Fix bug in univariate Ordered and SumTo1 transform logp

docs/source/api/distributions/transforms.rst

@@ -19,6 +19,7 @@ Transform instances are the entities that should be used in the
     logodds
     simplex
     sum_to_1
+    ordered
 
 
 Specific Transform Classes

pymc/distributions/discrete.py

@@ -1259,7 +1259,7 @@ class OrderedLogistic:
         # Ordered logistic regression
         with pm.Model() as model:
             cutpoints = pm.Normal("cutpoints", mu=[-1,1], sigma=10, shape=2,
-                                  transform=pm.distributions.transforms.univariate_ordered)
+                                  transform=pm.distributions.transforms.ordered)
             y_ = pm.OrderedLogistic("y", cutpoints=cutpoints, eta=x, observed=y)
             idata = pm.sample()
 

pymc/distributions/mixture.py

@@ -539,7 +539,7 @@ class NormalMixture:
                 mu=data.mean(),
                 sigma=10,
                 shape=n_components,
-                transform=pm.distributions.transforms.univariate_ordered,
+                transform=pm.distributions.transforms.ordered,
                 initval=[1, 2, 3],
             )
             σ = pm.HalfNormal("σ", sigma=10, shape=n_components)

pymc/distributions/transforms.py

@@ -11,6 +11,8 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+import warnings
+
 from functools import singledispatch
 
 import numpy as np
@@ -39,19 +41,28 @@
     "logodds",
     "Interval",
     "log_exp_m1",
-    "univariate_ordered",
-    "multivariate_ordered",
+    "ordered",
     "log",
     "sum_to_1",
-    "univariate_sum_to_1",
-    "multivariate_sum_to_1",
     "circular",
     "CholeskyCovPacked",
     "Chain",
     "ZeroSumTransform",
 ]
 
 
+def __getattr__(name):
+    if name in ("univariate_ordered", "multivariate_ordered"):
+        warnings.warn(f"{name} has been deprecated, use ordered instead.", FutureWarning)
+        return ordered
+
+    if name in ("univariate_sum_to_1, multivariate_sum_to_1"):
+        warnings.warn(f"{name} has been deprecated, use sum_to_1 instead.", FutureWarning)
+        return sum_to_1
+
+    raise AttributeError(f"module {__name__} has no attribute {name}")
+
+
 @singledispatch
 def _default_transform(op: Op, rv: TensorVariable):
     """Return default transform for a given Distribution `Op`"""
@@ -79,31 +90,24 @@ def log_jac_det(self, value, *inputs):
 class Ordered(RVTransform):
     name = "ordered"
 
-    def __init__(self, ndim_supp=0):
-        if ndim_supp > 1:
-            raise ValueError(
-                f"For Ordered transformation number of core dimensions"
-                f"(ndim_supp) must not exceed 1 but is {ndim_supp}"
-            )
-        self.ndim_supp = ndim_supp
+    def __init__(self, ndim_supp=None):
+        if ndim_supp is not None:
+            warnings.warn("ndim_supp argument is deprecated and has no effect", FutureWarning)
 
     def backward(self, value, *inputs):
         x = pt.zeros(value.shape)
-        x = pt.inc_subtensor(x[..., 0], value[..., 0])
-        x = pt.inc_subtensor(x[..., 1:], pt.exp(value[..., 1:]))
+        x = pt.set_subtensor(x[..., 0], value[..., 0])
+        x = pt.set_subtensor(x[..., 1:], pt.exp(value[..., 1:]))
         return pt.cumsum(x, axis=-1)
 
     def forward(self, value, *inputs):
         y = pt.zeros(value.shape)
-        y = pt.inc_subtensor(y[..., 0], value[..., 0])
-        y = pt.inc_subtensor(y[..., 1:], pt.log(value[..., 1:] - value[..., :-1]))
+        y = pt.set_subtensor(y[..., 0], value[..., 0])
+        y = pt.set_subtensor(y[..., 1:], pt.log(value[..., 1:] - value[..., :-1]))
         return y
 
     def log_jac_det(self, value, *inputs):
-        if self.ndim_supp == 0:
-            return pt.sum(value[..., 1:], axis=-1, keepdims=True)
-        else:
-            return pt.sum(value[..., 1:], axis=-1)
+        return pt.sum(value[..., 1:], axis=-1)
 
 
 class SumTo1(RVTransform):
@@ -114,13 +118,9 @@ class SumTo1(RVTransform):
 
     name = "sumto1"
 
-    def __init__(self, ndim_supp=0):
-        if ndim_supp > 1:
-            raise ValueError(
-                f"For SumTo1 transformation number of core dimensions"
-                f"(ndim_supp) must not exceed 1 but is {ndim_supp}"
-            )
-        self.ndim_supp = ndim_supp
+    def __init__(self, ndim_supp=None):
+        if ndim_supp is not None:
+            warnings.warn("ndim_supp argument is deprecated and has no effect", FutureWarning)
 
     def backward(self, value, *inputs):
         remaining = 1 - pt.sum(value[..., :], axis=-1, keepdims=True)
@@ -131,10 +131,7 @@ def forward(self, value, *inputs):
 
     def log_jac_det(self, value, *inputs):
         y = pt.zeros(value.shape)
-        if self.ndim_supp == 0:
-            return pt.sum(y, axis=-1, keepdims=True)
-        else:
-            return pt.sum(y, axis=-1)
+        return pt.sum(y, axis=-1)
 
 
 class CholeskyCovPacked(RVTransform):
@@ -359,38 +356,21 @@ def extend_axis_rev(array, axis):
 Instantiation of :class:`pymc.distributions.transforms.LogExpM1`
 for use in the ``transform`` argument of a random variable."""
 
-univariate_ordered = Ordered(ndim_supp=0)
-univariate_ordered.__doc__ = """
+# Deprecated
+ordered = Ordered()
+ordered.__doc__ = """
 Instantiation of :class:`pymc.distributions.transforms.Ordered`
-for use in the ``transform`` argument of a univariate random variable."""
-
-multivariate_ordered = Ordered(ndim_supp=1)
-multivariate_ordered.__doc__ = """
-Instantiation of :class:`pymc.distributions.transforms.Ordered`
-for use in the ``transform`` argument of a multivariate random variable."""
+for use in the ``transform`` argument of a random variable."""
 
 log = LogTransform()
 log.__doc__ = """
 Instantiation of :class:`pymc.logprob.transforms.LogTransform`
 for use in the ``transform`` argument of a random variable."""
 
-univariate_sum_to_1 = SumTo1(ndim_supp=0)
-univariate_sum_to_1.__doc__ = """
-Instantiation of :class:`pymc.distributions.transforms.SumTo1`
-for use in the ``transform`` argument of a univariate random variable."""
-
-multivariate_sum_to_1 = SumTo1(ndim_supp=1)
-multivariate_sum_to_1.__doc__ = """
-Instantiation of :class:`pymc.distributions.transforms.SumTo1`
-for use in the ``transform`` argument of a multivariate random variable."""
-
-# backwards compatibility
-sum_to_1 = SumTo1(ndim_supp=1)
+sum_to_1 = SumTo1()
 sum_to_1.__doc__ = """
 Instantiation of :class:`pymc.distributions.transforms.SumTo1`
-for use in the ``transform`` argument of a random variable.
-This instantiation is for backwards compatibility only.
-Please use `univariate_sum_to_1` or `multivariate_sum_to_1` instead."""
+for use in the ``transform`` argument of a random variable."""
 
 circular = CircularTransform()
 circular.__doc__ = """

pymc/logprob/transforms.py

@@ -195,6 +195,9 @@
             phi_inv = self.backward(value, *inputs)
             return pt.log(pt.abs(pt.nlinalg.det(pt.atleast_2d(jacobian(phi_inv, [value])[0]))))
 
+    def __str__(self):
+        return f"{self.__class__.__name__}"
+
 
 @node_rewriter(tracks=None)
 def transform_values(fgraph: FunctionGraph, node: Node) -> Optional[List[Node]]:
@@ -1219,22 +1222,46 @@
         if not isinstance(logprobs, Sequence):
             logprobs = [logprobs]
 
-        if use_jacobian:
-            assert len(values) == len(logprobs) == len(op.transforms)
-            logprobs_jac = []
-            for value, transform, logp in zip(values, op.transforms, logprobs):
-                if transform is None:
-                    logprobs_jac.append(logp)
-                    continue
-                assert isinstance(value.owner.op, TransformedVariable)
-                original_forward_value = value.owner.inputs[1]
-                jacobian = transform.log_jac_det(original_forward_value, *inputs).copy()
+        # Handle jacobian
+        assert len(values) == len(logprobs) == len(op.transforms)
+        logprobs_jac = []
+        for value, transform, logp in zip(values, op.transforms, logprobs):
+            if transform is None:
+                logprobs_jac.append(logp)
+                continue
+
+            assert isinstance(value.owner.op, TransformedVariable)
+            original_forward_value = value.owner.inputs[1]
+            log_jac_det = transform.log_jac_det(original_forward_value, *inputs).copy()
+            # The jacobian determinant has less dims than the logp
+            # when a multivariate transform (like Simplex or Ordered) is applied to univariate distributions.
+            # In this case we have to reduce the last logp dimensions, as they are no longer independent
+            if log_jac_det.ndim < logp.ndim:
+                diff_ndims = logp.ndim - log_jac_det.ndim
+                logp = logp.sum(axis=np.arange(-diff_ndims, 0))
+            # This case is sometimes, but not always, trivial to accomodate depending on the "space rank" of the
+            # multivariate distribution. See https://proceedings.mlr.press/v130/radul21a.html
+            elif log_jac_det.ndim > logp.ndim:
+                raise NotImplementedError(
+                    f"Univariate transform {transform} cannot be applied to multivariate {rv_op}"
+                )
+            else:
+                # Check there is no broadcasting between logp and jacobian
+                if logp.type.broadcastable != log_jac_det.type.broadcastable:
+                    raise ValueError(
+                        f"The logp of {rv_op} and log_jac_det of {transform} are not allowed to broadcast together. "
+                        "There is a bug in the implementation of either one."
+                    )
+
+            if use_jacobian:
                 if value.name:
-                    jacobian.name = f"{value.name}_jacobian"
-                logprobs_jac.append(logp + jacobian)
-            logprobs = logprobs_jac
+                    log_jac_det.name = f"{value.name}_jacobian"
+                logprobs_jac.append(logp + log_jac_det)
+            else:
+                # We still want to use the reduced logp, even though the jacobian isn't included
+                logprobs_jac.append(logp)
 
-        return logprobs
+        return logprobs_jac
 
     new_op = copy(rv_op)
     new_op.__class__ = new_op_type