def test_dynamic_supports():
true_coef = 0.9
data = true_coef + random.normal(random.PRNGKey(0), (1000,))
def actual_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), transforms.AffineTransform(0, alpha)))
numpyro.sample('obs', dist.Normal(loc, 0.1), obs=data)
def expected_model(data):
alpha = numpyro.sample('alpha', dist.Uniform(0, 1))
loc = numpyro.sample('loc', dist.Uniform(0, 1)) * alpha
numpyro.sample('obs', dist.Normal(loc, 0.1), obs=data)
adam = optim.Adam(0.01)
rng_key_init = random.PRNGKey(1)
guide = AutoDiagonalNormal(actual_model)
svi = SVI(actual_model, guide, adam, Trace_ELBO())
svi_state = svi.init(rng_key_init, data)
actual_opt_params = adam.get_params(svi_state.optim_state)
actual_params = svi.get_params(svi_state)
actual_values = guide.median(actual_params)
actual_loss = svi.evaluate(svi_state, data)
guide = AutoDiagonalNormal(expected_model)
svi = SVI(expected_model, guide, adam, Trace_ELBO())
svi_state = svi.init(rng_key_init, data)
expected_opt_params = adam.get_params(svi_state.optim_state)
expected_params = svi.get_params(svi_state)
expected_values = guide.median(expected_params)
expected_loss = svi.evaluate(svi_state, data)
# test auto_loc, auto_scale
check_eq(actual_opt_params, expected_opt_params)
check_eq(actual_params, expected_params)
# test latent values
assert_allclose(actual_values['alpha'], expected_values['alpha'])
assert_allclose(actual_values['loc_base'], expected_values['loc'])
assert_allclose(actual_loss, expected_loss)
def test_subsample_guide(auto_class):
# The model adapted from tutorial/source/easyguide.ipynb
def model(batch, subsample, full_size):
drift = numpyro.sample("drift", dist.LogNormal(-1, 0.5))
with handlers.substitute(data={"data": subsample}):
plate = numpyro.plate("data",
full_size,
subsample_size=len(subsample))
assert plate.size == 50
def transition_fn(z_prev, y_curr):
with plate:
z_curr = numpyro.sample("state", dist.Normal(z_prev, drift))
y_curr = numpyro.sample("obs",
dist.Bernoulli(logits=z_curr),
obs=y_curr)
return z_curr, y_curr
_, result = scan(transition_fn,
jnp.zeros(len(subsample)),
batch,
length=num_time_steps)
return result
def create_plates(batch, subsample, full_size):
with handlers.substitute(data={"data": subsample}):
return numpyro.plate("data",
full_size,
subsample_size=subsample.shape[0])
guide = auto_class(model, create_plates=create_plates)
full_size = 50
batch_size = 20
num_time_steps = 8
with handlers.seed(rng_seed=0):
data = model(None, jnp.arange(full_size), full_size)
assert data.shape == (num_time_steps, full_size)
svi = SVI(model, guide, optim.Adam(0.02), Trace_ELBO())
svi_state = svi.init(random.PRNGKey(0),
data[:, :batch_size],
jnp.arange(batch_size),
full_size=full_size)
update_fn = jit(svi.update, static_argnums=(3, ))
for epoch in range(2):
beg = 0
while beg < full_size:
end = min(full_size, beg + batch_size)
subsample = jnp.arange(beg, end)
batch = data[:, beg:end]
beg = end
svi_state, loss = update_fn(svi_state, batch, subsample, full_size)
def test_tracegraph_normal_normal():
# normal-normal; known covariance
lam0 = jnp.array([0.1, 0.1]) # precision of prior
loc0 = jnp.array([0.0, 0.5]) # prior mean
# known precision of observation noise
lam = jnp.array([6.0, 4.0])
data = []
data.append(jnp.array([-0.1, 0.3]))
data.append(jnp.array([0.0, 0.4]))
data.append(jnp.array([0.2, 0.5]))
data.append(jnp.array([0.1, 0.7]))
n_data = len(data)
sum_data = data[0] + data[1] + data[2] + data[3]
analytic_lam_n = lam0 + n_data * lam
analytic_log_sig_n = -0.5 * jnp.log(analytic_lam_n)
analytic_loc_n = sum_data * (lam / analytic_lam_n) + loc0 * (
lam0 / analytic_lam_n)
class FakeNormal(dist.Normal):
reparametrized_params = []
def model():
with numpyro.plate("plate", 2):
loc_latent = numpyro.sample(
"loc_latent", FakeNormal(loc0, jnp.power(lam0, -0.5)))
for i, x in enumerate(data):
numpyro.sample(
"obs_{}".format(i),
dist.Normal(loc_latent, jnp.power(lam, -0.5)),
obs=x,
)
return loc_latent
def guide():
loc_q = numpyro.param("loc_q",
analytic_loc_n + jnp.array([0.334, 0.334]))
log_sig_q = numpyro.param(
"log_sig_q", analytic_log_sig_n + jnp.array([-0.29, -0.29]))
sig_q = jnp.exp(log_sig_q)
with numpyro.plate("plate", 2):
loc_latent = numpyro.sample("loc_latent", FakeNormal(loc_q, sig_q))
return loc_latent
adam = optim.Adam(step_size=0.0015, b1=0.97, b2=0.999)
svi = SVI(model, guide, adam, loss=TraceGraph_ELBO())
svi_result = svi.run(jax.random.PRNGKey(0), 5000)
loc_error = jnp.sum(
jnp.power(analytic_loc_n - svi_result.params["loc_q"], 2.0))
log_sig_error = jnp.sum(
jnp.power(analytic_log_sig_n - svi_result.params["log_sig_q"], 2.0))
assert_allclose(loc_error, 0, atol=0.05)
assert_allclose(log_sig_error, 0, atol=0.05)
def test_neutra_reparam_unobserved_model():
model = dirichlet_categorical
data = jnp.ones(10, dtype=jnp.int32)
guide = AutoIAFNormal(model)
svi = SVI(model, guide, Adam(1e-3), Trace_ELBO())
svi_state = svi.init(random.PRNGKey(0), data)
params = svi.get_params(svi_state)
neutra = NeuTraReparam(guide, params)
reparam_model = neutra.reparam(model)
with handlers.seed(rng_seed=0):
reparam_model(data=None)
def test_plate_inconsistent(size, dim):
def model():
with numpyro.plate("a", 10, dim=-1):
numpyro.sample("x", dist.Normal(0, 1))
with numpyro.plate("a", size, dim=dim):
numpyro.sample("y", dist.Normal(0, 1))
guide = AutoDelta(model)
svi = SVI(model, guide, numpyro.optim.Adam(step_size=0.1), Trace_ELBO())
with pytest.raises(AssertionError, match="has inconsistent dim or size"):
svi.run(random.PRNGKey(0), 10)
def test_subsample_model_with_deterministic():
def model():
x = numpyro.sample("x", dist.Normal(0, 1))
numpyro.deterministic("x2", x * 2)
with numpyro.plate("N", 10, subsample_size=5):
numpyro.sample("obs", dist.Normal(x, 1), obs=jnp.ones(5))
guide = AutoNormal(model)
svi = SVI(model, guide, optim.Adam(1.0), Trace_ELBO())
svi_result = svi.run(random.PRNGKey(0), 10)
samples = guide.sample_posterior(random.PRNGKey(1), svi_result.params)
assert "x2" in samples
def test_svi_discrete_latent():
def model():
numpyro.sample("x", dist.Bernoulli(0.5))
def guide():
probs = numpyro.param("probs", 0.2)
numpyro.sample("x", dist.Bernoulli(probs))
svi = SVI(model, guide, optim.Adam(1), Trace_ELBO())
with pytest.warns(UserWarning,
match="SVI does not support models with discrete"):
svi.run(random.PRNGKey(0), 10)
def run_svi(model, guide_family, args, X, Y):
if guide_family == "AutoDelta":
guide = autoguide.AutoDelta(model)
elif guide_family == "AutoDiagonalNormal":
guide = autoguide.AutoDiagonalNormal(model)
optimizer = numpyro.optim.Adam(0.001)
svi = SVI(model, guide, optimizer, Trace_ELBO())
svi_results = svi.run(PRNGKey(1), args.maxiter, X=X, Y=Y)
params = svi_results.params
return params, guide
def test_stable_run(stable_run):
def model():
var = numpyro.sample("var", dist.Exponential(1))
numpyro.sample("obs", dist.Normal(0, jnp.sqrt(var)), obs=0.0)
def guide():
loc = numpyro.param("loc", 0.0)
numpyro.sample("var", dist.Normal(loc, 10))
svi = SVI(model, guide, optim.Adam(1), Trace_ELBO())
svi_result = svi.run(random.PRNGKey(0), 1000, stable_update=stable_run)
assert jnp.isfinite(svi_result.params["loc"]) == stable_run
def test_iaf():
# test for substitute logic for exposed methods `sample_posterior` and `get_transforms`
N, dim = 3000, 3
data = random.normal(random.PRNGKey(0), (N, dim))
true_coefs = jnp.arange(1.0, dim + 1.0)
logits = jnp.sum(true_coefs * data, axis=-1)
labels = dist.Bernoulli(logits=logits).sample(random.PRNGKey(1))
def model(data, labels):
coefs = numpyro.sample("coefs", dist.Normal(jnp.zeros(dim), jnp.ones(dim)))
offset = numpyro.sample("offset", dist.Uniform(-1, 1))
logits = offset + jnp.sum(coefs * data, axis=-1)
return numpyro.sample("obs", dist.Bernoulli(logits=logits), obs=labels)
adam = optim.Adam(0.01)
rng_key_init = random.PRNGKey(1)
guide = AutoIAFNormal(model)
svi = SVI(model, guide, adam, Trace_ELBO())
svi_state = svi.init(rng_key_init, data, labels)
params = svi.get_params(svi_state)
x = random.normal(random.PRNGKey(0), (dim + 1,))
rng_key = random.PRNGKey(1)
actual_sample = guide.sample_posterior(rng_key, params)
actual_output = guide._unpack_latent(guide.get_transform(params)(x))
flows = []
for i in range(guide.num_flows):
if i > 0:
flows.append(transforms.PermuteTransform(jnp.arange(dim + 1)[::-1]))
arn_init, arn_apply = AutoregressiveNN(
dim + 1,
[dim + 1, dim + 1],
permutation=jnp.arange(dim + 1),
skip_connections=guide._skip_connections,
nonlinearity=guide._nonlinearity,
)
arn = partial(arn_apply, params["auto_arn__{}$params".format(i)])
flows.append(InverseAutoregressiveTransform(arn))
flows.append(guide._unpack_latent)
transform = transforms.ComposeTransform(flows)
_, rng_key_sample = random.split(rng_key)
expected_sample = transform(
dist.Normal(jnp.zeros(dim + 1), 1).sample(rng_key_sample)
)
expected_output = transform(x)
assert_allclose(actual_sample["coefs"], expected_sample["coefs"])
assert_allclose(
actual_sample["offset"],
transforms.biject_to(constraints.interval(-1, 1))(expected_sample["offset"]),
)
check_eq(actual_output, expected_output)
def svi(model, guide, num_steps, lr, rng_key, X, Y):
"""
Helper function for doing SVI inference.
"""
svi = SVI(model, guide, optim.Adam(lr), ELBO(num_particles=1), X=X, Y=Y)
svi_state = svi.init(rng_key)
print('Optimizing...')
state, loss = lax.scan(lambda x, i: svi.update(x), svi_state,
np.zeros(num_steps))
return loss, svi.get_params(state)
def test_logistic_regression(auto_class, Elbo):
N, dim = 3000, 3
data = random.normal(random.PRNGKey(0), (N, dim))
true_coefs = jnp.arange(1.0, dim + 1.0)
logits = jnp.sum(true_coefs * data, axis=-1)
labels = dist.Bernoulli(logits=logits).sample(random.PRNGKey(1))
def model(data, labels):
coefs = numpyro.sample("coefs",
dist.Normal(0, 1).expand([dim]).to_event())
logits = numpyro.deterministic("logits", jnp.sum(coefs * data,
axis=-1))
with numpyro.plate("N", len(data)):
return numpyro.sample("obs",
dist.Bernoulli(logits=logits),
obs=labels)
adam = optim.Adam(0.01)
rng_key_init = random.PRNGKey(1)
guide = auto_class(model, init_loc_fn=init_strategy)
svi = SVI(model, guide, adam, Elbo())
svi_state = svi.init(rng_key_init, data, labels)
# smoke test if analytic KL is used
if auto_class is AutoNormal and Elbo is TraceMeanField_ELBO:
_, mean_field_loss = svi.update(svi_state, data, labels)
svi.loss = Trace_ELBO()
_, elbo_loss = svi.update(svi_state, data, labels)
svi.loss = TraceMeanField_ELBO()
assert abs(mean_field_loss - elbo_loss) > 0.5
def body_fn(i, val):
svi_state, loss = svi.update(val, data, labels)
return svi_state
svi_state = fori_loop(0, 2000, body_fn, svi_state)
params = svi.get_params(svi_state)
if auto_class not in (AutoDAIS, AutoIAFNormal, AutoBNAFNormal):
median = guide.median(params)
assert_allclose(median["coefs"], true_coefs, rtol=0.1)
# test .quantile method
if auto_class is not AutoDelta:
median = guide.quantiles(params, [0.2, 0.5])
assert_allclose(median["coefs"][1], true_coefs, rtol=0.1)
# test .sample_posterior method
posterior_samples = guide.sample_posterior(random.PRNGKey(1),
params,
sample_shape=(1000, ))
expected_coefs = jnp.array([0.97, 2.05, 3.18])
assert_allclose(jnp.mean(posterior_samples["coefs"], 0),
expected_coefs,
rtol=0.1)
def test_beta_bernoulli(auto_class):
data = jnp.array([[1.0] * 8 + [0.0] * 2, [1.0] * 4 + [0.0] * 6]).T
N = len(data)
def model(data):
f = numpyro.sample("beta",
dist.Beta(jnp.ones(2), jnp.ones(2)).to_event())
with numpyro.plate("N", N):
numpyro.sample("obs", dist.Bernoulli(f).to_event(1), obs=data)
adam = optim.Adam(0.01)
if auto_class == AutoDAIS:
guide = auto_class(model,
init_loc_fn=init_strategy,
base_dist="cholesky")
else:
guide = auto_class(model, init_loc_fn=init_strategy)
svi = SVI(model, guide, adam, Trace_ELBO())
svi_state = svi.init(random.PRNGKey(1), data)
def body_fn(i, val):
svi_state, loss = svi.update(val, data)
return svi_state
svi_state = fori_loop(0, 3000, body_fn, svi_state)
params = svi.get_params(svi_state)
true_coefs = (jnp.sum(data, axis=0) + 1) / (data.shape[0] + 2)
# test .sample_posterior method
posterior_samples = guide.sample_posterior(random.PRNGKey(1),
params,
sample_shape=(1000, ))
posterior_mean = jnp.mean(posterior_samples["beta"], 0)
assert_allclose(posterior_mean, true_coefs, atol=0.05)
if auto_class not in [AutoDAIS, AutoDelta, AutoIAFNormal, AutoBNAFNormal]:
quantiles = guide.quantiles(params, [0.2, 0.5, 0.8])
assert quantiles["beta"].shape == (3, 2)
# Predictive can be instantiated from posterior samples...
predictive = Predictive(model, posterior_samples=posterior_samples)
predictive_samples = predictive(random.PRNGKey(1), None)
assert predictive_samples["obs"].shape == (1000, N, 2)
# ... or from the guide + params
predictive = Predictive(model,
guide=guide,
params=params,
num_samples=1000)
predictive_samples = predictive(random.PRNGKey(1), None)
assert predictive_samples["obs"].shape == (1000, N, 2)
def test_autodais_subsampling_error():
data = jnp.array([1.0] * 8 + [0.0] * 2)
def model(data):
f = numpyro.sample("beta", dist.Beta(1, 1))
with numpyro.plate("plate", 20, 10, dim=-1):
numpyro.sample("obs", dist.Bernoulli(f), obs=data)
adam = optim.Adam(0.01)
guide = AutoDAIS(model)
svi = SVI(model, guide, adam, Trace_ELBO())
with pytest.raises(NotImplementedError, match=".*data subsampling.*"):
svi.init(random.PRNGKey(1), data)
def test_laplace_approximation_custom_hessian():
def model(x, y):
a = numpyro.sample("a", dist.Normal(0, 10))
b = numpyro.sample("b", dist.Normal(0, 10))
mu = a + b * x
numpyro.sample("y", dist.Normal(mu, 1), obs=y)
x = random.normal(random.PRNGKey(0), (100, ))
y = 1 + 2 * x
guide = AutoLaplaceApproximation(
model, hessian_fn=lambda f, x: jacobian(jacobian(f))(x))
svi = SVI(model, guide, optim.Adam(0.1), Trace_ELBO(), x=x, y=y)
svi_result = svi.run(random.PRNGKey(0), 10000, progress_bar=False)
guide.get_transform(svi_result.params)
def init_svi(self, X: DeviceArray, *, lr: float, **kwargs):
"""Initialize the SVI state
Args:
X: input data
lr: learning rate
kwargs: other keyword arguments for optimizer
"""
self.optim = self.optim_builder(lr, **kwargs)
self.svi = SVI(self.model, self.guide, self.optim, self.loss)
svi_state = self.svi.init(self.rng_key, X)
if self.svi_state is None:
self.svi_state = svi_state
return self
def test_improper():
y = random.normal(random.PRNGKey(0), (100,))
def model(y):
lambda1 = numpyro.sample('lambda1', dist.ImproperUniform(dist.constraints.real, (), ()))
lambda2 = numpyro.sample('lambda2', dist.ImproperUniform(dist.constraints.real, (), ()))
sigma = numpyro.sample('sigma', dist.ImproperUniform(dist.constraints.positive, (), ()))
mu = numpyro.deterministic('mu', lambda1 + lambda2)
numpyro.sample('y', dist.Normal(mu, sigma), obs=y)
guide = AutoDiagonalNormal(model)
svi = SVI(model, guide, optim.Adam(0.003), Trace_ELBO(), y=y)
svi_state = svi.init(random.PRNGKey(2))
lax.scan(lambda state, i: svi.update(state), svi_state, jnp.zeros(10000))
def test_module():
x = random.normal(random.PRNGKey(0), (100, 10))
y = random.normal(random.PRNGKey(1), (100,))
def model(x, y):
nn = numpyro.module("nn", Dense(1), (10,))
mu = nn(x).squeeze(-1)
sigma = numpyro.sample("sigma", dist.HalfNormal(1))
numpyro.sample("y", dist.Normal(mu, sigma), obs=y)
guide = AutoDiagonalNormal(model)
svi = SVI(model, guide, optim.Adam(0.003), Trace_ELBO(), x=x, y=y)
svi_state = svi.init(random.PRNGKey(2))
lax.scan(lambda state, i: svi.update(state), svi_state, jnp.zeros(1000))
def test_reparam_log_joint(model, kwargs):
guide = AutoIAFNormal(model)
svi = SVI(model, guide, Adam(1e-10), Trace_ELBO(), **kwargs)
svi_state = svi.init(random.PRNGKey(0))
params = svi.get_params(svi_state)
neutra = NeuTraReparam(guide, params)
reparam_model = neutra.reparam(model)
_, pe_fn, _, _ = initialize_model(random.PRNGKey(1), model, model_kwargs=kwargs)
init_params, pe_fn_neutra, _, _ = initialize_model(random.PRNGKey(2), reparam_model, model_kwargs=kwargs)
latent_x = list(init_params[0].values())[0]
pe_transformed = pe_fn_neutra(init_params[0])
latent_y = neutra.transform(latent_x)
log_det_jacobian = neutra.transform.log_abs_det_jacobian(latent_x, latent_y)
pe = pe_fn(guide._unpack_latent(latent_y))
assert_allclose(pe_transformed, pe - log_det_jacobian)
def test_collapse_beta_binomial():
total_count = 10
data = 3.
def model1():
c1 = numpyro.param("c1", 0.5, constraint=dist.constraints.positive)
c0 = numpyro.param("c0", 1.5, constraint=dist.constraints.positive)
with handlers.collapse():
probs = numpyro.sample("probs", dist.Beta(c1, c0))
numpyro.sample("obs", dist.Binomial(total_count, probs), obs=data)
def model2():
c1 = numpyro.param("c1", 0.5, constraint=dist.constraints.positive)
c0 = numpyro.param("c0", 1.5, constraint=dist.constraints.positive)
numpyro.sample("obs", dist.BetaBinomial(c1, c0, total_count), obs=data)
trace1 = handlers.trace(model1).get_trace()
trace2 = handlers.trace(model2).get_trace()
assert "probs" in trace1
assert "obs" not in trace1
assert "probs" not in trace2
assert "obs" in trace2
svi1 = SVI(model1, lambda: None, numpyro.optim.Adam(1), Trace_ELBO())
svi2 = SVI(model2, lambda: None, numpyro.optim.Adam(1), Trace_ELBO())
svi_state1 = svi1.init(random.PRNGKey(0))
svi_state2 = svi2.init(random.PRNGKey(0))
params1 = svi1.get_params(svi_state1)
params2 = svi2.get_params(svi_state2)
assert_allclose(params1["c1"], params2["c1"])
assert_allclose(params1["c0"], params2["c0"])
params1 = svi1.get_params(svi1.update(svi_state1)[0])
params2 = svi2.get_params(svi2.update(svi_state2)[0])
assert_allclose(params1["c1"], params2["c1"])
assert_allclose(params1["c0"], params2["c0"])
def test_laplace_approximation_warning():
def model(x, y):
a = numpyro.sample("a", dist.Normal(0, 10))
b = numpyro.sample("b", dist.Normal(0, 10), sample_shape=(3,))
mu = a + b[0] * x + b[1] * x ** 2 + b[2] * x ** 3
numpyro.sample("y", dist.Normal(mu, 0.001), obs=y)
x = random.normal(random.PRNGKey(0), (3,))
y = 1 + 2 * x + 3 * x ** 2 + 4 * x ** 3
guide = AutoLaplaceApproximation(model)
svi = SVI(model, guide, optim.Adam(0.1), Trace_ELBO(), x=x, y=y)
init_state = svi.init(random.PRNGKey(0))
svi_state = fori_loop(0, 10000, lambda i, val: svi.update(val)[0], init_state)
params = svi.get_params(svi_state)
with pytest.warns(UserWarning, match="Hessian of log posterior"):
guide.sample_posterior(random.PRNGKey(1), params)
def test_logistic_regression(auto_class, Elbo):
N, dim = 3000, 3
data = random.normal(random.PRNGKey(0), (N, dim))
true_coefs = jnp.arange(1., dim + 1.)
logits = jnp.sum(true_coefs * data, axis=-1)
labels = dist.Bernoulli(logits=logits).sample(random.PRNGKey(1))
def model(data, labels):
coefs = numpyro.sample('coefs',
dist.Normal(jnp.zeros(dim), jnp.ones(dim)))
logits = jnp.sum(coefs * data, axis=-1)
return numpyro.sample('obs', dist.Bernoulli(logits=logits), obs=labels)
adam = optim.Adam(0.01)
rng_key_init = random.PRNGKey(1)
guide = auto_class(model, init_loc_fn=init_strategy)
svi = SVI(model, guide, adam, Elbo())
svi_state = svi.init(rng_key_init, data, labels)
# smoke test if analytic KL is used
if auto_class is AutoNormal and Elbo is TraceMeanField_ELBO:
_, mean_field_loss = svi.update(svi_state, data, labels)
svi.loss = Trace_ELBO()
_, elbo_loss = svi.update(svi_state, data, labels)
svi.loss = TraceMeanField_ELBO()
assert abs(mean_field_loss - elbo_loss) > 0.5
def body_fn(i, val):
svi_state, loss = svi.update(val, data, labels)
return svi_state
svi_state = fori_loop(0, 2000, body_fn, svi_state)
params = svi.get_params(svi_state)
if auto_class not in (AutoIAFNormal, AutoBNAFNormal):
median = guide.median(params)
assert_allclose(median['coefs'], true_coefs, rtol=0.1)
# test .quantile method
median = guide.quantiles(params, [0.2, 0.5])
assert_allclose(median['coefs'][1], true_coefs, rtol=0.1)
# test .sample_posterior method
posterior_samples = guide.sample_posterior(random.PRNGKey(1),
params,
sample_shape=(1000, ))
assert_allclose(jnp.mean(posterior_samples['coefs'], 0),
true_coefs,
rtol=0.1)
def run_svi_inference(model, guide, rng_key, X, Y, optimizer, n_epochs=1_000):
# initialize svi
svi = SVI(model, guide, optimizer, loss=Trace_ELBO())
# initialize state
init_state = svi.init(rng_key, X, Y.squeeze())
# Run optimizer for 1000 iteratons.
state, losses = jax.lax.scan(
lambda state, i: svi.update(state, X, Y.squeeze()), init_state, n_epochs
)
# Extract surrogate posterior.
params = svi.get_params(state)
return params
def test_collapse_beta_bernoulli():
data = 0.
def model():
c = numpyro.sample("c", dist.Gamma(1, 1))
with handlers.collapse():
probs = numpyro.sample("probs", dist.Beta(c, 2))
numpyro.sample("obs", dist.Bernoulli(probs), obs=data)
def guide():
a = numpyro.param("a", 1., constraint=constraints.positive)
b = numpyro.param("b", 1., constraint=constraints.positive)
numpyro.sample("c", dist.Gamma(a, b))
svi = SVI(model, guide, numpyro.optim.Adam(1), Trace_ELBO())
svi_state = svi.init(random.PRNGKey(0))
svi.update(svi_state)
def main(_args):
data = generate_data()
init_rng_key = PRNGKey(1273)
# nuts = NUTS(gmm)
# mcmc = MCMC(nuts, 100, 1000)
# mcmc.print_summary()
seeded_gmm = seed(gmm, init_rng_key)
model_trace = trace(seeded_gmm).get_trace(data)
max_plate_nesting = _guess_max_plate_nesting(model_trace)
enum_gmm = enum(config_enumerate(gmm), - max_plate_nesting - 1)
svi = SVI(enum_gmm, gmm_guide, Adam(0.1), RenyiELBO(-10.))
svi_state = svi.init(init_rng_key, data)
upd_fun = jax.jit(svi.update)
with tqdm.trange(100_000) as pbar:
for i in pbar:
svi_state, loss = upd_fun(svi_state, data)
pbar.set_description(f"SVI {loss}", True)
def test_pickle_autoguide(guide_class):
x = np.random.poisson(1.0, size=(100,))
guide = guide_class(poisson_regression)
optim = numpyro.optim.Adam(1e-2)
svi = SVI(poisson_regression, guide, optim, numpyro.infer.Trace_ELBO())
svi_result = svi.run(random.PRNGKey(1), 3, x, len(x))
pickled_guide = pickle.loads(pickle.dumps(guide))
predictive = Predictive(
poisson_regression,
guide=pickled_guide,
params=svi_result.params,
num_samples=1,
return_sites=["param", "x"],
)
samples = predictive(random.PRNGKey(1), None, 1)
assert set(samples.keys()) == {"param", "x"}
def test_autoguide(deterministic):
GLOBAL["count"] = 0
guide = AutoDiagonalNormal(model)
svi = SVI(model,
guide,
optim.Adam(0.1),
Trace_ELBO(),
deterministic=deterministic)
svi_state = svi.init(random.PRNGKey(0))
svi_state = lax.fori_loop(0, 100, lambda i, val: svi.update(val)[0],
svi_state)
params = svi.get_params(svi_state)
guide.sample_posterior(random.PRNGKey(1), params, sample_shape=(100, ))
if deterministic:
assert GLOBAL["count"] == 5
else:
assert GLOBAL["count"] == 4
def test_collapse_beta_binomial_plate():
data = np.array([0., 1., 5., 5.])
def model():
c = numpyro.sample("c", dist.Gamma(1, 1))
with handlers.collapse():
probs = numpyro.sample("probs", dist.Beta(c, 2))
with numpyro.plate("plate", len(data)):
numpyro.sample("obs", dist.Binomial(10, probs), obs=data)
def guide():
a = numpyro.param("a", 1., constraint=constraints.positive)
b = numpyro.param("b", 1., constraint=constraints.positive)
numpyro.sample("c", dist.Gamma(a, b))
svi = SVI(model, guide, numpyro.optim.Adam(1), Trace_ELBO())
svi_state = svi.init(random.PRNGKey(0))
svi.update(svi_state)
def test_run(progress_bar):
data = jnp.array([1.0] * 8 + [0.0] * 2)
def model(data):
f = numpyro.sample("beta", dist.Beta(1., 1.))
numpyro.sample("obs", dist.Bernoulli(f), obs=data)
def guide(data):
alpha_q = numpyro.param("alpha_q", lambda key: random.normal(key),
constraint=constraints.positive)
beta_q = numpyro.param("beta_q", lambda key: random.exponential(key),
constraint=constraints.positive)
numpyro.sample("beta", dist.Beta(alpha_q, beta_q))
svi = SVI(model, guide, optim.Adam(0.05), Trace_ELBO())
params, losses = svi.run(random.PRNGKey(1), 1000, data, progress_bar=progress_bar)
assert losses.shape == (1000,)
assert_allclose(params['alpha_q'] / (params['alpha_q'] + params['beta_q']), 0.8, atol=0.05, rtol=0.05)
def fit_advi(model, num_iter, learning_rate=0.01, seed=0):
"""Automatic Differentiation Variational Inference using a Normal variational distribution
with a diagonal covariance matrix.
"""
rng_key = random.PRNGKey(seed)
adam = Adam(learning_rate)
# Automatically create a variational distribution (aka "guide" in Pyro's terminology)
guide = AutoDiagonalNormal(model)
svi = SVI(model, guide, adam, AutoContinuousELBO())
svi_state = svi.init(rng_key)
# Run optimization
last_state, losses = lax.scan(lambda state, i: svi.update(state),
svi_state, np.zeros(num_iter))
results = ADVIResults(svi=svi,
guide=guide,
state=last_state,
losses=losses)
return results