support for padded arrays in hmm inference

dynamax/hidden_markov_model/inference.py

@@ -101,7 +101,8 @@ def hmm_filter(
     transition_matrix: Union[Float[Array, "num_timesteps num_states num_states"],
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
-    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]] = None
+    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]] = None,
+    num_timesteps: Optional[Int] = None,
 ) -> HMMPosteriorFiltered:
     r"""Forwards filtering
 
@@ -115,27 +116,32 @@ def hmm_filter(
         transition_matrix: $p(z_{t+1} \mid z_t, u_t, \theta)$
         log_likelihoods: $p(y_t \mid z_t, u_t, \theta)$ for $t=1,\ldots, T$.
         transition_fn: function that takes in an integer time index and returns a $K \times K$ transition matrix.
+        num_timesteps: number of "valid" timesteps, to support vmapping with padded arrays.
 
     Returns:
         filtered posterior distribution
 
     """
-    num_timesteps, num_states = log_likelihoods.shape
+    max_num_timesteps = log_likelihoods.shape[0]
+    num_timesteps = num_timesteps if num_timesteps is not None else max_num_timesteps
 
     def _step(carry, t):
         log_normalizer, predicted_probs = carry
 
         A = get_trans_mat(transition_matrix, transition_fn, t)
         ll = log_likelihoods[t]
 
+        # Ignore observations after specified number of timesteps
+        ll = jnp.where(t < num_timesteps, ll, 0.0)
+
         filtered_probs, log_norm = _condition_on(predicted_probs, ll)
         log_normalizer += log_norm
         predicted_probs_next = _predict(filtered_probs, A)
 
         return (log_normalizer, predicted_probs_next), (filtered_probs, predicted_probs)
 
     carry = (0.0, initial_distribution)
-    (log_normalizer, _), (filtered_probs, predicted_probs) = lax.scan(_step, carry, jnp.arange(num_timesteps))
+    (log_normalizer, _), (filtered_probs, predicted_probs) = lax.scan(_step, carry, jnp.arange(max_num_timesteps))
 
     post = HMMPosteriorFiltered(marginal_loglik=log_normalizer,
                                 filtered_probs=filtered_probs,
@@ -149,7 +155,8 @@ def hmm_backward_filter(
     transition_matrix: Union[Float[Array, "num_timesteps num_states num_states"],
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
-    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None
+    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None,
+    num_timesteps: Optional[Int] = None
 ) -> Tuple[Float, Float[Array, "num_timesteps num_states"]]:
     r"""Run the filter backwards in time. This is the second step of the forward-backward algorithm.
 
@@ -163,30 +170,33 @@ def hmm_backward_filter(
         transition_matrix: $p(z_{t+1} \mid z_t, u_t, \theta)$
         log_likelihoods: $p(y_t \mid z_t, u_t, \theta)$ for $t=1,\ldots, T$.
         transition_fn: function that takes in an integer time index and returns a $K \times K$ transition matrix.
+        num_timesteps: number of "valid" timesteps, to support vmapping with padded arrays.
 
     Returns:
         marginal log likelihood and backward messages.
 
     """
-    num_timesteps, num_states = log_likelihoods.shape
+    max_num_timesteps, num_states = log_likelihoods.shape
+    num_timesteps = num_timesteps if num_timesteps is not None else max_num_timesteps
 
     def _step(carry, t):
         log_normalizer, backward_pred_probs = carry
 
         A = get_trans_mat(transition_matrix, transition_fn, t)
         ll = log_likelihoods[t]
 
+        # Ignore observations after specified number of timesteps
+        ll = jnp.where(t < num_timesteps, ll, 0.0)
+
         # Condition on emission at time t, being careful not to overflow.
         backward_filt_probs, log_norm = _condition_on(backward_pred_probs, ll)
-        # Update the log normalizer.
-        log_normalizer += log_norm
+
         # Predict the next state (going backward in time).
         next_backward_pred_probs = _predict(backward_filt_probs, A.T)
         return (log_normalizer, next_backward_pred_probs), backward_pred_probs
 
     carry = (0.0, jnp.ones(num_states))
-    (log_normalizer, _), rev_backward_pred_probs = lax.scan(_step, carry, jnp.arange(num_timesteps)[::-1])
-    backward_pred_probs = rev_backward_pred_probs[::-1]
+    (log_normalizer, _), backward_pred_probs = lax.scan(_step, carry, jnp.arange(max_num_timesteps), reverse=True)
     return log_normalizer, backward_pred_probs
 
 
@@ -197,6 +207,7 @@ def hmm_two_filter_smoother(
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
     transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None,
+    num_timesteps: Optional[Int] = None,
     compute_trans_probs: bool = True
 ) -> HMMPosterior:
     r"""Computed the smoothed state probabilities using the two-filter
@@ -212,16 +223,19 @@ def hmm_two_filter_smoother(
         transition_matrix: $p(z_{t+1} \mid z_t, u_t, \theta)$
         log_likelihoods: $p(y_t \mid z_t, u_t, \theta)$ for $t=1,\ldots, T$.
         transition_fn: function that takes in an integer time index and returns a $K \times K$ transition matrix.
+        num_timesteps: number of "valid" timesteps, to support vmapping with padded arrays.
 
     Returns:
         posterior distribution
 
     """
-    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn)
+    # Forward
+    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn, num_timesteps)
     ll = post.marginal_loglik
     filtered_probs, predicted_probs = post.filtered_probs, post.predicted_probs
 
-    _, backward_pred_probs = hmm_backward_filter(transition_matrix, log_likelihoods, transition_fn)
+    # Backward
+    _, backward_pred_probs = hmm_backward_filter(transition_matrix, log_likelihoods, transition_fn, num_timesteps)
 
     # Compute smoothed probabilities
     smoothed_probs = filtered_probs * backward_pred_probs
@@ -251,6 +265,7 @@ def hmm_smoother(
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
     transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None,
+    num_timesteps: Optional[Int]=None,
     compute_trans_probs: bool = True
 ) -> HMMPosterior:
     r"""Computed the smoothed state probabilities using a general
@@ -268,15 +283,17 @@ def hmm_smoother(
         transition_matrix: $p(z_{t+1} \mid z_t, u_t, \theta)$
         log_likelihoods: $p(y_t \mid z_t, u_t, \theta)$ for $t=1,\ldots, T$.
         transition_fn: function that takes in an integer time index and returns a $K \times K$ transition matrix.
+        num_timesteps: number of "valid" timesteps, to support vmapping with padded arrays.
 
     Returns:
         posterior distribution
 
     """
-    num_timesteps, num_states = log_likelihoods.shape
+    max_num_timesteps, _ = log_likelihoods.shape
+    num_timesteps = num_timesteps if num_timesteps is not None else max_num_timesteps
 
     # Run the HMM filter
-    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn)
+    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn, num_timesteps)
     ll = post.marginal_loglik
     filtered_probs, predicted_probs = post.filtered_probs, post.predicted_probs
 
@@ -294,16 +311,15 @@ def _step(carry, args):
                                         smoothed_probs_next / predicted_probs_next)
         smoothed_probs = filtered_probs * (A @ relative_probs_next)
         smoothed_probs /= smoothed_probs.sum()
-
         return smoothed_probs, smoothed_probs
 
     # Run the HMM smoother
     carry = filtered_probs[-1]
-    args = (jnp.arange(num_timesteps - 2, -1, -1), filtered_probs[:-1][::-1], predicted_probs[1:][::-1])
-    _, rev_smoothed_probs = lax.scan(_step, carry, args)
+    args = (jnp.arange(max_num_timesteps - 1), filtered_probs[:-1], predicted_probs[1:])
+    _, smoothed_probs = lax.scan(_step, carry, args, reverse=True)
 
     # Reverse the arrays and return
-    smoothed_probs = jnp.vstack([rev_smoothed_probs[::-1], filtered_probs[-1]])
+    smoothed_probs = jnp.vstack([smoothed_probs, filtered_probs[-1]])
 
     # Package into a posterior
     posterior = HMMPosterior(
@@ -352,6 +368,7 @@ def hmm_fixed_lag_smoother(
         posterior distribution
 
     """
+    # TODO: Update to allow variable length time series
     num_timesteps, num_states = log_likelihoods.shape
 
     def _step(carry, t):
@@ -441,7 +458,8 @@ def hmm_posterior_mode(
     transition_matrix: Union[Float[Array, "num_timesteps num_states num_states"],
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
-    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None
+    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]]= None,
+    num_timesteps: Optional[Int]=None,
 ) -> Int[Array, "num_timesteps"]:
     r"""Compute the most likely state sequence. This is called the Viterbi algorithm.
 
@@ -450,12 +468,14 @@ def hmm_posterior_mode(
         transition_matrix: $p(z_{t+1} \mid z_t, u_t, \theta)$
         log_likelihoods: $p(y_t \mid z_t, u_t, \theta)$ for $t=1,\ldots, T$.
         transition_fn: function that takes in an integer time index and returns a $K \times K$ transition matrix.
+        num_timesteps: number of "valid" timesteps, to support vmapping with padded arrays.
 
     Returns:
         most likely state sequence
 
     """
-    num_timesteps, num_states = log_likelihoods.shape
+    max_num_timesteps, _ = log_likelihoods.shape
+    num_timesteps = num_timesteps if num_timesteps is not None else max_num_timesteps
 
     # Run the backward pass
     def _backward_pass(best_next_score, t):
@@ -464,14 +484,19 @@ def _backward_pass(best_next_score, t):
         scores = jnp.log(A) + best_next_score + log_likelihoods[t + 1]
         best_next_state = jnp.argmax(scores, axis=1)
         best_next_score = jnp.max(scores, axis=1)
+
+        # Only update if log_likelihoods[t+1] is valid
+        best_next_score = jnp.where(t + 1 < num_timesteps, best_next_score, jnp.zeros(num_states))
+        best_next_state = jnp.where(t + 1 < num_timesteps, best_next_state, jnp.zeros(num_states, dtype=int))
+
         return best_next_score, best_next_state
 
     num_states = log_likelihoods.shape[1]
-    best_second_score, rev_best_next_states = lax.scan(
-        _backward_pass, jnp.zeros(num_states), jnp.arange(num_timesteps - 2, -1, -1)
+    best_second_score, best_next_states = lax.scan(
+        _backward_pass, jnp.zeros(num_states), jnp.arange(max_num_timesteps - 1),
+        reverse=True
     )
-    best_next_states = rev_best_next_states[::-1]
-
+
     # Run the forward pass
     def _forward_pass(state, best_next_state):
         next_state = best_next_state[state]
@@ -490,7 +515,8 @@ def hmm_posterior_sample(
     transition_matrix: Union[Float[Array, "num_timesteps num_states num_states"],
                              Float[Array, "num_states num_states"]],
     log_likelihoods: Float[Array, "num_timesteps num_states"],
-    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]] = None
+    transition_fn: Optional[Callable[[Int], Float[Array, "num_states num_states"]]] = None,
+    num_timesteps: Optional[Int] = None,
 ) -> Int[Array, "num_timesteps"]:
     r"""Sample a latent sequence from the posterior.
 
@@ -505,10 +531,11 @@ def hmm_posterior_sample(
         :sample of the latent states, $z_{1:T}$
 
     """
-    num_timesteps, num_states = log_likelihoods.shape
+    max_num_timesteps, num_states = log_likelihoods.shape
+    num_timesteps = num_timesteps if num_timesteps is not None else max_num_timesteps
 
     # Run the HMM filter
-    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn)
+    post = hmm_filter(initial_distribution, transition_matrix, log_likelihoods, transition_fn, num_timesteps)
     log_normalizer, filtered_probs = post.marginal_loglik, post.filtered_probs
 
     # Run the sampler backward in time
@@ -528,13 +555,13 @@ def _step(carry, args):
         return state, state
 
     # Run the HMM smoother
-    rngs = jr.split(rng, num_timesteps)
+    rngs = jr.split(rng, max_num_timesteps)
     last_state = jr.choice(rngs[-1], a=num_states, p=filtered_probs[-1])
-    args = (jnp.arange(num_timesteps - 1, 0, -1), rngs[:-1][::-1], filtered_probs[:-1][::-1])
-    _, rev_states = lax.scan(_step, last_state, args)
+    args = (jnp.arange(max_num_timesteps - 1), rngs[:-1], filtered_probs[:-1])
+    _, states = lax.scan(_step, last_state, args, reverse=True)
 
     # Reverse the arrays and return
-    states = jnp.concatenate([rev_states[::-1], jnp.array([last_state])])
+    states = jnp.concatenate([states, jnp.array([last_state])])
     return log_normalizer, states
 
 def _compute_sum_transition_probs(

dynamax/hidden_markov_model/inference_test.py

@@ -5,6 +5,7 @@
 import dynamax.hidden_markov_model.inference as core
 import dynamax.hidden_markov_model.parallel_inference as parallel
 
+from jax import vmap
 from jax.scipy.special import logsumexp
 
 def big_log_joint(initial_probs, transition_matrix, log_likelihoods):
@@ -259,6 +260,43 @@ def trans_mat_callable(t):
     assert jnp.allclose(sample, sample2)
 
 
+def test_hmm_padding(key=0, num_timesteps=10, num_states=5, padding=3):
+    if isinstance(key, int):
+        key = jr.PRNGKey(key)
+
+    initial_probs, transition_matrix, log_lkhds = random_hmm_args(key, num_timesteps + padding, num_states)
+
+    # Run the HMM filter with a 3d list of transition matrices and a callable
+    post = core.hmm_filter(initial_probs, transition_matrix, log_lkhds[:num_timesteps])
+    post2 = core.hmm_filter(initial_probs, transition_matrix, log_lkhds, num_timesteps=num_timesteps)
+    assert jnp.allclose(post.marginal_loglik, post2.marginal_loglik, atol=1e-4)
+    assert jnp.allclose(post.filtered_probs, post2.filtered_probs[:num_timesteps], atol=1e-4)
+
+    # Run the HMM smoother with a 3d list of transition matrices and a callable
+    post = core.hmm_smoother(initial_probs, transition_matrix, log_lkhds[:num_timesteps])
+    post2 = core.hmm_smoother(initial_probs, transition_matrix, log_lkhds, num_timesteps=num_timesteps)
+    assert jnp.allclose(post.smoothed_probs, post2.smoothed_probs[:num_timesteps], atol=1e-4)
+
+    # Run Viterbi
+    mode = core.hmm_posterior_mode(initial_probs, transition_matrix, log_lkhds[:num_timesteps])
+    mode2 = core.hmm_posterior_mode(initial_probs, transition_matrix, log_lkhds, num_timesteps=num_timesteps)
+    assert jnp.allclose(mode, mode2[:num_timesteps])
+
+
+# Test vmap
+def test_hmm_variable_length_vmap(key=0, max_num_timesteps=10, num_states=5, num_seqs=10):
+    if isinstance(key, int):
+        key = jr.PRNGKey(key)
+
+    all_args = vmap(random_hmm_args, in_axes=(0, None, None))(
+        jr.split(key, num_seqs), max_num_timesteps, num_states)
+
+    all_num_timesteps = jr.randint(key, (num_seqs,), 1, max_num_timesteps)
+
+    # Just make sure vmap runs without throwing a concretization error
+    posteriors = vmap(core.hmm_filter)(*all_args, num_timesteps=all_num_timesteps)
+
+
 def test_parallel_filter(key=0, num_timesteps=100, num_states=3):
     if isinstance(key, int):
         key = jr.PRNGKey(key)

dynamax/nonlinear_gaussian_ssm/inference_ekf.py

@@ -341,5 +341,6 @@ def _step(carry, _):
         smoothed_posterior = extended_kalman_smoother(params, emissions, smoothed_prior, inputs)
         return smoothed_posterior, None
 
+    # TODO: Does this even work with None as initial carry?
     smoothed_posterior, _ = lax.scan(_step, None, jnp.arange(num_iter))
     return smoothed_posterior