def optimize(self, reset=False):
# Bounded region of parameter space
pbounds = {
'men_kappa_fulltime': (0.3, 0.6),
'men_kappa_parttime':
(0.3, 0.7), #'men_mu_scale': (0.01,0.3), 'men_mu_age': (57,62),
'women_kappa_fulltime': (0.3, 0.6),
'women_kappa_parttime': (0.3, 0.7)
} #, 'women_mu_scale': (0.01,0.3), 'women_mu_age': (57,62)}
optimizer = BayesianOptimization(
f=self.black_box_function,
pbounds=pbounds,
verbose=
2, # verbose = 1 prints only when a maximum is observed, verbose = 0 is silent
random_state=1,
)
LOG_DIR = Path().absolute() / 'bayes_opt_logs'
LOG_DIR.mkdir(exist_ok=True)
filename = 'log_0.json'
# talletus
logfile = str(LOG_DIR / filename)
logger = JSONLogger(path=logfile)
if Path(logfile).exists() and not reset:
load_logs(optimizer, logs=[logfile])
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
optimizer.maximize(
init_points=2,
n_iter=20,
)
print('The best parameters found {}'.format(optimizer.max))
def optimize(self, load_from: str = None):
self.idx = 0
Popen('ulimit -n 4096', shell=True)
optimizer = BayesianOptimization(
f=self._black_box_function,
pbounds=self.p_bounds,
random_state=1,
)
logger = JSONLogger(path=self.opt_filepath)
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
if load_from is not None:
logfile = os.path.join(self.out_path, load_from)
if Path(logfile).is_file():
logging.info('Loading logs from ' + logfile)
load_logs(optimizer, logs=[logfile])
else:
logging.info('Could not find a log file under {}'.format(logfile))
optimizer.maximize(
init_points=self.init_points,
n_iter=self.n_iter,
)
def optimizer(self,
log_json=False,
load_log=False,
log_path=None,
**kwargs):
allow = ['n_init_explore_point', 'n_bayesian_iterations']
self.__dict__.update((k, v) for k, v in kwargs.items() if k in allow)
b_opt = BayesianOptimization(
f=self.bb_partial,
pbounds=self.parameters,
verbose=self.opt_verbose,
random_state=0,
)
if log_json:
logger = JSONLogger(path=r'./Logs/' + self.type_nn + '_' +
str(self.rnn_kind) + '.json')
b_opt.subscribe(Events.OPTMIZATION_STEP, logger)
if load_log and log_path is not None:
load_logs(b_opt, logs=log_path)
b_opt.maximize(
init_points=self.n_init_explore_point,
n_iter=self.n_bayesian_iterations,
acq=
"poi", # Acquisition Function "Probability of Improvement" --> Prefer exploration (with xi=0.1)
xi=1e-1)
print('best parameters:', b_opt.max, '\n')
return b_opt
def get_optimizer():
optimizer = BayesianOptimization(f=train,
pbounds=pbounds,
random_state=3,
verbose=2)
if os.path.isfile('./oldlogs.json'):
load_logs(optimizer, logs=["./oldlogs.json"])
print("New optimizer is now aware of {} points.".format(
len(optimizer.space)))
else:
optimizer.probe(
params={
"contrast": 1,
"hue": 0,
"lr": 0.12,
"rotations": 0
},
lazy=True,
)
logger = BasicObserver("./logs.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
optimizer.subscribe(Events.OPTMIZATION_START, logger.screenlogger)
optimizer.subscribe(Events.OPTMIZATION_END, logger.screenlogger)
return optimizer
def optimize():
global ITERATIONS
ITERATIONS = 1
MAX_EVALS = 10
from bayes_opt import BayesianOptimization
# Bounded region of parameter space
pbounds = {'alpha': (0.001, 0.999), 'beta': (0.001, 1.5)}
optimizer = BayesianOptimization(
f=objective,
pbounds=pbounds,
random_state=1,
)
try:
from bayes_opt.util import load_logs
load_logs(optimizer, logs=["logs.json"])
print("Rerunning from {} trials".format(len(optimizer.res)))
except:
print("Starting from scratch: new trials.")
from bayes_opt.observer import JSONLogger
from bayes_opt.event import Events
logger = JSONLogger(path="logs.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
# Results will be saved in ./logs.json
optimizer.maximize(
init_points=20, #max(0, 5 - len(optimizer.res)),
n_iter=MAX_EVALS,
)
print(optimizer.max)
def get():
pbounds = {
'batch_size_continuous': (20, 20),
# Possibly as small as possible to reduce model construction time.
# Effect of large batch size is the same as large lr because
# the training batch is repeative (no variance between batches).
'lr_exp': (1.02, 1.02),
# As large as possible to allows larger initial gradient
'momentum': (0.8, 0.8),
'layer_size_continuous': (20, 20),
# As large as possible to increase model complexity, since no overfitting is presented.)
'layer_count_continuous': (1, 1)
# As small as possible because large layer count leads to slower optimization.
}
optimizer = BayesianOptimization(
f=initial_acc, # initial_slop,
pbounds=pbounds
)
load_logs(optimizer, logs=["./baysian_logs.json"])
res_list = []
for i, res in enumerate(optimizer.res):
print("Iteration {}: \n\t{}".format(i, res))
res_list.append(res)
# print("Final Max:", optimizer.max)
return res_list
def maximize(self,
LHS_path=None,
init_points=5,
is_LHS=False,
n_iter=25,
acq='ucb',
kappa=2.576,
xi=0.0,
**gp_params):
"""Mazimize your function"""
self._prime_subscriptions()
self.dispatch(Events.OPTMIZATION_START)
if LHS_path == None:
if is_LHS:
self._prime_queue_LHS(init_points)
else:
self._prime_queue(init_points)
else:
from bayes_opt.util import load_logs
load_logs(self, logs=[LHS_path])
self.set_gp_params(**gp_params)
util = UtilityFunction(kind=acq, kappa=kappa, xi=xi)
iteration = 0
while not self._queue.empty or iteration < n_iter:
try:
x_probe = next(self._queue)
except StopIteration:
x_probe = self.suggest(util)
iteration += 1
self.probe(x_probe, lazy=False)
self.dispatch(Events.OPTMIZATION_END)
def optimize_bayes_wo_param(parse_model_param):
def crossval(*args_model, **kwargs_model):
estimator = parse_model_param(*args_model, **kwargs_model)
return cross_val_score(estimator,
X=X,
y=y,
*args_eval,
**kwargs_eval).mean()
optimizer = BayesianOptimization(crossval, pbounds=pbounds)
optimizer_log_dir = (LOG_DIR / log_dir)
if optimizer_log_dir.exists():
all_log = [str(path) for path in optimizer_log_dir.iterdir()]
load_logs(optimizer, logs=all_log)
filename = 'log_{}.json'.format(len(all_log))
else:
optimizer_log_dir.mkdir()
filename = 'log_0.json'
logger = JSONLogger(path=str(optimizer_log_dir / filename))
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
optimizer.maximize(init_points, n_iter, kappa=kappa, acq=acq)
best_model = parse_model_param(**optimizer.max['params'])
best_model.fit(X=X, y=y)
return best_model
def load_hyperparameters(self):
"""
This method loads the best hyperparameters from the Hyperparameter_Selection History to the current instance
"""
optimizer = BayesianOptimization(
f=None,
pbounds=self.hyperparameter,
verbose=
2, # verbose = 1 prints only when a maximum is observed, verbose = 0 is silent
random_state=1)
#Load Hyperparamter Selection History Logs
logger_name = self.model_name
if os.path.exists(saved_models_path + logger_name + ".json"):
load_logs(optimizer,
logs=[saved_models_path + logger_name + ".json"])
#Save best hyperparameter
best_model = optimizer.max
if self.ridge_2 != None:
self.ridge_1 = best_model['params']['ridge_1']
self.ridge_2 = best_model['params']['ridge_2']
else:
self.ridge_1 = best_model['params']['ridge_1']
print(
"The optimizer is now aware of {num_pts} points and the best result is {Result}."
.format(Result=best_model['target'],
num_pts=len(optimizer.space)))
else:
print('No Hyperparameters was tested.')
return None
def hyperParameterOptimizer():
def blackbox(c1Filters, c1KernelSize, c1Strides, c2Filters, c2KernelSize,
c2Strides, c3Filters, c3KernelSize, c3Strides, fcc1Units,
fcc2Units, dropout1, dropout2):
hyperParams = HyperParams()
hyperParams.c1Filters = int(round(c1Filters))
hyperParams.c1KernelSize = int(round(c1KernelSize))
hyperParams.c1Strides = int(round(c1Strides))
hyperParams.c2Filters = int(round(c2Filters))
hyperParams.c2KernelSize = int(round(c2KernelSize))
hyperParams.c2Strides = int(round(c2Strides))
hyperParams.c3Filters = int(round(c3Filters))
hyperParams.c3KernelSize = int(round(c3KernelSize))
hyperParams.c3Strides = int(round(c3Strides))
hyperParams.fcc1Units = int(round(fcc1Units))
hyperParams.fcc2Units = int(round(fcc2Units))
hyperParams.dropout1 = round(dropout1, 2)
hyperParams.dropout2 = round(dropout2, 2)
checkpoint = train(200, None, hyperParams)
return checkpoint.validationAccuracy
bounds = {
'c1Filters': (100, 128),
'c1KernelSize': (2, 2),
'c1Strides': (2, 2),
'c2Filters': (64, 100),
'c2KernelSize': (2, 2),
'c2Strides': (2, 2),
'c3Filters': (32, 64),
'c3KernelSize': (2, 2),
'c3Strides': (2, 2),
'fcc1Units': (32, 150),
'fcc2Units': (32, 150),
'dropout1': (0.2, 0.5),
'dropout2': (0.2, 0.5),
}
optimizer = BayesianOptimization(
f=blackbox,
pbounds=bounds,
random_state=1,
)
logger = JSONLogger(path="./logs.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
load_logs(optimizer, logs=["./oldlogs.json"])
optimizer.maximize(
init_points=2,
n_iter=36,
)
print(optimizer.max)
def xgb_optimization(X, y, params, random_state=1337):
training_data = xgb.DMatrix(X, y)
def xgb_model(
feature_fraction,
bagging_fraction,
lambda_l1,
lambda_l2,
max_depth,
num_leaves,
min_split_gain,
min_child_weight,
learning_rate,
n_estimators,
):
params["feature_fraction"] = max(min(feature_fraction, 1), 0)
params["bagging_fraction"] = max(min(bagging_fraction, 1), 0)
params["lambda_l1"] = max(lambda_l1, 0)
params["lambda_l2"] = max(lambda_l2, 0)
params["max_depth"] = int(round(max_depth))
params["num_leaves"] = int(round(num_leaves))
params["min_split_gain"] = min_split_gain
params["min_child_weight"] = min_child_weight
params["learning_rate"] = learning_rate
params["n_estimators"] = int(round(n_estimators))
params.update({
"objective": "reg:squarederror",
"max_bin": 255,
"bagging_freq": 1,
"min_child_samples": 20,
"boosting": "gbdt",
"verbosity": 1,
"early_stopping_round": 200,
"metric": "rmse",
})
clf = xgb.cv(params,
training_data,
nfold=5,
seed=random_state,
verbose_eval=1)
return (-1 * np.array(clf["test-rmse-mean"])).max()
optimizer = BayesianOptimization(f=xgb_model,
pbounds=params,
random_state=1337)
logger_path = os.path.join(LOGS_DIR, "logs_xgb.json")
if os.path.exists(logger_path):
load_logs(optimizer, logs=logger_path)
logger = JSONLogger(path=logger_path)
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
optimizer.maximize(init_points=5, n_iter=25, acq="ucb")
return optimizer.max["params"]
def optimize_2d(path=None,
steps=None,
init_points=None,
bounds=None,
true_function=None,
plot=False,
load=False):
def wrapper(x, y):
os.environ['NW'] = "%f" % (x)
os.environ['NN'] = "%f" % (y)
res = -F.func_para()
return res
opt = BayesianOptimization(f=wrapper,
pbounds=bounds,
verbose=2,
random_state=92898)
log_file = new_log_file_name()
logger = JSONLogger(path=log_file)
screen_logger = ScreenLogger(verbose=2)
opt.subscribe(Events.OPTMIZATION_STEP, logger)
opt.subscribe(Events.OPTMIZATION_START, screen_logger)
opt.subscribe(Events.OPTMIZATION_STEP, screen_logger)
opt.subscribe(Events.OPTMIZATION_END, screen_logger)
print('Logging to logfile: ', os.path.abspath(log_file))
dump_bounds(log_file, bounds)
no_log_files_found = False
if load:
files = find_log_files()
if len(files) > 0:
print('Loading previous runs from logfile(s):')
for f in files:
print(f)
load_logs(opt, logs=files)
else:
no_log_files_found = True
if (init_points is not None) and (init_points > 0):
if no_log_files_found or not load:
opt.maximize(init_points=init_points, n_iter=0, alpha=1e-5)
first_step = True
opt.unsubscribe(Events.OPTMIZATION_END, screen_logger)
print('')
if _check_steps_finite(steps):
for _ in range(steps):
opt.maximize(init_points=0, n_iter=1, alpha=1e-5)
if first_step:
opt.unsubscribe(Events.OPTMIZATION_START, screen_logger)
first_step = False
else:
while True:
opt.maximize(init_points=0, n_iter=1, alpha=1e-5)
print("MAX: ", opt.max)
return opt
def optimize():
# define bounds for the params you want to optimize. Can be multivariate. Check https://github.com/fmfn/BayesianOptimization on how to
bounds = {
'localAreaDensity': (0.01, 0.15),
'permanenceIncrement': (0.01, 0.1),
}
optimizer = BayesianOptimization(
f=target_func,
pbounds=bounds,
random_state=1,
)
# We can start from saved logs
if os.path.isfile('./local_area_density_optimization_logs_base.json'):
print('Loading Logs...')
load_logs(optimizer, logs=["./local_area_density_optimization_logs_base.json"]);
# The new log file to write to
json_logger = JSONLogger(path="./local_area_density_optimization_logs.json")
optimizer.subscribe(Events.OPTIMIZATION_STEP, json_logger)
# Additionally log to console
screen_logger = ScreenLogger()
optimizer.subscribe(Events.OPTIMIZATION_STEP, screen_logger)
# If you want to guide the optimization process
val = 0.02
while val <= 0.04:
optimizer.probe(
params={
'localAreaDensity': val,
'permanenceIncrement': 0.04,
},
lazy=True,
)
val = round(val + 0.001, 3)
optimizer.maximize(
init_points=20,
n_iter=50,
)
print(optimizer.max)
# cleanup temp dir
shutil.rmtree(os.path.join('temp'))
def bayes_opt(fn, params, probes=None):
name = fn.__name__
opt = BayesianOptimization(fn, params, verbose=2)
if os.path.exists(f'./bayes_opt_logs/{name}.json'):
print('Loading logs...')
load_logs(opt, logs=[f'./bayes_opt_logs/{name}.json'])
logger = JSONLogger(path=f'./bayes_opt_logs/{name}.json')
opt.subscribe(Events.OPTMIZATION_STEP, logger)
# Probe with a set of know "good" params
if probes:
for probe in probes:
opt.probe(params=probe, lazy=True)
opt.maximize(n_iter=100, init_points=60)
print(opt.max)
def print_max(self):
optimizer = BayesianOptimization(
f=self.cost,
pbounds=self.pbounds,
random_state=1,
verbose=2,
)
load_logs(optimizer,
logs=[
"ABC_Results/user_parameters_p{}.json".format(
self.participant)
])
x_obs = optimizer.space._params
y_obs = optimizer.space._target
gp = optimizer._gp
gp.fit(x_obs, y_obs)
print(optimizer.max)
def hyper():
opt = BayesianOptimization(f=train,
pbounds={
'lr': (0.0001, 0.001),
'lm': (0.75, 0.95),
'tpri': (10, 150),
'rpr': (0.25, 0.75),
'dmc': (0.6, 0.9),
'wd': (0.00001, 0.001)
},
verbose=2)
logger = JSONLogger(path="./bo_logs.json")
opt.subscribe(Events.OPTIMIZATION_STEP, logger)
opt.maximize(init_points=3, n_iter=10)
load_logs(opt, logs=["./bo_logs.json"])
print('maximum: ', opt.max)
def get():
pbounds = {
'squeeze_scale_exp': (1.5, 1.5), # 2
'small_filter_rate': (0.5, 0.5), # 10
'max_lr_exp': (-4, -2), # 6
'max_momentum': (0.8, 0.99),
'num_epoch': (20, 50)
}
optimizer = BayesianOptimization(f=OneCycleTrain, pbounds=pbounds)
load_logs(optimizer, logs=["./one_cycle_baysian_logs.json"])
res_list = []
for i, res in enumerate(optimizer.res):
print("Iteration {}: \n\t{}".format(i, res))
res_list.append(res)
# print("Final Max:", optimizer.max)
return res_list
def optimize(self):
"""
Main function for optimization
"""
# Initialize optimizer
self.bo = BayesianOptimization(self._eval_fun, self.param_boundaries)
self.bo.subscribe(Events.OPTMIZATION_STEP, self.logger)
if self.load_log:
load_logs(self.bo, logs=[self.prev_log])
# Explore the input and target space on predefined points
if self.probe:
self._explore_target_space()
# Set parameters for Gaussian Process
gp_params = {}
# {'kernel': None, 'alpha': 1e-5}
self.bo.maximize(init_points=self.NR_INIT_POINTS,
n_iter=self.NR_ITERATIONS,
acq='ei',
**gp_params)
def test_logs():
import pytest
def f(x, y):
return -x**2 - (y - 1)**2 + 1
optimizer = BayesianOptimization(f=f,
pbounds={
"x": (-2, 2),
"y": (-2, 2)
},
ptypes={
'x': float,
'y': float
})
assert len(optimizer.space) == 0
load_logs(optimizer, "./tests/test_logs.json")
assert len(optimizer.space) == 5
load_logs(optimizer, ["./tests/test_logs.json"])
assert len(optimizer.space) == 5
other_optimizer = BayesianOptimization(f=lambda x: -x**2,
pbounds={"x": (-2, 2)})
with pytest.raises(ValueError):
load_logs(other_optimizer, ["./tests/test_logs.json"])
def optimize_local_area_density():
# optimize localAreaDensity
bounds = {
'localAreaDensity': (0.01, 0.15),
}
optimizer = BayesianOptimization(
f=target_func,
pbounds=bounds,
random_state=1,
)
if os.path.isfile('./local_area_density_optimization_logs_base.json'):
print('Loading Logs...')
load_logs(optimizer,
logs=["./local_area_density_optimization_logs_base.json"])
logger = JSONLogger(path="./local_area_density_optimization_logs.json")
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
val = 0.02
while val <= 0.04:
print('Adding', val)
optimizer.probe(
params={
'localAreaDensity': val,
},
lazy=True,
)
val = round(val + 0.001, 3)
print('Starting optimization...')
optimizer.maximize(
init_points=20,
n_iter=50,
)
print(optimizer.max)
return accuracy
pbounds = {
'alphabet_size': (64.0, 64.0),
'dropout': (0.0, 0.4),
'embedding_size': (32.0, 64.0),
'label_smoothing': (0.0, 0.2),
'layer_size': (1280.0, 1280.0),
'learning_rate': (-4.0, -2.0),
'learning_rate_final': (-5.0, -3.0),
'window': (8.0, 8.0)
}
optimizer = BayesianOptimization(f=model_accuracy,
pbounds=pbounds,
verbose=2,
random_state=1)
if os.path.isfile("./parameters_log.json"):
load_logs(optimizer, logs=["./parameters_log.json"])
print("Loaded {} model evaluations".format(len(optimizer.space)))
logger = JSONLogger(path="./parameters_log_new.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
optimizer.subscribe(Events.OPTMIZATION_STEP, ScreenLogger())
optimizer.maximize(
init_points=max(0, 20 - len(optimizer.space)),
n_iter=40 - max(len(optimizer.space) - 20, 0),
)
def plot2(self):
optimizer = BayesianOptimization(
f=self.cost,
pbounds=self.pbounds,
random_state=1,
verbose=2,
)
load_logs(optimizer,
logs=[
"ABC_Results/user_parameters_p{}.json".format(
self.participant)
])
x_obs = optimizer.space._params
y_obs = optimizer.space._target
gp = optimizer._gp
# kernel = Matern(nu=4.5)
kernel = RBF(length_scale=1e-5)
# kernel = RationalQuadratic(length_scale=1,
# alpha=10) # length_scale_bounds=(1e-05, 100000.0), alpha_bounds=(1e-05, 100000.0)),
# kernel=DotProduct(sigma_0=3e7)
# sigma = 1e1
# kernel = DotProduct(sigma_0=sigma) * DotProduct(sigma_0=sigma)
gp = GaussianProcessRegressor(
kernel=kernel,
normalize_y=True,
alpha=0.5,
n_restarts_optimizer=25,
)
gp.fit(x_obs, y_obs)
max_x = np.array([
optimizer.max['params']['max_motor_units'],
optimizer.max['params']['w_vel']
])
max_y = optimizer.max['target']
num_vals = 101
heatmap = np.zeros((num_vals, num_vals))
w_vel = np.linspace(self.pbounds["w_vel"][0], self.pbounds["w_vel"][1],
num_vals)
max_motor_units = np.linspace(self.pbounds["max_motor_units"][0],
self.pbounds["max_motor_units"][1],
num_vals)
# calculate heat map
for i in range(num_vals):
for j in range(num_vals):
heatmap[i, j] = gp.predict(
np.array([max_motor_units[j], w_vel[i]]).reshape(1, -1))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(x_obs[:, 0], x_obs[:, 1], y_obs, color='g')
ax.scatter(max_x[0], max_x[1], max_y, color='r')
xv, yv = np.meshgrid(max_motor_units, w_vel)
ax.plot_wireframe(xv, yv, heatmap)
# ax.plot_surface(xv, yv, heatmap)
ax.set_xlabel("motor")
ax.set_ylabel("w_vel")
plt.show()
'ridge_alpha': 0.0006696012127733874
}
]
optimizer = BayesianOptimization(
f=black_box_function,
pbounds=pbounds,
random_state=42,
)
for point in start_points:
optimizer.probe(
params=point,
lazy=True,
)
if LOAD_PREV:
load_logs(optimizer, logs=["./calc_shifts_params.json"]);
logger = JSONLogger(path="./calc_shifts_params.json")
scrlogger = ScreenLogger()
optimizer.subscribe(Events.OPTIMIZATION_STEP, scrlogger)
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
optimizer.maximize(
init_points=500,
n_iter=500,
)
print(optimizer.max)
'T': (0, 1),
'Tsin': (0, 1),
} #constrained optimization technique, so you must specify the minimum and maximum values that can be probed for each parameter
optimizer = BayesianOptimization(
f=bayesOpt_function, #function that is optimized
pbounds=pbounds, #opt.-range of parameters
random_state=1,
verbose=
0 # verbose = 1 prints only when a maximum is observed, verbose = 0 is silent, verbose = 2 prints everything
)
#load existing optimizer
log_already_available = 0
if os.path.isfile("./logs_CNN_seq2seq_GWLt-1_" + Well_ID + ".json"):
load_logs(optimizer,
logs=["./logs_CNN_seq2seq_GWLt-1_" + Well_ID + ".json"])
print("\nExisting optimizer is already aware of {} points.".format(
len(optimizer.space)))
log_already_available = 1
# Saving progress
logger = newJSONLogger(path="./logs_CNN_seq2seq_GWLt-1_" + Well_ID +
".json")
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
# random exploration as a start
f = open('./timelog_CNN_seq2seq_GWLt-1_' + Well_ID + '.txt', "w")
print("Starttime of first iteration: {}\n".format(
datetime.datetime.now()),
file=f) #this is not looged in json file
def plot(self, p, i):
optimizer = BayesianOptimization(
f=self.cost,
pbounds=self.pbounds,
random_state=1,
verbose=2,
)
load_logs(optimizer,
logs=[
"ABC_Results/user_parameters_p{}.json".format(
self.participant)
])
x_obs = np.array([[res["params"][p]] for res in optimizer.res])[:i + 1]
y_obs = np.array([res["target"] for res in optimizer.res])[:i + 1]
gp = optimizer._gp
gp.fit(x_obs, y_obs)
# # kernel = Matern(nu=4.5)
# kernel = RBF(length_scale=1e-5)
# kernel = RationalQuadratic(length_scale=1,
# alpha=10) # length_scale_bounds=(1e-05, 100000.0), alpha_bounds=(1e-05, 100000.0)),
# # kernel=DotProduct(sigma_0=3e7)
sigma = 1e0
kernel = DotProduct(sigma_0=sigma) * DotProduct(sigma_0=sigma)
#
gp = GaussianProcessRegressor(
kernel=kernel,
normalize_y=True,
alpha=1e-6,
n_restarts_optimizer=5,
)
gp.fit(x_obs, y_obs)
# max_x = np.array([optimizer.max['params'][p]])
# max_y = optimizer.max['target']
xmin, xmax = self.pbounds[p]
x = np.linspace(xmin, xmax, 100)
num_vals = len(x)
w_vel = np.linspace(self.pbounds[p][0], self.pbounds[p][1], num_vals)
mu, sigma = gp.predict(w_vel.reshape(-1, 1), return_std=True)
fig = plt.figure(i)
ax = fig.add_subplot(111)
ax.scatter(x_obs.flatten(), y_obs, color='g', label="observations")
# ax.scatter(max_x, max_y, color='r', label="Max value")
ax.plot(w_vel, mu, 'k--', label="prediction")
ax.fill_between(w_vel,
mu - sigma,
mu + sigma,
label="SD Confidence",
alpha=0.5)
ax.set_xlabel(p)
ax.set_ylabel("target")
ax.set_xlim(0, 1000)
ax.set_ylim(-15, 1)
plt.legend()
counter = str(i).zfill(3)
plt.savefig("ABC_Results\images\w_vel_p999_{}.png".format(counter))
plt.close()
def bayesian_search(
config_path,
inferencecfg,
pbounds,
edgewisecondition=True,
shuffle=1,
trainingsetindex=0,
modelprefix="",
snapshotindex=-1,
target="rpck_test",
maximize=True,
init_points=20,
n_iter=50,
acq="ei",
log_file=None,
dcorr=5,
leastbpts=3,
printingintermediatevalues=True,
): #
if "rpck" in target:
assert maximize == True
if "rmse" in target:
assert maximize == False
cfg = auxiliaryfunctions.read_config(config_path)
evaluationfolder = os.path.join(
cfg["project_path"],
str(
auxiliaryfunctions.GetEvaluationFolder(
cfg["TrainingFraction"][int(trainingsetindex)],
shuffle,
cfg,
modelprefix=modelprefix,
)),
)
DLCscorer, DLCscorerlegacy = auxiliaryfunctions.GetScorerName(
cfg,
shuffle,
cfg["TrainingFraction"][int(trainingsetindex)],
cfg["iteration"],
modelprefix=modelprefix,
)
# load params
fns = return_evaluate_network_data(
config_path,
shuffle=shuffle,
trainingsetindex=trainingsetindex,
modelprefix=modelprefix,
)
predictionsfn = fns[snapshotindex]
data, metadata = auxfun_multianimal.LoadFullMultiAnimalData(predictionsfn)
params = set_up_evaluation(data)
columns = ["train_iter", "train_frac", "shuffle"]
columns += [
"_".join((b, a)) for a in ("train", "test")
for b in ("rmse", "hits", "misses", "falsepos", "ndetects", "pck",
"rpck")
]
train_iter = trainingsetindex # int(predictionsfn.split('-')[-1].split('.')[0])
train_frac = cfg["TrainingFraction"][
train_iter] # int(predictionsfn.split('trainset')[1].split('shuffle')[0])
trainIndices = metadata["data"]["trainIndices"]
testIndices = metadata["data"]["testIndices"]
if edgewisecondition:
mf = str(
auxiliaryfunctions.GetModelFolder(
cfg["TrainingFraction"][int(trainingsetindex)],
shuffle,
cfg,
modelprefix=modelprefix,
))
modelfolder = os.path.join(cfg["project_path"], mf)
path_inferencebounds_config = (Path(modelfolder) / "test" /
"inferencebounds.yaml")
try:
inferenceboundscfg = auxiliaryfunctions.read_plainconfig(
path_inferencebounds_config)
except FileNotFoundError:
print("Computing distances...")
from deeplabcut.pose_estimation_tensorflow import calculatepafdistancebounds
inferenceboundscfg = calculatepafdistancebounds(
config_path, shuffle, trainingsetindex)
auxiliaryfunctions.write_plainconfig(path_inferencebounds_config,
inferenceboundscfg)
partaffinityfield_graph = params["paf_graph"]
upperbound = np.array([
float(inferenceboundscfg[str(edge[0]) + "_" +
str(edge[1])]["intra_max"])
for edge in partaffinityfield_graph
])
lowerbound = np.array([
float(inferenceboundscfg[str(edge[0]) + "_" +
str(edge[1])]["intra_min"])
for edge in partaffinityfield_graph
])
upperbound *= inferencecfg["upperbound_factor"]
lowerbound *= inferencecfg["lowerbound_factor"]
else:
lowerbound = None
upperbound = None
def dlc_hyperparams(**kwargs):
inferencecfg.update(kwargs)
# Ensure type consistency
for k, (bound, _) in pbounds.items():
inferencecfg[k] = type(bound)(inferencecfg[k])
stats = compute_crossval_metrics_preloadeddata(
params,
columns,
inferencecfg,
data,
trainIndices,
testIndices,
train_iter,
train_frac,
shuffle,
lowerbound,
upperbound,
dcorr=dcorr,
leastbpts=leastbpts,
)
# stats = compute_crossval_metrics(config_path, inferencecfg, shuffle,trainingsetindex,
# dcorr=dcorr,leastbpts=leastbpts,modelprefix=modelprefix)
if printingintermediatevalues:
print(
"rpck",
stats["rpck_test"].values[0],
"rpck train:",
stats["rpck_train"].values[0],
)
print(
"rmse",
stats["rmse_test"].values[0],
"miss",
stats["misses_test"].values[0],
"hit",
stats["hits_test"].values[0],
)
# val = stats['rmse_test'].values[0]*(1+stats['misses_test'].values[0]*1./stats['hits_test'].values[0])
val = stats[target].values[0]
if np.isnan(val):
if maximize: # pck case
val = -1e9 # random small number
else: # RMSE, return a large RMSE
val = 1e9
if not maximize:
val = -val
return val
opt = BayesianOptimization(f=dlc_hyperparams,
pbounds=pbounds,
random_state=42)
if log_file:
load_logs(opt, log_file)
logger = JSONLogger(path=os.path.join(evaluationfolder, "opti_log" +
DLCscorer + ".json"))
opt.subscribe(Events.OPTIMIZATION_STEP, logger)
opt.maximize(init_points=init_points, n_iter=n_iter, acq=acq)
inferencecfg.update(opt.max["params"])
for k, (bound, _) in pbounds.items():
tmp = type(bound)(inferencecfg[k])
if isinstance(tmp, np.floating):
tmp = np.round(tmp, 2).item()
inferencecfg[k] = tmp
return inferencecfg, opt
def main():
# Parse arguments
import argparse
parser = argparse.ArgumentParser(description='Runs a bayesian optimisation for some of the algorithms defined in the PTSP framework')
parser.add_argument('--algorithm',
choices=["QD-MCTS", "S-MCTS", "MS-MCTS", "VanillaGA", "VanillaMCTS"],
help='The algorithm that should be optimized',
default="S-MCTS")
parser.add_argument('--outputDir',
default="./optimizationResults",
help='The output directory for all data generated by the optimization')
parser.add_argument("--ptspPath",
default="./ptsp.jar",
help="The path to the .jar file containing the PTSP framework")
parser.add_argument("--iters",
default="10",
type=int,
help="Number of parameter-points to test by the bayesian optimization")
args = parser.parse_args()
args.outputPath = f"{args.outputDir}/{args.algorithm}"
# Find all previous logs for this optimization
logs = glob.glob(f"{args.outputPath}/optimizationLogs*.json")
csvLogs = glob.glob(f"{args.outputPath}/*.csv")
# Launch the JVM
jpype.startJVM()
jpype.addClassPath(args.ptspPath)
import framework.Optimization as optim
# Move java output into a file
from java.lang import System
from java.io import PrintStream, FileOutputStream
pathlib.Path(args.outputPath).mkdir(parents=True, exist_ok=True)
System.setOut(PrintStream(FileOutputStream(f"{args.outputPath}/cout.txt", True)))
# Algorithm specific data
bounds = {
"QD-MCTS" : {
"lowER": (0.01, 10), # Exploration rate low-level search
"highER": (0.01, 10), # Exploration rate high-level search
"steps": (300, 600), # Number of steps for low-level search
"rd": (10, 30) # rolloutDepth
},
"S-MCTS" : {
"cellSize": (5, 30), # Size of a cell in the subgoal grid (aka distance between subgoals)
"er": (0.01, 10), # Exploration rate high-level search
"steps": (300, 600), # Number of steps for low-level search
"rd": (10, 30) # rolloutDepth
},
"MS-MCTS" : {
"cellSize": (5, 30), # Size of a cell in the subgoal grid (aka distance between subgoals)
"er": (0.01, 10), # Exploration rate high-level search
"steps": (300, 600), # Number of steps for low-level search
"rd": (10, 30) # rolloutDepth
},
"VanillaGA" : {
"gl": (10, 30), # How many base-actions does a genome contain
"ps": (1, 100), # How many genomes in one population
"mr": (0.1, 0.9), # Probability that an action is mutated
},
"VanillaMCTS" : {
"er": (0.01, 10), # Exploration rate
"rd": (10, 30), # RolloutDepth
}
}
funcs = {
"QD-MCTS" : lambda lowER, highER, steps, rd: execSafe(optim.runQD_MCTS, lowER, highER, round(steps), round(rd)),
"S-MCTS" : lambda cellSize, er, steps, rd: execSafe(optim.runSMCTS, cellSize, er, round(steps), round(rd)),
"MS-MCTS" : lambda cellSize, er, steps, rd: execSafe(optim.runMS_MCTS, cellSize, er, round(steps), round(rd)),
"VanillaGA" : lambda gl, ps, mr: execSafe(optim.runVanillaGA, round(gl), round(ps), mr),
"VanillaMCTS" : lambda er, rd: execSafe(optim.runVanillaMCTS, er, round(rd))
}
# Probe points for each algorithm, only one which I've used previously
probes = {
"QD-MCTS" : {"lowER": math.sqrt(2), "highER": 4, "steps": 400, "rd": 25},
"S-MCTS" : {"cellSize": 20, "er": 4, "steps": 400, "rd": 25},
"MS-MCTS" : {"cellSize": 20, "er": 4, "steps": 400, "rd": 25},
"VanillaGA" : {"gl": 20, "ps": 50, "mr": 1. / 20},
"VanillaMCTS" : {"er": math.sqrt(2), "rd": 12}
}
# Initialize optimization
optim.setupRun(len(logs) * 11) # Different seed for each run
optim.RUN_COUNTER = len(csvLogs) # Make sure java logs into a new csv file
optim.NUM_TRIALS = 10
optim.OutputDir = args.outputPath
optim.m_mapNames = glob.glob("./maps/**/*.map", recursive=True)
optimizer = BayesianOptimization(
f=funcs[args.algorithm],
pbounds=bounds[args.algorithm],
random_state=len(logs) * 11, # Change behaviour for each run
)
print(f"Optimizing {args.algorithm} with bounds:")
print(bounds[args.algorithm])
# Probe if necessary
init_points = 0
if len(logs) == 0:
print("Found no previous logs... Probing to improve results:")
print(probes[args.algorithm])
optimizer.probe(params=probes[args.algorithm], lazy=True)
init_points = 5
else: # If we found logs, load them
print(f"Reading previous logs into optimizer...")
load_logs(optimizer, logs=logs);
for log in logs:
print(f"Successfully loaded {log}")
logger = JSONLogger(path=f"{args.outputPath}/optimizationLogs{len(logs) + 1}.json")
optimizer.subscribe(Events.OPTIMIZATION_STEP, logger)
# Run optimization
print(f"Starting optimisation for {args.algorithm}...")
optimizer.maximize(init_points=init_points, n_iter=args.iters)
print("Finished optimisation")
print(optimizer.max)
model_paths.append(os.path.join(dirpath, filename))
model_paths = sorted(model_paths, key=str.lower)
optimizer = BayesianOptimization(f='',
pbounds={
'batch_size': (0, 1),
'n_hidden_1': (32, 4096),
'n_hidden_2': (32, 4096),
'learning_rate': (1e-5, 1e-3),
'dropout': (0, 1)
},
verbose=0,
random_state=5)
load_logs(optimizer, logs=[log_path])
print("Loading train dataset ... ", end='')
with open(train_data_path, 'rb') as train_data_file:
X, y = pickle.load(train_data_file)
dataset = Dataset(X, y)
print("Done.")
print("Splitting dataset ... ", end='')
num_train = int(len(dataset) * 0.8)
num_val = len(dataset) - num_train
torch.manual_seed(123)
[train_set, val_set] = torch.utils.data.random_split(dataset,
(num_train, num_val))
X_train = X[train_set.indices]
return latency
# Bounded region of parameter space
pbounds = {'buffer_pool': (128, buffer_pool_max), 'log_file': (48, log_file_max),'flush_method': (0, flush_method_max),
'thread_cache': (9, thread_cache_max),'thread_sleep': (0, thread_sleep_max), 'max_connect': (151, max_connect_max)}
optimizer = BayesianOptimization(
f=objFunction,
pbounds=pbounds,
random_state=1,
)
load_logs(optimizer, logs=[setLoggerRoute()])
logger = JSONLogger(path="./logsResumed.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
print("New optimizer is now aware of {} points.".format(len(optimizer.space)))
count=len(optimizer.space)
optimizer.maximize(
init_points=0,
n_iter=defineOptIterations(),
)
print(optimizer.max)
)
logger = JSONLogger(path="./logs.json")
optimizer.subscribe(Events.OPTMIZATION_STEP, logger)
# By default these will be explored lazily (lazy=True), meaning these points will be evaluated only the next time you call maximize.
print(optimizer.space.keys)
optimizer.maximize(init_points=0, n_iter=6)
for i, res in enumerate(optimizer.res):
print("Iteration {}: \n\t{}".format(i, res))
print(optimizer.max)
#load_logs
new_optimizer = BayesianOptimization(
f=black_box_function,
pbounds={"x": (-2, 2), "y": (-2, 2)},
verbose=2,
random_state=7,
)
print(len(new_optimizer.space))
load_logs(new_optimizer, logs=["./logs.json"])
print("New optimizer is now aware of {} points.".format(len(new_optimizer.space)))
new_optimizer.maximize(
init_points=0,
n_iter=10,
)
