Implement Symmetric and Asymmetric Multivariate Laplace distributions

conda-envs/environment-test.yml

@@ -10,6 +10,6 @@ dependencies:
 - xhistogram
 - statsmodels
 - pip:
-  - pymc>=5.17.0  # CI was failing to resolve
+  - pymc>=5.18.0  # CI was failing to resolve
   - blackjax
   - scikit-learn

conda-envs/windows-environment-test.yml

@@ -10,6 +10,6 @@ dependencies:
 - xhistogram
 - statsmodels
 - pip:
-  - pymc>=5.17.0  # CI was failing to resolve
+  - pymc>=5.18.0  # CI was failing to resolve
   - blackjax
   - scikit-learn

docs/api_reference.rst

@@ -39,6 +39,8 @@ Distributions
    GeneralizedPoisson
    BetaNegativeBinomial
    GenExtreme
+   MvAsymmetricLaplace
+   MvLaplace
    R2D2M2CP
    Skellam
    histogram_approximation

pymc_experimental/distributions/__init__.py

@@ -24,14 +24,17 @@
     Skellam,
 )
 from pymc_experimental.distributions.histogram_utils import histogram_approximation
-from pymc_experimental.distributions.multivariate import R2D2M2CP
+from pymc_experimental.distributions.multivariate.laplace import MvAsymmetricLaplace, MvLaplace
+from pymc_experimental.distributions.multivariate.r2d2m2cp import R2D2M2CP
 from pymc_experimental.distributions.timeseries import DiscreteMarkovChain
 
 __all__ = [
     "BetaNegativeBinomial",
     "DiscreteMarkovChain",
     "GeneralizedPoisson",
     "GenExtreme",
+    "MvAsymmetricLaplace",
+    "MvLaplace",
     "R2D2M2CP",
     "Skellam",
     "histogram_approximation",

pymc_experimental/distributions/multivariate/__init__.py

@@ -1,3 +0,0 @@
-from pymc_experimental.distributions.multivariate.r2d2m2cp import R2D2M2CP
-
-__all__ = ["R2D2M2CP"]

pymc_experimental/distributions/multivariate/laplace.py

@@ -0,0 +1,276 @@
+import numpy as np
+import pytensor.tensor as pt
+import scipy
+
+from pymc.distributions.dist_math import check_parameters
+from pymc.distributions.distribution import Continuous, SymbolicRandomVariable, _support_point
+from pymc.distributions.moments.means import _mean
+from pymc.distributions.multivariate import (
+    _logdet_from_cholesky,
+    nan_lower_cholesky,
+    quaddist_chol,
+    quaddist_matrix,
+    solve_lower,
+)
+from pymc.distributions.shape_utils import implicit_size_from_params, rv_size_is_none
+from pymc.logprob.basic import _logprob
+from pymc.pytensorf import normalize_rng_param
+from pytensor.gradient import grad_not_implemented
+from pytensor.scalar import BinaryScalarOp, upgrade_to_float
+from pytensor.tensor.elemwise import Elemwise
+from pytensor.tensor.random.utils import normalize_size_param
+
+
+class Kv(BinaryScalarOp):
+    """
+    Modified Bessel function of the second kind of real order v.
+    """
+
+    nfunc_spec = ("scipy.special.kv", 2, 1)
+
+    @staticmethod
+    def st_impl(v, x):
+        return scipy.special.kv(v, x)
+
+    def impl(self, v, x):
+        return self.st_impl(v, x)
+
+    def L_op(self, inputs, outputs, output_grads):
+        v, x = inputs
+        [out] = outputs
+        [g_out] = output_grads
+        dx = -(v / x) * out - self.kv(v - 1, x)
+        return [grad_not_implemented(self, 0, v), g_out * dx]
+
+    def c_code(self, *args, **kwargs):
+        raise NotImplementedError()
+
+
+kv = Elemwise(Kv(upgrade_to_float, name="kv"))
+
+
+class MvLaplaceRV(SymbolicRandomVariable):
+    name = "multivariate_laplace"
+    extended_signature = "[rng],[size],(m),(m,m)->[rng],(m)"
+    _print_name = ("MultivariateLaplace", "\\operatorname{MultivariateLaplace}")
+
+    @classmethod
+    def rv_op(cls, mu, cov, *, size=None, rng=None):
+        mu = pt.as_tensor(mu)
+        cov = pt.as_tensor(cov)
+        rng = normalize_rng_param(rng)
+        size = normalize_size_param(size)
+
+        assert mu.type.ndim >= 1
+        assert cov.type.ndim >= 2
+
+        if rv_size_is_none(size):
+            size = implicit_size_from_params(mu, cov, ndims_params=(1, 2))
+
+        next_rng, e = pt.random.exponential(size=size, rng=rng).owner.outputs
+        next_rng, z = pt.random.multivariate_normal(
+            mean=pt.zeros(mu.shape[-1]), cov=cov, size=size, rng=next_rng
+        ).owner.outputs
+        rv = mu + pt.sqrt(e)[..., None] * z
+
+        return cls(
+            inputs=[rng, size, mu, cov],
+            outputs=[next_rng, rv],
+        )(rng, size, mu, cov)
+
+
+class MvLaplace(Continuous):
+    r"""Multivariate (Symmetric) Laplace distribution.
+
+    The pdf of this distribution is
+
+    .. math::
+
+        pdf(x \mid \mu, \Sigma) =
+            \frac{2}{(2\pi)^{k/2} |\Sigma|^{1/2}}
+            ( \frac{(x-\mu)'\Sigma^{-1}(x-mu)}{2} )^{v/2}
+            \K_v (\sqrt{2(x-\mu)' \Sigma^{-1} (x - \mu)}})
+
+    where :math:`v = 1 - k/2` and :math:`\K_v` is the modified Bessel function of the second kind.
+
+    ========  ==========================
+    Support   :math:`x \in \mathbb{R}^k`
+    Mean      :math:`\mu`
+    Variance  :math:`\Sigma`
+    ========  ==========================
+
+    Parameters
+    ----------
+    mu : tensor_like of float
+        Location.
+    cov : tensor_like of float, optional
+        Covariance matrix. Exactly one of cov, tau, or chol is needed.
+    tau : tensor_like of float, optional
+        Precision matrix. Exactly one of cov, tau, or chol is needed.
+    chol : tensor_like of float, optional
+        Cholesky decomposition of covariance matrix. Exactly one of cov,
+        tau, or chol is needed.
+    lower: bool, default=True
+        Whether chol is the lower tridiagonal cholesky factor.
+    """
+
+    rv_type = MvLaplaceRV
+    rv_op = MvLaplaceRV.rv_op
+
+    @classmethod
+    def dist(cls, mu=0, cov=None, *, tau=None, chol=None, lower=True, **kwargs):
+        cov = quaddist_matrix(cov, chol, tau, lower)
+
+        mu = pt.atleast_1d(pt.as_tensor_variable(mu))
+        if mu.type.broadcastable[-1] and not cov.type.broadcastable[-1]:
+            mu, _ = pt.broadcast_arrays(mu, cov[..., -1])
+        return super().dist([mu, cov], **kwargs)
+
+
+class MvAsymmetricLaplaceRV(SymbolicRandomVariable):
+    name = "multivariate_asymmetric_laplace"
+    extended_signature = "[rng],[size],(m),(m,m)->[rng],(m)"
+    _print_name = ("MultivariateAsymmetricLaplace", "\\operatorname{MultivariateAsymmetricLaplace}")
+
+    @classmethod
+    def rv_op(cls, mu, cov, *, size=None, rng=None):
+        mu = pt.as_tensor(mu)
+        cov = pt.as_tensor(cov)
+        rng = normalize_rng_param(rng)
+        size = normalize_size_param(size)
+
+        assert mu.type.ndim >= 1
+        assert cov.type.ndim >= 2
+
+        if rv_size_is_none(size):
+            size = implicit_size_from_params(mu, cov, ndims_params=(1, 2))
+
+        next_rng, e = pt.random.exponential(size=size, rng=rng).owner.outputs
+        next_rng, z = pt.random.multivariate_normal(
+            mean=pt.zeros(mu.shape[-1]), cov=cov, size=size, rng=next_rng
+        ).owner.outputs
+        e = e[..., None]
+        rv = e * mu + pt.sqrt(e) * z
+
+        return cls(
+            inputs=[rng, size, mu, cov],
+            outputs=[next_rng, rv],
+        )(rng, size, mu, cov)
+
+
+class MvAsymmetricLaplace(Continuous):
+    r"""Multivariate Asymmetric Laplace distribution.
+
+    The pdf of this distribution is
+
+    .. math::
+
+        pdf(x \mid \mu, \Sigma) =
+            \frac{2}{(2\pi)^{k/2} |\Sigma|^{1/2}}
+            ( \frac{(x-\mu)'\Sigma^{-1}(x-mu)}{2} )^{v/2}
+            \K_v (\sqrt{2(x-\mu)' \Sigma^{-1} (x - \mu)}})
+
+    where :math:`v = 1 - k/2` and :math:`\K_v` is the modified Bessel function of the second kind.
+
+    ========  ==========================
+    Support   :math:`x \in \mathbb{R}^k`
+    Mean      :math:`\mu`
+    Variance  :math:`\Sigma + \mu' \mu`
+    ========  ==========================
+
+    Parameters
+    ----------
+    mu : tensor_like of float
+        Location.
+    cov : tensor_like of float, optional
+        Covariance matrix. Exactly one of cov, tau, or chol is needed.
+    tau : tensor_like of float, optional
+        Precision matrix. Exactly one of cov, tau, or chol is needed.
+    chol : tensor_like of float, optional
+        Cholesky decomposition of covariance matrix. Exactly one of cov,
+        tau, or chol is needed.
+    lower: bool, default=True
+        Whether chol is the lower tridiagonal cholesky factor.
+    """
+
+    rv_type = MvAsymmetricLaplaceRV
+    rv_op = MvAsymmetricLaplaceRV.rv_op
+
+    @classmethod
+    def dist(cls, mu=0, cov=None, *, tau=None, chol=None, lower=True, **kwargs):
+        cov = quaddist_matrix(cov, chol, tau, lower)
+
+        mu = pt.atleast_1d(pt.as_tensor_variable(mu))
+        if mu.type.broadcastable[-1] and not cov.type.broadcastable[-1]:
+            mu, _ = pt.broadcast_arrays(mu, cov[..., -1])
+        return super().dist([mu, cov], **kwargs)
+
+
+@_logprob.register(MvLaplaceRV)
+def mv_laplace_logp(op, values, rng, size, mu, cov, **kwargs):
+    [value] = values
+    quaddist, logdet, posdef = quaddist_chol(value, mu, cov)
+
+    k = value.shape[-1].astype("floatX")
+    norm = np.log(2) - (k / 2) * np.log(2 * np.pi) - logdet
+
+    v = 1 - (k / 2)
+    kernel = ((v / 2) * pt.log(quaddist / 2)) + pt.log(kv(v, pt.sqrt(2 * quaddist)))
+
+    logp_val = norm + kernel
+    return check_parameters(logp_val, posdef, msg="posdef scale")
+
+
+@_logprob.register(MvAsymmetricLaplaceRV)
+def mv_asymmetric_laplace_logp(op, values, rng, size, mu, cov, **kwargs):
+    [value] = values
+
+    chol_cov = nan_lower_cholesky(cov)
+    logdet, posdef = _logdet_from_cholesky(chol_cov)
+
+    # solve_triangular will raise if there are nans
+    # (which happens if the cholesky fails)
+    chol_cov = pt.switch(posdef[..., None, None], chol_cov, 1)
+
+    solve_x = solve_lower(chol_cov, value, b_ndim=1)
+    solve_mu = solve_lower(chol_cov, mu, b_ndim=1)
+
+    x_quaddist = (solve_x**2).sum(-1)
+    mu_quaddist = (solve_mu**2).sum(-1)
+    x_mu_quaddist = (value * solve_mu).sum(-1)
+
+    k = value.shape[-1].astype("floatX")
+    norm = np.log(2) - (k / 2) * np.log(2 * np.pi) - logdet
+
+    v = 1 - (k / 2)
+    kernel = (
+        x_mu_quaddist
+        + ((v / 2) * (pt.log(x_quaddist) - pt.log(2 + mu_quaddist)))
+        + pt.log(kv(v, pt.sqrt((2 + mu_quaddist) * x_quaddist)))
+    )
+
+    logp_val = norm + kernel
+    return check_parameters(logp_val, posdef, msg="posdef scale")
+
+
+@_mean.register(MvLaplaceRV)
+@_mean.register(MvAsymmetricLaplaceRV)
+def mv_laplace_mean(op, rv, rng, size, mu, cov):
+    if rv_size_is_none(size):
+        bcast_mu, _ = pt.random.utils.broadcast_params([mu, cov], ndims_params=[1, 2])
+    else:
+        bcast_mu = pt.broadcast_to(mu, pt.concatenate([size, [mu.shape[-1]]]))
+    return bcast_mu
+
+
+@_support_point.register(MvLaplaceRV)
+@_support_point.register(MvAsymmetricLaplaceRV)
+def mv_laplace_support_point(op, rv, rng, size, mu, cov):
+    # We have a 0 * inf when value = mu. I assume density is infinite, which isn't a good starting point.
+    point = mu + 1
+    if rv_size_is_none(size):
+        bcast_point, _ = pt.random.utils.broadcast_params([point, cov], ndims_params=[1, 2])
+    else:
+        bcast_shape = pt.concatenate([size, [point.shape[-1]]])
+        bcast_point = pt.broadcast_to(point, bcast_shape)
+    return bcast_point

requirements.txt

@@ -1,2 +1,2 @@
-pymc>=5.17.0
+pymc>=5.18.0
 scikit-learn

tests/distributions/__init__.py

@@ -1,19 +0,0 @@
-#   Copyright 2022 The PyMC Developers
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   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.
-
-
-from pymc_experimental.distributions import histogram_utils
-from pymc_experimental.distributions.histogram_utils import histogram_approximation
-
-__all__ = ["histogram_utils", "histogram_approximation"]