arianna-ppl 0.1.24

Arianna probabilistic programming language

Arianna

A probabilistic programming language for python built on numpy.

Installation

To install from PyPI (recommended):

pip

pip install arianna-ppl

uv

uv add arianna-ppl

To install the absolute latest version from main:

pip

pip install git+https://github.com/lanl/arianna-ppl.git

uv

uv add git+https://github.com/lanl/arianna-ppl.git

Usage

Model Specification (linear regression)

from typing import Optional

import numpy as np
from numpy.random import default_rng

from arianna.distributions import Gamma, Normal
from arianna.ppl.context import Context, Predictive
from arianna.ppl.inference import (
    AIES,
    AffineInvariantMCMC,
    Chain,
    LaplaceApproximation,
    ParallelAIES,
    RandomWalkMetropolis,
)

# Type annotation are, of course, optional. Provided only for clarity.
def linear_regression(
    ctx: Context,
    X: np.ndarray,
    y: Optional[np.ndarray]=None,
    bias: bool=True
) -> None:
    _, p = X.shape
    beta = ctx.rv("beta", Normal(np.zeros(p), 10))
    sigma = ctx.rv("sigma", Gamma(1, 1))
    mu = ctx.cached("mu", X @ beta)
    if bias:
        alpha = ctx.rv("alpha", Normal(0, 10))
        mu += alpha

    ctx.rv("y", Normal(mu, sigma), obs=y)

Simulate data from Prior Predictive

nobs = 100
rng = np.random.default_rng(0)

# Generate random predictors (X).
X = rng.normal(0, 1, (nobs, 1))

# Simulate from prior predictive using Predictive.
sim_truth = Predictive.run(
    linear_regression,  # supplied model here.
    state=dict(sigma=0.7),
    rng=rng,
    X=X,
    # since y is None, the returned dictionary will contain y sampled from it's
    # predictive distributions.
    y=None,
    # Not return cached values, so the sim_truth will contain only parameters
    # and y.
    return_cached=False,  
)

# pop y so that sim_truth contains only model parameters.
y = sim_truth.pop("y")

# Now sim_truth is a dict containing ("beta", "sigma", "alpha").

Affine invariant ensemble sampler

aies = AIES(
    linear_regression,  # model function.
    nwalkers=10,  # number of walkers.
    # Whether or not to transform parameters into unconstrained space.
    transform=True,  # Set to true when possible.
    # Random number generator for reproducibility.
    rng=default_rng(0),
    # Provide data.
    X=X, y=y,
)

# Does 3000 steps, with 10 walkers, after burning for 3000, and thins by 1. At
# the end, 3000 = 3000*10 samples will be aggregated from all 10 walkers. Then,
# by default, these samples are passed into an importance sampler to reweight
# the samples, yielding 3000 samples.
chain = aies.fit(nsteps=3000, burn=3000, thin=1)

chain is an object that contains posterior samples (states). You can iterate over chain.

for state in chain:
    print(state)  # state is a e.g., dict(alpha=1.3, beta=2.5, sigma=0.6, mu=some_long_array)
    break # just print the first one.

You can convert chain into a large dict with bundle = chain.bundle, which is a dict[str, ndarray].

You can also get the samples directly with chain.samples.

Parallel Affine invariant ensemble sampler Works only in python 3.13t. But 3.13t does not yet work with jupyter.

from concurrent.futures import ThreadPoolExecutor

paies = ParallelAIES(
    linear_regression,  # model function.
    ThreadPoolExecutor(4)  # use 4 cores.
    nwalkers=10,  # number of walkers.
    # Whether or not to transform parameters into unconstrained space.
    transform=True,  # Set to true when possible.
    # Random number generator for reproducibility.
    rng=default_rng(0),
    # Provide data.
    X=X, y=y,
)

# Same as non-parallel version, but will be faster in python 3.13t.
# Will be slightly slower than the non-parallel version in GIL enabled python
# builds, i.e. python 3.9, 3.10, 3.11, 3.12, 3.13.
chain = paies.fit(nsteps=3000, burn=3000, thin=1)

Laplace Approximation

la = LaplaceApproximation(
    linear_regression,
    transform=True,
    rng=default_rng(0),
    X=X, y=y,
)

# The MAP estimate and inverse Hessian are computed via L-BFGS optimization.
# Those estimates are used to construct a MvNormal object. 3000 samples are
# drawn from that resulting MvNormal.
chain = la.fit(nsamples=3000)

Posterior Predictive

rng = default_rng
xnew = np.linspace(-3, 3, 50)
Xnew = xnew.reshape(-1, 1)
ynew = Chain(
    Predictive.run(
        linear_regression, state=state, rng=rng, X=Xnew, y=None
    )
    for state in chain
).get("y")

See demos.

Threading

As of 8 Jan 2025, jupyter does not work with the threaded (no-gil) version of python 3.13 (3.13t). You can install arianna with python 3.13 or python 3.13t but you cannot install jupyter also. If you must use jupyter, use python 3.10, 3.11, 3.12, 3.13 (but not 3.13t).

LANL Software Release Information

• O4856