def test_trace_handler(model, backend):
with pyro_backend(backend), handlers.seed(
rng_seed=2), xfail_if_not_implemented():
f = MODELS[model]()
model, model_args, model_kwargs = f['model'], f.get(
'model_args', ()), f.get('model_kwargs', {})
# should be implemented
handlers.trace(model).get_trace(*model_args, **model_kwargs)
def test_constraints(backend, jit):
data = torch.tensor(0.5)
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
steps = 2
assert_ok(constrained_model, guide_constrained_model, elbo, steps, data)
def test_mcmc_interface(model, backend):
with pyro_backend(backend), handlers.seed(rng_seed=20):
f = MODELS[model]()
model, args, kwargs = f['model'], f.get('model_args',
()), f.get('model_kwargs', {})
nuts_kernel = infer.NUTS(model=model)
mcmc = infer.MCMC(nuts_kernel, num_samples=10, warmup_steps=10)
mcmc.run(*args, **kwargs)
mcmc.summary()
def test_generate_data(backend):
def model(data=None):
loc = pyro.param("loc", torch.tensor(2.0))
scale = pyro.param("scale", torch.tensor(1.0))
x = pyro.sample("x", dist.Normal(loc, scale), obs=data)
return x
with pyro_backend(backend):
data = model().data
assert data.shape == ()
def elbo_test_case(backend, jit, expected_elbo, data, steps=None):
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
if steps:
assert_ok(constrained_model, guide_constrained_model, elbo, steps, data)
if backend == "pyro":
# TODO: this is a difference between the two implementations
elbo = elbo.loss
assert elbo(constrained_model, guide_constrained_model, data) == approx(expected_elbo, rel=0.1)
def test_rng_seed(model, backend):
with pyro_backend(backend), handlers.seed(
rng_seed=2), xfail_if_not_implemented():
f = MODELS[model]()
model, model_args = f['model'], f.get('model_args', ())
with handlers.seed(rng_seed=0):
expected = model(*model_args)
if expected is None:
pytest.skip()
with handlers.seed(rng_seed=0):
actual = model(*model_args)
assert ops.allclose(actual, expected)
def test_nonempty_model_empty_guide_ok(backend, jit):
def model(data):
loc = pyro.param("loc", torch.tensor(0.0))
pyro.sample("x", dist.Normal(loc, 1.), obs=data)
def guide(data):
pass
data = torch.tensor(2.)
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
assert_ok(model, guide, elbo, data)
def test_mean_field_warn(backend):
def model():
x = pyro.sample("x", dist.Normal(0., 1.))
pyro.sample("y", dist.Normal(x, 1.))
def guide():
loc = pyro.param("loc", torch.tensor(0.))
y = pyro.sample("y", dist.Normal(loc, 1.))
pyro.sample("x", dist.Normal(y, 1.))
with pyro_backend(backend):
elbo = infer.TraceMeanField_ELBO()
assert_warning(model, guide, elbo)
def test_gaussian_probit_hmm_smoke(exact, jit):
def model(data):
T, N, D = data.shape # time steps, individuals, features
# Gaussian initial distribution.
init_loc = pyro.param("init_loc", torch.zeros(D))
init_scale = pyro.param("init_scale",
1e-2 * torch.eye(D),
constraint=constraints.lower_cholesky)
# Linear dynamics with Gaussian noise.
trans_const = pyro.param("trans_const", torch.zeros(D))
trans_coeff = pyro.param("trans_coeff", torch.eye(D))
noise = pyro.param("noise",
1e-2 * torch.eye(D),
constraint=constraints.lower_cholesky)
obs_plate = pyro.plate("channel", D, dim=-1)
with pyro.plate("data", N, dim=-2):
state = None
for t in range(T):
# Transition.
if t == 0:
loc = init_loc
scale_tril = init_scale
else:
loc = trans_const + funsor.torch.torch_tensordot(
trans_coeff, state, 1)
scale_tril = noise
state = pyro.sample("state_{}".format(t),
dist.MultivariateNormal(loc, scale_tril),
infer={"exact": exact})
# Factorial probit likelihood model.
with obs_plate:
pyro.sample("obs_{}".format(t),
dist.Bernoulli(logits=state["channel"]),
obs=data[t])
def guide(data):
pass
data = torch.distributions.Bernoulli(0.5).sample((3, 4, 2))
with pyro_backend("funsor"):
Elbo = infer.JitTraceEnum_ELBO if jit else infer.TraceEnum_ELBO
elbo = Elbo()
adam = optim.Adam({"lr": 1e-3})
svi = infer.SVI(model, guide, adam, elbo)
svi.step(data)
def main(args):
# Define a basic model with a single Normal latent random variable `loc`
# and a batch of Normally distributed observations.
def model(data):
loc = pyro.sample("loc", dist.Normal(0., 1.))
with pyro.plate("data", len(data), dim=-1):
pyro.sample("obs", dist.Normal(loc, 1.), obs=data)
# Define a guide (i.e. variational distribution) with a Normal
# distribution over the latent random variable `loc`.
def guide(data):
guide_loc = pyro.param("guide_loc", torch.tensor(0.))
guide_scale = pyro.param("guide_scale",
torch.tensor(1.),
constraint=constraints.positive)
pyro.sample("loc", dist.Normal(guide_loc, guide_scale))
# Generate some data.
torch.manual_seed(0)
data = torch.randn(100) + 3.0
# Because the API in minipyro matches that of Pyro proper,
# training code works with generic Pyro implementations.
with pyro_backend(args.backend), interpretation(monte_carlo):
# Construct an SVI object so we can do variational inference on our
# model/guide pair.
Elbo = infer.JitTrace_ELBO if args.jit else infer.Trace_ELBO
elbo = Elbo()
adam = optim.Adam({"lr": args.learning_rate})
svi = infer.SVI(model, guide, adam, elbo)
# Basic training loop
pyro.get_param_store().clear()
for step in range(args.num_steps):
loss = svi.step(data)
if args.verbose and step % 100 == 0:
print("step {} loss = {}".format(step, loss))
# Report the final values of the variational parameters
# in the guide after training.
if args.verbose:
for name in pyro.get_param_store():
value = pyro.param(name).data
print("{} = {}".format(name, value.detach().cpu().numpy()))
# For this simple (conjugate) model we know the exact posterior. In
# particular we know that the variational distribution should be
# centered near 3.0. So let's check this explicitly.
assert (pyro.param("guide_loc") - 3.0).abs() < 0.1
def test_elbo_plate_plate(backend, outer_dim, inner_dim):
with pyro_backend(backend):
pyro.get_param_store().clear()
num_particles = 1
q = pyro.param("q", torch.tensor([0.75, 0.25], requires_grad=True))
p = 0.2693204236205713 # for which kl(Categorical(q), Categorical(p)) = 0.5
p = torch.tensor([p, 1 - p])
def model():
d = dist.Categorical(p)
context1 = pyro.plate("outer", outer_dim, dim=-1)
context2 = pyro.plate("inner", inner_dim, dim=-2)
pyro.sample("w", d)
with context1:
pyro.sample("x", d)
with context2:
pyro.sample("y", d)
with context1, context2:
pyro.sample("z", d)
def guide():
d = dist.Categorical(pyro.param("q"))
context1 = pyro.plate("outer", outer_dim, dim=-1)
context2 = pyro.plate("inner", inner_dim, dim=-2)
pyro.sample("w", d, infer={"enumerate": "parallel"})
with context1:
pyro.sample("x", d, infer={"enumerate": "parallel"})
with context2:
pyro.sample("y", d, infer={"enumerate": "parallel"})
with context1, context2:
pyro.sample("z", d, infer={"enumerate": "parallel"})
kl_node = kl_divergence(
torch.distributions.Categorical(funsor.to_data(q)),
torch.distributions.Categorical(funsor.to_data(p)))
kl = (1 + outer_dim + inner_dim + outer_dim * inner_dim) * kl_node
expected_loss = kl
expected_grad = grad(kl, [funsor.to_data(q)])[0]
elbo = infer.TraceEnum_ELBO(num_particles=num_particles,
vectorize_particles=True,
strict_enumeration_warning=True)
elbo = elbo.differentiable_loss if backend == "pyro" else elbo
actual_loss = funsor.to_data(elbo(model, guide))
actual_loss.backward()
actual_grad = funsor.to_data(pyro.param('q')).grad
assert_close(actual_loss, expected_loss, atol=1e-5)
assert_close(actual_grad, expected_grad, atol=1e-5)
def test_generate_data_plate(backend):
num_points = 1000
def model(data=None):
loc = pyro.param("loc", torch.tensor(2.0))
scale = pyro.param("scale", torch.tensor(1.0))
with pyro.plate("data", 1000, dim=-1):
x = pyro.sample("x", dist.Normal(loc, scale), obs=data)
return x
with pyro_backend(backend):
data = model().data
assert data.shape == (num_points,)
mean = float(ops.sum(data)) / num_points
assert 1.9 <= mean <= 2.1
def test_optimizer(backend, optim_name, jit):
def model(data):
p = pyro.param("p", torch.tensor(0.5))
pyro.sample("x", dist.Bernoulli(p), obs=data)
def guide(data):
pass
data = torch.tensor(0.)
with pyro_backend(backend):
pyro.get_param_store().clear()
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
optimizer = getattr(optim, optim_name)({"lr": 1e-6})
inference = infer.SVI(model, guide, optimizer, elbo)
for i in range(2):
inference.step(data)
def test_constraints(backend, jit):
data = torch.tensor(0.5)
def model():
locs = pyro.param("locs", torch.randn(3), constraint=constraints.real)
scales = pyro.param("scales", ops.exp(torch.randn(3)), constraint=constraints.positive)
p = torch.tensor([0.5, 0.3, 0.2])
x = pyro.sample("x", dist.Categorical(p))
pyro.sample("obs", dist.Normal(locs[x], scales[x]), obs=data)
def guide():
q = pyro.param("q", ops.exp(torch.randn(3)), constraint=constraints.simplex)
pyro.sample("x", dist.Categorical(q))
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
assert_ok(model, guide, elbo)
def test_plate_ok(backend, jit):
data = torch.randn(10)
def model():
locs = pyro.param("locs", torch.tensor([0.2, 0.3, 0.5]))
p = torch.tensor([0.2, 0.3, 0.5])
with pyro.plate("plate", len(data), dim=-1):
x = pyro.sample("x", dist.Categorical(p))
pyro.sample("obs", dist.Normal(locs[x], 1.0), obs=data)
def guide():
p = pyro.param("p", torch.tensor([0.5, 0.3, 0.2]))
with pyro.plate("plate", len(data), dim=-1):
pyro.sample("x", dist.Categorical(p))
with pyro_backend(backend):
elbo_factory = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = elbo_factory(ignore_jit_warnings=True)
assert_ok(model, guide, elbo)
def test_nested_plate_plate_ok(backend, jit):
data = torch.randn(2, 3)
def model():
loc = torch.tensor(3.0)
with pyro.plate("plate_outer", data.size(-1), dim=-1):
x = pyro.sample("x", dist.Normal(loc, 1.0))
with pyro.plate("plate_inner", data.size(-2), dim=-2):
pyro.sample("y", dist.Normal(x, 1.0), obs=data)
def guide():
loc = pyro.param("loc", torch.tensor(0.0))
scale = pyro.param("scale", torch.tensor(1.0))
with pyro.plate("plate_outer", data.size(-1), dim=-1):
pyro.sample("x", dist.Normal(loc, scale))
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
assert_ok(model, guide, elbo)
def test_local_param_ok(backend, jit):
data = torch.randn(10)
def model():
locs = pyro.param("locs", torch.tensor([-1.0, 0.0, 1.0]))
with pyro.plate("plate", len(data), dim=-1):
x = pyro.sample("x", dist.Categorical(torch.ones(3) / 3))
pyro.sample("obs", dist.Normal(locs[x], 1.0), obs=data)
def guide():
with pyro.plate("plate", len(data), dim=-1):
p = pyro.param("p", torch.ones(len(data), 3) / 3, event_dim=1)
pyro.sample("x", dist.Categorical(p))
return p
with pyro_backend(backend):
Elbo = infer.JitTrace_ELBO if jit else infer.Trace_ELBO
elbo = Elbo(ignore_jit_warnings=True)
assert_ok(model, guide, elbo)
# Check that pyro.param() can be called without init_value.
expected = guide()
actual = pyro.param("p")
assert_close(actual, expected)
def test_elbo_enumerate_plate_7(backend):
# Guide Model
# a -----> b
# | |
# +-|--------|----------------+
# | V V |
# | c -----> d -----> e N=2 |
# +---------------------------+
# This tests a mixture of model and guide enumeration.
with pyro_backend(backend):
pyro.param("model_probs_a",
torch.tensor([0.45, 0.55]),
constraint=constraints.simplex)
pyro.param("model_probs_b",
torch.tensor([[0.6, 0.4], [0.4, 0.6]]),
constraint=constraints.simplex)
pyro.param("model_probs_c",
torch.tensor([[0.75, 0.25], [0.55, 0.45]]),
constraint=constraints.simplex)
pyro.param("model_probs_d",
torch.tensor([[[0.4, 0.6], [0.3, 0.7]],
[[0.3, 0.7], [0.2, 0.8]]]),
constraint=constraints.simplex)
pyro.param("model_probs_e",
torch.tensor([[0.75, 0.25], [0.55, 0.45]]),
constraint=constraints.simplex)
pyro.param("guide_probs_a",
torch.tensor([0.35, 0.64]),
constraint=constraints.simplex)
pyro.param(
"guide_probs_c",
torch.tensor([[0., 1.], [1., 0.]]), # deterministic
constraint=constraints.simplex)
def auto_model(data):
probs_a = pyro.param("model_probs_a")
probs_b = pyro.param("model_probs_b")
probs_c = pyro.param("model_probs_c")
probs_d = pyro.param("model_probs_d")
probs_e = pyro.param("model_probs_e")
a = pyro.sample("a", dist.Categorical(probs_a))
b = pyro.sample("b",
dist.Categorical(probs_b[a]),
infer={"enumerate": "parallel"})
with pyro.plate("data", 2, dim=-1):
c = pyro.sample("c", dist.Categorical(probs_c[a]))
d = pyro.sample("d",
dist.Categorical(Vindex(probs_d)[b, c]),
infer={"enumerate": "parallel"})
pyro.sample("obs", dist.Categorical(probs_e[d]), obs=data)
def auto_guide(data):
probs_a = pyro.param("guide_probs_a")
probs_c = pyro.param("guide_probs_c")
a = pyro.sample("a",
dist.Categorical(probs_a),
infer={"enumerate": "parallel"})
with pyro.plate("data", 2, dim=-1):
pyro.sample("c", dist.Categorical(probs_c[a]))
def hand_model(data):
probs_a = pyro.param("model_probs_a")
probs_b = pyro.param("model_probs_b")
probs_c = pyro.param("model_probs_c")
probs_d = pyro.param("model_probs_d")
probs_e = pyro.param("model_probs_e")
a = pyro.sample("a", dist.Categorical(probs_a))
b = pyro.sample("b",
dist.Categorical(probs_b[a]),
infer={"enumerate": "parallel"})
for i in range(2):
c = pyro.sample("c_{}".format(i), dist.Categorical(probs_c[a]))
d = pyro.sample("d_{}".format(i),
dist.Categorical(Vindex(probs_d)[b, c]),
infer={"enumerate": "parallel"})
pyro.sample("obs_{}".format(i),
dist.Categorical(probs_e[d]),
obs=data[i])
def hand_guide(data):
probs_a = pyro.param("guide_probs_a")
probs_c = pyro.param("guide_probs_c")
a = pyro.sample("a",
dist.Categorical(probs_a),
infer={"enumerate": "parallel"})
for i in range(2):
pyro.sample("c_{}".format(i), dist.Categorical(probs_c[a]))
data = torch.tensor([0, 0])
elbo = infer.TraceEnum_ELBO(max_plate_nesting=1)
elbo = elbo.differentiable_loss if backend == "pyro" else elbo
auto_loss = elbo(auto_model, auto_guide, data)
elbo = infer.TraceEnum_ELBO(max_plate_nesting=0)
elbo = elbo.differentiable_loss if backend == "pyro" else elbo
hand_loss = elbo(hand_model, hand_guide, data)
_check_loss_and_grads(hand_loss, auto_loss)
def test_not_implemented(backend):
with pyro_backend(backend):
pyro.sample # should be implemented
pyro.param # should be implemented
with pytest.raises(NotImplementedError):
pyro.nonexistent_primitive
def test_elbo_enumerate_plates_1(backend):
# +-----------------+
# | a ----> b M=2 |
# +-----------------+
# +-----------------+
# | c ----> d N=3 |
# +-----------------+
# This tests two unrelated plates.
# Each should remain uncontracted.
with pyro_backend(backend):
pyro.param("probs_a",
torch.tensor([0.45, 0.55]),
constraint=constraints.simplex)
pyro.param("probs_b",
torch.tensor([[0.6, 0.4], [0.4, 0.6]]),
constraint=constraints.simplex)
pyro.param("probs_c",
torch.tensor([0.75, 0.25]),
constraint=constraints.simplex)
pyro.param("probs_d",
torch.tensor([[0.4, 0.6], [0.3, 0.7]]),
constraint=constraints.simplex)
b_data = torch.tensor([0, 1])
d_data = torch.tensor([0, 0, 1])
def auto_model():
probs_a = pyro.param("probs_a")
probs_b = pyro.param("probs_b")
probs_c = pyro.param("probs_c")
probs_d = pyro.param("probs_d")
with pyro.plate("a_axis", 2, dim=-1):
a = pyro.sample("a",
dist.Categorical(probs_a),
infer={"enumerate": "parallel"})
pyro.sample("b", dist.Categorical(probs_b[a]), obs=b_data)
with pyro.plate("c_axis", 3, dim=-1):
c = pyro.sample("c",
dist.Categorical(probs_c),
infer={"enumerate": "parallel"})
pyro.sample("d", dist.Categorical(probs_d[c]), obs=d_data)
def hand_model():
probs_a = pyro.param("probs_a")
probs_b = pyro.param("probs_b")
probs_c = pyro.param("probs_c")
probs_d = pyro.param("probs_d")
for i in range(2):
a = pyro.sample("a_{}".format(i),
dist.Categorical(probs_a),
infer={"enumerate": "parallel"})
pyro.sample("b_{}".format(i),
dist.Categorical(probs_b[a]),
obs=b_data[i])
for j in range(3):
c = pyro.sample("c_{}".format(j),
dist.Categorical(probs_c),
infer={"enumerate": "parallel"})
pyro.sample("d_{}".format(j),
dist.Categorical(probs_d[c]),
obs=d_data[j])
def guide():
pass
elbo = infer.TraceEnum_ELBO(max_plate_nesting=1)
elbo = elbo.differentiable_loss if backend == "pyro" else elbo
auto_loss = elbo(auto_model, guide)
elbo = infer.TraceEnum_ELBO(max_plate_nesting=0)
elbo = elbo.differentiable_loss if backend == "pyro" else elbo
hand_loss = elbo(hand_model, guide)
_check_loss_and_grads(hand_loss, auto_loss)
def test_model_sample(model, backend):
with pyro_backend(backend), handlers.seed(
rng_seed=2), xfail_if_not_implemented():
f = MODELS[model]()
model, model_args = f['model'], f.get('model_args', ())
model(*model_args)
