def _sample_at_x(self, x_best) -> Tuple[np.ndarray, np.ndarray]:
"""Evaluate the sampler object at these points.
This function is useful if we want to impose specific noise
on the measurements
Parameters
----------
x_best
Locations to sample at
Returns
-------
x : np.ndarray
Sampled locations x (this is useful in case of input noise)
y : np.ndarray
Values of y at the sampled locations
"""
if self.verbose > 1:
print("Sampling at selected location")
new_sample = self.sampler(x_best)
# new_sample_x = new_sample['x_sample']
# new_sample_y = new_sample['f_sample']
# return new_sample_x, new_sample_y
return x_best, new_sample
def get_next(self):
"""Finds the next point to sample at
Returns
-------
x_best : np.ndarray
Location to sample at
acq_at_x_best : float
Value of the acquisition function at the sampling locations
"""
assert self.batch_size == 1, "Batch BO not yet implemented..."
acq = self._create_acq_function()
best_eval = self._optimise_acq_func(acq)
x_best, acq_at_x_best = best_eval
if self.verbose > 1:
print("Optimised acq_dict function")
print("x, acq_dict(x) = {}".format(best_eval))
mu, _ = self.surrogate.predict(x_best)
return x_best, acq_at_x_best
def _update_surrogate_with_new_data(self, new_sample_x, new_sample_y):
if self.verbose > 1:
print("Updating the surrogate model's data arrays")
model_x, model_y = self.surrogate.X, self.surrogate.Y_raw
new_x = np.vstack((model_x, new_sample_x))
new_y = np.vstack((model_y, new_sample_y))
self.surrogate.set_XY(X=new_x, Y=new_y)
def run(self):
"""
Run the BayesOpt loop
"""
t0 = time.time()
if self.verbose:
print("Started BayesOpt.run()")
self._initialise_bo_df()
for self.curr_bo_step in range(0, self.n_bo_steps):
# try:
if True:
# if True:
t1 = time.time()
if self.verbose:
print("**--** Starting BayesOpt iteration {}/{} **--**".
format(self.curr_bo_step + 1, self.n_bo_steps))
self.optimize_surrogate_if_needed()
self.x_min, self.y_min, self.var_at_y_min = self._get_y_min()
x_best, acq_at_x_best = self.get_next()
t2 = time.time()
time_taken = t2 - t1
if self.create_plots:
self.plot_step(x_best=x_best)
# get new y
new_sample_x, new_sample_y = self._sample_at_x(x_best)
self._update_surrogate_with_new_data(new_sample_x,
new_sample_y)
self.save_history(acq_at_x_best)
# update variables for plotting
self.sampling_locs[self.curr_bo_step] = x_best
self._update_bo_df(x_best, acq_at_x_best, new_sample_x,
new_sample_y, time_taken)
if self.curr_bo_step == self.n_bo_steps - 1: # last step
if self.verbose > 1:
print("Used up budget.")
print("Minimum at",
self.surrogate.X[np.argmin(self.surrogate.Y)])
# except np.linalg.linalg.LinAlgError:
# print("WARNING: BayesOpt crashed at iteration {}!"
# .format(self.curr_bo_step))
# break
if self.verbose:
print(f"Completed BO exp in {round(time.time() - t0, 2)}s")
def save_plots_to_disk(self, fig):
folder = (self.save_plots
if isinstance(self.save_plots, str) else './plots/')
if not os.path.exists(folder):
os.makedirs(folder)
prefix = ('' if self.plots_prefix in (None,
False) else self.plots_prefix)
fname = os.path.join(folder, f"{prefix}{self.curr_bo_step}.png")
fig.savefig(fname)
if self.verbose:
print("Saved plot ", fname)
plt.close()
def optimize_surrogate_if_needed(self):
run_opt = False
if self.optimise_surrogate_model_flag == 'data':
if len(self.surrogate.Y) >= self.opt_next_at_n_data:
self.opt_next_at_n_data += self.optimize_every_n_data
run_opt = True
elif self.optimise_surrogate_model_flag == 'iter':
if len(self.curr_bo_step) >= self.opt_next_at_iter:
self.opt_next_at_iter += self.optimize_every_n_iter
run_opt = True
elif self.optimise_surrogate_model_flag == 'always':
run_opt = True
if run_opt:
if self.verbose >= 1:
print("Optimising surrogate model...")
self.surrogate.optimize()
if self.verbose > 1:
print(f"Surrogate model optimisation complete. "
f"New param_array = {self.surrogate.param_array}")
self.param_array_hist.append(self.surrogate.param_array)
def plot_acq(self, acq_func=None, x_batch=None, x_best=None, x_busy=None):
import pylab as plt
assert self.surrogate.X.shape[1] == 1, "Debugging acq only in 1D!"
if x_batch is not None:
x_batch = np.vstack(x_batch)
if x_busy is not None:
x_busy = np.vstack(x_busy)
x_dense = np.linspace(self.bounds[0, 0], self.bounds[0, 1], 1000)
if acq_func is not None:
fig, axes = plt.subplots(nrows=2, ncols=1, figsize=(12, 9))
acq_dense = acq_func(x_dense[:, None])
if x_best is None:
x_best = np.atleast_2d(x_dense[np.argmax(acq_dense)])
else:
fig, axes = plt.subplots(nrows=1, ncols=1, figsize=(7, 9))
axes = axes,
acq_dense = None
f_mean, f_var = self.surrogate.predict(x_dense[:, None])
f_var[f_var < 1e-10] = 1e-10
f_mean = f_mean.flatten()
f_var = f_var.flatten()
f_std = np.sqrt(f_var)
# Mean and variance of surrogate
axes[0].plot(x_dense, f_mean, 'k', label='Surrogate')
axes[0].fill_between(x_dense,
f_mean + 2 * f_std,
f_mean - 2 * f_std,
color='b',
alpha=0.2)
axes[0].set_title(f'{acq_func} Surrogate model')
# Data in the surrogate
if len(self.surrogate.X) > 0:
axes[0].plot(self.surrogate.X,
self.surrogate.Y_raw,
'b*',
markersize=16,
label='Data')
# New point(s)
axes[0].plot(x_best,
self.surrogate.predict(np.atleast_2d(x_best))[0],
'r*',
markersize=16,
label='New')
if x_batch is not None:
axes[0].plot(x_batch,
self.surrogate.predict(x_batch)[0],
'g*',
label="Batch",
markersize=16)
if acq_func is not None:
axes[1].plot(x_batch,
acq_func(x_batch),
'g*',
label="Batch",
markersize=16)
if x_busy is not None and len(x_busy) > 0:
axes[0].plot(x_busy,
self.surrogate.predict(x_busy)[0],
'k*',
label="Busy",
markersize=16)
if acq_func is not None:
axes[1].plot(x_busy,
acq_func(x_busy),
'k*',
label="Busy",
markersize=16)
if acq_func is not None:
# Acquisition function
axes[1].plot(x_dense, acq_dense, 'k')
# New point(s)
if x_best is not None:
axes[1].plot(x_best,
acq_func(x_best),
'r*',
markersize=16,
label='New')
folder = (self.save_plots
if isinstance(self.save_plots, str) else './plots/')
if not os.path.exists(folder):
os.makedirs(folder)
if x_batch is None:
x_batch = []
fname = os.path.join(folder, f"{self.curr_bo_step}_{len(x_batch)}.pdf")
fig.savefig(fname)
if self.verbose:
print("Saved plot ", fname)
plt.close()
fig.show()
def __init__(self,
sampler: Callable,
surrogate: GP,
bounds: np.ndarray,
batch_size: int = 1,
acq_dict: Optional[Dict] = None,
y_min_opt_params: Optional[dict] = None,
acq_opt_params: Optional[dict] = None,
n_bo_steps: Optional[int] = 30,
optimise_surrogate_model: Optional[bool] = True,
optimize_every_n_data: Optional[int] = None,
optimize_every_n_iter: Optional[int] = None,
track_cond_k: Optional[bool] = True,
min_acq: Optional[float] = None,
create_plots: Optional[bool] = False,
save_plots: Optional[bool] = False,
plots_prefix: Optional[str] = False,
verbose: Optional[Union[bool, int]] = False,
debug: Optional[bool] = False,
**kwargs):
self.verbose = verbose
self.debug = debug
self.df = None
self.curr_bo_step = None
self.batch_size = batch_size
if self.verbose:
print("Initialising BayesOpt instance...")
if acq_dict is None:
self.acq_dict = {'type': 'EI'}
else:
self.acq_dict = acq_dict
self.min_acq = min_acq
if y_min_opt_params is None:
self.y_min_opt_params = {'method': 'direct', 'n_direct_evals': 100}
else:
self.y_min_opt_params = y_min_opt_params
if acq_opt_params is None:
self.acq_opt_params = {'method': 'direct', 'n_direct_evals': 100}
else:
self.acq_opt_params = acq_opt_params
self.n_bo_steps = n_bo_steps
self.param_array_hist = []
self.surrogate = surrogate
self.sampler = sampler
self.bounds = bounds
if optimize_every_n_data is not None:
self.optimise_surrogate_model_flag = 'data'
self.optimize_every_n_data = optimize_every_n_data
self.opt_next_at_n_data = \
len(self.surrogate.Y) + self.optimize_every_n_data
elif optimize_every_n_iter is not None:
raise NotImplementedError # not tested yet
self.optimise_surrogate_model_flag = 'iter'
self.optimize_every_n_iter = optimize_every_n_iter
self.opt_next_at_iter = None
elif optimise_surrogate_model:
self.optimise_surrogate_model_flag = 'always'
self.counter_since_last_surrogate_opt = 0
self.x_min = None
self.y_min = None
self.var_at_y_min = None
self.acq_hist = np.zeros(self.n_bo_steps)
self.sampling_locs = np.zeros((self.n_bo_steps, self.bounds.shape[0]))
# For debugging numerical issues
self.track_cond_k = track_cond_k
if self.track_cond_k:
self.cond_k_hist = np.zeros(self.n_bo_steps)
else:
self.cond_k_hist = None
# Keep a record of the best sample so far
self.y_min_hist = np.zeros(self.n_bo_steps)
self.var_at_y_min_hist = np.zeros(self.n_bo_steps)
self.x_min_hist = np.zeros((self.n_bo_steps, self.bounds.shape[0]))
self.create_plots = create_plots
self.save_plots = save_plots
self.plots_prefix = plots_prefix
if self.verbose:
print("Initialisation of BayesOpt instance done.")
def plot_step(self,
x_best=None,
save_plots=None,
external_call=False,
**kwargs):
"""
Plots a summary of the BayesOpt step and saves the image to a
specified folder
"""
if save_plots is None:
save_plots = self.save_plots
text = "Task"
figsize = (12, 9)
acq = self._create_acq_function()
# Get the best EI/ best minimum
# if x_best is None:
# best_eval = self._optimise_acq_func(acq)
# x_best = best_eval[0]
p = x_best
if len(self.bounds) == 1: # 1D
n_x = 100
x_dense = np.linspace(self.bounds[0, 0], self.bounds[0, 1], n_x)
# get mean and std over the domain
f_mean, f_var = self.surrogate.predict(x_dense[:, None])
f_mean = f_mean.flatten()
f_var = f_var.flatten()
f_std = np.sqrt(f_var)
acq_dense = acq.evaluate(x_dense[:, None])
if self.verbose:
print("Preparing plots")
fig, axes = plt.subplots(nrows=2,
ncols=1,
figsize=figsize,
sharex='all')
# Mean and variance of surrogate
axes[0].plot(x_dense, f_mean, 'k', label='Surrogate')
axes[0].fill_between(x_dense,
f_mean + 2 * f_std,
f_mean - 2 * f_std,
color='b',
alpha=0.2)
axes[0].set_title(f'Step {self.curr_bo_step} Surrogate model')
# Data in the surrogate
if len(self.surrogate.X) > 0:
axes[0].plot(self.surrogate.X,
self.surrogate.Y_raw,
'b*',
markersize=16,
label='Data')
# New point(s)
if x_best is not None:
axes[0].plot(x_best,
self.surrogate.predict(x_best)[0],
'r*',
markersize=16,
label='New')
# Acquisition function
axes[1].plot(x_dense, acq_dense, 'k')
# New point(s)
if x_best is not None:
axes[1].plot(x_best,
acq.evaluate(x_best),
'r*',
markersize=16,
label='New')
axes[1].set_title('Acquisition function')
if not external_call:
axes[0].legend(numpoints=1)
axes[1].legend(numpoints=1)
elif len(self.bounds) == 2: # 2D
n_x1, n_x2 = 20, 20
x1 = np.linspace(self.bounds[0, 0], self.bounds[0, 1], n_x1)
x2 = np.linspace(self.bounds[1, 0], self.bounds[1, 1], n_x2)[::-1]
x1x2 = np.dstack(np.meshgrid(x1, x2)).reshape(-1, 2)
y_grid = self.sampler(x1x2)['f_of_x']
# get mean and std over the domain
f_mean, f_var = self.surrogate.predict(x1x2)
f_mean = f_mean[:, 0]
f_var = f_var[:, 0]
f_std = np.sqrt(f_var)
acq_dense = acq.evaluate(x1x2)
if self.verbose:
print("Preparing plots")
fig, axes = plt.subplots(nrows=2, ncols=2, figsize=figsize)
fig.suptitle("Step " + str(self.curr_bo_step), fontsize=16)
levels = np.linspace(np.min(y_grid), np.max(y_grid), 10)
# Mean of the GP
im1 = axes[0, 0].contourf(x1,
x2,
f_mean.reshape(n_x1, n_x2),
levels=levels)
axes[0, 0].plot(self.surrogate.X[:, 0],
self.surrogate.X[:, 1],
'r*',
markersize=15)
if self.curr_bo_step > 0:
axes[0, 0].plot(p[0][0, 0], p[0][0, 1], 'c*', markersize=20)
axes[0, 0].plot(self.x_min[0], self.x_min[1], 'y*', markersize=18)
axes[0, 0].set_title('Mean of the GP')
# Chosen task
im2 = axes[0, 1].contourf(x1,
x2,
y_grid.reshape(n_x1, n_x2),
levels=levels)
axes[0, 1].plot(self.surrogate.X[:, 0],
self.surrogate.X[:, 1],
'r*',
markersize=15)
if self.curr_bo_step > 0:
axes[0, 1].plot(p[0][0, 0], p[0][0, 1], 'c*', markersize=20)
axes[0, 1].plot(self.x_min[0], self.x_min[1], 'y*', markersize=18)
axes[0, 1].set_title(text)
# Stdev of GP
im3 = axes[1, 0].contourf(x1, x2, f_std.reshape(n_x1, n_x2))
fig.colorbar(im3, ax=axes[1, 0])
axes[1, 0].plot(self.surrogate.X[:, 0],
self.surrogate.X[:, 1],
'r*',
markersize=15)
if self.curr_bo_step > 0:
axes[1, 0].plot(p[0][0, 0], p[0][0, 1], 'c*', markersize=20)
axes[1, 0].set_title('Stdev of the GP')
# Acquisition function
im4 = axes[1, 1].contourf(x1, x2, acq_dense.reshape(n_x1, n_x2))
fig.colorbar(im4, ax=axes[1, 1])
axes[1, 1].plot(self.surrogate.X[:, 0],
self.surrogate.X[:, 1],
'r*',
markersize=15)
if self.curr_bo_step > 0:
axes[1, 1].plot(p[0][0, 0], p[0][0, 1], 'c*', markersize=20)
axes[1, 1].set_title('Acquisition Function')
# fig.subplots_adjust(right=0.8)
cax = fig.add_axes([0.91, 0.55, 0.015, 0.35])
cb = fig.colorbar(im2, cax=cax)
else:
raise NotImplementedError
if not external_call:
if save_plots:
self.save_plots_to_disk(fig)
else:
plt.show()
return fig, axes
def _get_y_min(self):
"""
Get y_min for EI computation
Returns smallest y_min of the model. Can change this to evaluate
lowest y over domain later.
"""
if self.verbose:
print("Finding y_min")
def optimiser_func(x):
return self.surrogate.predict(np.atleast_2d(x))[0].flatten()
if self.y_min_opt_params['method'] == 'standard':
idx = np.argmin(self.surrogate.Y_raw)
x_min = self.surrogate.X[idx]
y_min = self.surrogate.Y_raw[idx]
elif self.y_min_opt_params['method'] == 'direct':
def optimiser_func(x):
return self.surrogate.predict(np.array([x]))[0]
n_direct_evals = self.y_min_opt_params['n_direct_evals']
res = scipydirect.minimize(optimiser_func,
self.bounds,
maxf=n_direct_evals)
x_min = res.x
y_min = res.fun
elif self.y_min_opt_params['method'] == 'multigrad':
num_restarts = self.y_min_opt_params['num_restarts']
res = minimize_with_restarts(optimiser_func,
self.bounds,
num_restarts=num_restarts,
verbose=False)
x_min = res.x
y_min = res.fun
elif self.y_min_opt_params['method'] == 'samplegrad':
op = self.y_min_opt_params
if 'minimize_options' in op.keys():
minimize_options = op['minimize_options']
else:
minimize_options = None
if 'num_samples' in op.keys():
num_samples = op['num_samples']
else:
num_samples = 1000
if 'num_local' in op.keys():
num_local = op['num_local']
else:
num_local = 5
if 'evaluate_sequentially' in op.keys():
evaluate_sequentially = \
op['evaluate_sequentially']
else:
evaluate_sequentially = False
res = sample_then_minimize(
optimiser_func,
self.bounds,
num_samples=num_samples,
num_local=num_local,
minimize_options=minimize_options,
evaluate_sequentially=evaluate_sequentially,
extra_locs=self.surrogate.X,
verbose=False)
x_min = res.x
y_min = res.fun
else:
raise NotImplementedError
_, var_at_y_min = self.surrogate.predict(np.atleast_2d(x_min))
if self.verbose:
print(f"Current y_min = {y_min}")
return x_min, y_min.item(), var_at_y_min.item()
def _optimise_acq_func(self, acq, max_or_min='max', acq_opt_params=None):
"""
Run the chosen optimisation procedure
"""
if self.verbose:
print(f"Optimising acquisition function ({max_or_min})")
if acq_opt_params is None:
acq_opt_params = self.acq_opt_params
if max_or_min == 'max':
def optimiser_func(x):
return -acq.evaluate(np.atleast_2d(x))
elif max_or_min == 'min':
def optimiser_func(x):
return acq.evaluate(np.atleast_2d(x))
else:
raise NotImplementedError
if acq_opt_params['method'] == 'direct':
n_direct_evals = acq_opt_params['n_direct_evals']
res = scipydirect.minimize(optimiser_func,
self.bounds,
maxf=n_direct_evals)
elif acq_opt_params['method'] == 'multigrad':
num_restarts = acq_opt_params['num_restarts']
if 'minimize_options' in acq_opt_params.keys():
minimize_options = acq_opt_params['minimize_options']
else:
minimize_options = None
res = minimize_with_restarts(optimiser_func,
self.bounds,
num_restarts=num_restarts,
hard_bounds=self.bounds,
minimize_options=minimize_options,
verbose=False)
elif acq_opt_params['method'] == 'samplegrad':
if 'minimize_options' in acq_opt_params.keys():
minimize_options = acq_opt_params['minimize_options']
else:
minimize_options = None
if 'num_samples' in acq_opt_params.keys():
num_samples = acq_opt_params['num_samples']
else:
num_samples = 1000
if 'num_local' in acq_opt_params.keys():
num_local = acq_opt_params['num_local']
else:
num_local = 5
if 'num_chunks' in acq_opt_params.keys():
num_chunks = acq_opt_params['num_chunks']
else:
num_chunks = 5
if 'evaluate_sequentially' in acq_opt_params.keys():
evaluate_sequentially = \
acq_opt_params['evaluate_sequentially']
else:
evaluate_sequentially = True
res = sample_then_minimize(
optimiser_func,
self.bounds,
num_samples=num_samples,
num_local=num_local,
num_chunks=num_chunks,
minimize_options=minimize_options,
evaluate_sequentially=evaluate_sequentially,
verbose=False)
else:
raise NotImplementedError
best_x = np.atleast_2d(res.x)
# if isinstance(acq, AcquisitionOnSubspace):
# best_x = np.hstack((np.atleast_2d(acq.fixed_vals),
# np.atleast_2d(best_x)))
# Return the correct value for the acquisition function depending on
# whether we minimized or maximized
if max_or_min == 'max':
best_eval = best_x, -res.fun
elif max_or_min == 'min':
best_eval = best_x, res.fun
else:
raise NotImplementedError
return best_eval
def run(self):
"""
Run the Async BayesOpt loop
"""
t_starting_run = time.time()
if self.verbose:
print("Started BayesOpt.run()")
self._initialise_bo_df()
if self.starting_jobs is not None:
for job in self.starting_jobs:
self.interface.add_job_to_queue(job)
for self.curr_bo_step in range(0, self.n_bo_steps):
new_sample_x, new_sample_y = None, None
# try:
if True:
t_beginning_of_bo_step = time.time()
if self.verbose:
print("**--** Starting BayesOpt iteration {}/{} **--**".
format(self.curr_bo_step + 1, self.n_bo_steps))
# Move time ahead until we have the correct number of free
# workers
self.interface.run_until_n_free(self.batch_size)
n_free_workers = self.interface.status['n_free_workers']
completed_jobs = self.interface.get_completed_jobs()
if len(completed_jobs) > 0:
new_sample_x, new_sample_y = \
self._add_completed_jobs_to_surrogate(completed_jobs)
assert n_free_workers >= self.batch_size
t_before_opt_surrogate = time.time()
# if self.verbose:
# print(f"Surrogate n_data = {len(self.surrogate.X)}")
# if self.optimise_surrogate_model_flag:
# if self.verbose > 1:
# print("Optimising surrogate model...")
# self.surrogate.optimize()
# self.param_array_hist.append(self.surrogate.param_array)
# if self.verbose > 1:
# print(
# f"Surrogate model optimisation complete. "
# f"New param_array = {self.surrogate.param_array}")
self.optimize_surrogate_if_needed()
t_after_opt_surrogate = time.time()
t_before_find_y_min = time.time()
self.x_min, self.y_min, self.var_at_y_min = self._get_y_min()
t_after_find_y_min = t_before_get_next = time.time()
if self.verbose:
print("Selecting next point(s)...")
x_batch, acq_at_x_batch = self.get_next()
t_after_get_next = t_end_of_bo_step = time.time()
time_taken_opt_surrogate = \
(t_after_opt_surrogate - t_before_opt_surrogate)
time_taken_find_y_min = \
(t_after_find_y_min - t_before_find_y_min)
time_taken_get_next = \
(t_after_get_next - t_before_get_next)
time_taken_bo_step = \
(t_end_of_bo_step - t_beginning_of_bo_step)
time_taken_dict = {
'time_taken_opt_surrogate': time_taken_opt_surrogate,
'time_taken_find_y_min': time_taken_find_y_min,
'time_taken_get_next': time_taken_get_next,
'time_taken_bo_step': time_taken_bo_step,
}
if self.create_plots:
self.plot_step(x_batch=x_batch)
# queue the jobs
jobs = []
for ii in range(len(x_batch)):
job = {'x': x_batch[ii], 'f': self.sampler}
jobs.append(job)
self.interface.add_job_to_queue(jobs)
self.save_history(None)
if self.curr_bo_step == self.n_bo_steps - 1: # last step
if self.verbose > 1:
print("Used up budget.")
print("Minimum at",
self.surrogate.X[np.argmin(self.surrogate.Y)])
self._update_bo_df(x_batch, acq_at_x_batch, new_sample_x,
new_sample_y, time_taken_dict)
# Attempting to force SLURM to update the output file
sys.stdout.flush()
# except np.linalg.linalg.LinAlgError:
# print("WARNING: BayesOpt crashed at iteration {}!".format(
# self.curr_bo_step))
# break
if self.verbose:
print(f"Completed BO exp in;"
f" {round(time.time() - t_starting_run, 2)}s")
