def test_unnormalized_normal_chain(kernel, kwargs, num_chains):
from numpyro.contrib.tfp import mcmc
# TODO: remove when this issue is fixed upstream
# https://github.com/tensorflow/probability/pull/1087
if num_chains == 2 and kernel == "ReplicaExchangeMC":
pytest.xfail(
"ReplicaExchangeMC is not fully compatible with omnistaging yet.")
kernel_class = getattr(mcmc, kernel)
true_mean, true_std = 1., 0.5
warmup_steps, num_samples = (1000, 8000)
def potential_fn(z):
return 0.5 * ((z - true_mean) / true_std)**2
init_params = jnp.array(0.) if num_chains == 1 else jnp.array([0., 2.])
tfp_kernel = kernel_class(potential_fn=potential_fn, **kwargs)
mcmc = MCMC(tfp_kernel,
warmup_steps,
num_samples,
num_chains=num_chains,
progress_bar=False)
mcmc.run(random.PRNGKey(0), init_params=init_params)
mcmc.print_summary()
hmc_states = mcmc.get_samples()
assert_allclose(jnp.mean(hmc_states), true_mean, rtol=0.07)
assert_allclose(jnp.std(hmc_states), true_std, rtol=0.07)
def test_mcmc_kernels(kernel, kwargs):
from numpyro.contrib.tfp import mcmc
kernel_class = getattr(mcmc, kernel)
true_coef = 0.9
num_warmup, num_samples = 1000, 1000
def model(data):
alpha = numpyro.sample('alpha', dist.Uniform(0, 1))
with numpyro.handlers.reparam(config={'loc': TransformReparam()}):
loc = numpyro.sample(
'loc',
dist.TransformedDistribution(dist.Uniform(0, 1),
AffineTransform(0, alpha)))
numpyro.sample('obs', dist.Normal(loc, 0.1), obs=data)
data = true_coef + random.normal(random.PRNGKey(0), (1000, ))
tfp_kernel = kernel_class(model=model, **kwargs)
mcmc = MCMC(tfp_kernel, num_warmup=num_warmup, num_samples=num_samples)
mcmc.warmup(random.PRNGKey(2), data, collect_warmup=True)
warmup_samples = mcmc.get_samples()
mcmc.run(random.PRNGKey(3), data)
samples = mcmc.get_samples()
assert len(warmup_samples['loc']) == num_warmup
assert len(samples['loc']) == num_samples
assert_allclose(jnp.mean(samples['loc'], 0), true_coef, atol=0.05)
def test_mcmc_kernels(kernel, kwargs):
from numpyro.contrib.tfp import mcmc
if ("CI" in os.environ) and kernel == "SliceSampler":
# TODO: Look into this issue if some users are using SliceSampler
# with NumPyro model.
pytest.skip("SliceSampler freezes CI for unknown reason.")
kernel_class = getattr(mcmc, kernel)
true_coef = 0.9
num_warmup, num_samples = 1000, 1000
def model(data):
alpha = numpyro.sample("alpha", dist.Uniform(0, 1))
with numpyro.handlers.reparam(config={"loc": TransformReparam()}):
loc = numpyro.sample(
"loc",
dist.TransformedDistribution(dist.Uniform(0, 1),
AffineTransform(0, alpha)),
)
numpyro.sample("obs", dist.Normal(loc, 0.1), obs=data)
data = true_coef + random.normal(random.PRNGKey(0), (1000, ))
tfp_kernel = kernel_class(model=model, **kwargs)
mcmc = MCMC(tfp_kernel, num_warmup=num_warmup, num_samples=num_samples)
mcmc.warmup(random.PRNGKey(2), data, collect_warmup=True)
warmup_samples = mcmc.get_samples()
mcmc.run(random.PRNGKey(3), data)
samples = mcmc.get_samples()
assert len(warmup_samples["loc"]) == num_warmup
assert len(samples["loc"]) == num_samples
assert_allclose(jnp.mean(samples["loc"], 0), true_coef, atol=0.05)
def test_mcmc_unwrapped_tfp_distributions():
from tensorflow_probability.substrates.jax import distributions as tfd
def model(y):
theta = numpyro.sample("p", tfd.Beta(1, 1))
with numpyro.plate("plate", y.size):
numpyro.sample("y", tfd.Bernoulli(probs=theta), obs=y)
mcmc = MCMC(NUTS(model), num_warmup=1000, num_samples=1000)
mcmc.run(random.PRNGKey(0), jnp.array([0, 0, 1, 1, 1]))
samples = mcmc.get_samples()
assert_allclose(jnp.mean(samples["p"]), 4 / 7, atol=0.05)