bayinx 0.2.27__py3-none-any.whl → 0.2.28__py3-none-any.whl

bayinx/core/constraints.py

@@ -9,16 +9,12 @@ from jaxtyping import Array, ArrayLike, Scalar, ScalarLike
 class Constraint(eqx.Module):
     """
     Abstract base class for defining parameter constraints.
-
-    Subclasses should implement the `constrain` method to apply the
-    transformation and compute the ladj adjustment.
     """
+
     @abstractmethod
     def constrain(self, x: ArrayLike) -> Tuple[Array, Scalar]:
         """
-        Applies the constraining transformation to an unconstrained input
-        and computes the log absolute determinant of the Jacobian (ladj)
-        of this transformation.
+        Applies the constraining transformation to an unconstrained input and computes the log-absolute-jacobian of the transformation.
 
         # Parameters
         - `x`: The unconstrained JAX Array-like input.
@@ -26,7 +22,7 @@ class Constraint(eqx.Module):
         # Returns
         A tuple containing:
             - The constrained JAX Array.
-            - A scalar JAX Array representing the ladj of the transformation.
+            - A scalar JAX Array representing the laj of the transformation.
         """
         pass
 
@@ -35,6 +31,7 @@ class LowerBound(Constraint):
     """
     Enforces a lower bound on the parameter.
     """
+
     lb: ScalarLike
 
     def __init__(self, lb: ScalarLike):
@@ -42,7 +39,7 @@ class LowerBound(Constraint):
 
     def constrain(self, x: ArrayLike) -> Tuple[Array, Scalar]:
         """
-        Applies the lower bound constraint and computes the ladj.
+        Applies the lower bound constraint and computes the laj.
 
         # Parameters
         - `x`: The unconstrained JAX Array-like input.
@@ -50,10 +47,10 @@ class LowerBound(Constraint):
         # Parameters
         A tuple containing:
             - The constrained JAX Array (x > self.lb).
-            - A scalar JAX Array representing the ladj of the transformation.
+            - A scalar JAX Array representing the laj of the transformation.
         """
         # Compute transformation adjustment
-        ladj = jnp.sum(x)
+        ladj: Scalar = jnp.sum(x)
 
         # Compute transformation
         x = jnp.exp(x) + self.lb

bayinx/core/flow.py

@@ -8,11 +8,11 @@ from jaxtyping import Array, Float
 
 class Flow(eqx.Module):
     """
-    A superclass used to define continuously parameterized diffeomorphisms for normalizing flows.
+    An abstract base class for a flow(of a normalizing flow).
 
     # Attributes
     - `pars`: A dictionary of JAX Arrays representing parameters of the diffeomorphism.
-    - `constraints`: A dictionary of functions that constrain their corresponding parameter.
+    - `constraints`: A dictionary of simple functions that constrain their corresponding parameter.
     """
 
     params: Dict[str, Float[Array, "..."]]
@@ -28,10 +28,10 @@ class Flow(eqx.Module):
     @abstractmethod
     def adjust_density(self, draws: Array) -> Tuple[Array, Array]:
         """
-        Computes the log-absolute-determinant of the Jacobian at `draws` and applies the forward transformation.
+        Computes the log-absolute-Jacobian at `draws` and applies the forward transformation.
 
         # Returns
-        A tuple of JAX Arrays containing the log-absolute-determinant of the Jacobians and transformed draws.
+        A tuple of JAX Arrays containing the transformed draws and log-absolute-Jacobians.
         """
         pass
 

bayinx/core/model.py

@@ -11,11 +11,11 @@ from bayinx.core.constraints import Constraint
 
 class Model(eqx.Module):
     """
-    A superclass used to define probabilistic models.
+    An abstract base class used to define probabilistic models.
 
     # Attributes
     - `params`: A dictionary of JAX Arrays representing parameters of the model.
-    - `constraints`: A dictionary of functions that constrain their corresponding parameter.
+    - `constraints`: A dictionary of constraints.
     """
 
     params: Dict[str, Array]
@@ -63,7 +63,7 @@ class Model(eqx.Module):
 
         return t_params, target
 
-
+    # Add default transform method
     def transform_pars(self) -> Tuple[Dict[str, Array], Scalar]:
         """
         Apply a custom transformation to `params` if needed.

bayinx/core/variational.py

@@ -8,7 +8,7 @@ import jax.lax as lax
 import jax.numpy as jnp
 import jax.random as jr
 import optax as opx
-from jaxtyping import Array, Float, Key, PyTree, Scalar
+from jaxtyping import Array, Key, PyTree, Scalar
 from optax import GradientTransformation, OptState, Schedule
 
 from bayinx.core import Model
@@ -16,16 +16,23 @@ from bayinx.core import Model
 
 class Variational(eqx.Module):
     """
-    A superclass used to define variational methods.
+    An abstract base class used to define variational methods.
 
     # Attributes
     - `_unflatten`: A static function to transform draws from the variational distribution back to a `Model`.
     - `_constraints`: A static partitioned `Model` with the constraints of the `Model` used to initialize the `Variational` object.
     """
 
-    _unflatten: Callable[[Float[Array, "..."]], Model]
+    _unflatten: Callable[[Array], Model]
     _constraints: Model
 
+    @abstractmethod
+    def filter_spec(self):
+        """
+        Filter specification for dynamic and static components of the `Variational`.
+        """
+        pass
+
     @abstractmethod
     def sample(self, n: int, key: Key) -> Array:
         """
@@ -54,13 +61,6 @@ class Variational(eqx.Module):
         """
         pass
 
-    @abstractmethod
-    def filter_spec(self):
-        """
-        Filter specification for dynamic and static components of the `Variational`.
-        """
-        pass
-
     @eqx.filter_jit
     @partial(jax.vmap, in_axes=(None, 0, None))
     def eval_model(self, draws: Array, data: Any = None) -> Array:
@@ -135,7 +135,7 @@ class Variational(eqx.Module):
             # Update PRNG key
             key, _ = jr.split(key)
 
-            # Combine variational
+            # Reconstruct variational
             vari = eqx.combine(dyn, static)
 
             # Compute gradient of the ELBO

bayinx/dists/normal.py

@@ -19,7 +19,7 @@ def prob(
     The PDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `mu`, and `sigma`.
     """
 
-    return _lax.exp(-0.5 * _lax.square((x - mu) / sigma)) / ( # pyright: ignore
+    return _lax.exp(-0.5 * _lax.square((x - mu) / sigma)) / (  # pyright: ignore
         sigma * _lax.sqrt(2.0 * __PI)
     )
 
@@ -39,7 +39,9 @@ def logprob(
     The log of the PDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `mu`, and `sigma`.
     """
 
-    return -_lax.log(sigma * _lax.sqrt(2.0 * __PI)) - 0.5 * _lax.square((x - mu) / sigma) # pyright: ignore
+    return -_lax.log(sigma * _lax.sqrt(2.0 * __PI)) - 0.5 * _lax.square(
+        (x - mu) / sigma # pyright: ignore
+    )
 
 
 def uprob(
@@ -57,7 +59,7 @@ def uprob(
     The uPDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `mu`, and `sigma`.
     """
 
-    return _lax.exp(-0.5 * _lax.square((x - mu) / sigma)) / sigma # pyright: ignore
+    return _lax.exp(-0.5 * _lax.square((x - mu) / sigma)) / sigma  # pyright: ignore
 
 
 def ulogprob(
@@ -75,4 +77,4 @@ def ulogprob(
     The log uPDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `mu`, and `sigma`.
     """
 
-    return -_lax.log(sigma) - 0.5 * _lax.square((x - mu) / sigma) # pyright: ignore
+    return -_lax.log(sigma) - 0.5 * _lax.square((x - mu) / sigma)  # pyright: ignore

bayinx/dists/uniform.py

@@ -18,7 +18,7 @@ def prob(
     The PDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `lb`, and `ub`.
     """
 
-    return 1.0 / (ub - lb) # pyright: ignore
+    return 1.0 / (ub - lb)  # pyright: ignore
 
 
 def logprob(
@@ -36,7 +36,7 @@ def logprob(
     The log of the PDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `lb`, and `ub`.
     """
 
-    return _lax.log(1.0) - _lax.log(ub - lb) # pyright: ignore
+    return _lax.log(1.0) - _lax.log(ub - lb)  # pyright: ignore
 
 
 def uprob(
@@ -54,7 +54,7 @@ def uprob(
     The uPDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `lb`, and `ub`.
     """
 
-    return jnp.ones(jnp.broadcast_arrays(x,lb,ub))
+    return jnp.ones(jnp.broadcast_arrays(x, lb, ub))
 
 
 def ulogprob(
@@ -72,4 +72,4 @@ def ulogprob(
     The log uPDF evaluated at `x`. The output will have the broadcasted shapes of `x`, `lb`, and `ub`.
     """
 
-    return jnp.zeros(jnp.broadcast_arrays(x,lb,ub))
+    return jnp.zeros(jnp.broadcast_arrays(x, lb, ub))

bayinx/mhx/vi/flows/fullaffine.py

@@ -1,29 +1,26 @@
 from functools import partial
-from typing import Callable, Dict, Tuple
+from typing import Tuple
 
 import equinox as eqx
 import jax
 import jax.numpy as jnp
-from jaxtyping import Array, Float, Scalar
+from jaxtyping import Array, Scalar
 
 from bayinx.core import Flow
 
 
 class FullAffine(Flow):
     """
-    An affine flow.
+    A full affine flow.
 
     # Attributes
     - `params`: A dictionary containing the JAX Arrays representing the scale and shift parameters.
     - `constraints`: A dictionary of constraining transformations.
     """
 
-    params: Dict[str, Float[Array, "..."]]
-    constraints: Dict[str, Callable[[Float[Array, "..."]], Float[Array, "..."]]]
-
     def __init__(self, dim: int):
         """
-        Initializes an affine flow.
+        Initializes a full affine flow.
 
         # Parameters
         - `dim`: The dimension of the parameter space.
@@ -35,21 +32,18 @@ class FullAffine(Flow):
 
         self.constraints = {"scale": lambda m: jnp.tril(m)}
 
+    @eqx.filter_jit
     def transform_pars(self):
-        # Get constrained parameters
         params = self.constrain_pars()
 
         # Extract diagonal and apply exponential
-        diag: Array = jnp.exp(jnp.diag(params['scale']))
+        diag: Array = jnp.exp(jnp.diag(params["scale"]))
 
         # Fill diagonal
-        params['scale'] = jnp.fill_diagonal(params['scale'], diag, inplace=False)
-
+        params["scale"] = jnp.fill_diagonal(params["scale"], diag, inplace=False)
 
         return params
 
-
-
     @eqx.filter_jit
     def forward(self, draws: Array) -> Array:
         params = self.transform_pars()
@@ -65,7 +59,7 @@ class FullAffine(Flow):
 
     @eqx.filter_jit
     @partial(jax.vmap, in_axes=(None, 0))
-    def adjust_density(self, draws: Array) -> Tuple[Scalar, Array]:
+    def adjust_density(self, draws: Array) -> Tuple[Array, Scalar]:
         params = self.transform_pars()
 
         # Extract parameters
@@ -75,7 +69,7 @@ class FullAffine(Flow):
         # Compute forward transformation
         draws = draws @ scale + shift
 
-        # Compute ladj
-        ladj: Scalar = jnp.log(jnp.diag(scale)).sum()
+        # Compute laj
+        laj: Scalar = jnp.log(jnp.diag(scale)).sum()
 
-        return ladj, draws
+        return draws, laj

bayinx/mhx/vi/flows/planar.py

@@ -53,7 +53,7 @@ class Planar(Flow):
 
     @eqx.filter_jit
     @partial(jax.vmap, in_axes=(None, 0))
-    def adjust_density(self, draws: Array) -> Tuple[Scalar, Array]:
+    def adjust_density(self, draws: Array) -> Tuple[Array, Scalar]:
         params = self.transform_pars()
 
         # Extract parameters
@@ -67,8 +67,8 @@ class Planar(Flow):
         # Compute forward transformation
         draws = draws + u * jnp.tanh(x)
 
-        # Compute ladj
+        # Compute laj
         h_prime: Scalar = 1.0 - jnp.square(jnp.tanh(x))
-        ladj: Scalar = jnp.log(jnp.abs(1.0 + h_prime * u.dot(w)))
+        laj: Scalar = jnp.log(jnp.abs(1.0 + h_prime * u.dot(w)))
 
-        return ladj, draws
+        return draws, laj

bayinx/mhx/vi/flows/radial.py

@@ -66,7 +66,7 @@ class Radial(Flow):
 
     @partial(jax.vmap, in_axes=(None, 0))
     @eqx.filter_jit
-    def adjust_density(self, draws: Array) -> Tuple[Scalar, Array]:
+    def adjust_density(self, draws: Array) -> Tuple[Array, Scalar]:
         params = self.transform_pars()
 
         # Extract parameters
@@ -84,11 +84,11 @@ class Radial(Flow):
         draws = draws + (x) * (draws - center)
 
         # Compute density adjustment
-        ladj = jnp.log(
+        laj = jnp.log(
             jnp.abs(
                 (1.0 + alpha * beta / (alpha + r) ** 2.0)
                 * (1.0 + x) ** (center.size - 1.0)
             )
         )
 
-        return ladj, draws
+        return draws, laj

bayinx/mhx/vi/meanfield.py

@@ -20,8 +20,8 @@ class MeanField(Variational):
     """
 
     var_params: Dict[str, Float[Array, "..."]]
-    _unflatten: Callable[[Float[Array, "..."]], Model] = eqx.field(static=True)
-    _constraints: Model = eqx.field(static=True)
+    _unflatten: Callable[[Float[Array, "..."]], Model]
+    _constraints: Model
 
     def __init__(self, model: Model):
         """
@@ -63,25 +63,24 @@ class MeanField(Variational):
 
     @eqx.filter_jit
     def filter_spec(self):
+        # Generate empty specification
         filter_spec = jtu.tree_map(lambda _: False, self)
+
+        # Specify variational parameters
         filter_spec = eqx.tree_at(
             lambda mf: mf.var_params,
             filter_spec,
             replace=True,
         )
+
         return filter_spec
 
     @eqx.filter_jit
     def elbo(self, n: int, key: Key, data: Any = None) -> Scalar:
-        """
-        Estimate the ELBO and its gradient(w.r.t the variational parameters).
-        """
-        # Partition variational
         dyn, static = eqx.partition(self, self.filter_spec())
 
         @eqx.filter_jit
         def elbo(dyn: Self, n: int, key: Key, data: Any = None) -> Scalar:
-            # Combine
             vari = eqx.combine(dyn, static)
 
             # Sample draws from variational distribution
@@ -100,7 +99,6 @@ class MeanField(Variational):
 
     @eqx.filter_jit
     def elbo_grad(self, n: int, key: Key, data: Any = None) -> Self:
-        # Partition
         dyn, static = eqx.partition(self, self.filter_spec())
 
         @eqx.filter_grad

bayinx/mhx/vi/normalizing_flow.py

@@ -1,11 +1,11 @@
-from typing import Any, Callable, Self, Tuple
+from typing import Any, Self, Tuple
 
 import equinox as eqx
 import jax.flatten_util as jfu
 import jax.numpy as jnp
 import jax.random as jr
 import jax.tree_util as jtu
-from jaxtyping import Array, Float, Key, Scalar
+from jaxtyping import Array, Key, Scalar
 
 from bayinx.core import Flow, Model, Variational
 
@@ -17,14 +17,11 @@ class NormalizingFlow(Variational):
 
     # Attributes
     - `base`: A base variational distribution.
-    - `flows`: An ordered collection of continuously parameterized
-        diffeomorphisms.
+    - `flows`: An ordered collection of continuously parameterized diffeomorphisms.
     """
 
     flows: list[Flow]
     base: Variational
-    _unflatten: Callable[[Float[Array, "..."]], Model]
-    _constraints: Model
 
     def __init__(self, base: Variational, flows: list[Flow], model: Model):
         """
@@ -44,6 +41,19 @@ class NormalizingFlow(Variational):
         self.base = base
         self.flows = flows
 
+    def filter_spec(self):
+        # Generate empty specification
+        filter_spec = jtu.tree_map(lambda _: False, self)
+
+        # Specify variational parameters based on each flow's filter spec.
+        filter_spec = eqx.tree_at(
+            lambda vari: vari.flows,
+            filter_spec,
+            replace=[flow.filter_spec() for flow in self.flows],
+        )
+
+        return filter_spec
+
     @eqx.filter_jit
     def sample(self, n: int, key: Key = jr.PRNGKey(0)):
         """
@@ -65,19 +75,18 @@ class NormalizingFlow(Variational):
 
         for map in self.flows:
             # Compute adjustment
-            ladj, draws = map.adjust_density(draws)
+            laj, draws = map.adjust_density(draws)
 
             # Adjust variational density
-            variational_evals = variational_evals - ladj
+            variational_evals = variational_evals - laj
 
         return variational_evals
 
     @eqx.filter_jit
     def __eval(self, draws: Array, data=None) -> Tuple[Array, Array]:
         """
-        Evaluate the posterior and variational densities at the transformed
-        `draws` to avoid extra compute when requiring variational draws for
-        the posterior evaluation.
+        Evaluate the posterior and variational densities together at the
+        transformed `draws` to avoid extra compute.
 
         # Parameters
         - `draws`: Draws from the base variational distribution.
@@ -91,29 +100,16 @@ class NormalizingFlow(Variational):
 
         for map in self.flows:
             # Compute adjustment
-            ladj, draws = map.adjust_density(draws)
+            draws, laj = map.adjust_density(draws)
 
             # Adjust variational density
-            variational_evals = variational_evals - ladj
+            variational_evals = variational_evals - laj
 
         # Evaluate posterior at final variational draws
         posterior_evals = self.eval_model(draws, data)
 
         return posterior_evals, variational_evals
 
-    def filter_spec(self):
-        # Generate empty specification
-        filter_spec = jtu.tree_map(lambda _: False, self)
-
-        # Specify variational parameters based on each flow's filter spec.
-        filter_spec = eqx.tree_at(
-            lambda vari: vari.flows,
-            filter_spec,
-            replace=[flow.filter_spec() for flow in self.flows],
-        )
-
-        return filter_spec
-
     @eqx.filter_jit
     def elbo(self, n: int, key: Key = jr.PRNGKey(0), data: Any = None) -> Scalar:
         dyn, static = eqx.partition(self, self.filter_spec())

{bayinx-0.2.27.dist-info → bayinx-0.2.28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bayinx
-Version: 0.2.27
+Version: 0.2.28
 Summary: Bayesian Inference with JAX
 Requires-Python: >=3.12
 Requires-Dist: equinox>=0.11.12

bayinx-0.2.28.dist-info/RECORD

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bayinx/core/utils.py

@@ -1 +0,0 @@
-

bayinx-0.2.27.dist-info/RECORD

@@ -1,28 +0,0 @@
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