def test_gaussian_noise_multi(self):
# Multi-output test for known/unknown Gaussian noise log-likelihood
# methods.
model = pints.toy.FitzhughNagumoModel()
parameters = [0.5, 0.5, 0.5]
sigma = 0.1
times = np.linspace(0, 100, 100)
values = model.simulate(parameters, times)
values += np.random.normal(0, sigma, values.shape)
problem = pints.MultiOutputProblem(model, times, values)
# Test if known/unknown give same result
l1 = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
l2 = pints.GaussianKnownSigmaLogLikelihood(problem, [sigma, sigma])
l3 = pints.GaussianLogLikelihood(problem)
self.assertAlmostEqual(l1(parameters), l2(parameters),
l3(parameters + [sigma, sigma]))
# Test invalid constructors
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, 0)
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, -1)
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, [1])
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, [1, 2, 3, 4])
self.assertRaises(ValueError, pints.GaussianKnownSigmaLogLikelihood,
problem, [1, 2, -3])
def test_sum_of_independent_log_pdfs(self):
# Test single output
model = pints.toy.LogisticModel()
x = [0.015, 500]
sigma = 0.1
times = np.linspace(0, 1000, 100)
values = model.simulate(x, times) + 0.1
problem = pints.SingleOutputProblem(model, times, values)
l1 = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
l2 = pints.GaussianLogLikelihood(problem)
ll = pints.SumOfIndependentLogPDFs([l1, l1, l1])
self.assertEqual(l1.n_parameters(), ll.n_parameters())
self.assertEqual(3 * l1(x), ll(x))
# Test single output derivatives
y, dy = ll.evaluateS1(x)
self.assertEqual(y, ll(x))
self.assertEqual(dy.shape, (2, ))
y1, dy1 = l1.evaluateS1(x)
self.assertTrue(np.all(3 * dy1 == dy))
# Wrong number of arguments
self.assertRaises(TypeError, pints.SumOfIndependentLogPDFs)
self.assertRaises(ValueError, pints.SumOfIndependentLogPDFs, [l1])
# Wrong types
self.assertRaises(ValueError, pints.SumOfIndependentLogPDFs, [l1, 1])
self.assertRaises(ValueError, pints.SumOfIndependentLogPDFs,
[problem, l1])
# Mismatching dimensions
self.assertRaises(ValueError, pints.SumOfIndependentLogPDFs, [l1, l2])
# Test multi-output
model = pints.toy.FitzhughNagumoModel()
x = model.suggested_parameters()
nt = 10
nx = model.n_parameters()
times = np.linspace(0, 10, nt)
values = model.simulate(x, times) + 0.01
problem = pints.MultiOutputProblem(model, times, values)
sigma = 0.01
l1 = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
ll = pints.SumOfIndependentLogPDFs([l1, l1, l1])
self.assertEqual(l1.n_parameters(), ll.n_parameters())
self.assertEqual(3 * l1(x), ll(x))
# Test multi-output derivatives
y, dy = ll.evaluateS1(x)
# Note: y and ll(x) differ a bit, because the solver acts slightly
# different when evaluating with and without sensitivities!
self.assertAlmostEqual(y, ll(x), places=3)
self.assertEqual(dy.shape, (nx, ))
y1, dy1 = l1.evaluateS1(x)
self.assertTrue(np.all(3 * dy1 == dy))
def test_build_tree_nan(self):
# This method gives nan in the hamiltonian_dash
# in the build_tree function
# Needed for coverage
model = pints.toy.LogisticModel()
real_parameters = np.array([0.015, 20])
times = np.linspace(0, 1000, 50)
org_values = model.simulate(real_parameters, times)
np.random.seed(1)
noise = 0.1
values = org_values + np.random.normal(0, noise, org_values.shape)
problem = pints.SingleOutputProblem(model, times, values)
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, noise)
log_prior = pints.UniformLogPrior([0.0001, 1], [1, 500])
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
xs = [[0.36083914, 1.99013825]]
nuts_mcmc = pints.MCMCController(log_posterior,
len(xs),
xs,
method=pints.NoUTurnMCMC)
nuts_mcmc.set_max_iterations(50)
nuts_mcmc.set_log_to_screen(False)
np.random.seed(5)
nuts_chains = nuts_mcmc.run()
self.assertFalse(np.isnan(np.sum(nuts_chains)))
def setUpClass(cls):
""" Prepare for the test. """
# Create toy model
model = pints.toy.LogisticModel()
cls.real_parameters = [0.015, 500]
times = np.linspace(0, 1000, 1000)
values = model.simulate(cls.real_parameters, times)
# Add noise
np.random.seed(1)
cls.noise = 10
values += np.random.normal(0, cls.noise, values.shape)
cls.real_parameters.append(cls.noise)
# Create an object with links to the model and time series
problem = pints.SingleOutputProblem(model, times, values)
# Create a uniform prior over both the parameters and the new noise
# variable
cls.log_prior = pints.UniformLogPrior(
[0.01, 400],
[0.02, 600]
)
# Create a log-likelihood
cls.log_likelihood = pints.GaussianKnownSigmaLogLikelihood(
problem, cls.noise)
def test_model_that_gives_nan(self):
# This model will return a nan in the gradient evaluation, which
# originally tripped up the find_reasonable_epsilon function in nuts.
# Run it for a bit so that we get coverage on the if statement!
model = pints.toy.LogisticModel()
real_parameters = model.suggested_parameters()
times = model.suggested_parameters()
org_values = model.simulate(real_parameters, times)
np.random.seed(1)
noise = 0.2
values = org_values + np.random.normal(0, noise, org_values.shape)
problem = pints.SingleOutputProblem(model, times, values)
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, noise)
log_prior = pints.UniformLogPrior([0.01, 40], [0.2, 60])
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
xs = [real_parameters * 1.1]
nuts_mcmc = pints.MCMCController(log_posterior,
len(xs),
xs,
method=pints.NoUTurnMCMC)
nuts_mcmc.set_max_iterations(10)
nuts_mcmc.set_log_to_screen(False)
nuts_chains = nuts_mcmc.run()
self.assertFalse(np.isnan(np.sum(nuts_chains)))
def run(model, real_parameters, noise_used, log_prior_used):
# Create some toy data
times = np.linspace(1, 1000, 50)
org_values = model.simulate(real_parameters, times)
# Add noise
noise = 10
values = org_values + np.random.normal(0, noise, org_values.shape)
real_parameters = np.array(real_parameters)
# Create an object with links to the model and time series
problem = pints.SingleOutputProblem(model, times, values)
# Create a log-likelihood function (adds an extra parameter!)
log_likelihood_used = pints.GaussianKnownSigmaLogLikelihood(problem, [noise_used])
# Create a uniform prior over both the parameters and the new noise variable
# Create a posterior log-likelihood (log(likelihood * prior))
log_posterior = pints.LogPosterior(log_likelihood_used, log_prior_used)
# Choose starting points for 3 mcmc chains
xs = [
real_parameters,
real_parameters * 1.01,
real_parameters * 0.99,
]
# Create mcmc routine with four chains
mcmc = pints.MCMCController(log_posterior, 3, xs, method=pints.HaarioACMC)
sample_size = 4000
# Add stopping criterion
mcmc.set_max_iterations(sample_size)
# Start adapting after 1000 iterations
mcmc.set_initial_phase_iterations(sample_size//4)
# Disable logging mode
mcmc.set_log_to_screen(False)
# Run!
print('Running...')
chains = mcmc.run()
print('Done!')
s = sample_size//4+1
#HMC: s = 1
b = False
while s < sample_size:
chains_cut = chains[:,sample_size//4:s+1]
rhat = pints.rhat(chains_cut)
s+=1
if rhat[0] < 1.05:
b = True
break
print(s)
return chains[0][s:][:, 0]
def test_known_noise_gaussian_single_and_multi(self):
"""
Tests the output of single-series against multi-series known noise
log-likelihoods.
"""
# Define boring 1-output and 2-output models
class NullModel1(pints.ForwardModel):
def n_parameters(self):
return 1
def simulate(self, x, times):
return np.zeros(times.shape)
class NullModel2(pints.ForwardModel):
def n_parameters(self):
return 1
def n_outputs(self):
return 2
def simulate(self, x, times):
return np.zeros((len(times), 2))
# Create two single output problems
times = np.arange(10)
np.random.seed(1)
sigma1 = 3
sigma2 = 5
values1 = np.random.uniform(0, sigma1, times.shape)
values2 = np.random.uniform(0, sigma2, times.shape)
model1d = NullModel1()
problem1 = pints.SingleOutputProblem(model1d, times, values1)
problem2 = pints.SingleOutputProblem(model1d, times, values2)
log1 = pints.GaussianKnownSigmaLogLikelihood(problem1, sigma1)
log2 = pints.GaussianKnownSigmaLogLikelihood(problem2, sigma2)
# Create one multi output problem
values3 = np.array([values1, values2]).swapaxes(0, 1)
model2d = NullModel2()
problem3 = pints.MultiOutputProblem(model2d, times, values3)
log3 = pints.GaussianKnownSigmaLogLikelihood(
problem3, [sigma1, sigma2])
# Check if we get the right output
self.assertAlmostEqual(log1(0) + log2(0), log3(0))
def test_log_posterior(self):
# Create a toy problem and log likelihood
model = pints.toy.LogisticModel()
real_parameters = [0.015, 500]
x = [0.014, 501]
sigma = 0.001
times = np.linspace(0, 1000, 100)
values = model.simulate(real_parameters, times)
problem = pints.SingleOutputProblem(model, times, values)
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
# Create a prior
log_prior = pints.UniformLogPrior([0, 0], [1, 1000])
# Test
p = pints.LogPosterior(log_likelihood, log_prior)
self.assertEqual(p(x), log_likelihood(x) + log_prior(x))
y = [-1, 500]
self.assertEqual(log_prior(y), -float('inf'))
self.assertEqual(p(y), -float('inf'))
self.assertEqual(p(y), log_prior(y))
# Test derivatives
log_prior = pints.ComposedLogPrior(pints.GaussianLogPrior(0.015, 0.3),
pints.GaussianLogPrior(500, 100))
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
x = [0.013, 540]
y, dy = log_posterior.evaluateS1(x)
self.assertEqual(y, log_posterior(x))
self.assertEqual(dy.shape, (2, ))
y1, dy1 = log_prior.evaluateS1(x)
y2, dy2 = log_likelihood.evaluateS1(x)
self.assertTrue(np.all(dy == dy1 + dy2))
# Test getting the prior and likelihood back again
self.assertIs(log_posterior.log_prior(), log_prior)
self.assertIs(log_posterior.log_likelihood(), log_likelihood)
# First arg must be a LogPDF
self.assertRaises(ValueError, pints.LogPosterior, 'hello', log_prior)
# Second arg must be a log_prior
self.assertRaises(ValueError, pints.LogPosterior, log_likelihood,
log_likelihood)
# Prior and likelihood must have same dimension
self.assertRaises(ValueError, pints.LogPosterior, log_likelihood,
pints.GaussianLogPrior(0.015, 0.3))
def create_pints_log_likelihood(self):
problem, fitted_children = self.create_pints_problem()
if self.form == self.Form.NORMAL:
noise_param = self.parameters.get(index=1)
if noise_param.child.form == noise_param.child.Form.FIXED:
value = noise_param.value
return pints.GaussianKnownSigmaLogLikelihood(
problem, value), fitted_children
else:
return pints.GaussianLogLikelihood(
problem), fitted_children + [noise_param.child]
elif self.form == LogLikelihood.Form.LOGNORMAL:
noise_param = self.parameters.get(index=1)
return pints.LogNormalLogLikelihood(
problem), fitted_children + [noise_param.child]
raise RuntimeError('unknown log_likelihood form')
def __init__(self, name):
super(TestPlot, self).__init__(name)
# Create toy model (single output)
self.model = toy.LogisticModel()
self.real_parameters = [0.015, 500]
self.times = np.linspace(0, 1000, 100) # small problem
self.values = self.model.simulate(self.real_parameters, self.times)
# Add noise
self.noise = 10
self.values += np.random.normal(0, self.noise, self.values.shape)
self.real_parameters.append(self.noise)
self.real_parameters = np.array(self.real_parameters)
# Create an object with links to the model and time series
self.problem = pints.SingleOutputProblem(self.model, self.times,
self.values)
# Create a uniform prior over both the parameters and the new noise
# variable
self.lower = [0.01, 400, self.noise * 0.1]
self.upper = [0.02, 600, self.noise * 100]
self.log_prior = pints.UniformLogPrior(self.lower, self.upper)
# Create a log likelihood
self.log_likelihood = pints.GaussianLogLikelihood(self.problem)
# Create an un-normalised log-posterior (log-likelihood + log-prior)
self.log_posterior = pints.LogPosterior(self.log_likelihood,
self.log_prior)
# Run MCMC
self.x0 = [
self.real_parameters * 1.1, self.real_parameters * 0.9,
self.real_parameters * 1.05
]
mcmc = pints.MCMCController(self.log_posterior, 3, self.x0)
mcmc.set_max_iterations(300) # make it as small as possible
mcmc.set_log_to_screen(False)
self.samples = mcmc.run()
# Create toy model (multi-output)
self.model2 = toy.LotkaVolterraModel()
self.real_parameters2 = self.model2.suggested_parameters()
self.times2 = self.model2.suggested_times()[::10] # down sample it
self.values2 = self.model2.simulate(self.real_parameters2, self.times2)
# Add noise
self.noise2 = 0.05
self.values2 += np.random.normal(0, self.noise2, self.values2.shape)
# Create an object with links to the model and time series
self.problem2 = pints.MultiOutputProblem(self.model2, self.times2,
self.values2)
# Create a uniform prior over both the parameters and the new noise
# variable
self.log_prior2 = pints.UniformLogPrior([1, 1, 1, 1], [6, 6, 6, 6])
# Create a log likelihood
self.log_likelihood2 = pints.GaussianKnownSigmaLogLikelihood(
self.problem2, self.noise2)
# Create an un-normalised log-posterior (log-likelihood + log-prior)
self.log_posterior2 = pints.LogPosterior(self.log_likelihood2,
self.log_prior2)
# Run MCMC
self.x02 = [
self.real_parameters2 * 1.1, self.real_parameters2 * 0.9,
self.real_parameters2 * 1.05
]
mcmc = pints.MCMCController(self.log_posterior2, 3, self.x02)
mcmc.set_max_iterations(300) # make it as small as possible
mcmc.set_log_to_screen(False)
self.samples2 = mcmc.run()
# Create toy model (single-output, single-parameter)
self.real_parameters3 = [0]
self.log_posterior3 = toy.GaussianLogPDF(self.real_parameters3, [1])
self.lower3 = [-3]
self.upper3 = [3]
# Run MCMC
self.x03 = [[1], [-2], [3]]
mcmc = pints.MCMCController(self.log_posterior3, 3, self.x03)
mcmc.set_max_iterations(300) # make it as small as possible
mcmc.set_log_to_screen(False)
self.samples3 = mcmc.run()
ax = plt.hist([], bins=range(L + 2), align='left')
rankstats = []
columns = [str(x) for x in range(N)]
df = pd.DataFrame(columns=columns)
for n in range(N):
print(n)
theta = log_prior.sample(n=1)[0]
times = np.linspace(1, 1000, 25)
org_values = model.simulate(theta, times)
# Add noise
noise = 10
ys = org_values + np.random.normal(0, noise, org_values.shape)
# Create an object with links to the model and time series
problem = pints.SingleOutputProblem(model, times, ys)
# Create a log-likelihood function (adds an extra parameter!)
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, [noise])
log_prior_incorrect = pints.UniformLogPrior([200], [800])
log_posterior = pints.LogPosterior(log_likelihood, log_prior)
# Choose starting points for 3 mcmc chains
xs = [theta, theta * 1.01, theta * 0.99]
isinf = False
for x in xs:
if (math.isinf(log_posterior.evaluateS1(x)[0])):
isinf = True
d += 1
break
if (isinf == True):
continue
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)
def test_known_noise_gaussian_single_S1(self):
# Simple tests for single known noise Gaussian log-likelihood with
# sensitivities.
model = pints.toy.LogisticModel()
x = [0.015, 500]
sigma = 0.1
times = np.linspace(0, 1000, 100)
values = model.simulate(x, times)
values += np.random.normal(0, sigma, values.shape)
problem = pints.SingleOutputProblem(model, times, values)
# Test if values are correct
f = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
L1 = f(x)
L2, dL = f.evaluateS1(x)
self.assertEqual(L1, L2)
self.assertEqual(dL.shape, (2, ))
# Test with MultiOutputProblem
problem = pints.MultiOutputProblem(model, times, values)
f2 = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
L3 = f2(x)
L4, dL = f2.evaluateS1(x)
self.assertEqual(L3, L4)
self.assertEqual(L1, L3)
self.assertEqual(dL.shape, (2, ))
# Test without noise
values = model.simulate(x, times)
problem = pints.SingleOutputProblem(model, times, values)
f = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
L1 = f(x)
L2, dL = f.evaluateS1(x)
self.assertEqual(L1, L2)
self.assertEqual(dL.shape, (2, ))
# Test if zero at optimum
self.assertTrue(np.all(dL == 0))
# Test if positive to the left, negative to the right
L, dL = f.evaluateS1(x + np.array([-1e-9, 0]))
self.assertTrue(dL[0] > 0)
L, dL = f.evaluateS1(x + np.array([1e-9, 0]))
self.assertTrue(dL[0] < 0)
# Test if positive to the left, negative to the right
L, dL = f.evaluateS1(x + np.array([0, -1e-9]))
self.assertTrue(dL[1] > 0)
L, dL = f.evaluateS1(x + np.array([0, 1e-9]))
self.assertTrue(dL[1] < 0)
# Plot derivatives
if False:
import matplotlib.pyplot as plt
plt.figure()
r = np.linspace(x[0] * 0.95, x[0] * 1.05, 100)
L = []
dL1 = []
dL2 = []
for y in r:
a, b = f.evaluateS1([y, x[1]])
L.append(a)
dL1.append(b[0])
dL2.append(b[1])
plt.subplot(3, 1, 1)
plt.plot(r, L)
plt.subplot(3, 1, 2)
plt.plot(r, dL1)
plt.grid(True)
plt.subplot(3, 1, 3)
plt.plot(r, dL2)
plt.grid(True)
plt.figure()
r = np.linspace(x[1] * 0.95, x[1] * 1.05, 100)
L = []
dL1 = []
dL2 = []
for y in r:
a, b = f.evaluateS1([x[0], y])
L.append(a)
dL1.append(b[0])
dL2.append(b[1])
plt.subplot(3, 1, 1)
plt.plot(r, L)
plt.subplot(3, 1, 2)
plt.plot(r, dL1)
plt.grid(True)
plt.subplot(3, 1, 3)
plt.plot(r, dL2)
plt.grid(True)
plt.show()
# value-based tests (single output tests are above)
# multiple outputs
model = pints.toy.ConstantModel(3)
parameters = [0, 0, 0]
times = [1, 2, 3, 4]
values = model.simulate(parameters, 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)
sigma = [3.5, 1, 12]
log_likelihood = pints.GaussianKnownSigmaLogLikelihood(problem, sigma)
# 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), -50.508848609684783)
l, dl = log_likelihood.evaluateS1(parameters)
self.assertAlmostEqual(l, -50.508848609684783)
self.assertAlmostEqual(dl[0], 1.820408163265306)
self.assertAlmostEqual(dl[1], 3.7000000000000002)
self.assertAlmostEqual(dl[2], -0.021527777777777774)
def test_scaled_log_likelihood(self):
model = pints.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.SingleOutputProblem(model, times, values)
# Create a scaled and not scaled log_likelihood
log_likelihood_not_scaled = pints.GaussianKnownSigmaLogLikelihood(
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)
# Test bad constructor
self.assertRaises(ValueError, pints.ScaledLogLikelihood, model)
# Test single-output derivatives
y1, dy1 = log_likelihood_not_scaled.evaluateS1(test_parameters)
y2, dy2 = log_likelihood_scaled.evaluateS1(test_parameters)
self.assertEqual(y1, log_likelihood_not_scaled(test_parameters))
self.assertEqual(dy1.shape, (2, ))
self.assertEqual(y2, log_likelihood_scaled(test_parameters))
self.assertEqual(dy2.shape, (2, ))
dy3 = dy2 * len(times)
self.assertAlmostEqual(dy1[0] / dy3[0], 1)
self.assertAlmostEqual(dy1[1] / dy3[1], 1)
# Test on multi-output problem
model = pints.toy.FitzhughNagumoModel()
nt = 10
no = model.n_outputs()
times = np.linspace(0, 100, nt)
values = model.simulate([0.5, 0.5, 0.5], times)
problem = pints.MultiOutputProblem(model, times, values)
unscaled = pints.GaussianKnownSigmaLogLikelihood(problem, 1)
scaled = pints.ScaledLogLikelihood(unscaled)
p = [0.1, 0.1, 0.1]
x = unscaled(p)
y = scaled(p)
self.assertAlmostEqual(y, x / nt / no)
# Test multi-output derivatives
y1, dy1 = unscaled.evaluateS1(p)
y2, dy2 = scaled.evaluateS1(p)
self.assertAlmostEqual(y1, unscaled(p), places=6)
self.assertEqual(dy1.shape, (3, ))
self.assertAlmostEqual(y2, scaled(p))
self.assertEqual(dy2.shape, (3, ))
dy3 = dy2 * nt * no
self.assertAlmostEqual(dy1[0] / dy3[0], 1)
self.assertAlmostEqual(dy1[1] / dy3[1], 1)
# test values of log-likelihood and derivatives
model = pints.toy.ConstantModel(3)
times = [1, 2, 3, 4]
parameters = [0, 0, 0]
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)
f2 = pints.GaussianKnownSigmaLogLikelihood(problem, [3.5, 1, 12])
log_likelihood = pints.ScaledLogLikelihood(f2)
# 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),
-50.508848609684783 / 12.0)
l, dl = log_likelihood.evaluateS1(parameters)
self.assertAlmostEqual(l, -50.508848609684783 / 12.0)
self.assertAlmostEqual(dl[0], 1.820408163265306 / 12.0)
self.assertAlmostEqual(dl[1], 3.7000000000000002 / 12.0)
self.assertAlmostEqual(dl[2], -0.021527777777777774 / 12.0)
def Algorithm1WithConvergence(L,
N,
model,
log_prior,
log_prior_used,
times,
noise,
noise_used,
MCMCmethod,
param=0):
time_start = time.time()
sum_p = 0
sum_p_theta = 0
sum_p_y = 0
c = 1
for i in range(c):
print(i)
res1 = []
res2 = []
thetatildeArray = [] #np.empty(N, dtype=float)
ytildeArray = [] #np.empty(N, dtype=float)
d = 0
for n in range(N):
print(n)
thetatilde = log_prior.sample(n=1)[0]
org_values = model.simulate(thetatilde, times)
ytilde_n = org_values + np.random.normal(0, noise,
org_values.shape)
problem = pints.SingleOutputProblem(model, times, ytilde_n)
log_likelihood_used = pints.GaussianKnownSigmaLogLikelihood(
problem, [noise_used])
log_posterior = pints.LogPosterior(log_likelihood_used,
log_prior_used)
#Start from thetatilde
xs = [thetatilde, thetatilde * 1.01, thetatilde * 0.99]
isinf = False
for x in xs:
#print(x)
if (math.isinf(log_posterior.evaluateS1(x)[0])):
isinf = True
d += 1
break
if (isinf == True):
print('isinf:', isinf)
continue
#Run Markov chain L steps from thetatilde'''
mcmc = pints.MCMCController(log_posterior,
len(xs),
xs,
method=MCMCmethod)
# Add stopping criterion
sample_size = 3000
mcmc.set_max_iterations(sample_size)
# Start adapting after sample_size//4 iterations
mcmc.set_initial_phase_iterations(sample_size // 4)
# Disable logging mode
mcmc.set_log_to_screen(False)
chains = mcmc.run()
s = sample_size // 4 + 1
b = False
while s < sample_size:
chains_cut = chains[:, sample_size // 4:s + 1]
#HMC: chains_cut = chains[:,0:s+1]
rhat = pints.rhat(chains_cut)
s += 1
if rhat[0] < 1.05:
print('converge')
b = True
break
if b == False:
d += 1
continue
print(s)
thetatilde_n = chains[0][(s + sample_size) // 2 - 1]
print(thetatilde)
thetatildeArray.append(thetatilde_n[param])
ytildeArray.append(ytilde_n[param])
res1.append((thetatilde_n[param], ytilde_n[param]))
thetaArray = np.empty(N - d, dtype=float)
yArray = np.empty(N - d, dtype=float)
for n in range(N - d):
theta_n = log_prior.sample(n=1)[0]
org_values = model.simulate(theta_n, times)
y_n = org_values + np.random.normal(0, noise, org_values.shape)
thetaArray[n] = theta_n[param]
yArray[n] = y_n[param]
res2.append((theta_n[param], y_n[param]))
p = ks2d2s(thetatildeArray, ytildeArray, thetaArray, yArray)
statistic_theta, p_theta = ks_2samp(thetatildeArray, thetaArray)
statistic_y, p_y = ks_2samp(ytildeArray, yArray)
sum_p += p
sum_p_theta += p_theta
sum_p_y += p_y
time_end = time.time()
duration = time_end - time_start
average_p = sum_p / c
average_p_theta = sum_p_theta / c
average_p_y = sum_p_y / c
print('average_p:', average_p)
print('average_p_theta:', average_p_theta)
print('average_p_y:', average_p_y)
return average_p, average_p_theta, average_p_y, duration, thetatildeArray, thetaArray, ytildeArray, yArray
def setUpClass(cls):
# Number of samples: Make this as small as possible to speed up testing
n_samples = 300
# Create toy model (single output)
cls.model = toy.LogisticModel()
cls.real_parameters = [0.015, 500]
cls.times = np.linspace(0, 1000, 100) # small problem
cls.values = cls.model.simulate(cls.real_parameters, cls.times)
# Add noise
cls.noise = 10
cls.values += np.random.normal(0, cls.noise, cls.values.shape)
cls.real_parameters.append(cls.noise)
cls.real_parameters = np.array(cls.real_parameters)
# Create an object with links to the model and time series
cls.problem = pints.SingleOutputProblem(cls.model, cls.times,
cls.values)
# Create a uniform prior over both the parameters and the new noise
# variable
cls.lower = [0.01, 400, cls.noise * 0.1]
cls.upper = [0.02, 600, cls.noise * 100]
cls.log_prior = pints.UniformLogPrior(cls.lower, cls.upper)
# Create a log likelihood
cls.log_likelihood = pints.GaussianLogLikelihood(cls.problem)
# Create an un-normalised log-posterior (log-likelihood + log-prior)
cls.log_posterior = pints.LogPosterior(cls.log_likelihood,
cls.log_prior)
# Run MCMC
cls.x0 = [
cls.real_parameters * 1.1, cls.real_parameters * 0.9,
cls.real_parameters * 1.05
]
mcmc = pints.MCMCController(cls.log_posterior, 3, cls.x0)
mcmc.set_max_iterations(n_samples)
mcmc.set_log_to_screen(False)
cls.samples = mcmc.run()
# Create toy model (multi-output)
cls.model2 = toy.LotkaVolterraModel()
cls.real_parameters2 = cls.model2.suggested_parameters()
cls.times2 = cls.model2.suggested_times()[::10] # downsample it
cls.values2 = cls.model2.simulate(cls.real_parameters2, cls.times2)
# Add noise
cls.noise2 = 0.05
cls.values2 += np.random.normal(0, cls.noise2, cls.values2.shape)
# Create an object with links to the model and time series
cls.problem2 = pints.MultiOutputProblem(cls.model2, cls.times2,
np.log(cls.values2))
# Create a uniform prior over both the parameters and the new noise
# variable
cls.log_prior2 = pints.UniformLogPrior([0, 0, 0, 0], [6, 6, 6, 6])
# Create a log likelihood
cls.log_likelihood2 = pints.GaussianKnownSigmaLogLikelihood(
cls.problem2, cls.noise2)
# Create an un-normalised log-posterior (log-likelihood + log-prior)
cls.log_posterior2 = pints.LogPosterior(cls.log_likelihood2,
cls.log_prior2)
# Run MCMC
cls.x02 = [
cls.real_parameters2 * 1.1, cls.real_parameters2 * 0.9,
cls.real_parameters2 * 1.05
]
mcmc = pints.MCMCController(cls.log_posterior2, 3, cls.x02)
mcmc.set_max_iterations(n_samples)
mcmc.set_log_to_screen(False)
cls.samples2 = mcmc.run()
# Create toy model (single-output, single-parameter)
cls.real_parameters3 = [0]
cls.log_posterior3 = toy.GaussianLogPDF(cls.real_parameters3, [1])
cls.lower3 = [-3]
cls.upper3 = [3]
# Run MCMC
cls.x03 = [[1], [-2], [3]]
mcmc = pints.MCMCController(cls.log_posterior3, 3, cls.x03)
mcmc.set_max_iterations(n_samples)
mcmc.set_log_to_screen(False)
cls.samples3 = mcmc.run()
set_ion=info.ions_conc,
transform=transform_to_model_param,
temperature=273.15 + info.temperature, # K
)
LogPrior = {
'model_A': priors.ModelALogPrior,
'model_B': priors.ModelBLogPrior,
}
# Update protocol
model.set_fixed_form_voltage_protocol(protocol, protocol_times)
# Create Pints stuffs
problem = pints.SingleOutputProblem(model, times, data)
loglikelihood = pints.GaussianKnownSigmaLogLikelihood(problem, noise_sigma)
logprior = LogPrior[info_id](transform_to_model_param,
transform_from_model_param)
logposterior = pints.LogPosterior(loglikelihood, logprior)
# Check logposterior is working fine
priorparams = np.copy(info.base_param)
transform_priorparams = transform_from_model_param(priorparams)
print('Score at prior parameters: ', logposterior(transform_priorparams))
for _ in range(10):
assert(logposterior(transform_priorparams) ==\
logposterior(transform_priorparams))
# Run
try:
N = int(sys.argv[2])
def Algorithm1Rankstat(N,
L,
Ldashdash,
model,
log_prior,
log_prior_used,
times,
noise,
noise_used,
MCMCmethod,
param=0):
time_start = time.time()
sum_p = 0
sum_p_theta = 0
sum_p_y = 0
rankstats = []
d = 0
for n in range(N):
print(n)
thetaArray = np.empty(L, dtype=float)
thetatilde = log_prior.sample(n=1)[0]
org_values = model.simulate(thetatilde, times)
ytilde_n = org_values + np.random.normal(0, noise, org_values.shape)
problem = pints.SingleOutputProblem(model, times, ytilde_n)
log_likelihood_used = pints.GaussianKnownSigmaLogLikelihood(
problem, [noise_used])
log_posterior = pints.LogPosterior(log_likelihood_used, log_prior_used)
for l in range(L):
#Run Markov chain L steps from thetatilde
xs = [thetatilde]
mcmc = pints.MCMCController(log_posterior,
1,
xs,
method=MCMCmethod)
# Add stopping criterion
sample_size = Ldashdash + 1
mcmc.set_max_iterations(sample_size)
# Start adapting after sample_size//4 iterations
mcmc.set_initial_phase_iterations(sample_size // 4)
# Disable logging mode
mcmc.set_log_to_screen(False)
chain = mcmc.run()[0]
theta_l = chain[Ldashdash]
thetaArray[l] = theta_l[param]
rankstat = rank_statistic(thetaArray, thetatilde)
rankstats.append(rankstat)
current_date_and_time = datetime.now()
current_date_and_time_string = str(current_date_and_time)
plt.hist(rankstats, bins=range(N + 2), align='left')
plt.axhline(y=c / (N + 1), color='r', linestyle='-')
plt.axhline(y=binom.ppf(0.005, N, 1 / (L + 1)), color='b')
plt.axhline(y=binom.ppf(0.995, N, 1 / (L + 1)), color='b')
plt.savefig('./Gandy2020AlgorithmRankstat' + current_date_and_time_string +
'.png',
dpi=500,
bbox_inches='tight')
time_end = time.time()
print('total running time', time_end - time_start)
plt.show()
