import blackjax as bj
import jax
from jax import random as jr
from sbijax._src.mcmc.util import sample_and_post_process_from_blackjax_samples
# ruff: noqa: PLR0913,D417,E501
[docs]
def sample_with_nuts(
rng_key, lp, prior, *, n_chains=4, n_samples=2_000, n_warmup=1_000, **kwargs
):
r"""Sample from a distribution using the No-U-Turn sampler.
Args:
rng_key: a jax random key
lp: the logdensity you wish to sample from
prior: a function that returns a prior sample
n_chains: number of chains to sample
n_samples: number of samples per chain
n_warmup: number of samples to discard
Examples:
>>> import functools as ft
>>> from jax import numpy as jnp, random as jr
>>> from tensorflow_probability.substrates.jax import distributions as tfd
...
>>> prior = tfd.JointDistributionNamed(
... dict(theta=tfd.Normal(jnp.zeros(2), 1.0))
... )
>>> def log_prob(theta, y):
... lp_prior = prior.log_prob(theta)
... lp_data = tfd.Normal(theta["theta"], 1.0).log_prob(y)
... return jnp.sum(lp_data) + jnp.sum(lp_prior)
...
>>> prop_posterior_lp = ft.partial(log_prob, y=jnp.array([-1.0, 1.0]))
>>> samples = sample_with_nuts(jr.PRNGKey(0), prop_posterior_lp, prior)
Returns:
a JAX pytree with keys corresponding to the variables names
and tensor values of dimension `n_chains x n_samples x dim_variable`
"""
def _inference_loop(rng_key, kernel, initial_state, n_samples):
@jax.jit
def _step(states, rng_key):
keys = jax.random.split(rng_key, n_chains)
states, _ = jax.vmap(kernel)(keys, states)
return states, states
sampling_keys = jax.random.split(rng_key, n_samples)
_, states = jax.lax.scan(_step, initial_state, sampling_keys)
return states
init_key, rng_key = jr.split(rng_key)
initial_states, kernel = _nuts_init(init_key, n_chains, prior, lp)
samples = sample_and_post_process_from_blackjax_samples(
rng_key,
_inference_loop,
kernel,
initial_states,
n_chains,
n_samples,
n_warmup,
)
return samples
# pylint: disable=missing-function-docstring
def _nuts_init(rng_key, n_chains, prior, lp):
init_key, rng_key = jr.split(rng_key)
initial_positions = prior.sample(seed=init_key, sample_shape=(n_chains,))
init_keys = jr.split(rng_key, n_chains)
warmup = bj.window_adaptation(bj.nuts, lp)
initial_states, kernel_params = jax.vmap(
lambda seed, param: warmup.run(seed, param)[0]
)(init_keys, initial_positions)
kernel_params = {k: v[0] for k, v in kernel_params.items()}
_, kernel = bj.nuts(lp, **kernel_params)
return initial_states, kernel
