def __init__(self,
lower: Tensor,
upper: Tensor,
return_numpy: bool = False):
self.lower = lower
self.upper = upper
self.dist = BoxUniform(lower, upper)
self.return_numpy = return_numpy
def test_process_matrix_observation():
prior = BoxUniform(torch.zeros(4), torch.ones(4))
observed_data = np.zeros((1, 2, 2))
simulator = matrix_simulator
observed_data, observation_dim = process_observed_data(
observed_data, simulator, prior)
def test_nograd_after_inference_train(inference_method) -> None:
num_dim = 2
prior_ = BoxUniform(-torch.ones(num_dim), torch.ones(num_dim))
simulator, prior = prepare_for_sbi(diagonal_linear_gaussian, prior_)
inference = inference_method(
prior,
**(
dict(classifier="resnet")
if inference_method in [SNRE_A, SNRE_B]
else dict(
density_estimator=(
"mdn_snpe_a" if inference_method == SNPE_A else "maf"
)
)
),
show_progress_bars=False,
)
theta, x = simulate_for_sbi(simulator, prior, 32)
inference = inference.append_simulations(theta, x)
posterior_estimator = inference.train(max_num_epochs=2)
def check_no_grad(model):
for p in model.parameters():
assert p.grad is None
check_no_grad(posterior_estimator)
check_no_grad(inference._neural_net)
def test_simulate_in_batches(
num_sims,
batch_size,
simulator=diagonal_linear_gaussian,
prior=BoxUniform(zeros(5), ones(5)),
):
"""Test combinations of num_sims and simulation_batch_size. """
theta = prior.sample((num_sims,))
simulate_in_batches(simulator, theta, batch_size)
def test_reinterpreted_batch_dim_prior():
"""Test whether the right warning and error are raised for reinterpreted priors."""
# Both must raise ValueError because we don't reinterpret batch dims anymore.
with pytest.raises(ValueError):
process_prior(Uniform(zeros(3), ones(3)))
with pytest.raises(ValueError):
process_prior(MultivariateNormal(zeros(2, 3), ones(3)))
# This must pass without warnings or errors.
process_prior(BoxUniform(zeros(3), ones(3)))
def test_simulate_in_batches(
num_sims,
batch_size,
simulator,
prior=BoxUniform(zeros(5), ones(5)),
):
"""Test combinations of num_sims and simulation_batch_size. """
simulator, prior = prepare_for_sbi(simulator, prior)
theta = prior.sample((num_sims, ))
simulate_in_batches(simulator, theta, batch_size)
def test_nonlinearGaussian_based_on_mmd():
simulator = non_linear_gaussian
# Ground truth parameters as specified in 'Sequential Neural Likelihood' paper.
ground_truth_parameters = torch.tensor([-0.7, -2.9, -1.0, -0.9, 0.6])
# ground truth observation using same seed as 'Sequential Neural Likelihood' paper.
ground_truth_observation = torch.tensor([
-0.97071232,
-2.94612244,
-0.44947218,
-3.42318484,
-0.13285634,
-3.36401699,
-0.85367595,
-2.42716377,
])
# assume batch dims
parameter_dim = ground_truth_parameters.shape[0]
observation_dim = ground_truth_observation.shape[0]
prior = BoxUniform(
low=-3 * torch.ones(parameter_dim),
high=3 * torch.ones(parameter_dim),
)
infer = SnpeC(
simulator=simulator,
true_observation=ground_truth_observation[None, ],
prior=prior,
num_atoms=-1,
z_score_obs=True,
use_combined_loss=False,
retrain_from_scratch_each_round=False,
discard_prior_samples=False,
)
num_rounds, num_simulations_per_round = 2, 1000
posterior = infer(num_rounds=num_rounds,
num_simulations_per_round=num_simulations_per_round)
samples = posterior.sample(1000)
# Sample from (analytically tractable) target distribution.
target_samples = get_ground_truth_posterior_samples_nonlinear_gaussian(
num_samples=1000)
# Compute and check if MMD is larger than expected.
mmd = utils.unbiased_mmd_squared(target_samples.float(), samples.float())
max_mmd = 0.16 # mean mmd plus 2 stds.
assert mmd < max_mmd, f"MMD={mmd} larger than mean plus 2 stds."
class UserNumpyUniform:
"""User defined numpy uniform prior.
Used for testing to mimick a user-defined prior with valid .sample and .log_prob
methods.
"""
def __init__(self, lower: Tensor, upper: Tensor, return_numpy: bool = False):
self.lower = lower
self.upper = upper
self.dist = BoxUniform(lower, upper)
self.return_numpy = return_numpy
def sample(self, sample_shape=torch.Size([])):
samples = self.dist.sample(sample_shape)
return samples.numpy() if self.return_numpy else samples
def log_prob(self, values):
if self.return_numpy:
values = torch.as_tensor(values)
log_probs = self.dist.log_prob(values)
return log_probs.numpy() if self.return_numpy else log_probs
def test_simulate_in_batches(
num_samples,
batch_size,
simulator=linear_gaussian,
prior=BoxUniform(torch.zeros(5), torch.ones(5)),
):
"""Test combinations of num_samples and simulation_batch_size. """
simulate_in_batches(
simulator,
lambda n: prior.sample((n, )),
num_samples,
batch_size,
torch.Size([5]),
)
def process_pytorch_prior(
prior: Distribution) -> Tuple[Distribution, int, bool]:
"""Return PyTorch prior adapted to the requirements for sbi.
Args:
prior: PyTorch distribution prior provided by the user.
Raises:
ValueError: If prior is defined over an unwrapped scalar variable.
Returns:
prior: PyTorch distribution prior.
theta_numel: Number of parameters - elements in a single sample from the prior.
prior_returns_numpy: False.
"""
# Turn off validation of input arguments to allow `log_prob()` on samples outside
# of the support.
prior.set_default_validate_args(False)
# Reject unwrapped scalar priors.
# This will reject Uniform priors with dimension larger than 1.
if prior.sample().ndim == 0:
raise ValueError(
"Detected scalar prior. Please make sure to pass a PyTorch prior with "
"`batch_shape=torch.Size([1])` or `event_shape=torch.Size([1])`.")
# Cast 1D Uniform to BoxUniform to avoid shape error in mdn log prob.
elif isinstance(prior, Uniform) and prior.batch_shape.numel() == 1:
prior = BoxUniform(low=prior.low, high=prior.high)
warnings.warn(
"Casting 1D Uniform prior to BoxUniform to match sbi batch requirements."
)
check_prior_batch_behavior(prior)
check_prior_batch_dims(prior)
if not prior.sample().dtype == float32:
prior = PytorchReturnTypeWrapper(prior,
return_type=float32,
validate_args=False)
# This will fail for float64 priors.
check_prior_return_type(prior)
theta_numel = prior.sample().numel()
return prior, theta_numel, False
def test_train_with_different_data_and_training_device(
inference_method, data_device: str, training_device: str
) -> None:
assert torch.cuda.is_available(), "this test requires that cuda is available."
num_dim = 2
prior_ = BoxUniform(
-torch.ones(num_dim), torch.ones(num_dim), device=training_device
)
simulator, prior = prepare_for_sbi(diagonal_linear_gaussian, prior_)
inference = inference_method(
prior,
**(
dict(classifier="resnet")
if inference_method in [SNRE_A, SNRE_B]
else dict(
density_estimator=(
"mdn_snpe_a" if inference_method == SNPE_A else "maf"
)
)
),
show_progress_bars=False,
device=training_device,
)
theta, x = simulate_for_sbi(simulator, prior, 32)
theta, x = theta.to(data_device), x.to(data_device)
x_o = torch.zeros(x.shape[1])
inference = inference.append_simulations(theta, x)
posterior_estimator = inference.train(max_num_epochs=2)
# Check for default device for inference object
weights_device = next(inference._neural_net.parameters()).device
assert torch.device(training_device) == weights_device
_ = DirectPosterior(
posterior_estimator=posterior_estimator, prior=prior
).set_default_x(x_o)
# Test log prob on batch of thetas.
log_probs = prior.log_prob(theta)
assert isinstance(log_probs, Tensor)
assert log_probs.shape[0] == batch_size
@pytest.mark.parametrize(
"prior",
(
pytest.param(Uniform(0.0, 1.0), marks=pytest.mark.xfail),
pytest.param(Uniform(torch.zeros(3), torch.ones(3)),
marks=pytest.mark.xfail),
pytest.param(Uniform(torch.zeros((1, 3)), torch.ones((1, 3))),
marks=pytest.mark.xfail),
Uniform(torch.zeros(1), torch.ones(1)),
BoxUniform(torch.zeros(3), torch.ones(3)),
MultivariateNormal(torch.zeros(3), torch.eye(3)),
UserNumpyUniform(torch.zeros(3), torch.ones(3), return_numpy=False),
UserNumpyUniform(torch.zeros(3), torch.ones(3), return_numpy=True),
),
)
def test_process_prior(prior):
prior, parameter_dim, numpy_simulator = process_prior(prior)
batch_size = 2
theta = prior.sample((batch_size, ))
assert theta.shape == torch.Size(
(batch_size,
parameter_dim)), "Number of sampled parameters must match batch size."
assert (prior.log_prob(theta).shape[0] == batch_size
return theta.reshape(1, 2, 2)
@pytest.mark.parametrize(
"wrapper, prior",
(
(
CustomPytorchWrapper,
UserNumpyUniform(zeros(3), ones(3), return_numpy=True),
),
(ScipyPytorchWrapper, multivariate_normal()),
(ScipyPytorchWrapper, uniform()),
(ScipyPytorchWrapper, beta(a=1, b=1)),
(
PytorchReturnTypeWrapper,
BoxUniform(zeros(3, dtype=torch.float64),
ones(3, dtype=torch.float64)),
),
),
)
def test_prior_wrappers(wrapper, prior):
"""Test prior wrappers to pytorch distributions."""
prior = wrapper(prior)
# use 2 here to test for minimal case >1
batch_size = 2
theta = prior.sample((batch_size, ))
assert isinstance(theta, Tensor)
assert theta.shape[0] == batch_size
# Test log prob on batch of thetas.
log_probs = prior.log_prob(theta)
def test_training_and_mcmc_on_device(
method,
model,
data_device,
mcmc_method,
training_device,
prior_device,
prior_type="gaussian",
):
"""Test training on devices.
This test does not check training speeds.
"""
num_dim = 2
num_samples = 10
num_simulations = 100
max_num_epochs = 5
x_o = zeros(1, num_dim).to(data_device)
likelihood_shift = -1.0 * ones(num_dim).to(prior_device)
likelihood_cov = 0.3 * eye(num_dim).to(prior_device)
if prior_type == "gaussian":
prior_mean = zeros(num_dim).to(prior_device)
prior_cov = eye(num_dim).to(prior_device)
prior = MultivariateNormal(loc=prior_mean, covariance_matrix=prior_cov)
else:
prior = BoxUniform(
low=-2 * torch.ones(num_dim),
high=2 * torch.ones(num_dim),
device=prior_device,
)
def simulator(theta):
return linear_gaussian(theta, likelihood_shift, likelihood_cov)
training_device = process_device(training_device)
if method in [SNPE_A, SNPE_C]:
kwargs = dict(
density_estimator=utils.posterior_nn(model=model, num_transforms=2)
)
elif method == SNLE:
kwargs = dict(
density_estimator=utils.likelihood_nn(model=model, num_transforms=2)
)
elif method in (SNRE_A, SNRE_B):
kwargs = dict(classifier=utils.classifier_nn(model=model))
else:
raise ValueError()
inferer = method(show_progress_bars=False, device=training_device, **kwargs)
proposals = [prior]
# Test for two rounds.
for _ in range(2):
theta, x = simulate_for_sbi(simulator, proposals[-1], num_simulations)
theta, x = theta.to(data_device), x.to(data_device)
estimator = inferer.append_simulations(theta, x).train(
training_batch_size=100, max_num_epochs=max_num_epochs
)
if method == SNLE:
potential_fn, theta_transform = likelihood_estimator_based_potential(
estimator, prior, x_o
)
elif method == SNPE_A or method == SNPE_C:
potential_fn, theta_transform = posterior_estimator_based_potential(
estimator, prior, x_o
)
elif method == SNRE_A or method == SNRE_B:
potential_fn, theta_transform = ratio_estimator_based_potential(
estimator, prior, x_o
)
else:
raise ValueError
if mcmc_method == "rejection":
posterior = RejectionPosterior(
proposal=prior,
potential_fn=potential_fn,
device=training_device,
)
elif mcmc_method == "direct":
posterior = DirectPosterior(
posterior_estimator=estimator, prior=prior
).set_default_x(x_o)
else:
posterior = MCMCPosterior(
potential_fn=potential_fn,
theta_transform=theta_transform,
proposal=prior,
method=mcmc_method,
device=training_device,
)
proposals.append(posterior)
# Check for default device for inference object
weights_device = next(inferer._neural_net.parameters()).device
assert torch.device(training_device) == weights_device
samples = proposals[-1].sample(sample_shape=(num_samples,))
proposals[-1].potential(samples)
