Allow creating MarginalModel from existing Model

Author: ricardoV94

Diff for: docs/api_reference.rst

@@ -10,6 +10,7 @@ methods in the current release of PyMC experimental.
 
    as_model
    MarginalModel
+   marginalize
    model_builder.ModelBuilder
 
 Inference

Diff for: pymc_experimental/model/marginal_model.py

@@ -1,5 +1,5 @@
 import warnings
-from typing import Sequence
+from typing import Sequence, Union
 
 import numpy as np
 import pymc
@@ -25,10 +25,12 @@
 from pytensor.tensor.shape import Shape
 from pytensor.tensor.special import log_softmax
 
-__all__ = ["MarginalModel"]
+__all__ = ["MarginalModel", "marginalize"]
 
 from pymc_experimental.distributions import DiscreteMarkovChain
 
+ModelRVs = TensorVariable | Sequence[TensorVariable] | str | Sequence[str]
+
 
 class MarginalModel(Model):
     """Subclass of PyMC Model that implements functionality for automatic
@@ -207,35 +209,50 @@ def logp(self, vars=None, **kwargs):
             vars = [m[var.name] for var in vars]
         return m._logp(vars=vars, **kwargs)
 
-    def clone(self):
-        m = MarginalModel(coords=self.coords)
-        model_vars = self.basic_RVs + self.potentials + self.deterministics + self.marginalized_rvs
-        data_vars = [var for name, var in self.named_vars.items() if var not in model_vars]
+    @staticmethod
+    def from_model(model: Union[Model, "MarginalModel"]) -> "MarginalModel":
+        new_model = MarginalModel(coords=model.coords)
+        if isinstance(model, MarginalModel):
+            marginalized_rvs = model.marginalized_rvs
+            marginalized_named_vars_to_dims = model._marginalized_named_vars_to_dims
+        else:
+            marginalized_rvs = []
+            marginalized_named_vars_to_dims = {}
+
+        model_vars = model.basic_RVs + model.potentials + model.deterministics + marginalized_rvs
+        data_vars = [var for name, var in model.named_vars.items() if var not in model_vars]
         vars = model_vars + data_vars
         cloned_vars = clone_replace(vars)
         vars_to_clone = {var: cloned_var for var, cloned_var in zip(vars, cloned_vars)}
-        m.vars_to_clone = vars_to_clone
-
-        m.named_vars = treedict({name: vars_to_clone[var] for name, var in self.named_vars.items()})
-        m.named_vars_to_dims = self.named_vars_to_dims
-        m.values_to_rvs = {i: vars_to_clone[rv] for i, rv in self.values_to_rvs.items()}
-        m.rvs_to_values = {vars_to_clone[rv]: i for rv, i in self.rvs_to_values.items()}
-        m.rvs_to_transforms = {vars_to_clone[rv]: i for rv, i in self.rvs_to_transforms.items()}
-        m.rvs_to_initial_values = {
-            vars_to_clone[rv]: i for rv, i in self.rvs_to_initial_values.items()
+        new_model.vars_to_clone = vars_to_clone
+
+        new_model.named_vars = treedict(
+            {name: vars_to_clone[var] for name, var in model.named_vars.items()}
+        )
+        new_model.named_vars_to_dims = model.named_vars_to_dims
+        new_model.values_to_rvs = {vv: vars_to_clone[rv] for vv, rv in model.values_to_rvs.items()}
+        new_model.rvs_to_values = {vars_to_clone[rv]: vv for rv, vv in model.rvs_to_values.items()}
+        new_model.rvs_to_transforms = {
+            vars_to_clone[rv]: tr for rv, tr in model.rvs_to_transforms.items()
+        }
+        new_model.rvs_to_initial_values = {
+            vars_to_clone[rv]: iv for rv, iv in model.rvs_to_initial_values.items()
         }
-        m.free_RVs = [vars_to_clone[rv] for rv in self.free_RVs]
-        m.observed_RVs = [vars_to_clone[rv] for rv in self.observed_RVs]
-        m.potentials = [vars_to_clone[pot] for pot in self.potentials]
-        m.deterministics = [vars_to_clone[det] for det in self.deterministics]
+        new_model.free_RVs = [vars_to_clone[rv] for rv in model.free_RVs]
+        new_model.observed_RVs = [vars_to_clone[rv] for rv in model.observed_RVs]
+        new_model.potentials = [vars_to_clone[pot] for pot in model.potentials]
+        new_model.deterministics = [vars_to_clone[det] for det in model.deterministics]
 
-        m.marginalized_rvs = [vars_to_clone[rv] for rv in self.marginalized_rvs]
-        m._marginalized_named_vars_to_dims = self._marginalized_named_vars_to_dims
-        return m
+        new_model.marginalized_rvs = [vars_to_clone[rv] for rv in marginalized_rvs]
+        new_model._marginalized_named_vars_to_dims = marginalized_named_vars_to_dims
+        return new_model
+
+    def clone(self):
+        return self.from_model(self)
 
     def marginalize(
         self,
-        rvs_to_marginalize: TensorVariable | Sequence[TensorVariable] | str | Sequence[str],
+        rvs_to_marginalize: ModelRVs,
     ):
         if not isinstance(rvs_to_marginalize, Sequence):
             rvs_to_marginalize = (rvs_to_marginalize,)
@@ -491,6 +508,35 @@ def transform_input(inputs):
             return rv_dataset
 
 
+def marginalize(model: Model, rvs_to_marginalize: ModelRVs) -> MarginalModel:
+    """Marginalize a subset of variables in a PyMC model.
+
+    This creates a class of `MarginalModel` from an existing `Model`, with the specified
+    variables marginalized.
+
+    See documentation for `MarginalModel` for more information.
+
+    Parameters
+    ----------
+    model : Model
+        PyMC model to marginalize. Original variables well be cloned.
+    rvs_to_marginalize : Sequence[TensorVariable]
+        Variables to marginalize in the returned model.
+
+    Returns
+    -------
+    marginal_model: MarginalModel
+        Marginal model with the specified variables marginalized.
+    """
+    if not isinstance(rvs_to_marginalize, tuple | list):
+        rvs_to_marginalize = (rvs_to_marginalize,)
+    rvs_to_marginalize = [rv if isinstance(rv, str) else rv.name for rv in rvs_to_marginalize]
+
+    marginal_model = MarginalModel.from_model(model)
+    marginal_model.marginalize(rvs_to_marginalize)
+    return marginal_model
+
+
 class MarginalRV(SymbolicRandomVariable):
     """Base class for Marginalized RVs"""
 

Diff for: pymc_experimental/tests/model/test_marginal_model.py

@@ -10,6 +10,7 @@
 from pymc import ImputationWarning, inputvars
 from pymc.distributions import transforms
 from pymc.logprob.abstract import _logprob
+from pymc.model.fgraph import fgraph_from_model
 from pymc.util import UNSET
 from scipy.special import log_softmax, logsumexp
 from scipy.stats import halfnorm, norm
@@ -19,7 +20,9 @@
     FiniteDiscreteMarginalRV,
     MarginalModel,
     is_conditional_dependent,
+    marginalize,
 )
+from pymc_experimental.tests.utils import equal_computations_up_to_root
 
 
 @pytest.fixture
@@ -776,3 +779,33 @@ def test_mutable_indexing_jax_backend():
         pm.LogNormal("y", mu=cat_effect[cat_effect_idx], sigma=1 + is_outlier, observed=data)
     model.marginalize(["is_outlier"])
     get_jaxified_logp(model)
+
+
+def test_marginal_model_func():
+    def create_model(model_class):
+        with model_class(coords={"trial": range(10)}) as m:
+            idx = pm.Bernoulli("idx", p=0.5, dims="trial")
+            mu = pt.where(idx, 1, -1)
+            sigma = pm.HalfNormal("sigma")
+            y = pm.Normal("y", mu=mu, sigma=sigma, dims="trial", observed=[1] * 10)
+        return m
+
+    marginal_m = marginalize(create_model(pm.Model), ["idx"])
+    assert isinstance(marginal_m, MarginalModel)
+
+    reference_m = create_model(MarginalModel)
+    reference_m.marginalize(["idx"])
+
+    # Check forward graph representation is the same
+    marginal_fgraph, _ = fgraph_from_model(marginal_m)
+    reference_fgraph, _ = fgraph_from_model(reference_m)
+    assert equal_computations_up_to_root(marginal_fgraph.outputs, reference_fgraph.outputs)
+
+    # Check logp graph is the same
+    # This fails because OpFromGraphs comparison is broken
+    # assert equal_computations_up_to_root([marginal_m.logp()], [reference_m.logp()])
+    ip = marginal_m.initial_point()
+    np.testing.assert_allclose(
+        marginal_m.compile_logp()(ip),
+        reference_m.compile_logp()(ip),
+    )

Diff for: pymc_experimental/tests/utils.py

@@ -0,0 +1,31 @@
+from typing import Sequence
+
+from pytensor.compile import SharedVariable
+from pytensor.graph import Constant, graph_inputs
+from pytensor.graph.basic import Variable, equal_computations
+from pytensor.tensor.random.type import RandomType
+
+
+def equal_computations_up_to_root(
+    xs: Sequence[Variable], ys: Sequence[Variable], ignore_rng_values=True
+) -> bool:
+    # Check if graphs are equivalent even if root variables have distinct identities
+
+    x_graph_inputs = [var for var in graph_inputs(xs) if not isinstance(var, Constant)]
+    y_graph_inputs = [var for var in graph_inputs(ys) if not isinstance(var, Constant)]
+    if len(x_graph_inputs) != len(y_graph_inputs):
+        return False
+    for x, y in zip(x_graph_inputs, y_graph_inputs):
+        if x.type != y.type:
+            return False
+        if x.name != y.name:
+            return False
+        if isinstance(x, SharedVariable):
+            if not isinstance(y, SharedVariable):
+                return False
+            if isinstance(x.type, RandomType) and ignore_rng_values:
+                continue
+            if not x.type.values_eq(x.get_value(), y.get_value()):
+                return False
+
+    return equal_computations(xs, ys, in_xs=x_graph_inputs, in_ys=y_graph_inputs)