pymc-extras 0.2.0__py3-none-any.whl

pymc_extras/model/transforms/autoreparam.py

@@ -0,0 +1,434 @@
+import logging
+
+from collections.abc import Sequence
+from dataclasses import dataclass
+from functools import singledispatch
+
+import numpy as np
+import pymc as pm
+import pytensor
+import pytensor.tensor as pt
+import scipy.special
+
+from pymc.distributions import SymbolicRandomVariable
+from pymc.logprob.transforms import Transform
+from pymc.model.fgraph import (
+    ModelDeterministic,
+    ModelNamed,
+    fgraph_from_model,
+    model_deterministic,
+    model_free_rv,
+    model_from_fgraph,
+    model_named,
+)
+from pymc.pytensorf import toposort_replace
+from pytensor.graph.basic import Apply, Variable
+from pytensor.tensor.random.op import RandomVariable
+
+_log = logging.getLogger("pmx")
+
+
+@dataclass
+class VIP:
+    r"""Helper to reparemetrize VIP model.
+
+    Manipulation of :math:`\lambda` in the below equation is done using this helper class.
+
+    .. math::
+
+        \begin{align*}
+        \eta_{k} &\sim \text{normal}(\lambda_{k} \cdot \mu, \sigma^{\lambda_{k}})\\
+        \theta_{k} &= \mu + \sigma^{1 - \lambda_{k}} ( \eta_{k}  - \lambda_{k} \cdot \mu)
+        \sim \text{normal}(\mu, \sigma).
+        \end{align*}
+    """
+
+    _logit_lambda: dict[str, pytensor.tensor.sharedvar.TensorSharedVariable]
+
+    @property
+    def variational_parameters(self) -> list[pytensor.tensor.sharedvar.TensorSharedVariable]:
+        r"""Return raw :math:`\operatorname{logit}(\lambda_k)` for custom optimization.
+
+        Examples
+        --------
+        with model:
+            # set all parameterizations to mix of centered and non-centered
+            vip.set_all_lambda(0.5)
+
+            pm.fit(more_obj_params=vip.variational_parameters, method="fullrank_advi")
+        """
+        return list(self._logit_lambda.values())
+
+    def truncate_lambda(self, **kwargs: float):
+        r"""Truncate :math:`\lambda_k` with :math:`\varepsilon`.
+
+        .. math::
+
+            \hat \lambda_k = \begin{cases}
+                0, \quad &\lambda_k \le \varepsilon\\
+                \lambda_k, \quad &\varepsilon \lt \lambda_k \lt 1-\varepsilon\\
+                1, \quad &\lambda_k \ge 1-\varepsilon\\
+            \end{cases}
+
+        Parameters
+        ----------
+        kwargs : Dict[str, float]
+            Variable to :math:`\varepsilon` mapping.
+            If :math:`\lambda` (or :math:`1-\lambda`) is not passing
+            the threshold of :math:`\varepsilon`, it will be clipped
+            to 1 or zero if rounding is turned on.
+        """
+        lambdas = self.get_lambda()
+        update = dict()
+        for var, eps in kwargs.items():
+            lam = lambdas[var]
+            update[var] = np.piecewise(
+                lam,
+                [lam < eps, lam > (1 - eps)],
+                [0, 1, lambda x: x],
+            )
+        self.set_lambda(**update)
+
+    def truncate_all_lambda(self, value: float):
+        r"""Truncate all :math:`\lambda_k` with :math:`\varepsilon`.
+
+        .. math::
+
+            \hat \lambda_k = \begin{cases}
+                0, \quad &\lambda_k \le \varepsilon\\
+                \lambda_k, \quad &\varepsilon \lt \lambda_k \lt 1-\varepsilon\\
+                1, \quad &\lambda_k \ge 1-\varepsilon\\
+            \end{cases}
+
+
+
+        Parameters
+        ----------
+        value : float
+            :math:`\varepsilon`
+        """
+        truncate = dict.fromkeys(
+            self._logit_lambda.keys(),
+            value,
+        )
+        self.truncate_lambda(**truncate)
+
+    def get_lambda(self) -> dict[str, np.ndarray]:
+        r"""Get :math:`\lambda_k` that are currently used by the model.
+
+        Returns
+        -------
+        Dict[str, np.ndarray]
+            Mapping from variable name to :math:`\lambda_k`.
+        """
+        return {
+            name: scipy.special.expit(shared.get_value())
+            for name, shared in self._logit_lambda.items()
+        }
+
+    def set_lambda(self, **kwargs: dict[str, np.ndarray | float]):
+        r"""Set :math:`\lambda_k` per variable."""
+        for key, value in kwargs.items():
+            logit_lam = scipy.special.logit(value)
+            shared = self._logit_lambda[key]
+            fill = np.broadcast_to(
+                logit_lam,
+                shared.type.shape,
+            )
+            shared.set_value(fill)
+
+    def set_all_lambda(self, value: np.ndarray | float):
+        r"""Set :math:`\lambda_k` globally."""
+        config = dict.fromkeys(
+            self._logit_lambda.keys(),
+            value,
+        )
+        self.set_lambda(**config)
+
+    def fit(self, *args, **kwargs) -> pm.Approximation:
+        r"""Set :math:`\lambda_k` using Variational Inference.
+
+        Examples
+        --------
+
+        .. code-block:: python
+
+            with model:
+                # set all parameterizations to mix of centered and non-centered
+                vip.set_all_lambda(0.5)
+
+                # fit using ADVI
+                mf = vip.fit(random_seed=42)
+        """
+        kwargs.setdefault("obj_optimizer", pm.adagrad_window(learning_rate=0.1))
+        kwargs.setdefault("method", "advi")
+        return pm.fit(
+            *args,
+            more_obj_params=self.variational_parameters,
+            **kwargs,
+        )
+
+
+def vip_reparam_node(
+    op: RandomVariable,
+    node: Apply,
+    name: str,
+    dims: list[Variable],
+    transform: Transform | None,
+) -> tuple[ModelDeterministic, ModelNamed]:
+    if not isinstance(node.op, RandomVariable | SymbolicRandomVariable):
+        raise TypeError("Op should be RandomVariable type")
+    # FIXME: This is wrong when size is None
+    _, size, *_ = node.inputs
+    eval_size = size.eval(mode="FAST_COMPILE")
+    if eval_size is not None:
+        rv_shape = tuple(eval_size)
+    else:
+        rv_shape = ()
+    lam_name = f"{name}::lam_logit__"
+    _log.debug(f"Creating {lam_name} with shape of {rv_shape}")
+    logit_lam_ = pytensor.shared(
+        np.zeros(rv_shape),
+        shape=rv_shape,
+        name=lam_name,
+    )
+    logit_lam = model_named(logit_lam_, *dims)
+    lam = pt.sigmoid(logit_lam)
+    return (
+        _vip_reparam_node(
+            op,
+            node=node,
+            name=name,
+            dims=dims,
+            transform=transform,
+            lam=lam,
+        ),
+        logit_lam,
+    )
+
+
+@singledispatch
+def _vip_reparam_node(
+    op: RandomVariable,
+    node: Apply,
+    name: str,
+    dims: list[Variable],
+    transform: Transform | None,
+    lam: pt.TensorVariable,
+) -> ModelDeterministic:
+    raise NotImplementedError
+
+
+@_vip_reparam_node.register
+def _(
+    op: pm.Normal,
+    node: Apply,
+    name: str,
+    dims: list[Variable],
+    transform: Transform | None,
+    lam: pt.TensorVariable,
+) -> ModelDeterministic:
+    rng, size, loc, scale = node.inputs
+    if transform is not None:
+        raise NotImplementedError("Reparametrization of Normal with Transform is not implemented")
+    vip_rv_ = pm.Normal.dist(
+        lam * loc,
+        scale**lam,
+        size=size,
+        rng=rng,
+    )
+    vip_rv_.name = f"{name}::tau_"
+
+    vip_rv = model_free_rv(
+        vip_rv_,
+        vip_rv_.clone(),
+        None,
+        *dims,
+    )
+
+    vip_rep_ = loc + scale ** (1 - lam) * (vip_rv - lam * loc)
+
+    vip_rep_.name = name
+
+    vip_rep = model_deterministic(vip_rep_, *dims)
+    return vip_rep
+
+
+@_vip_reparam_node.register
+def _(
+    op: pm.Exponential,
+    node: Apply,
+    name: str,
+    dims: list[Variable],
+    transform: Transform | None,
+    lam: pt.TensorVariable,
+) -> ModelDeterministic:
+    rng, size, scale = node.inputs
+    scale_centered = scale**lam
+    scale_noncentered = scale ** (1 - lam)
+    vip_rv_ = pm.Exponential.dist(
+        scale=scale_centered,
+        size=size,
+        rng=rng,
+    )
+    vip_rv_value_ = vip_rv_.clone()
+    vip_rv_.name = f"{name}::tau_"
+    if transform is not None:
+        vip_rv_value_.name = f"{vip_rv_.name}_{transform.name}__"
+    else:
+        vip_rv_value_.name = vip_rv_.name
+    vip_rv = model_free_rv(
+        vip_rv_,
+        vip_rv_value_,
+        transform,
+        *dims,
+    )
+
+    vip_rep_ = scale_noncentered * vip_rv
+
+    vip_rep_.name = name
+
+    vip_rep = model_deterministic(vip_rep_, *dims)
+    return vip_rep
+
+
+def vip_reparametrize(
+    model: pm.Model,
+    var_names: Sequence[str],
+) -> tuple[pm.Model, VIP]:
+    r"""Repametrize Model using Variationally Informed Parametrization (VIP).
+
+    .. math::
+
+        \begin{align*}
+        \eta_{k} &\sim \text{normal}(\lambda_{k} \cdot \mu, \sigma^{\lambda_{k}})\\
+        \theta_{k} &= \mu + \sigma^{1 - \lambda_{k}} ( \eta_{k}  - \lambda_{k} \cdot \mu)
+        \sim \text{normal}(\mu, \sigma).
+        \end{align*}
+
+    Parameters
+    ----------
+    model : Model
+        Model with centered parameterizations for variables.
+    var_names : Sequence[str]
+        Target variables to reparemetrize.
+
+    Returns
+    -------
+    Tuple[Model, VIP]
+        Updated model and VIP helper to reparametrize or infer parametrization of the model.
+
+    Examples
+    --------
+    The traditional eight schools.
+
+    .. code-block:: python
+
+        import pymc as pm
+        import numpy as np
+
+        J = 8
+        y = np.array([28.0, 8.0, -3.0, 7.0, -1.0, 1.0, 18.0, 12.0])
+        sigma = np.array([15.0, 10.0, 16.0, 11.0, 9.0, 11.0, 10.0, 18.0])
+
+        with pm.Model() as Centered_eight:
+            mu = pm.Normal("mu", mu=0, sigma=5)
+            tau = pm.HalfCauchy("tau", beta=5)
+            theta = pm.Normal("theta", mu=mu, sigma=tau, shape=J)
+            obs = pm.Normal("obs", mu=theta, sigma=sigma, observed=y)
+
+    The regular model definition with centered parametrization is sufficient to use VIP.
+    To change the model parametrization use the following function.
+
+    .. code-block:: python
+
+        from pymc_extras.model.transforms.autoreparam import vip_reparametrize
+        Reparam_eight, vip = vip_reparametrize(Centered_eight, ["theta"])
+
+        with Reparam_eight:
+            # set all parameterizations to cenered (not needed)
+            vip.set_all_lambda(1)
+
+            # set all parameterizations to non-cenered (desired)
+            vip.set_all_lambda(0)
+
+            # or per variable
+            vip.set_lambda(theta=0)
+
+            # just set non-centered parameterization
+            trace = pm.sample()
+
+    However, setting it manually is not always great experience, we can learn it.
+
+    .. code-block:: python
+
+        with Reparam_eight:
+            # set all parameterizations to mix of centered and non-centered
+            vip.set_all_lambda(0.5)
+
+            # fit using ADVI
+            mf = vip.fit(random_seed=42)
+
+            # display lambdas
+            print(vip.get_lambda())
+
+            # {'theta': array([0.01473405, 0.02221006, 0.03656685, 0.03798879, 0.04876761,
+            #    0.0300203 , 0.02733082, 0.01817754])}
+
+    Now you can use sampling again:
+
+    .. code-block:: python
+
+        with Reparam_eight:
+            trace = pm.sample()
+
+    Sometimes it makes sense to enable clipping (that is off by default).
+    The idea is to round :math:`\varepsilon` to the closest extremum (:math:`0` or :math:`0`)
+
+    .. math::
+
+        \hat \lambda_k = \begin{cases}
+            0, \quad &\lambda_k \le \varepsilon\\
+            \lambda_k, \quad &\varepsilon \lt \lambda_k \lt 1-\varepsilon\\
+            1, \quad &\lambda_k \ge 1-\varepsilon
+        \end{cases}
+
+    .. code-block:: python
+
+        vip.truncate_all_lambda(0.1)
+
+    Sampling has to be performed again
+
+    .. code-block:: python
+
+        with Reparam_eight:
+            trace = pm.sample()
+
+    References
+    ----------
+    - Automatic Reparameterisation of Probabilistic Programs,
+        Maria I. Gorinova, Dave Moore, Matthew D. Hoffman (2019)
+    """
+    fmodel, memo = fgraph_from_model(model)
+    lambda_names = []
+    replacements = []
+    for name in var_names:
+        old = memo[model.named_vars[name]]
+        rv, _, *dims = old.owner.inputs
+        new, lam = vip_reparam_node(
+            rv.owner.op,
+            rv.owner,
+            name=rv.name,
+            dims=dims,
+            transform=old.owner.op.transform,
+        )
+        replacements.append((old, new))
+        lambda_names.append(lam.name)
+    toposort_replace(fmodel, replacements, reverse=True)
+    reparam_model = model_from_fgraph(fmodel)
+    model_lambdas = {
+        var_name: reparam_model[lambda_name]
+        for lambda_name, var_name in zip(lambda_names, var_names)
+    }
+    vip = VIP(model_lambdas)
+    return reparam_model, vip