def test_scaled_log_likelihood(self):
import pints
import pints.toy as toy
import numpy as np
model = toy.LogisticModel()
real_parameters = [0.015, 500]
test_parameters = [0.014, 501]
sigma = 0.001
times = np.linspace(0, 1000, 100)
values = model.simulate(real_parameters, times)
# Create an object with links to the model and time series
problem = pints.SingleSeriesProblem(model, times, values)
# Create a scaled and not scaled log_likelihood
log_likelihood_not_scaled = pints.KnownNoiseLogLikelihood(
problem, sigma)
log_likelihood_scaled = pints.ScaledLogLikelihood(
log_likelihood_not_scaled)
eval_not_scaled = log_likelihood_not_scaled(test_parameters)
eval_scaled = log_likelihood_scaled(test_parameters)
self.assertEqual(int(eval_not_scaled), -20959169232)
self.assertAlmostEqual(eval_scaled * len(times), eval_not_scaled)
def sample(self, x, parallel=False):
"""
Runs the sampler, this method:
(1) generates simulated data and adds noise
(2) sets up the sampler with the method given,
using an KnownNoiseLogLikelihood, and a UniformLogPrior
(3) runs the sampler
(4) returns:
- the calculated rhat value
- the average of ess across all chains, returning the
minimum result across all parameters
- the total time taken by the sampler
"""
the_model = self.model()
values = the_model.simulate(self.real_parameters, self.times)
value_range = np.max(values) - np.min(values)
values += np.random.normal(0, self.noise * value_range, values.shape)
problem = pints.MultiOutputProblem(the_model, self.times, values)
log_likelihood = pints.KnownNoiseLogLikelihood(
problem, value_range * self.noise)
# lower = list(self.lower) + [value_range *
# self.noise / 10.0]*the_model.n_outputs()
#upper = list(self.upper) + [value_range * self.noise * 10]*the_model.n_outputs()
lower = list(self.lower)
upper = list(self.upper)
middle = [0.5 * (u + l) for l, u in zip(lower, upper)]
sigma = [u - l for l, u in zip(lower, upper)]
log_prior = pints.UniformLogPrior(lower, upper)
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
n_chains = int(x[-1])
xs = [[
np.random.uniform() * (u - l) + l for l, u in zip(lower, upper)
] for c in range(n_chains)]
mcmc = pints.MCMCSampling(log_posterior,
n_chains,
xs,
method=self.method)
[sampler.set_hyper_parameters(x[:-1]) for sampler in mcmc.samplers()]
if parallel:
mcmc.set_parallel(int(os.environ['OMP_NUM_THREADS']))
mcmc.set_log_interval(1000)
start = timer()
chains = mcmc.run()
end = timer()
rhat = np.max(pints._diagnostics.rhat_all_params(chains))
ess = np.zeros(chains[0].shape[1])
for chain in chains:
ess += np.array(pints._diagnostics.effective_sample_size(chain))
ess /= n_chains
ess = np.min(ess)
print('rhat:', rhat)
print('ess:', ess)
print('time:', end - start)
return rhat, ess, end - start
def test_known_unknown_log_likelihood(self):
import pints
import pints.toy as toy
import numpy as np
model = toy.LogisticModel()
parameters = [0.015, 500]
sigma = 0.1
times = np.linspace(0, 1000, 100)
values = model.simulate(parameters, times)
problem = pints.SingleSeriesProblem(model, times, values)
# Test if known/unknown give same result
l1 = pints.KnownNoiseLogLikelihood(problem, sigma)
l2 = pints.UnknownNoiseLogLikelihood(problem)
self.assertAlmostEqual(l1(parameters), l2(parameters + [sigma]))
def run_model(model,
cell,
protocol,
time,
voltage,
current,
plot='unfold',
label=None,
axes=None):
# Select protocol file
protocol_file = os.path.join(root, protocol + '.mmt')
print(protocol_file)
myokit_protocol = myokit.load_protocol(protocol_file)
# Estimate noise from start of data
sigma_noise = np.std(current[:2000], ddof=1)
# fetch cmaes parameters
obtained_parameters = model.fetch_parameters()
# Cell-specific parameters
temperature = model.temperature(cell)
lower_conductance = model.conductance_limit(cell)
# Apply capacitance filter based on protocol
print('Applying capacitance filtering')
time, voltage, current = model.capacitance(myokit_protocol, 0.1, time,
voltage, current)
forward_model = model.ForwardModel(myokit_protocol,
temperature,
sine_wave=False)
problem = pints.SingleOutputProblem(forward_model, time, current)
log_likelihood = pints.KnownNoiseLogLikelihood(problem, sigma_noise)
log_prior = model.LogPrior(lower_conductance)
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
# Show obtained parameters and score
obtained_log_posterior = log_posterior(obtained_parameters)
print('Kylie sine-wave parameters:')
for x in obtained_parameters:
print(pints.strfloat(x))
print('Final log-posterior:')
print(pints.strfloat(obtained_log_posterior))
# Simulate
simulated = forward_model.simulate(obtained_parameters, time)
if plot == 'unfold':
axes[0].plot(time, voltage, color='red') #, label='voltage')
#axes[0].legend(loc='upper right')
axes[1].plot(time, current, alpha=0.3,
color='red') #, label='measured current')
if label == 0:
model_name = 'circularCOIIC'
axes[1].plot(time,
simulated,
alpha=1,
color='blue',
label=model_name)
elif label == 1:
model_name = 'linearCOI'
axes[1].plot(time,
simulated,
alpha=1,
color='magenta',
label=model_name)
elif label == 2:
model_name = 'linearCCOI'
axes[1].plot(time,
simulated,
alpha=1,
color='seagreen',
label=model_name)
elif label == 3:
model_name = 'linearCCCOI'
axes[1].plot(time,
simulated,
alpha=1,
color='seagreen',
label=model_name)
#axes.subplot(2,1,1)
else:
IkrModel.fold_plot(protocol, time, voltage, [current, simulated])
temperature,
myo_model,
rate_dict,
transform,
sine_wave=sw)
n_params = model.n_params
#
# Define problem
#
problem = pints.SingleOutputProblem(model, time, current)
#
# Define log-posterior
#
log_likelihood = pints.KnownNoiseLogLikelihood(problem, sigma_noise)
log_prior = prior.LogPrior(rate_dict, lower_conductance, n_params,
transform)
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
rate_checker = Rates.ratesPrior(transform, lower_conductance)
# Define parameter set from best ones we have found so far.
# Only refresh thse on the first sine wave fit protocol
if protocol_name == 'sine-wave':
parameter_set = np.loadtxt(cmaes_result_files + model_name +
'-cell-' + str(cell) + '-cmaes.txt')
ll_score = log_likelihood(parameter_set)
print('CMAES model parameters start point: ', parameter_set)
print('LogLikelihood (proportional to square error): ', ll_score)
mcmc_best_param_file = mcmc_result_files + model_name + '-cell-' + str(
def test_gaussian_log_likelihoods_single_output(self):
# Single-output test for known/unknown noise log-likelihood methods
model = pints.toy.LogisticModel()
parameters = [0.015, 500]
sigma = 0.1
times = np.linspace(0, 1000, 100)
values = model.simulate(parameters, times)
values += np.random.normal(0, sigma, values.shape)
problem = pints.SingleOutputProblem(model, times, values)
# Test if known/unknown give same result
l1 = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
l2 = pints.GaussianLogLikelihood(problem)
self.assertAlmostEqual(l1(parameters), l2(parameters + [sigma]))
# Test invalid constructors
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, 0)
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, -1)
# known noise value checks
model = pints.toy.ConstantModel(1)
times = np.linspace(0, 10, 10)
values = model.simulate([2], times)
org_values = np.arange(10) / 5.0
problem = pints.SingleOutputProblem(model, times, org_values)
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, 1.5)
self.assertAlmostEqual(log_likelihood([-1]), -21.999591968683927)
l, dl = log_likelihood.evaluateS1([3])
self.assertAlmostEqual(l, -23.777369746461702)
self.assertAlmostEqual(dl[0], -9.3333333333333321)
self.assertEqual(len(dl), 1)
# unknown noise value checks
log_likelihood = pints.GaussianLogLikelihood(problem)
self.assertAlmostEqual(log_likelihood([-3, 1.5]), -47.777369746461702)
# unknown noise check sensitivity
model = pints.toy.ConstantModel(1)
times = np.linspace(0, 10, 10)
values = model.simulate([2], times)
org_values = np.arange(10) / 5.0
problem = pints.SingleOutputProblem(model, times, org_values)
log_likelihood = pints.GaussianLogLikelihood(problem)
l, dl = log_likelihood.evaluateS1([7, 2.0])
self.assertAlmostEqual(l, -63.04585713764618)
self.assertAlmostEqual(dl[0], -15.25)
self.assertAlmostEqual(dl[1], 41.925000000000004)
# Test deprecated aliases
l1 = pints.KnownNoiseLogLikelihood(problem, sigma)
self.assertIsInstance(l1, pints.GaussianKnownSigmaLogLikelihood)
l2 = pints.UnknownNoiseLogLikelihood(problem)
self.assertIsInstance(l2, pints.GaussianLogLikelihood)
# test multiple output unknown noise
model = pints.toy.ConstantModel(3)
parameters = [0, 0, 0]
times = [1, 2, 3, 4]
values = model.simulate([0, 0, 0], times)
org_values = [[10.7, 3.5, 3.8], [1.1, 3.2, -1.4], [9.3, 0.0, 4.5],
[1.2, -3, -10]]
problem = pints.MultiOutputProblem(model, times, org_values)
log_likelihood = pints.GaussianLogLikelihood(problem)
# Test Gaussian_logpdf((10.7, 1.1, 9.3, 1.2)|mean=0, sigma=3.5) +
# Gaussian_logpdf((3.5, 3.2, 0.0, -3)|mean=0, sigma=1) +
# Gaussian_logpdf((3.8, -1.4, 4.5, -10)|mean=0, sigma=12)
# = -50.5088...
self.assertAlmostEqual(log_likelihood(parameters + [3.5, 1, 12]),
-50.508848609684783)
l, dl = log_likelihood.evaluateS1(parameters + [3.5, 1, 12])
self.assertAlmostEqual(l, -50.508848609684783)
self.assertAlmostEqual(dl[0], 1.820408163265306)
self.assertAlmostEqual(dl[1], 3.7000000000000002)
self.assertAlmostEqual(dl[2], -0.021527777777777774)
self.assertAlmostEqual(dl[3], 3.6065306122448981)
self.assertAlmostEqual(dl[4], 27.490000000000002)
self.assertAlmostEqual(dl[5], -0.25425347222222222)
# test multiple output model dimensions of sensitivities
d = 20
model = pints.toy.ConstantModel(d)
parameters = [0 for i in range(d)]
times = [1, 2, 3, 4]
values = model.simulate(parameters, times)
org_values = np.ones((len(times), d))
extra_params = np.ones(d).tolist()
problem = pints.MultiOutputProblem(model, times, org_values)
log_likelihood = pints.GaussianLogLikelihood(problem)
l = log_likelihood(parameters + extra_params)
l1, dl = log_likelihood.evaluateS1(parameters + extra_params)
self.assertTrue(np.array_equal(len(dl),
len(parameters + extra_params)))
self.assertEqual(l, l1)
model_ap = forwardModel.ForwardModel(protocol_ap,
temperature,
myo_model,
rate_dict,
transform,
sine_wave=False)
npar = model.n_params
#
# Define problem
#
problem_sine = pints.SingleOutputProblem(model, time_sine, current_sine)
problem_ap = pints.SingleOutputProblem(model_ap, time_ap, current_ap)
#
# Define log-posterior
#
log_likelihood = pints.KnownNoiseLogLikelihood(problem_sine,
sigma_noise_sine)
log_likelihood_ap = pints.KnownNoiseLogLikelihood(problem_ap,
sigma_noise_ap)
log_prior = prior.LogPrior(rate_dict, lower_conductance, npar, transform)
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
log_posterior_ap = pints.LogPosterior(log_likelihood_ap, log_prior)
rate_checker = Rates.ratesPrior(transform, lower_conductance)
if args.mcmc:
model_metrics = np.zeros((5, 7))
root = os.path.abspath('mcmc_results')
param_filename = os.path.join(
root, model_name + '-cell-' + str(cell) + '-mcmc_traces.p')
trace = cPickle.load(open(param_filename, 'rb'))
burnin = 70000
def load_problem(problem_dict):
"""
Returns a dictionary containing an instantiated PINTS problem
"""
problem_instance = copy.deepcopy(problem_dict)
model = problem_dict["model"]()
parameters = problem_dict['parameters']
# simulate problem
if 'simulation_noise_percent' in problem_dict:
values, times, noise_stds = emutils.simulate(
model,
parameters=problem_dict['parameters'],
times=problem_dict['times'],
noise_range_percent=problem_dict['simulation_noise_percent'],
)
else:
values, times = emutils.simulate(
model,
parameters=problem_dict['parameters'],
times=problem_dict['times'],
noise_range_percent=None,
)
noise_stds = None
# create instance of a problem and
if problem_dict['n_outputs'] == 1:
problem = pints.SingleOutputProblem(model, times, values)
else:
problem = pints.MultiOutputProblem(model, times, values)
# create likelihood with or without known noise
# log_likelihood = pints.UnknownNoiseLogLikelihood(problem)
log_likelihood = pints.KnownNoiseLogLikelihood(problem, noise_stds)
# should either provide the percentage range for parameters
# or the parameter range itself
if 'param_range_percent' in problem_dict:
param_range_percent = problem_dict['param_range_percent']
params_lower = parameters - param_range_percent * np.abs(parameters)
params_upper = parameters + param_range_percent * np.abs(parameters)
else:
params_lower, params_upper = problem_dict['param_range']
# add noise
# noise_lower, noise_upper = problem_dict['noise_bounds']
bounds = pints.RectangularBoundaries(
lower=params_lower,
upper=params_upper,
)
log_prior = problem_dict['prior'](bounds)
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
# extend the dictionary with created variables
problem_instance.update({
'model': model,
'values': values,
'times': times,
'noise_stds': noise_stds,
'problem': problem,
'bounds': bounds,
'log_likelihood': log_likelihood,
'log_prior': log_prior,
'log_posterior': log_posterior
})
return problem_instance
