meridian.model.posterior_sampler.PosteriorMCMCSampler

A callable that samples from posterior distributions using MCMC.

meridian.model.posterior_sampler.PosteriorMCMCSampler(
    meridian: 'model.Meridian'
)

Attributes
model

Methods

__call__

View source

__call__(
    n_chains: (Sequence[int] | int),
    n_adapt: int,
    n_burnin: int,
    n_keep: int,
    current_state: (Mapping[str, backend.Tensor] | None) = None,
    init_step_size: (int | None) = None,
    dual_averaging_kwargs: (Mapping[str, int] | None) = None,
    max_tree_depth: int = 10,
    max_energy_diff: float = 500.0,
    unrolled_leapfrog_steps: int = 1,
    parallel_iterations: int = 10,
    seed: (Sequence[int] | int | None) = None,
    **pins
) -> None

Runs Markov Chain Monte Carlo (MCMC) sampling of posterior distributions.

For more information about the arguments, see windowed_adaptive_nuts.

Args
n_chains	Number of MCMC chains. Given a sequence of integers, windowed_adaptive_nuts will be called once for each element. The n_chains argument of each windowed_adaptive_nuts call will be equal to the respective integer element. Using a list of integers, one can split the chains of a windowed_adaptive_nuts call into multiple calls with fewer chains per call. This can reduce memory usage. This might require an increased number of adaptation steps for convergence, as the optimization is occurring across fewer chains per sampling call.
n_adapt	Number of adaptation draws per chain.
n_burnin	Number of burn-in draws per chain. Burn-in draws occur after adaptation draws and before the kept draws.
n_keep	Integer number of draws per chain to keep for inference.
current_state	Optional structure of tensors at which to initialize sampling. Use the same shape and structure as model.experimental_pin(**pins).sample(n_chains).
init_step_size	Optional integer determining where to initialize the step size for the leapfrog integrator. The structure must broadcast with current_state. For example, if the initial state is: { 'a': tf.zeros(n_chains), 'b': tf.zeros([n_chains, n_features]), } then any of 1., {'a': 1., 'b': 1.}, or {'a': tf.ones(n_chains), 'b': tf.ones([n_chains, n_features])} will work. Defaults to the dimension of the log density to the ¼ power.
dual_averaging_kwargs	Optional dict keyword arguments to pass to tfp.mcmc.DualAveragingStepSizeAdaptation. By default, a target_accept_prob of 0.85 is set, acceptance probabilities across chains are reduced using a harmonic mean, and the class defaults are used otherwise.
max_tree_depth	Maximum depth of the tree implicitly built by NUTS. The maximum number of leapfrog steps is bounded by 2**max_tree_depth, for example, the number of nodes in a binary tree max_tree_depth nodes deep. The default setting of 10 takes up to 1024 leapfrog steps.
max_energy_diff	Scalar threshold of energy differences at each leapfrog, divergence samples are defined as leapfrog steps that exceed this threshold. Default is 1000.
unrolled_leapfrog_steps	The number of leapfrogs to unroll per tree expansion step. Applies a direct linear multiplier to the maximum trajectory length implied by max_tree_depth. Defaults is 1.
parallel_iterations	Number of iterations allowed to run in parallel. Must be a positive integer. For more information, see tf.while_loop.
seed	An int32[2] Tensor or a Python list or tuple of 2 ints, which will be treated as stateless seeds; or a Python int or None, which will be converted into a stateless seed. See tfp.random.sanitize_seed.
**pins	These are used to condition the provided joint distribution, and are passed directly to joint_dist.experimental_pin(**pins).

Throws
MCMCOOMError	If the model is out of memory. Try reducing n_keep or pass a list of integers as n_chains to sample chains serially. For more information, see ResourceExhaustedError when running Meridian.sample_posterior.