def __call__(self, name, fn, obs):
fn, event_dim = self._unwrap(fn)
assert isinstance(fn, (dist.LinearHMM, dist.IndependentHMM))
if fn.duration is None:
raise ValueError(
"LinearHMMReparam requires duration to be specified "
"on targeted LinearHMM distributions")
# Unwrap IndependentHMM.
if isinstance(fn, dist.IndependentHMM):
if obs is not None:
obs = obs.transpose(-1, -2).unsqueeze(-1)
hmm, obs = self(name, fn.base_dist.to_event(1), obs)
hmm = dist.IndependentHMM(hmm.to_event(-1))
if obs is not None:
obs = obs.squeeze(-1).transpose(-1, -2)
return hmm, obs
# Reparameterize the initial distribution as conditionally Gaussian.
init_dist = fn.initial_dist
if self.init is not None:
init_dist, _ = self.init("{}_init".format(name),
self._wrap(init_dist, event_dim - 1),
None)
init_dist = init_dist.to_event(1 - init_dist.event_dim)
# Reparameterize the transition distribution as conditionally Gaussian.
trans_dist = fn.transition_dist
if self.trans is not None:
if trans_dist.batch_shape[-1] != fn.duration:
trans_dist = trans_dist.expand(trans_dist.batch_shape[:-1] +
(fn.duration, ))
trans_dist, _ = self.trans("{}_trans".format(name),
self._wrap(trans_dist, event_dim), None)
trans_dist = trans_dist.to_event(1 - trans_dist.event_dim)
# Reparameterize the observation distribution as conditionally Gaussian.
obs_dist = fn.observation_dist
if self.obs is not None:
if obs_dist.batch_shape[-1] != fn.duration:
obs_dist = obs_dist.expand(obs_dist.batch_shape[:-1] +
(fn.duration, ))
obs_dist, obs = self.obs("{}_obs".format(name),
self._wrap(obs_dist, event_dim), obs)
obs_dist = obs_dist.to_event(1 - obs_dist.event_dim)
# Reparameterize the entire HMM as conditionally Gaussian.
hmm = dist.GaussianHMM(init_dist,
fn.transition_matrix,
trans_dist,
fn.observation_matrix,
obs_dist,
duration=fn.duration)
hmm = self._wrap(hmm, event_dim)
# Apply any observation transforms.
if fn.transforms:
hmm = dist.TransformedDistribution(hmm, fn.transforms)
return hmm, obs
def test_independent_hmm_shape(init_shape, trans_mat_shape, trans_mvn_shape,
obs_mat_shape, obs_mvn_shape, hidden_dim,
obs_dim):
base_init_shape = init_shape + (obs_dim, )
base_trans_mat_shape = trans_mat_shape[:-1] + (obs_dim, trans_mat_shape[-1]
if trans_mat_shape else 6)
base_trans_mvn_shape = trans_mvn_shape[:-1] + (obs_dim, trans_mvn_shape[-1]
if trans_mvn_shape else 6)
base_obs_mat_shape = obs_mat_shape[:-1] + (obs_dim, obs_mat_shape[-1]
if obs_mat_shape else 6)
base_obs_mvn_shape = obs_mvn_shape[:-1] + (obs_dim, obs_mvn_shape[-1]
if obs_mvn_shape else 6)
init_dist = random_mvn(base_init_shape, hidden_dim)
trans_mat = torch.randn(base_trans_mat_shape + (hidden_dim, hidden_dim))
trans_dist = random_mvn(base_trans_mvn_shape, hidden_dim)
obs_mat = torch.randn(base_obs_mat_shape + (hidden_dim, 1))
obs_dist = random_mvn(base_obs_mvn_shape, 1)
d = dist.GaussianHMM(init_dist,
trans_mat,
trans_dist,
obs_mat,
obs_dist,
duration=6)
d = dist.IndependentHMM(d)
shape = broadcast_shape(init_shape + (6, ), trans_mat_shape,
trans_mvn_shape, obs_mat_shape, obs_mvn_shape)
expected_batch_shape, time_shape = shape[:-1], shape[-1:]
expected_event_shape = time_shape + (obs_dim, )
assert d.batch_shape == expected_batch_shape
assert d.event_shape == expected_event_shape
assert d.support.event_dim == d.event_dim
data = torch.randn(shape + (obs_dim, ))
assert data.shape == d.shape()
actual = d.log_prob(data)
assert actual.shape == expected_batch_shape
check_expand(d, data)
x = d.rsample()
assert x.shape == d.shape()
x = d.rsample((6, ))
assert x.shape == (6, ) + d.shape()
x = d.expand((6, 5)).rsample()
assert x.shape == (6, 5) + d.event_shape
def test_independent_hmm_shape(skew, batch_shape, duration, hidden_dim,
obs_dim):
base_batch_shape = batch_shape + (obs_dim, )
stability = dist.Uniform(0.5, 2).sample(base_batch_shape)
init_dist = random_stable(base_batch_shape + (hidden_dim, ),
stability.unsqueeze(-1),
skew=skew).to_event(1)
trans_mat = torch.randn(base_batch_shape +
(duration, hidden_dim, hidden_dim))
trans_dist = random_stable(
base_batch_shape + (duration, hidden_dim),
stability.unsqueeze(-1).unsqueeze(-1),
skew=skew,
).to_event(1)
obs_mat = torch.randn(base_batch_shape + (duration, hidden_dim, 1))
obs_dist = random_stable(
base_batch_shape + (duration, 1),
stability.unsqueeze(-1).unsqueeze(-1),
skew=skew,
).to_event(1)
hmm = dist.LinearHMM(init_dist,
trans_mat,
trans_dist,
obs_mat,
obs_dist,
duration=duration)
assert hmm.batch_shape == base_batch_shape
assert hmm.event_shape == (duration, 1)
hmm = dist.IndependentHMM(hmm)
assert hmm.batch_shape == batch_shape
assert hmm.event_shape == (duration, obs_dim)
def model(data=None):
with pyro.plate_stack("plates", batch_shape):
return pyro.sample("x", hmm, obs=data)
data = torch.randn(duration, obs_dim)
rep = SymmetricStableReparam() if skew == 0 else StableReparam()
with poutine.trace() as tr:
with poutine.reparam(config={"x": LinearHMMReparam(rep, rep, rep)}):
model(data)
assert isinstance(tr.trace.nodes["x"]["fn"], dist.IndependentHMM)
tr.trace.compute_log_prob() # smoke test only
def apply(self, msg):
name = msg["name"]
fn = msg["fn"]
value = msg["value"]
is_observed = msg["is_observed"]
fn, event_dim = self._unwrap(fn)
assert isinstance(fn, (dist.LinearHMM, dist.IndependentHMM))
if fn.duration is None:
raise ValueError(
"LinearHMMReparam requires duration to be specified "
"on targeted LinearHMM distributions")
# Unwrap IndependentHMM.
if isinstance(fn, dist.IndependentHMM):
indep_value = None
if value is not None:
indep_value = value.transpose(-1, -2).unsqueeze(-1)
msg = self.apply({
"name": name,
"fn": fn.base_dist.to_event(1),
"value": indep_value,
"is_observed": is_observed,
})
hmm = msg["fn"]
hmm = dist.IndependentHMM(hmm.to_event(-1))
if msg["value"] is not indep_value:
value = msg["value"].squeeze(-1).transpose(-1, -2)
return {"fn": hmm, "value": value, "is_observed": is_observed}
# Reparameterize the initial distribution as conditionally Gaussian.
init_dist = fn.initial_dist
if self.init is not None:
msg = self.init.apply({
"name": f"{name}_init",
"fn": self._wrap(init_dist, event_dim - 1),
"value": None,
"is_observed": False,
})
init_dist = msg["fn"]
init_dist = init_dist.to_event(1 - init_dist.event_dim)
# Reparameterize the transition distribution as conditionally Gaussian.
trans_dist = fn.transition_dist
if self.trans is not None:
if trans_dist.batch_shape[-1] != fn.duration:
trans_dist = trans_dist.expand(trans_dist.batch_shape[:-1] +
(fn.duration, ))
msg = self.trans.apply({
"name": f"{name}_trans",
"fn": self._wrap(trans_dist, event_dim),
"value": None,
"is_observed": False,
})
trans_dist = msg["fn"]
trans_dist = trans_dist.to_event(1 - trans_dist.event_dim)
# Reparameterize the observation distribution as conditionally Gaussian.
obs_dist = fn.observation_dist
if self.obs is not None:
if obs_dist.batch_shape[-1] != fn.duration:
obs_dist = obs_dist.expand(obs_dist.batch_shape[:-1] +
(fn.duration, ))
msg = self.obs.apply({
"name": f"{name}_obs",
"fn": self._wrap(obs_dist, event_dim),
"value": value,
"is_observed": is_observed,
})
obs_dist = msg["fn"]
obs_dist = obs_dist.to_event(1 - obs_dist.event_dim)
value = msg["value"]
is_observed = msg["is_observed"]
# Reparameterize the entire HMM as conditionally Gaussian.
hmm = dist.GaussianHMM(
init_dist,
fn.transition_matrix,
trans_dist,
fn.observation_matrix,
obs_dist,
duration=fn.duration,
)
hmm = self._wrap(hmm, event_dim)
# Apply any observation transforms.
if fn.transforms:
hmm = dist.TransformedDistribution(hmm, fn.transforms)
return {"fn": hmm, "value": value, "is_observed": is_observed}
def _(d, batch_shape):
base_shape = batch_shape + d.event_shape[-1:]
base_dist = reshape_batch(d.base_dist, base_shape)
return dist.IndependentHMM(base_dist)
def _(d, data):
base_data = data.transpose(-1, -2).unsqueeze(-1)
base_dist = prefix_condition(d.base_dist, base_data)
return dist.IndependentHMM(base_dist)
