# Source code for pyro.distributions.hmm

```
import torch
from torch.distributions import constraints
from pyro.distributions.torch import Categorical, MultivariateNormal
from pyro.distributions.torch_distribution import TorchDistribution
from pyro.distributions.util import broadcast_shape
from pyro.ops.gaussian import Gaussian, gaussian_tensordot, matrix_and_mvn_to_gaussian, mvn_to_gaussian
def _logmatmulexp(x, y):
"""
Numerically stable version of ``(x.log() @ y.log()).exp()``.
"""
x_shift = x.max(-1, keepdim=True)[0]
y_shift = y.max(-2, keepdim=True)[0]
xy = torch.matmul((x - x_shift).exp(), (y - y_shift).exp()).log()
return xy + x_shift + y_shift
def _sequential_logmatmulexp(logits):
"""
For a tensor ``x`` whose time dimension is -3, computes::
x[..., 0, :, :] @ x[..., 1, :, :] @ ... @ x[..., T-1, :, :]
but does so numerically stably in log space.
"""
batch_shape = logits.shape[:-3]
state_dim = logits.size(-1)
while logits.size(-3) > 1:
time = logits.size(-3)
even_time = time // 2 * 2
even_part = logits[..., :even_time, :, :]
x_y = even_part.reshape(batch_shape + (even_time // 2, 2, state_dim, state_dim))
x, y = x_y.unbind(-3)
contracted = _logmatmulexp(x, y)
if time > even_time:
contracted = torch.cat((contracted, logits[..., -1:, :, :]), dim=-3)
logits = contracted
return logits.squeeze(-3)
def _sequential_gaussian_tensordot(gaussian):
"""
Integrates a Gaussian ``x`` whose rightmost batch dimension is time, computes::
x[..., 0] @ x[..., 1] @ ... @ x[..., T-1]
"""
assert isinstance(gaussian, Gaussian)
assert gaussian.dim() % 2 == 0, "dim is not even"
batch_shape = gaussian.batch_shape[:-1]
state_dim = gaussian.dim() // 2
while gaussian.batch_shape[-1] > 1:
time = gaussian.batch_shape[-1]
even_time = time // 2 * 2
even_part = gaussian[..., :even_time]
x_y = even_part.reshape(batch_shape + (even_time // 2, 2))
x, y = x_y[..., 0], x_y[..., 1]
contracted = gaussian_tensordot(x, y, state_dim)
if time > even_time:
contracted = Gaussian.cat((contracted, gaussian[..., -1:]), dim=-1)
gaussian = contracted
return gaussian[..., 0]
[docs]class DiscreteHMM(TorchDistribution):
"""
Hidden Markov Model with discrete latent state and arbitrary observation
distribution. This uses [1] to parallelize over time, achieving
O(log(time)) parallel complexity.
The event_shape of this distribution includes time on the left::
event_shape = (num_steps,) + observation_dist.event_shape
This distribution supports any combination of homogeneous/heterogeneous
time dependency of ``transition_logits`` and ``observation_dist``. However,
because time is included in this distribution's event_shape, the
homogeneous+homogeneous case will have a broadcastable event_shape with
``num_steps = 1``, allowing :meth:`log_prob` to work with arbitrary length
data::
# homogeneous + homogeneous case:
event_shape = (1,) + observation_dist.event_shape
**References:**
[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019)
"Temporal Parallelization of Bayesian Filters and Smoothers"
https://arxiv.org/pdf/1905.13002.pdf
:param ~torch.Tensor initial_logits: A logits tensor for an initial
categorical distribution over latent states. Should have rightmost size
``state_dim`` and be broadcastable to ``batch_shape + (state_dim,)``.
:param ~torch.Tensor transition_logits: A logits tensor for transition
conditional distributions between latent states. Should have rightmost
shape ``(state_dim, state_dim)`` (old, new), and be broadcastable to
``batch_shape + (num_steps, state_dim, state_dim)``.
:param ~torch.distributions.Distribution observation_dist: A conditional
distribution of observed data conditioned on latent state. The
``.batch_shape`` should have rightmost size ``state_dim`` and be
broadcastable to ``batch_shape + (num_steps, state_dim)``. The
``.event_shape`` may be arbitrary.
"""
arg_constraints = {"initial_logits": constraints.real,
"transition_logits": constraints.real}
def __init__(self, initial_logits, transition_logits, observation_dist, validate_args=None):
if initial_logits.dim() < 1:
raise ValueError("expected initial_logits to have at least one dim, "
"actual shape = {}".format(initial_logits.shape))
if transition_logits.dim() < 2:
raise ValueError("expected transition_logits to have at least two dims, "
"actual shape = {}".format(transition_logits.shape))
if len(observation_dist.batch_shape) < 1:
raise ValueError("expected observation_dist to have at least one batch dim, "
"actual .batch_shape = {}".format(observation_dist.batch_shape))
shape = broadcast_shape(initial_logits.shape[:-1] + (1,),
transition_logits.shape[:-2],
observation_dist.batch_shape[:-1])
batch_shape, time_shape = shape[:-1], shape[-1:]
event_shape = time_shape + observation_dist.event_shape
self.initial_logits = initial_logits - initial_logits.logsumexp(-1, True)
self.transition_logits = transition_logits - transition_logits.logsumexp(-1, True)
self.observation_dist = observation_dist
super(DiscreteHMM, self).__init__(batch_shape, event_shape, validate_args=validate_args)
[docs] def expand(self, batch_shape, _instance=None):
new = self._get_checked_instance(DiscreteHMM, _instance)
batch_shape = torch.Size(broadcast_shape(self.batch_shape, batch_shape))
# We only need to expand one of the inputs, since batch_shape is determined
# by broadcasting all three. To save computation in _sequential_logmatmulexp(),
# we expand only initial_logits, which is applied only after the logmatmulexp.
# This is similar to the ._unbroadcasted_* pattern used elsewhere in distributions.
new.initial_logits = self.initial_logits.expand(batch_shape + (-1,))
new.transition_logits = self.transition_logits
new.observation_dist = self.observation_dist
super(DiscreteHMM, new).__init__(batch_shape, self.event_shape, validate_args=False)
new._validate_args = self.__dict__.get('_validate_args')
return new
[docs] def log_prob(self, value):
# Combine observation and transition factors.
value = value.unsqueeze(-1 - self.observation_dist.event_dim)
observation_logits = self.observation_dist.log_prob(value)
result = self.transition_logits + observation_logits.unsqueeze(-2)
# Eliminate time dimension.
result = _sequential_logmatmulexp(result)
# Combine initial factor.
result = self.initial_logits + result.logsumexp(-1)
# Marginalize out final state.
result = result.logsumexp(-1)
return result
[docs] def filter(self, value):
"""
Compute posterior over final state given a sequence of observations.
:param ~torch.Tensor value: A sequence of observations.
:return: A posterior distribution
over latent states at the final time step. ``result.logits`` can
then be used as ``initial_logits`` in a sequential Pyro model for
prediction.
:rtype: ~pyro.distributions.Categorical
"""
# Combine observation and transition factors.
value = value.unsqueeze(-1 - self.observation_dist.event_dim)
observation_logits = self.observation_dist.log_prob(value)
logp = self.transition_logits + observation_logits.unsqueeze(-2)
# Eliminate time dimension.
logp = _sequential_logmatmulexp(logp)
# Combine initial factor.
logp = (self.initial_logits.unsqueeze(-1) + logp).logsumexp(-2)
# Convert to a distribution.
return Categorical(logits=logp, validate_args=self._validate_args)
[docs]class GaussianHMM(TorchDistribution):
"""
Hidden Markov Model with Gaussians for initial, transition, and observation
distributions. This adapts [1] to parallelize over time to achieve
O(log(time)) parallel complexity, however it differs in that it tracks the
log normalizer to ensure :meth:`log_prob` is differentiable.
This corresponds to the generative model::
z = initial_distribution.sample()
x = []
for t in range(num_events):
z = z @ transition_matrix + transition_dist.sample()
x.append(z @ observation_matrix + observation_dist.sample())
The event_shape of this distribution includes time on the left::
event_shape = (num_steps,) + observation_dist.event_shape
This distribution supports any combination of homogeneous/heterogeneous
time dependency of ``transition_dist`` and ``observation_dist``. However,
because time is included in this distribution's event_shape, the
homogeneous+homogeneous case will have a broadcastable event_shape with
``num_steps = 1``, allowing :meth:`log_prob` to work with arbitrary length
data::
event_shape = (1, obs_dim) # homogeneous + homogeneous case
**References:**
[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019)
"Temporal Parallelization of Bayesian Filters and Smoothers"
https://arxiv.org/pdf/1905.13002.pdf
:ivar int hidden_dim: The dimension of the hidden state.
:ivar int obs_dim: The dimension of the observed state.
:param ~torch.distributions.MultivariateNormal initial_dist: A distribution
over initial states. This should have batch_shape broadcastable to
``self.batch_shape``. This should have event_shape ``(hidden_dim,)``.
:param ~torch.Tensor transition_matrix: A linear transformation of hidden
state. This should have shape broadcastable to
``self.batch_shape + (num_steps, hidden_dim, hidden_dim)`` where the
rightmost dims are ordered ``(old, new)``.
:param ~torch.distributions.MultivariateNormal transition_dist: A process
noise distribution. This should have batch_shape broadcastable to
``self.batch_shape + (num_steps,)``. This should have event_shape
``(hidden_dim,)``.
:param ~torch.Tensor observation_matrix: A linear transformation from hidden
to observed state. This should have shape broadcastable to
``self.batch_shape + (num_steps, hidden_dim, obs_dim)``.
:param observation_dist: An observation noise distribution. This should
have batch_shape broadcastable to ``self.batch_shape + (num_steps,)``.
This should have event_shape ``(obs_dim,)``.
:type observation_dist: ~torch.distributions.MultivariateNormal or
~torch.distributions.Independent of ~torch.distributions.Normal
"""
arg_constraints = {}
def __init__(self, initial_dist, transition_matrix, transition_dist,
observation_matrix, observation_dist, validate_args=None):
assert isinstance(initial_dist, torch.distributions.MultivariateNormal)
assert isinstance(transition_matrix, torch.Tensor)
assert isinstance(transition_dist, torch.distributions.MultivariateNormal)
assert isinstance(observation_matrix, torch.Tensor)
assert (isinstance(observation_dist, torch.distributions.MultivariateNormal) or
(isinstance(observation_dist, torch.distributions.Independent) and
isinstance(observation_dist.base_dist, torch.distributions.Normal)))
hidden_dim, obs_dim = observation_matrix.shape[-2:]
assert initial_dist.event_shape == (hidden_dim,)
assert transition_matrix.shape[-2:] == (hidden_dim, hidden_dim)
assert transition_dist.event_shape == (hidden_dim,)
assert observation_dist.event_shape == (obs_dim,)
shape = broadcast_shape(initial_dist.batch_shape + (1,),
transition_matrix.shape[:-2],
transition_dist.batch_shape,
observation_matrix.shape[:-2],
observation_dist.batch_shape)
batch_shape, time_shape = shape[:-1], shape[-1:]
event_shape = time_shape + (obs_dim,)
super(GaussianHMM, self).__init__(batch_shape, event_shape, validate_args=validate_args)
self.hidden_dim = hidden_dim
self.obs_dim = obs_dim
self._init = mvn_to_gaussian(initial_dist)
self._trans = matrix_and_mvn_to_gaussian(transition_matrix, transition_dist)
self._obs = matrix_and_mvn_to_gaussian(observation_matrix, observation_dist)
[docs] def expand(self, batch_shape, _instance=None):
new = self._get_checked_instance(GaussianHMM, _instance)
batch_shape = torch.Size(broadcast_shape(self.batch_shape, batch_shape))
new.hidden_dim = self.hidden_dim
new.obs_dim = self.obs_dim
# We only need to expand one of the inputs, since batch_shape is determined
# by broadcasting all three. To save computation in _sequential_gaussian_tensordot(),
# we expand only _init, which is applied only after _sequential_gaussian_tensordot().
new._init = self._init.expand(batch_shape)
new._trans = self._trans
new._obs = self._obs
super(GaussianHMM, new).__init__(batch_shape, self.event_shape, validate_args=False)
new._validate_args = self.__dict__.get('_validate_args')
return new
[docs] def log_prob(self, value):
# Combine observation and transition factors.
result = self._trans + self._obs.condition(value).event_pad(left=self.hidden_dim)
# Eliminate time dimension.
result = _sequential_gaussian_tensordot(result.expand(result.batch_shape))
# Combine initial factor.
result = gaussian_tensordot(self._init, result, dims=self.hidden_dim)
# Marginalize out final state.
result = result.event_logsumexp()
return result
[docs] def filter(self, value):
"""
Compute posterior over final state given a sequence of observations.
:param ~torch.Tensor value: A sequence of observations.
:return: A posterior
distribution over latent states at the final time step. ``result``
can then be used as ``initial_dist`` in a sequential Pyro model for
prediction.
:rtype: ~pyro.distributions.MultivariateNormal
"""
# Combine observation and transition factors.
logp = self._trans + self._obs.condition(value).event_pad(left=self.hidden_dim)
# Eliminate time dimension.
logp = _sequential_gaussian_tensordot(logp.expand(logp.batch_shape))
# Combine initial factor.
logp = gaussian_tensordot(self._init, logp, dims=self.hidden_dim)
# Convert to a distribution
precision = logp.precision
loc = logp.info_vec.unsqueeze(-1).cholesky_solve(precision.cholesky()).squeeze(-1)
return MultivariateNormal(loc, precision_matrix=precision,
validate_args=self._validate_args)
[docs]class GaussianMRF(TorchDistribution):
"""
Temporal Markov Random Field with Gaussian factors for initial, transition,
and observation distributions. This adapts [1] to parallelize over time to
achieve O(log(time)) parallel complexity, however it differs in that it
tracks the log normalizer to ensure :meth:`log_prob` is differentiable.
The event_shape of this distribution includes time on the left::
event_shape = (num_steps,) + observation_dist.event_shape
This distribution supports any combination of homogeneous/heterogeneous
time dependency of ``transition_dist`` and ``observation_dist``. However,
because time is included in this distribution's event_shape, the
homogeneous+homogeneous case will have a broadcastable event_shape with
``num_steps = 1``, allowing :meth:`log_prob` to work with arbitrary length
data::
event_shape = (1, obs_dim) # homogeneous + homogeneous case
**References:**
[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019)
"Temporal Parallelization of Bayesian Filters and Smoothers"
https://arxiv.org/pdf/1905.13002.pdf
:ivar int hidden_dim: The dimension of the hidden state.
:ivar int obs_dim: The dimension of the observed state.
:param ~torch.distributions.MultivariateNormal initial_dist: A distribution
over initial states. This should have batch_shape broadcastable to
``self.batch_shape``. This should have event_shape ``(hidden_dim,)``.
:param ~torch.distributions.MultivariateNormal transition_dist: A joint
distribution factor over a pair of successive time steps. This should
have batch_shape broadcastable to ``self.batch_shape + (num_steps,)``.
This should have event_shape ``(hidden_dim + hidden_dim,)`` (old+new).
:param ~torch.distributions.MultivariateNormal observation_dist: A joint
distribution factor over a hidden and an observed state. This should
have batch_shape broadcastable to ``self.batch_shape + (num_steps,)``.
This should have event_shape ``(hidden_dim + obs_dim,)``.
"""
arg_constraints = {}
def __init__(self, initial_dist, transition_dist, observation_dist, validate_args=None):
assert isinstance(initial_dist, torch.distributions.MultivariateNormal)
assert isinstance(transition_dist, torch.distributions.MultivariateNormal)
assert isinstance(observation_dist, torch.distributions.MultivariateNormal)
hidden_dim = initial_dist.event_shape[0]
assert transition_dist.event_shape[0] == hidden_dim + hidden_dim
obs_dim = observation_dist.event_shape[0] - hidden_dim
shape = broadcast_shape(initial_dist.batch_shape + (1,),
transition_dist.batch_shape,
observation_dist.batch_shape)
batch_shape, time_shape = shape[:-1], shape[-1:]
event_shape = time_shape + (obs_dim,)
super(GaussianMRF, self).__init__(batch_shape, event_shape, validate_args=validate_args)
self.hidden_dim = hidden_dim
self.obs_dim = obs_dim
self._init = mvn_to_gaussian(initial_dist)
self._trans = mvn_to_gaussian(transition_dist)
self._obs = mvn_to_gaussian(observation_dist)
[docs] def expand(self, batch_shape, _instance=None):
new = self._get_checked_instance(GaussianMRF, _instance)
batch_shape = torch.Size(broadcast_shape(self.batch_shape, batch_shape))
new.hidden_dim = self.hidden_dim
new.obs_dim = self.obs_dim
# We only need to expand one of the inputs, since batch_shape is determined
# by broadcasting all three. To save computation in _sequential_gaussian_tensordot(),
# we expand only _init, which is applied only after _sequential_gaussian_tensordot().
new._init = self._init.expand(batch_shape)
new._trans = self._trans
new._obs = self._obs
super(GaussianMRF, new).__init__(batch_shape, self.event_shape, validate_args=False)
new._validate_args = self.__dict__.get('_validate_args')
return new
[docs] def log_prob(self, value):
# We compute a normalized distribution as p(obs,hidden) / p(hidden).
logp_oh = self._trans
logp_h = self._trans
# Combine observation and transition factors.
logp_oh += self._obs.condition(value).event_pad(left=self.hidden_dim)
logp_h += self._obs.marginalize(right=self.obs_dim).event_pad(left=self.hidden_dim)
# Concatenate p(obs,hidden) and p(hidden) into a single Gaussian.
batch_dim = 1 + max(len(self._init.batch_shape) + 1, len(logp_oh.batch_shape))
batch_shape = (1,) * (batch_dim - len(logp_oh.batch_shape)) + logp_oh.batch_shape
logp = Gaussian.cat([logp_oh.expand(batch_shape),
logp_h.expand(batch_shape)])
# Eliminate time dimension.
logp = _sequential_gaussian_tensordot(logp)
# Combine initial factor.
logp = gaussian_tensordot(self._init, logp, dims=self.hidden_dim)
# Marginalize out final state.
logp_oh, logp_h = logp.event_logsumexp()
return logp_oh - logp_h # = log( p(obs,hidden) / p(hidden) )
```