Marginalize DiscreteMarkovChain

Co-authored-by: Jesse Grabowski <[email protected]>

Author: ricardoV94

pymc_experimental/model/marginal_model.py

@@ -10,21 +10,16 @@
 from pymc.distributions.discrete import Bernoulli, Categorical, DiscreteUniform
 from pymc.distributions.transforms import Chain
 from pymc.logprob.abstract import _logprob
-from pymc.logprob.basic import conditional_logp
+from pymc.logprob.basic import conditional_logp, logp
 from pymc.logprob.transforms import IntervalTransform
 from pymc.model import Model
 from pymc.pytensorf import compile_pymc, constant_fold, inputvars
 from pymc.util import _get_seeds_per_chain, dataset_to_point_list, treedict
-from pytensor import Mode
+from pytensor import Mode, scan
 from pytensor.compile import SharedVariable
 from pytensor.compile.builders import OpFromGraph
-from pytensor.graph import (
-    Constant,
-    FunctionGraph,
-    ancestors,
-    clone_replace,
-    vectorize_graph,
-)
+from pytensor.graph import Constant, FunctionGraph, ancestors, clone_replace
+from pytensor.graph.replace import vectorize_graph
 from pytensor.scan import map as scan_map
 from pytensor.tensor import TensorType, TensorVariable
 from pytensor.tensor.elemwise import Elemwise
@@ -33,6 +28,8 @@
 
 __all__ = ["MarginalModel"]
 
+from pymc_experimental.distributions import DiscreteMarkovChain
+
 
 class MarginalModel(Model):
     """Subclass of PyMC Model that implements functionality for automatic
@@ -247,16 +244,25 @@ def marginalize(
             self[var] if isinstance(var, str) else var for var in rvs_to_marginalize
         ]
 
-        supported_dists = (Bernoulli, Categorical, DiscreteUniform)
         for rv_to_marginalize in rvs_to_marginalize:
             if rv_to_marginalize not in self.free_RVs:
                 raise ValueError(
                     f"Marginalized RV {rv_to_marginalize} is not a free RV in the model"
                 )
-            if not isinstance(rv_to_marginalize.owner.op, supported_dists):
+
+            rv_op = rv_to_marginalize.owner.op
+            if isinstance(rv_op, DiscreteMarkovChain):
+                if rv_op.n_lags > 1:
+                    raise NotImplementedError(
+                        "Marginalization for DiscreteMarkovChain with n_lags > 1 is not supported"
+                    )
+                if rv_to_marginalize.owner.inputs[0].type.ndim > 2:
+                    raise NotImplementedError(
+                        "Marginalization for DiscreteMarkovChain with non-matrix transition probability is not supported"
+                    )
+            elif not isinstance(rv_op, (Bernoulli, Categorical, DiscreteUniform)):
                 raise NotImplementedError(
-                    f"RV with distribution {rv_to_marginalize.owner.op} cannot be marginalized. "
-                    f"Supported distribution include {supported_dists}"
+                    f"Marginalization of RV with distribution {rv_to_marginalize.owner.op} is not supported"
                 )
 
             if rv_to_marginalize.name in self.named_vars_to_dims:
@@ -492,6 +498,10 @@ class FiniteDiscreteMarginalRV(MarginalRV):
     """Base class for Finite Discrete Marginalized RVs"""
 
 
+class DiscreteMarginalMarkovChainRV(MarginalRV):
+    """Base class for Discrete Marginal Markov Chain RVs"""
+
+
 def static_shape_ancestors(vars):
     """Identify ancestors Shape Ops of static shapes (therefore constant in a valid graph)."""
     return [
@@ -620,11 +630,17 @@ def replace_finite_discrete_marginal_subgraph(fgraph, rv_to_marginalize, all_rvs
     replace_inputs.update({input_rv: input_rv.type() for input_rv in input_rvs})
     cloned_outputs = clone_replace(outputs, replace=replace_inputs)
 
-    marginalization_op = FiniteDiscreteMarginalRV(
+    if isinstance(rv_to_marginalize.owner.op, DiscreteMarkovChain):
+        marginalize_constructor = DiscreteMarginalMarkovChainRV
+    else:
+        marginalize_constructor = FiniteDiscreteMarginalRV
+
+    marginalization_op = marginalize_constructor(
         inputs=list(replace_inputs.values()),
         outputs=cloned_outputs,
         ndim_supp=ndim_supp,
     )
+
     marginalized_rvs = marginalization_op(*replace_inputs.keys())
     fgraph.replace_all(tuple(zip(rvs_to_marginalize, marginalized_rvs)))
     return rvs_to_marginalize, marginalized_rvs
@@ -640,14 +656,17 @@ def get_domain_of_finite_discrete_rv(rv: TensorVariable) -> Tuple[int, ...]:
     elif isinstance(op, DiscreteUniform):
         lower, upper = constant_fold(rv.owner.inputs[3:])
         return tuple(range(lower, upper + 1))
+    elif isinstance(op, DiscreteMarkovChain):
+        P = rv.owner.inputs[0]
+        return tuple(range(pt.get_vector_length(P[-1])))
 
     raise NotImplementedError(f"Cannot compute domain for op {op}")
 
 
 def _add_reduce_batch_dependent_logps(
     marginalized_type: TensorType, dependent_logps: Sequence[TensorVariable]
 ):
-    """Add the logps of dependent RVs while reducing extra batch dims as assessed from the `marginalized_type`."""
+    """Add the logps of dependent RVs while reducing extra batch dims relative to `marginalized_type`."""
 
     mbcast = marginalized_type.broadcastable
     reduced_logps = []
@@ -730,3 +749,69 @@ def logp_fn(marginalized_rv_const, *non_sequences):
 
     # We have to add dummy logps for the remaining value variables, otherwise PyMC will raise
     return joint_logps, *(pt.constant(0),) * (len(values) - 1)
+
+
+@_logprob.register(DiscreteMarginalMarkovChainRV)
+def marginal_hmm_logp(op, values, *inputs, **kwargs):
+
+    marginalized_rvs_node = op.make_node(*inputs)
+    inner_rvs = clone_replace(
+        op.inner_outputs,
+        replace={u: v for u, v in zip(op.inner_inputs, marginalized_rvs_node.inputs)},
+    )
+
+    chain_rv, *dependent_rvs = inner_rvs
+    P, n_steps_, init_dist_, rng = chain_rv.owner.inputs
+    domain = pt.arange(P.shape[-1], dtype="int32")
+
+    # Construct logp in two steps
+    # Step 1: Compute the probability of the data ("emissions") under every possible state (vec_logp_emission)
+
+    # First we need to vectorize the conditional logp graph of the data, in case there are batch dimensions floating
+    # around. To do this, we need to break the dependency between chain and the init_dist_ random variable. Otherwise,
+    # PyMC will detect a random variable in the logp graph (init_dist_), that isn't relevant at this step.
+    chain_value = chain_rv.clone()
+    dependent_rvs = clone_replace(dependent_rvs, {chain_rv: chain_value})
+    logp_emissions_dict = conditional_logp(dict(zip(dependent_rvs, values)))
+
+    # Reduce and add the batch dims beyond the chain dimension
+    reduced_logp_emissions = _add_reduce_batch_dependent_logps(
+        chain_rv.type, logp_emissions_dict.values()
+    )
+
+    # Add a batch dimension for the domain of the chain
+    chain_shape = constant_fold(tuple(chain_rv.shape))
+    batch_chain_value = pt.moveaxis(pt.full((*chain_shape, domain.size), domain), -1, 0)
+    batch_logp_emissions = vectorize_graph(reduced_logp_emissions, {chain_value: batch_chain_value})
+
+    # Step 2: Compute the transition probabilities
+    # This is the "forward algorithm", alpha_t = p(y | s_t) * sum_{s_{t-1}}(p(s_t | s_{t-1}) * alpha_{t-1})
+    # We do it entirely in logs, though.
+
+    # To compute the prior probabilities of each state, we evaluate the logp of the domain (all possible states) under
+    # the initial distribution. This is robust to everything the user can throw at it.
+    batch_logp_init_dist = pt.vectorize(lambda x: logp(init_dist_, x), "()->()")(
+        batch_chain_value[..., 0]
+    )
+    log_alpha_init = batch_logp_init_dist + batch_logp_emissions[..., 0]
+
+    def step_alpha(logp_emission, log_alpha, log_P):
+        step_log_prob = pt.logsumexp(log_alpha[:, None] + log_P, axis=0)
+        return logp_emission + step_log_prob
+
+    P_bcast_dims = (len(chain_shape) - 1) - (P.type.ndim - 2)
+    log_P = pt.shape_padright(pt.log(P), P_bcast_dims)
+    log_alpha_seq, _ = scan(
+        step_alpha,
+        non_sequences=[log_P],
+        outputs_info=[log_alpha_init],
+        # Scan needs the time dimension first, and we already consumed the 1st logp computing the initial value
+        sequences=pt.moveaxis(batch_logp_emissions[..., 1:], -1, 0),
+    )
+    # Final logp is just the sum of the last scan state
+    joint_logp = pt.logsumexp(log_alpha_seq[-1], axis=0)
+
+    # If there are multiple emission streams, we have to add dummy logps for the remaining value variables. The first
+    # return is the joint probability of everything together, but PyMC still expects one logp for each one.
+    dummy_logps = (pt.constant(0),) * (len(values) - 1)
+    return joint_logp, *dummy_logps

pymc_experimental/tests/model/test_marginal_model.py

@@ -14,6 +14,7 @@
 from scipy.special import log_softmax, logsumexp
 from scipy.stats import halfnorm, norm
 
+from pymc_experimental.distributions import DiscreteMarkovChain
 from pymc_experimental.model.marginal_model import (
     FiniteDiscreteMarginalRV,
     MarginalModel,
@@ -673,3 +674,87 @@ def dist(idx, size):
     ):
         pt = {"norm": test_value}
         np.testing.assert_allclose(logp_fn(pt), ref_logp_fn(pt))
+
+
+@pytest.mark.parametrize("batch_chain", (False, True), ids=lambda x: f"batch_chain={x}")
+@pytest.mark.parametrize("batch_emission", (False, True), ids=lambda x: f"batch_emission={x}")
+def test_marginalized_hmm_normal_emission(batch_chain, batch_emission):
+    if batch_chain and not batch_emission:
+        pytest.skip("Redundant implicit combination")
+
+    with MarginalModel() as m:
+        P = [[0, 1], [1, 0]]
+        init_dist = pm.Categorical.dist(p=[1, 0])
+        chain = DiscreteMarkovChain(
+            "chain", P=P, init_dist=init_dist, steps=3, shape=(3, 4) if batch_chain else None
+        )
+        emission = pm.Normal(
+            "emission", mu=chain * 2 - 1, sigma=1e-1, shape=(3, 4) if batch_emission else None
+        )
+
+    m.marginalize([chain])
+    logp_fn = m.compile_logp()
+
+    test_value = np.array([-1, 1, -1, 1])
+    expected_logp = pm.logp(pm.Normal.dist(0, 1e-1), np.zeros_like(test_value)).sum().eval()
+    if batch_emission:
+        test_value = np.broadcast_to(test_value, (3, 4))
+        expected_logp *= 3
+    np.testing.assert_allclose(logp_fn({f"emission": test_value}), expected_logp)
+
+
+@pytest.mark.parametrize(
+    "categorical_emission",
+    [
+        False,
+        # Categorical has a core vector parameter,
+        # so it is not possible to build a graph that uses elemwise operations exclusively
+        pytest.param(True, marks=pytest.mark.xfail(raises=NotImplementedError)),
+    ],
+)
+def test_marginalized_hmm_categorical_emission(categorical_emission):
+    """Example adapted from https://www.youtube.com/watch?v=9-sPm4CfcD0"""
+    with MarginalModel() as m:
+        P = np.array([[0.5, 0.5], [0.3, 0.7]])
+        init_dist = pm.Categorical.dist(p=[0.375, 0.625])
+        chain = DiscreteMarkovChain("chain", P=P, init_dist=init_dist, steps=2)
+        if categorical_emission:
+            emission = pm.Categorical(
+                "emission", p=pt.where(pt.eq(chain, 0)[..., None], [0.8, 0.2], [0.4, 0.6])
+            )
+        else:
+            emission = pm.Bernoulli("emission", p=pt.where(pt.eq(chain, 0), 0.2, 0.6))
+    m.marginalize([chain])
+
+    test_value = np.array([0, 0, 1])
+    expected_logp = np.log(0.1344)  # Shown at the 10m22s mark in the video
+    logp_fn = m.compile_logp()
+    np.testing.assert_allclose(logp_fn({f"emission": test_value}), expected_logp)
+
+
+@pytest.mark.parametrize("batch_emission1", (False, True))
+@pytest.mark.parametrize("batch_emission2", (False, True))
+def test_marginalized_hmm_multiple_emissions(batch_emission1, batch_emission2):
+    emission1_shape = (2, 4) if batch_emission1 else (4,)
+    emission2_shape = (2, 4) if batch_emission2 else (4,)
+    with MarginalModel() as m:
+        P = [[0, 1], [1, 0]]
+        init_dist = pm.Categorical.dist(p=[1, 0])
+        chain = DiscreteMarkovChain("chain", P=P, init_dist=init_dist, steps=3)
+        emission_1 = pm.Normal("emission_1", mu=chain * 2 - 1, sigma=1e-1, shape=emission1_shape)
+        emission_2 = pm.Normal(
+            "emission_2", mu=(1 - chain) * 2 - 1, sigma=1e-1, shape=emission2_shape
+        )
+
+    with pytest.warns(UserWarning, match="multiple dependent variables"):
+        m.marginalize([chain])
+
+    logp_fn = m.compile_logp()
+
+    test_value = np.array([-1, 1, -1, 1])
+    multiplier = 2 + batch_emission1 + batch_emission2
+    expected_logp = norm.logpdf(np.zeros_like(test_value), 0, 1e-1).sum() * multiplier
+    test_value_emission1 = np.broadcast_to(test_value, emission1_shape)
+    test_value_emission2 = np.broadcast_to(-test_value, emission2_shape)
+    test_point = {"emission_1": test_value_emission1, "emission_2": test_value_emission2}
+    np.testing.assert_allclose(logp_fn(test_point), expected_logp)