def sample(self, journal_file):
journal = Journal.fromFile(journal_file)
accepted_parameters = journal.get_accepted_parameters(-1)
accepted_weights = journal.get_weights(-1)
n_samples = journal.configuration["n_samples"]
self.accepted_parameters_manager.broadcast(self.backend, 1)
# Broadcast Accepted parameters and Accepted weights
self.accepted_parameters_manager.update_broadcast(self.backend, accepted_parameters=accepted_parameters,
accepted_weights=accepted_weights)
seed_arr = self.rng.randint(0, np.iinfo(np.uint32).max, size=n_samples, dtype=np.uint32)
rng_arr = np.array([np.random.RandomState(seed) for seed in seed_arr])
index_arr = np.arange(0,n_samples,1)
data_arr = []
for i in range(len(rng_arr)):
data_arr.append([rng_arr[i], index_arr[i]])
data_pds = self.backend.parallelize(data_arr)
parameters_simulations_pds = self.backend.map(self._sample_parameter, data_pds)
parameters_simulations = self.backend.collect(parameters_simulations_pds)
parameters, simulations = [list(t) for t in zip(*parameters_simulations)]
parameters = np.squeeze(np.array(parameters))
simulations = np.squeeze(np.array(simulations))
return parameters, simulations
def test_load_and_save(self):
params1 = np.zeros((2, 4))
weights1 = np.zeros((2, 4))
journal = Journal(0)
# journal.add_parameters(params1)
journal.add_weights(weights1)
journal.save('journal_tests_testfile.pkl')
new_journal = Journal.fromFile('journal_tests_testfile.pkl')
# np.testing.assert_equal(journal.parameters, new_journal.parameters)
np.testing.assert_equal(journal.weights, new_journal.weights)
def analyse_journal(journal):
# output parameters and weights
print(journal.parameters)
print(journal.weights)
# do post analysis
print(journal.posterior_mean())
print(journal.posterior_cov())
print(journal.posterior_histogram())
# print configuration
print(journal.configuration)
# save and load journal
journal.save("experiments.jnl")
from abcpy.output import Journal
new_journal = Journal.fromFile('experiments.jnl')
def analyse_journal(journal):
# output parameters and weights
print(journal.opt_values)
print(journal.get_weights())
# do post analysis
print(journal.posterior_mean())
print(journal.posterior_cov())
# print configuration
print(journal.configuration)
# plot posterior
journal.plot_posterior_distr(path_to_save="posterior.png")
# save and load journal
journal.save("experiments.jnl")
from abcpy.output import Journal
new_journal = Journal.fromFile('experiments.jnl')
def compute_posterior_mode(whichobs,
dim=None,
type='multiply',
data_type='_obs_'):
print(data_type)
journal_sabc = Journal.fromFile('Journals/sabc' + data_type +
str(whichobs) + '_' + type + '.jrnl')
# filenamere = '../APMCABC_Results/apmcabc_obs_' + str(whichobs) + '_re.jrnl'
# if os.path.isfile(filenamere):
# filename = '../APMCABC_Results/apmcabc_obs_'+str(whichobs)+'_re.jrnl'
# else:
# filename = '../APMCABC_Results/apmcabc_obs_'+str(whichobs)+'_reweighted.jrnl'
# journal_sabc = Journal.fromFile(filename)
### Converting posterior samples to a matrix
weights = np.concatenate(journal_sabc.get_weights(-1))
accepted_parameters = journal_sabc.get_accepted_parameters(-1)
parameters = []
for ind in range(511):
parameters.append(
np.array([x[0] for x in accepted_parameters[ind]]).reshape(-1, 1))
parameters = np.array(parameters).squeeze()
if dim is not None:
parameters = parameters[:, dim]
#print(weights.shape, parameters.shape)
kernel = stats.gaussian_kde(parameters.transpose(),
weights=weights,
bw_method=0.45)
def rosen(x):
return -np.log(kernel(x))
posterior_mean = np.mean(parameters, axis=0)
res = minimize(rosen,
posterior_mean,
method='nelder-mead',
options={
'xatol': 1e-8,
'disp': False
})
return (np.array(res.x).reshape(1, -1))
from abcpy.output import Journal
import numpy as np
import pylab as plt
from scipy.stats import gaussian_kde
type = 'simulated'
# type = 'observed'
if type == 'simulated':
#filename = 'VolcanojournalAPMCABC_triplet_simulated'
filename = 'VolcanojournalAPMCABC_simulated'
else:
#filename = 'VolcanojournalAPMCABC_triplet-fromfile_Pululagua'
filename = 'VolcanojournalAPMCABC_pululagua'
journal = Journal.fromFile(filename + '.jrnl')
# for ind in range(len(journal.weights)):
# journal.weights[ind] = journal.weights[ind]/sum(journal.weights[ind])
# journal.save(filename + '_normalized.jrnl')
mean = journal.posterior_mean()
print(journal.posterior_mean())
print(journal.posterior_cov())
k = -1
prioru = np.concatenate(journal.get_parameters(0)['U0'])
priorl = np.concatenate(journal.get_parameters(0)['L'])
postu = np.concatenate(journal.get_parameters(k)['U0']).reshape(-1, )
postl = np.concatenate(journal.get_parameters(k)['L']).reshape(-1, )
weights = np.concatenate(journal.get_weights(k))
# load the actual observation
if "fullLorenz95" in model:
x_obs = np.load(observation_folder +
"x_obs{}.npy".format(obs_index + 1))
else:
x_obs = np.load(observation_folder +
"timeseriers_obs{}.npy".format(obs_index + 1))
# theta_obs = np.load(observation_folder + "theta_obs{}.npy".format(obs_index + 1))
# reshape the observation:
x_obs = x_obs.reshape(num_vars_in_Lorenz, -1)
# print(x_obs.shape)
# load now the posterior for that observation
if inference_technique == "ABC":
jrnl_ABC = Journal.fromFile(inference_folder + "jrnl" +
namefile_postfix + ".jnl")
params, weights = extract_params_and_weights_from_journal(jrnl_ABC)
# subsample journal according to weights (bootstrap):
# params_ABC_subsampled = subsample_params_according_to_weights(params_ABC, weights_ABC,
# size=n_post_samples)
else:
trace_exchange = np.load(inference_folder +
f"exchange_mcmc_trace{obs_index + 1}.npy")
# subsample trace:
params = subsample_trace(trace_exchange,
size=subsample_size_exchange)
weights = None
# print("Results loaded correctly")
# now simulate for all the different param values
# epsilon_percentile = 70
#
# if "epsilon_arr" in jrnl.configuration.keys():
# eps = np.percentile(jrnl.distances[-1], epsilon_percentile)
# print("using epsilon from last step: ", eps)
#
# start_journal_path = results_folder + "journal_3.jrl"
# jrnl = ABC_inference("PMCABC", model, observation_france, final_distance, eps=eps, n_samples=500, n_steps=20,
# backend=backend, full_output=1, journal_file=start_journal_path,
# epsilon_percentile=epsilon_percentile,
# journal_file_save=results_folder + "journal_4")
#
# # save the journal
# jrnl.save(results_folder + "PMCABC_inf4.jrl")
print("Inference 5")
jrnl = Journal.fromFile(results_folder + "journal_4.jrl")
epsilon_percentile = 70
if "epsilon_arr" in jrnl.configuration.keys():
eps = np.percentile(jrnl.distances[-1], epsilon_percentile)
print("using epsilon from last step: ", eps)
start_journal_path = results_folder + "journal_4.jrl"
jrnl = ABC_inference("PMCABC", model, observation_france, final_distance, eps=eps, n_samples=500, n_steps=20,
backend=backend, full_output=1, journal_file=start_journal_path,
epsilon_percentile=epsilon_percentile,
journal_file_save=results_folder + "journal_5")
# save the journal
jrnl.save(results_folder + "PMCABC_inf5.jrl")
print('SABC Inferring')
# We use resultfakeobs1 as our observed dataset
journal_sabc = sampler.sample([resultfakeobs1],
steps=steps,
epsilon=epsilon,
n_samples=n_samples,
n_samples_per_param=n_samples_per_param,
ar_cutoff=ar_cutoff,
full_output=full_output,
journal_file=journal_file)
print(journal_sabc.posterior_mean())
journal_sabc.save('sabc_earthworm_fakeobs1.jrnl')
from abcpy.output import Journal
jrnl = Journal.fromFile('sabc_earthworm_fakeobs1.jrnl')
print(jrnl.configuration)
fig, ax = jrnl.plot_ESS()
fig.savefig('ess.pdf')
true_param_value = [
967, 0.25, 3.6, 10.6, 3.6, 3.5, 0.15, 0.011, 0.015, 0.5, 0.25, 0.177,
0.182, 0.004
]
parameters = [
'B_0', 'activation_energy', 'energy_tissue', 'energy_food',
'energy_synthesis', 'half_saturation_coeff', 'max_ingestion_rate',
'mass_birth', 'mass_cocoon', 'mass_maximum', 'mass_sexual_maturity',
'growth_constant', 'max_reproduction_rate', 'speed'
]
jrnl.plot_posterior_distr(path_to_save='posterior_1.pdf',
parameters_to_show=parameters[:5],
def sample(self,
observations,
steps,
epsilon_init,
n_samples=10000,
n_samples_per_param=1,
epsilon_percentile=10,
covFactor=2,
full_output=0,
journal_file=None,
journal_file_save=None):
"""Samples from the posterior distribution of the model parameter given the observed
data observations.
Parameters
----------
observations : list
A list, containing lists describing the observed data sets
steps : integer
Number of iterations in the sequential algoritm ("generations")
epsilon_init : numpy.ndarray
An array of proposed values of epsilon to be used at each steps. Can be supplied
A single value to be used as the threshold in Step 1 or a `steps`-dimensional array of values to be
used as the threshold in evry steps.
n_samples : integer, optional
Number of samples to generate. The default value is 10000.
n_samples_per_param : integer, optional
Number of data points in each simulated data set. The default value is 1.
epsilon_percentile : float, optional
A value between [0, 100]. The default value is 10.
covFactor : float, optional
scaling parameter of the covariance matrix. The default value is 2 as considered in [1].
full_output: integer, optional
If full_output==1, intermediate results are included in output journal.
The default value is 0, meaning the intermediate results are not saved.
journal_file: str, optional
Filename of a journal file to read an already saved journal file, from which the first iteration will start.
The default value is None.
Returns
-------
abcpy.output.Journal
A journal containing simulation results, metadata and optionally intermediate results.
"""
self.accepted_parameters_manager.broadcast(self.backend, observations)
self.n_samples = n_samples
self.n_samples_per_param = n_samples_per_param
if (journal_file is None):
journal = Journal(full_output)
journal.configuration["type_model"] = [
type(model).__name__ for model in self.model
]
journal.configuration["type_dist_func"] = type(
self.distance).__name__
journal.configuration["n_samples"] = self.n_samples
journal.configuration[
"n_samples_per_param"] = self.n_samples_per_param
journal.configuration["steps"] = steps
journal.configuration["epsilon_percentile"] = epsilon_percentile
else:
journal = Journal.fromFile(journal_file)
accepted_parameters = None
accepted_weights = None
accepted_cov_mats = None
# Define epsilon_arr
if len(epsilon_init) == steps:
epsilon_arr = epsilon_init
else:
if len(epsilon_init) == 1:
epsilon_arr = [None] * steps
epsilon_arr[0] = epsilon_init
else:
raise ValueError(
"The length of epsilon_init can only be equal to 1 or steps."
)
# main PMCABC algorithm
self.logger.info("Starting PMC iterations")
for aStep in range(steps):
self.logger.debug("iteration {} of PMC algorithm".format(aStep))
if (aStep == 0 and journal_file is not None):
accepted_parameters = journal.get_accepted_parameters(-1)
accepted_weights = journal.get_weights(-1)
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_parameters=accepted_parameters,
accepted_weights=accepted_weights)
kernel_parameters = []
for kernel in self.kernel.kernels:
kernel_parameters.append(
self.accepted_parameters_manager.
get_accepted_parameters_bds_values(kernel.models))
self.accepted_parameters_manager.update_kernel_values(
self.backend, kernel_parameters=kernel_parameters)
# 3: calculate covariance
self.logger.info("Calculateing covariance matrix")
new_cov_mats = self.kernel.calculate_cov(
self.accepted_parameters_manager)
# Since each entry of new_cov_mats is a numpy array, we can multiply like this
accepted_cov_mats = [
covFactor * new_cov_mat for new_cov_mat in new_cov_mats
]
seed_arr = self.rng.randint(0,
np.iinfo(np.uint32).max,
size=n_samples,
dtype=np.uint32)
rng_arr = np.array(
[np.random.RandomState(seed) for seed in seed_arr])
rng_pds = self.backend.parallelize(rng_arr)
# 0: update remotely required variables
# print("INFO: Broadcasting parameters.")
self.logger.info("Broadcasting parameters")
self.epsilon = epsilon_arr[aStep]
self.accepted_parameters_manager.update_broadcast(
self.backend, accepted_parameters, accepted_weights,
accepted_cov_mats)
# 1: calculate resample parameters
# print("INFO: Resampling parameters")
self.logger.info("Resampling parameters")
params_and_dists_and_counter_pds = self.backend.map(
self._resample_parameter, rng_pds)
params_and_dists_and_counter = self.backend.collect(
params_and_dists_and_counter_pds)
new_parameters, distances, counter = [
list(t) for t in zip(*params_and_dists_and_counter)
]
new_parameters = np.array(new_parameters)
distances = np.array(distances)
for count in counter:
self.simulation_counter += count
# Compute epsilon for next step
# print("INFO: Calculating acceptance threshold (epsilon).")
self.logger.info("Calculating acceptances threshold")
if aStep < steps - 1:
if epsilon_arr[aStep + 1] == None:
epsilon_arr[aStep + 1] = np.percentile(
distances, epsilon_percentile)
else:
epsilon_arr[aStep + 1] = np.max([
np.percentile(distances, epsilon_percentile),
epsilon_arr[aStep + 1]
])
# 2: calculate weights for new parameters
self.logger.info("Calculating weights")
new_parameters_pds = self.backend.parallelize(new_parameters)
self.logger.info("Calculate weights")
new_weights_pds = self.backend.map(self._calculate_weight,
new_parameters_pds)
new_weights = np.array(
self.backend.collect(new_weights_pds)).reshape(-1, 1)
sum_of_weights = 0.0
for w in new_weights:
sum_of_weights += w
new_weights = new_weights / sum_of_weights
# The calculation of cov_mats needs the new weights and new parameters
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_parameters=new_parameters,
accepted_weights=new_weights)
# The parameters relevant to each kernel have to be used to calculate n_sample times. It is therefore more efficient to broadcast these parameters once,
# instead of collecting them at each kernel in each step
kernel_parameters = []
for kernel in self.kernel.kernels:
kernel_parameters.append(
self.accepted_parameters_manager.
get_accepted_parameters_bds_values(kernel.models))
self.accepted_parameters_manager.update_kernel_values(
self.backend, kernel_parameters=kernel_parameters)
# 3: calculate covariance
self.logger.info("Calculating covariance matrix")
new_cov_mats = self.kernel.calculate_cov(
self.accepted_parameters_manager)
# Since each entry of new_cov_mats is a numpy array, we can multiply like this
new_cov_mats = [
covFactor * new_cov_mat for new_cov_mat in new_cov_mats
]
# 4: Update the newly computed values
accepted_parameters = new_parameters
accepted_weights = new_weights
accepted_cov_mats = new_cov_mats
self.logger.info("Save configuration to output journal")
if (full_output == 1
and aStep <= steps - 1) or (full_output == 0
and aStep == steps - 1):
journal.add_accepted_parameters(
copy.deepcopy(accepted_parameters))
journal.add_distances(copy.deepcopy(distances))
journal.add_weights(copy.deepcopy(accepted_weights))
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_parameters=accepted_parameters,
accepted_weights=accepted_weights)
names_and_parameters = self._get_names_and_parameters()
journal.add_user_parameters(names_and_parameters)
journal.number_of_simulations.append(self.simulation_counter)
print(journal_file_save)
if journal_file_save is not None:
if full_output == 1:
journal.save(
journal_file_save +
'.jrl') # avoid writing a lot of different files.
else:
journal.save(journal_file_save + '_' + str(aStep) +
'.jrl')
# Add epsilon_arr to the journal
journal.configuration["epsilon_arr"] = epsilon_arr
return journal
def sample(self,
observations,
steps,
epsilon,
n_samples=10000,
n_samples_per_param=1,
beta=2,
delta=0.2,
v=0.3,
ar_cutoff=0.1,
resample=None,
n_update=None,
full_output=0,
journal_file=None):
"""Samples from the posterior distribution of the model parameter given the observed
data observations.
Parameters
----------
observations : list
A list, containing lists describing the observed data sets
steps : integer
Number of maximum iterations in the sequential algoritm ("generations")
epsilon : numpy.float
A proposed value of threshold to start with.
n_samples : integer, optional
Number of samples to generate. The default value is 10000.
n_samples_per_param : integer, optional
Number of data points in each simulated data set. The default value is 1.
beta : numpy.float
Tuning parameter of SABC, default value is 2.
delta : numpy.float
Tuning parameter of SABC, default value is 0.2.
v : numpy.float, optional
Tuning parameter of SABC, The default value is 0.3.
ar_cutoff : numpy.float
Acceptance ratio cutoff, The default value is 0.1.
resample: int, optional
Resample after this many acceptance, The default value is None which takes value inside n_samples
n_update: int, optional
Number of perturbed parameters at each step, The default value is None which takes value inside n_samples
full_output: integer, optional
If full_output==1, intermediate results are included in output journal.
The default value is 0, meaning the intermediate results are not saved.
journal_file: str, optional
Filename of a journal file to read an already saved journal file, from which the first iteration will start.
The default value is None.
Returns
-------
abcpy.output.Journal
A journal containing simulation results, metadata and optionally intermediate results.
"""
global broken_preemptively
self.sample_from_prior(rng=self.rng)
self.accepted_parameters_manager.broadcast(self.backend, observations)
self.epsilon = epsilon
self.n_samples = n_samples
self.n_samples_per_param = n_samples_per_param
if (journal_file is None):
journal = Journal(full_output)
journal.configuration["type_model"] = [
type(model).__name__ for model in self.model
]
journal.configuration["type_dist_func"] = type(
self.distance).__name__
journal.configuration["type_kernel_func"] = type(self.kernel)
journal.configuration["n_samples"] = self.n_samples
journal.configuration[
"n_samples_per_param"] = self.n_samples_per_param
journal.configuration["beta"] = beta
journal.configuration["delta"] = delta
journal.configuration["v"] = v
journal.configuration["ar_cutoff"] = ar_cutoff
journal.configuration["resample"] = resample
journal.configuration["n_update"] = n_update
journal.configuration["full_output"] = full_output
else:
journal = Journal.fromFile(journal_file)
accepted_parameters = None
distances = np.zeros(shape=(n_samples, ))
smooth_distances = np.zeros(shape=(n_samples, ))
accepted_weights = np.ones(shape=(n_samples, 1))
all_distances = None
accepted_cov_mat = None
if resample == None:
resample = n_samples
if n_update == None:
n_update = n_samples
sample_array = np.ones(shape=(steps, ))
sample_array[0] = n_samples
sample_array[1:] = n_update
## Acceptance counter to determine the resampling step
accept = 0
samples_until = 0
## Counter whether broken preemptively
broken_preemptively = False
for aStep in range(0, steps):
self.logger.debug("step {}".format(aStep))
if (aStep == 0 and journal_file is not None):
accepted_parameters = journal.get_accepted_parameters(-1)
accepted_weights = journal.get_weights(-1)
#Broadcast Accepted parameters and Accedpted weights
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_parameters=accepted_parameters,
accepted_weights=accepted_weights)
kernel_parameters = []
for kernel in self.kernel.kernels:
kernel_parameters.append(
self.accepted_parameters_manager.
get_accepted_parameters_bds_values(kernel.models))
#Broadcast Accepted Kernel parameters
self.accepted_parameters_manager.update_kernel_values(
self.backend, kernel_parameters=kernel_parameters)
new_cov_mats = self.kernel.calculate_cov(
self.accepted_parameters_manager)
accepted_cov_mats = []
for new_cov_mat in new_cov_mats:
if not (new_cov_mat.size == 1):
accepted_cov_mats.append(beta * new_cov_mat + 0.0001 *
np.trace(new_cov_mat) *
np.eye(new_cov_mat.shape[0]))
else:
accepted_cov_mats.append(
(beta * new_cov_mat +
0.0001 * new_cov_mat).reshape(1, 1))
# Broadcast Accepted Covariance Matrix
self.accepted_parameters_manager.update_broadcast(
self.backend, accepted_cov_mats=accepted_cov_mats)
# main SABC algorithm
# print("INFO: Initialization of SABC")
seed_arr = self.rng.randint(0,
np.iinfo(np.uint32).max,
size=int(sample_array[aStep]),
dtype=np.uint32)
rng_arr = np.array(
[np.random.RandomState(seed) for seed in seed_arr])
index_arr = self.rng.randint(0,
self.n_samples,
size=int(sample_array[aStep]),
dtype=np.uint32)
data_arr = []
for i in range(len(rng_arr)):
data_arr.append([rng_arr[i], index_arr[i]])
data_pds = self.backend.parallelize(data_arr)
# 0: update remotely required variables
self.logger.info("Broadcasting parameters")
self.epsilon = epsilon
# 1: Calculate parameters
self.logger.info("Initial accepted parameters")
params_and_dists_pds = self.backend.map(self._accept_parameter,
data_pds)
params_and_dists = self.backend.collect(params_and_dists_pds)
new_parameters, filenames, index, acceptance, counter = [
list(t) for t in zip(*params_and_dists)
]
# Keeping counter of number of simulations
for count in counter:
self.simulation_counter += count
#new_parameters = np.array(new_parameters)
index = np.array(index)
acceptance = np.array(acceptance)
# Reading all_distances at Initial step
if aStep == 0:
index = np.linspace(0, n_samples - 1,
n_samples).astype(int).reshape(
n_samples, )
accept = 0
# Initialize/Update the accepted parameters and their corresponding distances
if accepted_parameters is None:
accepted_parameters = new_parameters
else:
for ind in range(len(acceptance)):
if acceptance[ind] == 1:
accepted_parameters[index[ind]] = new_parameters[ind]
# 1.5: Update the distance and recompute distances from observed data
self.logger.info("Updating distance")
distances = self.distance.distances[0].update(
filenames,
self.accepted_parameters_manager.observations_bds.value(),
self.backend)
self._update_broadcasts(distances=distances)
# 2: Compute epsilon
U = self._average_redefined_distance(distances,
epsilon * (1 - delta))
epsilon = self._schedule(U, v)
#U = np.mean(distances)
#epsilon = np.percentile(distances, .1 * 100)
print(epsilon)
# 4: Show progress and if acceptance rate smaller than a value break the iteration
if aStep > 0:
accept = accept + np.sum(acceptance)
samples_until = samples_until + sample_array[aStep]
acceptance_rate = accept / samples_until
msg = (
"updates= {:.2f}, epsilon= {}, u.mean={:e}, acceptance rate: {:.2f}"
.format(
np.sum(sample_array[1:aStep + 1]) /
np.sum(sample_array[1:]) * 100, epsilon, U,
acceptance_rate))
self.logger.debug(msg)
if acceptance_rate < ar_cutoff:
broken_preemptively = True
self.logger.debug(
"Stopping as acceptance rate is lower than cutoff")
break
# 5: Resampling if number of accepted particles greater than resample
if accept >= resample and U > 1e-100:
self.logger.info("Weighted resampling")
weight = np.exp(-distances * delta / U)
weight = weight / sum(weight)
index_resampled = self.rng.choice(np.arange(n_samples,
dtype=int),
n_samples,
replace=1,
p=weight)
accepted_parameters = [
accepted_parameters[i] for i in index_resampled
]
distances = distances[index_resampled]
## Update U and epsilon:
# # epsilon = epsilon * (1 - delta)
# U = np.mean(distances)
# # epsilon = self._schedule(U, v)
# epsilon = np.percentile(distances, .1 * 100)
U = self._average_redefined_distance(distances,
epsilon * (1 - delta))
epsilon = self._schedule(U, v)
## Print effective sampling size
print('Resampling: Effective sampling size: ',
1 / sum(pow(weight / sum(weight), 2)))
accept = 0
samples_until = 0
## Compute and broadcast accepted parameters, accepted kernel parameters and accepted Covariance matrix
# Broadcast Accepted parameters and add to journal
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_weights=accepted_weights,
accepted_parameters=accepted_parameters)
# Compute Accepetd Kernel parameters and broadcast them
kernel_parameters = []
for kernel in self.kernel.kernels:
kernel_parameters.append(
self.accepted_parameters_manager.
get_accepted_parameters_bds_values(kernel.models))
self.accepted_parameters_manager.update_kernel_values(
self.backend, kernel_parameters=kernel_parameters)
# Compute Kernel Covariance Matrix and broadcast it
new_cov_mats = self.kernel.calculate_cov(
self.accepted_parameters_manager)
accepted_cov_mats = []
for new_cov_mat in new_cov_mats:
if not (new_cov_mat.size == 1):
accepted_cov_mats.append(beta * new_cov_mat + 0.0001 *
np.trace(new_cov_mat) *
np.eye(new_cov_mat.shape[0]))
else:
accepted_cov_mats.append(
(beta * new_cov_mat +
0.0001 * new_cov_mat).reshape(1, 1))
self.accepted_parameters_manager.update_broadcast(
self.backend, accepted_cov_mats=accepted_cov_mats)
if (full_output == 1 and aStep <= steps - 1):
## Saving intermediate configuration to output journal.
print('Saving after resampling')
journal.add_accepted_parameters(
copy.deepcopy(accepted_parameters))
journal.add_weights(copy.deepcopy(accepted_weights))
journal.add_distances(copy.deepcopy(distances))
names_and_parameters = self._get_names_and_parameters()
journal.add_user_parameters(names_and_parameters)
journal.number_of_simulations.append(
self.simulation_counter)
else:
## Compute and broadcast accepted parameters, accepted kernel parameters and accepted Covariance matrix
# Broadcast Accepted parameters
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_weights=accepted_weights,
accepted_parameters=accepted_parameters)
# Compute Accepetd Kernel parameters and broadcast them
kernel_parameters = []
for kernel in self.kernel.kernels:
kernel_parameters.append(
self.accepted_parameters_manager.
get_accepted_parameters_bds_values(kernel.models))
self.accepted_parameters_manager.update_kernel_values(
self.backend, kernel_parameters=kernel_parameters)
# Compute Kernel Covariance Matrix and broadcast it
new_cov_mats = self.kernel.calculate_cov(
self.accepted_parameters_manager)
accepted_cov_mats = []
for new_cov_mat in new_cov_mats:
if not (new_cov_mat.size == 1):
accepted_cov_mats.append(beta * new_cov_mat + 0.0001 *
np.trace(new_cov_mat) *
np.eye(new_cov_mat.shape[0]))
else:
accepted_cov_mats.append(
(beta * new_cov_mat +
0.0001 * new_cov_mat).reshape(1, 1))
self.accepted_parameters_manager.update_broadcast(
self.backend, accepted_cov_mats=accepted_cov_mats)
if (full_output == 1 and aStep <= steps - 1):
## Saving intermediate configuration to output journal.
journal.add_accepted_parameters(
copy.deepcopy(accepted_parameters))
journal.add_weights(copy.deepcopy(accepted_weights))
journal.add_distances(copy.deepcopy(distances))
names_and_parameters = self._get_names_and_parameters()
journal.add_user_parameters(names_and_parameters)
journal.number_of_simulations.append(
self.simulation_counter)
# Add epsilon_arr, number of final steps and final output to the journal
# print("INFO: Saving final configuration to output journal.")
if (full_output == 0) or (full_output == 1 and broken_preemptively
and aStep <= steps - 1):
journal.add_accepted_parameters(copy.deepcopy(accepted_parameters))
journal.add_weights(copy.deepcopy(accepted_weights))
journal.add_distances(copy.deepcopy(distances))
self.accepted_parameters_manager.update_broadcast(
self.backend,
accepted_parameters=accepted_parameters,
accepted_weights=accepted_weights)
names_and_parameters = self._get_names_and_parameters()
journal.add_user_parameters(names_and_parameters)
journal.number_of_simulations.append(self.simulation_counter)
journal.configuration["steps"] = aStep + 1
journal.configuration["epsilon"] = epsilon
return journal
import pylab as plt
from sklearn.cluster import AgglomerativeClustering
from sklearn.metrics.cluster import adjusted_rand_score
from abcpy.output import Journal
import numpy as np
import os.path
from scipy.stats import gaussian_kde
names = ['pAD', 'pAg', 'pT', 'pF', 'aT', 'v_z_AP', 'v_z_NAP']
margmax, meanpost, ylabel = [], [], []
for ind in range(40):
whichobs = ind
filename = 'apmcabc_obs_' + str(whichobs) + '.jrnl'
if os.path.isfile(filename):
journal = Journal.fromFile(filename)
weights = np.concatenate(journal.get_weights())
post1 = np.concatenate(journal.get_parameters()['pAD'])
post2 = np.concatenate(journal.get_parameters()['pAg'])
post3 = np.concatenate(journal.get_parameters()['pT'])
post4 = np.concatenate(journal.get_parameters()['pF'])
post5 = np.concatenate(journal.get_parameters()['aT'])
post6 = np.concatenate(journal.get_parameters()['v_z_AP'])
post7 = np.concatenate(journal.get_parameters()['v_z_NAP'])
data = np.hstack((post1, post2, post3, post4, post5, post6, post7))
meanpost.append(
np.array([
np.mean(np.concatenate(journal.get_parameters()[x]))
for x in names
]))
#meanpost.append(np.array([journal.posterior_mean()[x] for x in names]))
# parameters, simulations = dp.sample(file=dircertory + "/"+'rejection_one_pcent.csv')
# np.savez(dircertory + "/"+'rejection_predict.npz', parameters=parameters, simulations=simulations)
from model import DrawFromPosterior
dp = DrawFromPosterior([Bass], backend)
print('Prediction')
parameters, simulations = dp.sample(journal_file=dircertory + "/" +
algorithm + '_' + problem +
'_obs.jrnl')
np.savez(dircertory + "/" + algorithm + '_' + 'predict.npz',
parameters=parameters,
simulations=simulations)
if plot:
from abcpy.output import Journal
journal_sabc = Journal.fromFile(dircertory + "/" + algorithm + "_" +
problem + '_obs.jrnl')
### Converting posterior samples to a matrix
accepted_parameters = journal_sabc.get_accepted_parameters(-1)
parameters = []
for ind in range(111):
parameters.append([x[0] for x in accepted_parameters[ind]])
parameters = np.array(parameters)
parameters[:, -1] = parameters[:, -1] * 1e+13
np.savetxt("Figures/sabc_parameters.csv",
np.array(parameters),
delimiter=",")
print(journal_sabc.configuration)
print(journal_sabc.posterior_mean())
print(journal_sabc.posterior_cov())
def main(epsilon,
sigma,
filename_prefix,
perform_standard_optimal_control=False,
perform_iterative_strategy=True,
use_sample_with_higher_weight=False,
use_posterior_median=False,
n_post_samples=None,
shift_each_iteration=1,
n_shifts=10,
window_size=30,
only_plot=False,
plot_file=None,
plot_days=None,
loss="deaths_Isc",
results_folder=None,
journal_file_name=None,
training_window_length=None,
use_mpi=False,
restart_at_index=None):
"""epsilon is an array with size 3, with order school, work, other
If use_sample_with_higher_weight is True: we do the procedure with that only, no posterior expectation
use_posterior_median: do the optimal control with the marginal posterior median.
n_post_samples: for the posterior expectation. Ignored if use_sample_with_higher_weight or use_posterior_median is True,
shift_each_iteration and n_shifts are for the iterative strategy.
"""
if use_mpi:
print("Using MPI")
backend = BackendMPI()
else:
backend = BackendDummy()
print("Epsilon: ", epsilon)
logging.basicConfig(level=logging.INFO)
############################ Load relevant data #################################################
if results_folder is None:
results_folder = "results/SEI4RD_france_infer_1Mar_31Aug/"
data_folder = "data/france_inference_data_1Mar_to_31Aug/"
alpha_home = 1 # set this to 1
mobility_work = np.load(data_folder + "mobility_work.npy")
mobility_other = np.load(data_folder + "mobility_other.npy")
mobility_school = np.load(data_folder + "mobility_school.npy")
france_pop = np.load(data_folder + "france_pop.npy", allow_pickle=True)
contact_matrix_home = np.load(data_folder + "contact_matrix_home.npy")
contact_matrix_work = np.load(data_folder + "contact_matrix_work.npy")
contact_matrix_school = np.load(data_folder + "contact_matrix_school.npy")
contact_matrix_other = np.load(data_folder + "contact_matrix_other.npy")
if journal_file_name is None:
jrnl = Journal.fromFile(results_folder + "PMCABC_inf3.jrl")
else:
jrnl = Journal.fromFile(results_folder + journal_file_name)
#################################### Define Model #################################################
# parameters
n = 5 # number of age groups
dt = 0.1 # integration timestep
if training_window_length is not None:
T = training_window_length
else:
T = mobility_school.shape[0] - 1 # horizon time in days
total_population = france_pop # population for each age group
# 16th March: Boris Johnson asked old people to isolate; we then learn a new alpha from the 18th March:
lockdown_day = 17
# alpha_home = np.repeat(alpha_home, np.int(1 / dt), axis=0)
mobility_work = np.repeat(mobility_work[0:T + 1], np.int(1 / dt), axis=0)
mobility_other = np.repeat(mobility_other[0:T + 1], np.int(1 / dt), axis=0)
mobility_school = np.repeat(mobility_school[0:T + 1],
np.int(1 / dt),
axis=0)
# daily_tests = np.repeat(daily_tests, np.int(1 / dt), axis=0)
# ABC model (priors need to be fixed better):
beta = Uniform(
[[0], [0.5]],
name='beta') # controls how fast the epidemics grows. Related to R_0
d_L = Uniform([[1], [16]], name='d_L') # average duration of incubation
d_C = Uniform([[1], [16]],
name='d_C') # average time before going to clinical
d_R = Uniform([[1], [16]], name='d_R') # average recovery time
d_RC = Uniform([[1], [16]], name='d_RC') # average recovery time
d_D = Uniform(
[[1], [16]], name='d_D'
) # average duration of infected clinical state (resulting in death)
p01 = Uniform([[0], [1]], name="p01")
p02 = Uniform([[0], [1]], name="p02")
p03 = Uniform([[0], [1]], name="p03")
p04 = Uniform([[0], [1]], name="p04")
p05 = Uniform([[0], [1]], name="p05")
p11 = Uniform([[0], [1]], name="p11")
p12 = Uniform([[0], [1]], name="p12")
p13 = Uniform([[0], [1]], name="p13")
p14 = Uniform([[0], [1]], name="p14")
p15 = Uniform([[0], [1]], name="p15")
initial_exposed = Uniform([[0], [500]], name="initial_exposed")
alpha_123 = Uniform([[0.3], [1]], name="alpha_123")
alpha_4 = Uniform([[0], [1]], name="alpha_4")
alpha_5 = Uniform([[0], [1]], name="alpha_5")
model = SEI4RD([
beta, d_L, d_C, d_R, d_RC, d_D, p01, p02, p03, p04, p05, p11, p12, p13,
p14, p15, initial_exposed, alpha_123, alpha_4, alpha_5
],
tot_population=total_population,
T=T,
contact_matrix_school=contact_matrix_school,
contact_matrix_work=contact_matrix_work,
contact_matrix_home=contact_matrix_home,
contact_matrix_other=contact_matrix_other,
alpha_school=mobility_school,
alpha_work=mobility_work,
alpha_home=alpha_home,
alpha_other=mobility_other,
modify_alpha_home=False,
dt=dt,
return_once_a_day=True,
learn_alphas_old=True,
lockdown_day=lockdown_day)
# guess for a phi function
NHS_max = 10000
def phi_func_sc(x): # this is an hard max function.
return np.maximum(0, x - NHS_max)
def phi_func_death(x): # this is an hard max function.
return np.maximum(0, x)
# def phi_func(x):
# return np.pow(np.maximum(0, x - NHS_max), 2)
# def phi_func(x, beta=.1): # this is the softplus, a smooth version of hard max
# threshold = 30
# shape = x.shape
# x = x.reshape(-1)
# new_x = x - NHS_max
# indices = new_x * beta < threshold
# phi_x = copy.deepcopy(new_x) # is deepcopy actually needed?
# phi_x[indices] = np.log(
# 1 + np.exp(new_x[indices] * beta)) / beta # approximate for numerical stability in other places
# return phi_x.reshape(shape)
# extract posterior sample points and bootstrap them:
seed = 1
np.random.seed(seed)
iteration = -1
weights = jrnl.get_weights(iteration) / np.sum(jrnl.get_weights(iteration))
params = jrnl.get_parameters(iteration)
if not use_posterior_median:
if use_sample_with_higher_weight:
post_samples = np.where(weights == weights.max())[0]
else:
# bootstrap
if n_post_samples is None:
n_post_samples = len(weights)
post_samples = np.random.choice(range(len(weights)),
p=weights.reshape(-1),
size=n_post_samples)
beta_values = np.array([params['beta'][i][0] for i in post_samples])
kappa_values = np.array(
[1 / params['d_L'][i][0] for i in post_samples])
gamma_c_values = np.array(
[1 / params['d_C'][i][0] for i in post_samples])
gamma_r_values = np.array(
[1 / params['d_R'][i][0] for i in post_samples])
gamma_rc_values = np.array(
[1 / params['d_RC'][i][0] for i in post_samples])
nu_values = np.array([1 / params['d_D'][i][0] for i in post_samples])
rho_values = np.array([
np.array([
params[key][i][0]
for key in ['p01', 'p02', 'p03', 'p04', 'p05']
]).reshape(-1) for i in post_samples
])
rho_prime_values = np.array([
np.array([
params[key][i][0]
for key in ['p11', 'p12', 'p13', 'p14', 'p15']
]).reshape(-1) for i in post_samples
])
alpha_123_values = np.array(
[params["alpha_123"][i][0] for i in post_samples])
alpha_4_values = np.array(
[params["alpha_4"][i][0] for i in post_samples])
alpha_5_values = np.array(
[params["alpha_5"][i][0] for i in post_samples])
initial_exposed_values = np.array(
[params["initial_exposed"][i][0] for i in post_samples])
else:
params_array = np.array(
[[params[key][i] for i in range(len(params[key]))]
for key in params.keys()]).squeeze()
marginal_medians = {
key: weighted_quantile(
np.array(params[key]).reshape(-1), [0.5], weights.squeeze())
for i in range(params_array.shape[0]) for key in params.keys()
}
beta_values = np.array([marginal_medians['beta'][0]])
kappa_values = np.array([1 / marginal_medians['d_L'][0]])
gamma_c_values = np.array([1 / marginal_medians['d_C'][0]])
gamma_r_values = np.array([1 / marginal_medians['d_R'][0]])
gamma_rc_values = np.array([1 / marginal_medians['d_RC'][0]])
nu_values = np.array([1 / marginal_medians['d_D'][0]])
rho_values = np.array([
np.array([
marginal_medians[key][0]
for key in ['p01', 'p02', 'p03', 'p04', 'p05']
]).reshape(-1)
])
rho_prime_values = np.array([
np.array([
marginal_medians[key][0]
for key in ['p11', 'p12', 'p13', 'p14', 'p15']
]).reshape(-1)
])
alpha_123_values = np.array([marginal_medians["alpha_123"][0]])
alpha_4_values = np.array([marginal_medians["alpha_4"][0]])
alpha_5_values = np.array([marginal_medians["alpha_5"][0]])
initial_exposed_values = np.array(
[marginal_medians["initial_exposed"][0]])
# instantiate the posterior cost class:
posterior_cost = PosteriorCost(model,
phi_func_sc=phi_func_sc,
phi_func_death=phi_func_death,
beta_vals=beta_values,
kappa_vals=kappa_values,
gamma_c_vals=gamma_c_values,
gamma_r_vals=gamma_r_values,
gamma_rc_vals=gamma_rc_values,
nu_vals=nu_values,
rho_vals=rho_values,
rho_prime_vals=rho_prime_values,
alpha_123_vals=alpha_123_values,
alpha_4_vals=alpha_4_values,
alpha_5_vals=alpha_5_values,
initial_exposed_vals=initial_exposed_values,
loss=loss)
if plot_days is None:
n_days = 120
else:
n_days = plot_days
end_training_mobility_values = [
mobility_school[-1], mobility_work[-1], mobility_other[-1]
]
# alpha initial is taken assuming values will be kept constant as it was on the last day observed
mobility_initial = copy.deepcopy(
np.stack((mobility_school[-1] * np.ones(shape=(n_days, )),
mobility_work[-1] * np.ones(shape=(n_days, )),
mobility_other[-1] * np.ones(shape=(n_days, ))))).flatten()
# Only plot using a mobility file
if only_plot:
mobility = np.load(results_folder + plot_file)[:, 0:n_days]
fig, ax = posterior_cost.produce_plot(mobility, n_days)
plt.savefig(results_folder + filename_prefix + ".pdf")
plt.close(fig)
return
# try cost computation:
t = time.time()
cost_initial = posterior_cost.compute_cost(mobility_initial, n_days, sigma,
epsilon, backend)
# fig, ax = posterior_cost.produce_plot(mobility_initial, n_days)
# plt.savefig(results_folder + filename_prefix + "evolution_under_final_training_lockdown_conditions.pdf")
# plt.close(fig)
cost_no_lockdown = posterior_cost.compute_cost(
np.ones_like(mobility_initial), n_days, sigma, epsilon, backend)
# fig, ax = posterior_cost.produce_plot(np.ones_like(mobility_initial), n_days)
# plt.savefig(results_folder + filename_prefix + "evolution_under_no_lockdown.pdf")
# plt.close(fig)
print("Initial cost: {:.2f}, no-lockdown cost: {:.2f}".format(
cost_initial, cost_no_lockdown))
print(time.time() - t)
# OPTIMAL CONTROL WITH NO MOVING WINDOW APPROACH
if perform_standard_optimal_control:
# bounds = different_bounds('startconstrained')
bounds = different_bounds('realistic', n_days, mobility_initial,
end_training_mobility_values)
results_da = optimize.dual_annealing(posterior_cost.compute_cost,
bounds=bounds,
args=(n_days, sigma, epsilon,
backend),
maxiter=10,
maxfun=1e3,
x0=mobility_initial)
# Plotting the figures
mobility_initial = mobility_initial.reshape(
3, n_days) # 3 instead of 4 as we are not using alpha_home
mobility_final = results_da.x.reshape(3, n_days)
cost_final = posterior_cost.compute_cost(mobility_final, n_days, sigma,
epsilon, backend)
np.save(results_folder + filename_prefix + "mobility_standard",
mobility_final)
# MOVING WINDOW APPROACH
if perform_iterative_strategy:
print("Iterative strategy")
# window_size = 30 # in days
mobility_initial = copy.deepcopy(
np.stack((mobility_school[-1] * np.ones(shape=(window_size, )),
mobility_work[-1] * np.ones(shape=(window_size, )),
mobility_other[-1] *
np.ones(shape=(window_size, ))))).flatten()
# shift_each_iteration = 10 # number of days by which to shift the sliding window at each iteration.
# n_shifts = 10
total_days = n_shifts * shift_each_iteration
print(total_days)
total_mobility = np.zeros((3, total_days))
if restart_at_index is not None:
total_mobility = np.load(results_folder + filename_prefix +
"mobility_iterative_" +
str(restart_at_index) + ".npy")
bounds = different_bounds(
'realistic',
n_days=window_size,
alpha_initial=mobility_initial,
end_training_alpha_values=end_training_mobility_values)
for shift_idx in range(n_shifts):
print('Running shift: ' + str(shift_idx))
if restart_at_index is not None and shift_idx <= restart_at_index:
# we exploit the same loop in order to restart, so that the evolution of the model will be the same.
mobility_final = np.zeros((3, window_size))
mobility_final[:, 0:shift_each_iteration] = \
total_mobility[:, shift_idx * shift_each_iteration:(shift_idx + 1) * shift_each_iteration]
# keep that constant for the future; this is only used to initialize the next optimal control iteration:
mobility_final[:,
shift_each_iteration:] = mobility_final[:,
shift_each_iteration
-
1].reshape(
3,
1)
else:
# do the optimal control stuff
results_da = optimize.dual_annealing(
posterior_cost.compute_cost,
bounds=bounds,
args=(window_size, sigma, epsilon, backend),
maxiter=10,
maxfun=1e3,
x0=mobility_initial)
# get the result of the optimization in that time window
mobility_final = results_da.x.reshape(3, window_size)
# save it to the total_mobility array:
total_mobility[:, shift_idx * shift_each_iteration:(shift_idx + 1) * shift_each_iteration] = \
mobility_final[:, 0:shift_each_iteration]
# Save in between mobility steps
np.save(
results_folder + filename_prefix + "mobility_iterative_" +
str(shift_idx), total_mobility)
# update now the state of the model:
posterior_cost.update_states(
shift_each_iteration, mobility_final[:, :shift_each_iteration])
# update mobility_initial as well, with the translated values of mobility_final, it may speed up convergence.
mobility_initial_tmp = np.zeros_like(mobility_final)
mobility_initial_tmp[:, 0:window_size -
shift_each_iteration] = mobility_final[:,
shift_each_iteration:
window_size]
mobility_initial_tmp[:, window_size -
shift_each_iteration:] = np.stack([
mobility_final[:, window_size -
shift_each_iteration - 1]
] * shift_each_iteration,
axis=1)
mobility_initial = mobility_initial_tmp.flatten()
np.save(results_folder + filename_prefix + "mobility_iterative",
total_mobility)
import numpy as np
from abcpy.output import Journal
import matplotlib.pyplot as plt
from scipy.stats import gaussian_kde
# Reading your journal file
claudio_journal = Journal.fromFile('apmcabc_fakeobs1.jrnl')
# Read what were the parameters used for this specific inference scheme which produced this result
# each key : value of the key
print('Lets find out the configuration of the inference: ' +
str(claudio_journal.configuration) + '\n')
# It shows you have run APMCABC for 4 steps with 10000 n_samples and etc.
# Most important is the epsilon_arr - This tells me the 'threshold vaklue' used at each of the 4 steps, this is automatically chosen.
# In this case, your final epsilon value is 0.1696, which is rather large.
# Our goal is to take this value as close to zeor possible
# TIPS: You have to choose big steps more than 4 and see how many do you need to lets say bring them down to 0.01?
# One thing you can do: start the inference APMCABC using the final samples stored in your previous journal file, which is
# in this case 'apmcabc_fakeobs1.jrnl'. To that in the inputs of APMCABC sample put journal_file = 'apmcabc_fakeobs1.jrnl'
# The posterior distribution is approximated by the 10000 (as n_samples=10000) samples drawn from the approximate posterior distribution
# First we read the posterior samples in samples_dictionary which is a python dictionary object
# (Here the samples we consider are stored at the end meaning after step 4)
samples_dictionary = claudio_journal.get_parameters()
# We first check what were parameters you were infering, this is stored as the keys
print('The parameters for which inference was done: ' +
str(samples_dictionary.keys()) + '\n')
# We also get the weights corresponding to each sample
weights = np.array(claudio_journal.get_weights()).reshape(10000, )
# Normalize weights
weights = weights / sum(weights)
