LUF + GLPK.GLP_BF_GR,
'btf+cbg': GLPK.GLP_BF_BTF + GLPK.GLP_BF_BG,
'btf+cgr': GLPK.GLP_BF_BTF + GLPK.GLP_BF_GR,
}[basis_fac]
_lib.glp_set_bfcp(prob, ctypes.byref(bfcp))
# Run the solver
if solver == 'simplex':
# Construct an initial basis
basis = simplex_options.get('init_basis', 'adv')
basis_fun = {
'std': _lib.glp_std_basis,
'adv': _lib.glp_adv_basis,
'bib': _lib.glp_cpx_basis,
}[basis]
basis_args = [prob]
if basis == 'adv':
# adv must have 0 as flags argument
basis_args.append(0)
basis_fun(*basis_args)
# Make control structure
smcp = glp_smcp()
_lib.glp_init_smcp(ctypes.byref(smcp))
# Set options
smcp.msg_lev = message_level*disp
smcp.meth = {
'primal': GLPK.GLP_PRIMAL,
'dual': GLPK.GLP_DUAL,
'dualp': GLPK.GLP_DUALP,
}[simplex_options.get('method', 'primal')]
smcp.pricing = {
True: GLPK.GLP_PT_PSE,
False: GLPK.GLP_PT_STD,
}[simplex_options.get('steep', True)]
smcp.r_test = {
'relax': GLPK.GLP_RT_HAR,
'norelax': GLPK.GLP_RT_STD,
'flip': GLPK.GLP_RT_FLIP,
}[simplex_options.get('ratio', 'relax')]
smcp.tol_bnd = simplex_options.get('tol_bnd', 1e-7)
smcp.tol_dj = simplex_options.get('tol_dj', 1e-7)
smcp.tol_piv = simplex_options.get('tol_piv', 1e-10)
if simplex_options.get('obj_ll', False):
smcp.obj_ll = simplex_options['obj_ll']
if simplex_options.get('obj_ul', False):
smcp.obj_ul = simplex_options['obj_ul']
smcp.it_lim = maxit
smcp.tm_lim = timeout
smcp.presolve = {
True: GLPK.GLP_ON,
False: GLPK.GLP_OFF,
}[simplex_options.get('presolve', True)]
# Simplex driver
if simplex_options.get('exact', False):
ret_code = _lib.glp_exact(prob, ctypes.byref(smcp))
else:
ret_code = _lib.glp_simplex(prob, ctypes.byref(smcp))
if ret_code != GLPK.SUCCESS:
warn('GLPK simplex not successful!', OptimizeWarning)
return OptimizeResult({
'message': GLPK.RET_CODES[ret_code],
})
# Figure out what happened
status = _lib.glp_get_status(prob)
message = GLPK.STATUS_CODES[status]
res = OptimizeResult({
'status': status,
'message': message,
'success': status == GLPK.GLP_OPT,
})
# We can read a solution:
if status == GLPK.GLP_OPT:
res.fun = _lib.glp_get_obj_val(prob)
res.x = np.array([_lib.glp_get_col_prim(prob, ii) for ii in range(1, _lib.glp_get_num_cols(prob)+1)])
res.dual = np.array([_lib.glp_get_row_dual(prob, ii) for ii in range(1, _lib.glp_get_num_rows(prob)+1)])
# We don't get slack without doing sensitivity analysis since GLPK
# uses auxiliary variables instead of slack!
res.slack = b_ub - A_ub @ res.x
res.con = b_eq - A_eq @ res.x
# We shouldn't be reading this field... But we will anyways
res.nit = prob.contents.it_cnt
elif solver == 'interior':
# Make a control structure
iptcp = glp_iptcp()
_lib.glp_init_iptcp(ctypes.byref(iptcp))
# Set options
iptcp.msg_lev = message_level*disp
iptcp.ord_alg = {
'nord': GLPK.GLP_ORD_NONE,
'qmd': GLPK.GLP_ORD_QMD,
'amd': GLPK.GLP_ORD_AMD,
'symamd': GLPK.GLP_ORD_SYMAMD,
}[ip_options.get('ordering', 'amd')]
# Run the solver
ret_code = _lib.glp_interior(prob, ctypes.byref(iptcp))
if ret_code != GLPK.SUCCESS:
warn('GLPK interior-point not successful!', OptimizeWarning)
return OptimizeResult({
'message': GLPK.RET_CODES[ret_code],
})
# Figure out what happened
status = _lib.glp_ipt_status(prob)
message = GLPK.STATUS_CODES[status]
res = OptimizeResult({
'status': status,
'message': message,
'success': status == GLPK.GLP_OPT,
})
# We can read a solution:
if status == GLPK.GLP_OPT:
res.fun = _lib.glp_ipt_obj_val(prob)
res.x = np.array([_lib.glp_ipt_col_prim(prob, ii) for ii in range(1, _lib.glp_get_num_cols(prob)+1)])
res.dual = np.array([_lib.glp_ipt_row_dual(prob, ii) for ii in range(1, _lib.gpl_get_num_rows(prob)+1)])
# We don't get slack without doing sensitivity analysis since GLPK uses
# auxiliary variables instead of slack!
res.slack = b_ub - A_ub @ res.x
res.con = b_eq - A_eq @ res.x
# We shouldn't be reading this field... But we will anyways
res.nit = prob.contents.it_cnt
elif solver == 'mip':
# Make a control structure
iocp = glp_iocp()
_lib.glp_init_iocp(ctypes.byref(iocp))
# Make variables integer- and binary-valued
if not mip_options.get('nomip', False):
intcon = mip_options.get('intcon', [])
for jj in intcon:
_lib.glp_set_col_kind(prob, jj+1, GLPK.GLP_IV)
bincon = mip_options.get('bincon', [])
for jj in bincon:
_lib.glp_set_col_kind(prob, jj+1, GLPK.GLP_BV)
# Set options
iocp.msg_lev = message_level*disp
iocp.br_tech = {
'first': GLPK.GLP_BR_FFV,
'last': GLPK.GLP_BR_LFV,
'mostf': GLPK.GLP_BR_MFV,
'drtom': GLPK.GLP_BR_DTH,
'pcost': GLPK.GLP_BR_PCH,
}[mip_options.get('branch', 'drtom')]
iocp.bt_tech = {
'dfs': GLPK.GLP_BT_DFS,
'bfs': GLPK.GLP_BT_BFS,
'bestp': GLPK.GLP_BT_BPH,
'bestb': GLPK.GLP_BT_BLB,
}[mip_options.get('backtrack', 'bestb')]
iocp.pp_teck = {
'none': GLPK.GLP_PP_NONE,
'root': GLPK.GLP_PP_ROOT,
'all': GLPK.GLP_PP_ALL,
}[mip_options.get('preprocess', 'all')]
iocp.sr_heur = {
True: GLPK.GLP_ON,
False: GLPK.GLP_OFF,
}[mip_options.get('round', True)]
iocp.fp_heur = {
True: GLPK.GLP_ON,
False: GLPK.GLP_OFF,
}[mip_options.get('fpump', False)]
ps_tm_lim = mip_options.get('proxy', 60)
if ps_tm_lim:
iocp.ps_heur = GLPK.GLP_ON
iocp.ps_tm_lim = ps_tm_lim*1000
else:
iocp.ps_heur = GLPK.GLP_OFF
iocp.ps_tm_lim = 0
cuts = set(list(mip_options.get('cuts', [])))
if 'all' in cuts:
cuts = {'gomory', 'mir', 'cover', 'clique'}
if 'gomory' in cuts:
iocp.gmi_cuts = GLPK.GLP_ON
if 'mir' in cuts:
iocp.mir_cuts = GLPK.GLP_ON
if 'cover' in cuts:
iocp.cov_cuts = GLPK.GLP_ON
if 'clique' in cuts:
iocp.clq_cuts = GLPK.GLP_ON
iocp.tol_int = mip_options.get('tol_int', 1e-5)
iocp.tol_obj = mip_options.get('tol_obj', 1e-7)
iocp.mip_gap = mip_options.get('mip_gap', 0.0)
iocp.tm_lim = timeout
iocp.presolve = {
True: GLPK.GLP_ON,
False: GLPK.GLP_OFF,
}[mip_options.get('presolve', True)]
iocp.binarize = {
True: GLPK.GLP_ON,
False: GLPK.GLP_OFF,
}[mip_options.get('binarize', False)]
# Run the solver
ret_code = _lib.glp_intopt(prob, ctypes.byref(iocp))
if ret_code != GLPK.SUCCESS:
warn('GLPK interior-point not successful!', OptimizeWarning)
return OptimizeResult({
'message': GLPK.RET_CODES[ret_code],
})
# Figure out what happened
status = _lib.glp_mip_status(prob)
message = GLPK.STATUS_CODES[status]
res = OptimizeResult({
'status': status,
'message': message,
'success': status in [GLPK.GLP_OPT, GLPK.GLP_FEAS],
})
# We can read a solution:
if res.success:
res.fun = _lib.glp_mip_obj_val(prob)
res.x = np.array([_lib.glp_mip_col_val(prob, ii) for ii in range(1, len(c)+1)])
else:
raise ValueError('"%s" is not a recognized solver.' % solver)
# We're done, cleanup!
_lib.glp_delete_prob(prob)
# Map status codes to scipy:
# res.status = {
# GLPK.GLP_OPT: 0,
# }[res.status]
return res
def dual_annealing(func,
bounds,
args=(),
maxiter=1000,
local_search_options={},
initial_temp=5230.,
restart_temp_ratio=2.e-5,
visit=2.62,
accept=-5.0,
maxfun=1e7,
seed=None,
no_local_search=False,
callback=None,
x0=None):
"""
Find the global minimum of a function using Dual Annealing.
Parameters
----------
func : callable
The objective function to be minimized. Must be in the form
``f(x, *args)``, where ``x`` is the argument in the form of a 1-D array
and ``args`` is a tuple of any additional fixed parameters needed to
completely specify the function.
bounds : sequence, shape (n, 2)
Bounds for variables. ``(min, max)`` pairs for each element in ``x``,
defining bounds for the objective function parameter.
args : tuple, optional
Any additional fixed parameters needed to completely specify the
objective function.
maxiter : int, optional
The maximum number of global search iterations. Default value is 1000.
local_search_options : dict, optional
Extra keyword arguments to be passed to the local minimizer
(`minimize`). Some important options could be:
``method`` for the minimizer method to use and ``args`` for
objective function additional arguments.
initial_temp : float, optional
The initial temperature, use higher values to facilitates a wider
search of the energy landscape, allowing dual_annealing to escape
local minima that it is trapped in. Default value is 5230. Range is
(0.01, 5.e4].
restart_temp_ratio : float, optional
During the annealing process, temperature is decreasing, when it
reaches ``initial_temp * restart_temp_ratio``, the reannealing process
is triggered. Default value of the ratio is 2e-5. Range is (0, 1).
visit : float, optional
Parameter for visiting distribution. Default value is 2.62. Higher
values give the visiting distribution a heavier tail, this makes
the algorithm jump to a more distant region. The value range is (0, 3].
accept : float, optional
Parameter for acceptance distribution. It is used to control the
probability of acceptance. The lower the acceptance parameter, the
smaller the probability of acceptance. Default value is -5.0 with
a range (-1e4, -5].
maxfun : int, optional
Soft limit for the number of objective function calls. If the
algorithm is in the middle of a local search, this number will be
exceeded, the algorithm will stop just after the local search is
done. Default value is 1e7.
seed : {int or `~numpy.random.mtrand.RandomState` instance}, optional
If `seed` is not specified the `~numpy.random.mtrand.RandomState`
singleton is used.
If `seed` is an int, a new ``RandomState`` instance is used,
seeded with `seed`.
If `seed` is already a ``RandomState`` instance, then that
instance is used.
Specify `seed` for repeatable minimizations. The random numbers
generated with this seed only affect the visiting distribution
function and new coordinates generation.
no_local_search : bool, optional
If `no_local_search` is set to True, a traditional Generalized
Simulated Annealing will be performed with no local search
strategy applied.
callback : callable, optional
A callback function with signature ``callback(x, f, context)``,
which will be called for all minima found.
``x`` and ``f`` are the coordinates and function value of the
latest minimum found, and ``context`` has value in [0, 1, 2], with the
following meaning:
- 0: minimum detected in the annealing process.
- 1: detection occurred in the local search process.
- 2: detection done in the dual annealing process.
If the callback implementation returns True, the algorithm will stop.
x0 : ndarray, shape(n,), optional
Coordinates of a single N-D starting point.
Returns
-------
res : OptimizeResult
The optimization result represented as a `OptimizeResult` object.
Important attributes are: ``x`` the solution array, ``fun`` the value
of the function at the solution, and ``message`` which describes the
cause of the termination.
See `OptimizeResult` for a description of other attributes.
Notes
-----
This function implements the Dual Annealing optimization. This stochastic
approach derived from [3]_ combines the generalization of CSA (Classical
Simulated Annealing) and FSA (Fast Simulated Annealing) [1]_ [2]_ coupled
to a strategy for applying a local search on accepted locations [4]_.
An alternative implementation of this same algorithm is described in [5]_
and benchmarks are presented in [6]_. This approach introduces an advanced
method to refine the solution found by the generalized annealing
process. This algorithm uses a distorted Cauchy-Lorentz visiting
distribution, with its shape controlled by the parameter :math:`q_{v}`
.. math::
g_{q_{v}}(\\Delta x(t)) \\propto \\frac{ \\
\\left[T_{q_{v}}(t) \\right]^{-\\frac{D}{3-q_{v}}}}{ \\
\\left[{1+(q_{v}-1)\\frac{(\\Delta x(t))^{2}} { \\
\\left[T_{q_{v}}(t)\\right]^{\\frac{2}{3-q_{v}}}}}\\right]^{ \\
\\frac{1}{q_{v}-1}+\\frac{D-1}{2}}}
Where :math:`t` is the artificial time. This visiting distribution is used
to generate a trial jump distance :math:`\\Delta x(t)` of variable
:math:`x(t)` under artificial temperature :math:`T_{q_{v}}(t)`.
From the starting point, after calling the visiting distribution
function, the acceptance probability is computed as follows:
.. math::
p_{q_{a}} = \\min{\\{1,\\left[1-(1-q_{a}) \\beta \\Delta E \\right]^{ \\
\\frac{1}{1-q_{a}}}\\}}
Where :math:`q_{a}` is a acceptance parameter. For :math:`q_{a}<1`, zero
acceptance probability is assigned to the cases where
.. math::
[1-(1-q_{a}) \\beta \\Delta E] < 0
The artificial temperature :math:`T_{q_{v}}(t)` is decreased according to
.. math::
T_{q_{v}}(t) = T_{q_{v}}(1) \\frac{2^{q_{v}-1}-1}{\\left( \\
1 + t\\right)^{q_{v}-1}-1}
Where :math:`q_{v}` is the visiting parameter.
.. versionadded:: 1.2.0
References
----------
.. [1] Tsallis C. Possible generalization of Boltzmann-Gibbs
statistics. Journal of Statistical Physics, 52, 479-487 (1998).
.. [2] Tsallis C, Stariolo DA. Generalized Simulated Annealing.
Physica A, 233, 395-406 (1996).
.. [3] Xiang Y, Sun DY, Fan W, Gong XG. Generalized Simulated
Annealing Algorithm and Its Application to the Thomson Model.
Physics Letters A, 233, 216-220 (1997).
.. [4] Xiang Y, Gong XG. Efficiency of Generalized Simulated
Annealing. Physical Review E, 62, 4473 (2000).
.. [5] Xiang Y, Gubian S, Suomela B, Hoeng J. Generalized
Simulated Annealing for Efficient Global Optimization: the GenSA
Package for R. The R Journal, Volume 5/1 (2013).
.. [6] Mullen, K. Continuous Global Optimization in R. Journal of
Statistical Software, 60(6), 1 - 45, (2014). DOI:10.18637/jss.v060.i06
Examples
--------
The following example is a 10-D problem, with many local minima.
The function involved is called Rastrigin
(https://en.wikipedia.org/wiki/Rastrigin_function)
>>> from scipy.optimize import dual_annealing
>>> func = lambda x: np.sum(x*x - 10*np.cos(2*np.pi*x)) + 10*np.size(x)
>>> lw = [-5.12] * 10
>>> up = [5.12] * 10
>>> ret = dual_annealing(func, bounds=list(zip(lw, up)), seed=1234)
>>> print("global minimum: xmin = {0}, f(xmin) = {1:.6f}".format(
... ret.x, ret.fun))
global minimum: xmin = [-4.26437714e-09 -3.91699361e-09 -1.86149218e-09 -3.97165720e-09
-6.29151648e-09 -6.53145322e-09 -3.93616815e-09 -6.55623025e-09
-6.05775280e-09 -5.00668935e-09], f(xmin) = 0.000000
""" # noqa: E501
if x0 is not None and not len(x0) == len(bounds):
raise ValueError('Bounds size does not match x0')
lu = list(zip(*bounds))
lower = np.array(lu[0])
upper = np.array(lu[1])
# Check that restart temperature ratio is correct
if restart_temp_ratio <= 0. or restart_temp_ratio >= 1.:
raise ValueError('Restart temperature ratio has to be in range (0, 1)')
# Checking bounds are valid
if (np.any(np.isinf(lower)) or np.any(np.isinf(upper))
or np.any(np.isnan(lower)) or np.any(np.isnan(upper))):
raise ValueError('Some bounds values are inf values or nan values')
# Checking that bounds are consistent
if not np.all(lower < upper):
raise ValueError('Bounds are not consistent min < max')
# Checking that bounds are the same length
if not len(lower) == len(upper):
raise ValueError('Bounds do not have the same dimensions')
# Wrapper for the objective function
func_wrapper = ObjectiveFunWrapper(func, maxfun, *args)
# Wrapper fot the minimizer
minimizer_wrapper = LocalSearchWrapper(bounds, func_wrapper,
**local_search_options)
# Initialization of RandomState for reproducible runs if seed provided
rand_state = check_random_state(seed)
# Initialization of the energy state
energy_state = EnergyState(lower, upper, callback)
energy_state.reset(func_wrapper, rand_state, x0)
# Minimum value of annealing temperature reached to perform
# re-annealing
temperature_restart = initial_temp * restart_temp_ratio
# VisitingDistribution instance
visit_dist = VisitingDistribution(lower, upper, visit, rand_state)
# Strategy chain instance
strategy_chain = StrategyChain(accept, visit_dist, func_wrapper,
minimizer_wrapper, rand_state, energy_state)
need_to_stop = False
iteration = 0
message = []
# OptimizeResult object to be returned
optimize_res = OptimizeResult()
optimize_res.success = True
optimize_res.status = 0
t1 = np.exp((visit - 1) * np.log(2.0)) - 1.0
# Run the search loop
while (not need_to_stop):
for i in range(maxiter):
# Compute temperature for this step
s = float(i) + 2.0
t2 = np.exp((visit - 1) * np.log(s)) - 1.0
temperature = initial_temp * t1 / t2
if iteration >= maxiter:
message.append("Maximum number of iteration reached")
need_to_stop = True
break
# Need a re-annealing process?
if temperature < temperature_restart:
energy_state.reset(func_wrapper, rand_state)
break
# starting strategy chain
val = strategy_chain.run(i, temperature)
if val is not None:
message.append(val)
need_to_stop = True
optimize_res.success = False
break
# Possible local search at the end of the strategy chain
if not no_local_search:
val = strategy_chain.local_search()
if val is not None:
message.append(val)
need_to_stop = True
optimize_res.success = False
break
iteration += 1
# Setting the OptimizeResult values
optimize_res.x = energy_state.xbest
optimize_res.fun = energy_state.ebest
optimize_res.nit = iteration
optimize_res.nfev = func_wrapper.nfev
optimize_res.njev = func_wrapper.ngev
optimize_res.nhev = func_wrapper.nhev
optimize_res.message = message
return optimize_res
def fmin_bfgs_f(f_g,
x0,
B0=None,
M=2,
gtol=1e-5,
Delta=10.0,
maxiter=None,
callback=None,
norm_ord=np.Inf,
**_kwargs):
"""test BFGS with nonmonote line search"""
fk, gk = f_g(x0)
if B0 is None:
Bk = np.eye(len(x0))
else:
Bk = B0
Hk = np.linalg.inv(Bk)
maxiter = 200 * len(x0) if maxiter is None else maxiter
xk = x0
norm = lambda x: np.linalg.norm(x, ord=norm_ord)
theta = 0.9
C = 0.5
k = 0
old_old_fval = fk + np.linalg.norm(gk) / 2
old_fval = fk
f_s = Seq(M)
f_s.add(fk)
flag = 0
re_search = 0
for k in range(maxiter):
if norm(gk) <= gtol:
break
dki = -np.dot(Hk, gk)
try:
pk = dki
f = f_g.fun
myfprime = f_g.grad
gfk = gk
old_fval = fk
(
alpha_k,
fc,
gc,
old_fval,
old_old_fval,
gfkp1,
) = line_search_wolfe2(f, myfprime, xk, pk, gfk, f_s.get_max(),
old_fval, old_old_fval)
except Exception as e:
print(e)
re_search += 1
xk = xk + dki
fk, gk = f_g(xk)
old_fval, old_old_fval = fk, old_fval
f_s.add(fk)
if re_search > 2:
flag = 1
break
continue
if alpha_k is None:
print("alpha is None")
xk = xk + dki
fk, gk = f_g(xk)
old_fval, old_old_fval = fk, old_fval
f_s.add(fk)
re_search += 1
if re_search > 2:
flag = 1
break
continue
dki = alpha_k * pk
# fki, gki = f_g(xk + dki)
fki, gki = old_fval, gfkp1
Aredk = fk - fki
Predk = -(np.dot(gk, dki) + 0.5 * np.dot(np.dot(Bk, dki), dki))
rk = Aredk / Predk
xk = xk + dki
fk = fki
yk = gki - gk
tk = C + max(0, -np.dot(yk, dki) / norm(dki)**2) / norm(gk)
ystark = (1 - theta) * yk + theta * tk * norm(gk) * dki
gk = gki
bs = np.dot(Bk, dki)
Bk = (Bk + np.outer(yk, yk) / np.dot(yk, dki) -
np.outer(bs, bs) / np.dot(bs, dki))
# sk = dki
# rhok = 1.0 / (np.dot(yk, sk))
# A1 = 1 - np.outer(sk, yk) * rhok
# A2 = 1 - np.outer(yk, sk) * rhok
# Hk = np.dot(A2, np.dot(Hk, A1)) - (rhok * np.outer(sk, sk))
# Bk = Bk + np.outer(ystark, ystark)/np.dot(ystark, dki) - \
# np.outer(bs, bs)/np.dot(bs, dki) # MBFGS
# print(np.dot(Hk, Bk))
try:
Hk = np.linalg.inv(Bk)
except Exception:
pass
f_s.add(fk)
if callback is not None:
callback(xk)
else:
flag = 2
# print("fit final: ", k, p, f_g.ncall)
s = OptimizeResult()
s.messgae = message_dict[flag]
s.fun = float(fk)
s.nit = k
s.nfev = f_g.ncall
s.njev = f_g.ncall
s.status = flag
s.x = np.array(xk)
s.jac = np.array(gk)
s.hess = np.array(Bk)
s.success = flag == 0
return s