def main(args):
pyro.set_rng_seed(args.seed)
model = SimpleHarmonicModel(args.process_noise, args.measurement_noise)
guide = SimpleHarmonicModel_Guide(model)
smc = SMCFilter(model,
guide,
num_particles=args.num_particles,
max_plate_nesting=0)
logging.info("Generating data")
zs, ys = generate_data(args)
logging.info("Filtering")
smc.init(initial=torch.tensor([1., 0.]))
for y in ys[1:]:
smc.step(y)
logging.info("At final time step:")
z = smc.get_empirical()["z"]
logging.info("truth: {}".format(zs[-1]))
logging.info("mean: {}".format(z.mean))
logging.info("std: {}".format(z.variance**0.5))
def main(args):
pyro.set_rng_seed(args.seed)
pyro.enable_validation(__debug__)
model = SimpleHarmonicModel(args.process_noise, args.measurement_noise)
guide = SimpleHarmonicModel_Guide(model)
smc = SMCFilter(model,
guide,
num_particles=args.num_particles,
max_plate_nesting=0)
logging.info('Generating data')
zs, ys = generate_data(args)
logging.info('Filtering')
smc.init(initial=torch.tensor([1., 0.]))
for y in ys[1:]:
smc.step(y)
logging.info('Marginals')
empirical = smc.get_empirical()
for t in range(1, 1 + args.num_timesteps):
z = empirical["z_{}".format(t)]
logging.info("{}\t{}\t{}\t{}".format(t, zs[t], z.mean, z.variance))
def test_smoke(max_plate_nesting, state_size, plate_size, num_steps):
model = SmokeModel(state_size, plate_size)
guide = SmokeGuide(state_size, plate_size)
smc = SMCFilter(model,
guide,
num_particles=100,
max_plate_nesting=max_plate_nesting)
true_model = SmokeModel(state_size, plate_size)
true_model.init()
truth = [true_model.step() for t in range(num_steps)]
smc.init()
for xy in truth:
smc.step(*xy)
smc.get_values_and_log_weights()
smc.get_empirical()
def test_smoke(max_plate_nesting, state_size, plate_size, num_steps):
model = SmokeModel(state_size, plate_size)
guide = SmokeGuide(state_size, plate_size)
smc = SMCFilter(model,
guide,
num_particles=100,
max_plate_nesting=max_plate_nesting)
true_model = SmokeModel(state_size, plate_size)
state = {}
true_model.init(state)
truth = [true_model.step(state) for t in range(num_steps)]
smc.init()
assert set(smc.state) == {"x_mean", "y_mean"}
for x, y in truth:
smc.step(x, y)
assert set(smc.state) == {"x_mean", "y_mean"}
smc.get_empirical()
def heuristic(self, num_particles=1024, ess_threshold=0.5, retries=10):
"""
Finds an initial feasible guess of all latent variables, consistent
with observed data. This is needed because not all hypotheses are
feasible and HMC needs to start at a feasible solution to progress.
The default implementation attempts to find a feasible state using
:class:`~pyro.infer.smcfilter.SMCFilter` with proprosals from the
prior. However this method may be overridden in cases where SMC
performs poorly e.g. in high-dimensional models.
:param int num_particles: Number of particles used for SMC.
:param float ess_threshold: Effective sample size threshold for SMC.
:returns: A dictionary mapping sample site name to tensor value.
:rtype: dict
"""
# Run SMC.
model = _SMCModel(self)
guide = _SMCGuide(self)
for attempt in range(1, 1 + retries):
smc = SMCFilter(model,
guide,
num_particles=num_particles,
ess_threshold=ess_threshold,
max_plate_nesting=self.max_plate_nesting)
try:
smc.init()
for t in range(1, self.duration):
smc.step()
break
except SMCFailed as e:
if attempt == retries:
raise
logger.info("{}. Retrying...".format(e))
continue
# Select the most probable hypothesis.
i = int(smc.state._log_weights.max(0).indices)
init = {key: value[i, 0] for key, value in smc.state.items()}
# Fill in sample site values.
init = self.generate(init)
aux = torch.stack([init[name] for name in self.compartments], dim=0)
init["auxiliary"] = clamp(aux, min=0.5, max=self.population - 0.5)
return init
def test_likelihood_ratio():
model = HarmonicModel()
guide = HarmonicGuide()
smc = SMCFilter(model, guide, num_particles=100, max_plate_nesting=0)
zs, ys = generate_data()
zs_true, ys_true = generate_data()
smc.init()
for y in ys_true[1:]:
smc.step(y)
values, logweights = smc.get_values_and_log_weights()
i = logweights.max(0)[1]
values = {k: v[i] for k, v in values.items()}
zs_pred = [torch.tensor([1., 0.])]
zs_pred += [values.get("z_{}".format(t)) for t in range(1, 51)]
assert (score_latent(zs_true, ys_true) > score_latent(zs, ys_true))
assert (score_latent(zs_pred, ys_true) > score_latent(zs_pred, ys))
assert (score_latent(zs_pred, ys_true) > score_latent(zs, ys_true))
def test_gaussian_filter():
dim = 4
init_dist = dist.MultivariateNormal(torch.zeros(dim),
scale_tril=torch.eye(dim) * 10)
trans_mat = torch.eye(dim)
trans_dist = dist.MultivariateNormal(torch.zeros(dim),
scale_tril=torch.eye(dim))
obs_mat = torch.eye(dim)
obs_dist = dist.MultivariateNormal(torch.zeros(dim),
scale_tril=torch.eye(dim) * 2)
hmm = dist.GaussianHMM(init_dist, trans_mat, trans_dist, obs_mat, obs_dist)
class Model:
def init(self, state):
state["z"] = pyro.sample("z_init", init_dist)
self.t = 0
def step(self, state, datum=None):
state["z"] = pyro.sample(
"z_{}".format(self.t),
dist.MultivariateNormal(state["z"],
scale_tril=trans_dist.scale_tril))
datum = pyro.sample(
"obs_{}".format(self.t),
dist.MultivariateNormal(state["z"],
scale_tril=obs_dist.scale_tril),
obs=datum)
self.t += 1
return datum
class Guide:
def init(self, state):
pyro.sample("z_init", init_dist)
self.t = 0
def step(self, state, datum):
pyro.sample(
"z_{}".format(self.t),
dist.MultivariateNormal(state["z"],
scale_tril=trans_dist.scale_tril * 2))
self.t += 1
# Generate data.
num_steps = 20
model = Model()
state = {}
model.init(state)
data = torch.stack([model.step(state) for _ in range(num_steps)])
# Perform inference.
model = Model()
guide = Guide()
smc = SMCFilter(model, guide, num_particles=1000, max_plate_nesting=0)
smc.init()
for t, datum in enumerate(data):
smc.step(datum)
expected = hmm.filter(data[:1 + t])
actual = smc.get_empirical()["z"]
assert_close(actual.variance**0.5,
expected.variance**0.5,
atol=0.1,
rtol=0.5)
sigma = actual.variance.max().item()**0.5
assert_close(actual.mean, expected.mean, atol=3 * sigma)