TinyGibbs
TinyGibbs is a small Gibbs sampler that makes use of the AbstractMCMC interface. It therefore allows for efficient Gibbs sampling including parallel sampling of multiple chains. Additionally, TinyGibbs can collect samples in two ways: (1) as a dictionary of tensors where each tensor or (2) as a MCMCChains.Chains type. Therefore, all the funcionality of MCMCChains can be exploited with TinyGibbs.
TinyGibbs goal is to be intuitive and as close as possible to research papers. That is, the goal is to have a syntax that is close to the notation used for Gibbs sampling procedures in research papers
How does it work?
using TinyGibbs
using StableRNGs
using Random, Distributions
using MCMCChains, AbstractMCMC
using LinearAlgebra
To achieve its goal of being as close as possible to research paper notation, TinyGibbs introduced the @tiny_gibbs
macro. This macro allows one to abstract away all the computational elements and to strictly focus on the Gibbs step logic - that is, on the way in which each parameter is drawn given the other parameters.
As an example, consider the Multivariate Normal Distribution
where
and
we then have the following rules:
and
We can therefore create the following Gibbs sampling procedure
@tiny_gibbs function gibbs_normal(mu, Σ)
# Drawing y: here a vector of all elements except the first
my = mu[2:end] + 1/Σ[1, 1]*Σ[2:end, 1]*(x - mu[1])
Σy = Σ[2:end, 2:end] - 1/Σ[1, 1]*Σ[2:end, 1]*Σ[1, 2:end]'
y ~ MultivariateNormal(my, Hermitian(Σy))
# drawing the first element conditional on the others
mx = mu[1] + Σ[1, 2:end]'*inv(Σ[2:end, 2:end])*(y - mu[2:end])
Σx = Σ[1, 1] - Σ[1, 2:end]'*inv(Σ[2:end, 2:end])*Σ[2:end, 1]
x ~ Normal(mx, sqrt(Σx))
end
This will create a function gibbs_normal
in our environment. This function takes as the first argument a dictionary of initial values. Each variable in the Gibbs sampling procedure that is on the LHS of a ~
must be a key in the dictionary and must therefore have an initial value. As the remaining arguments, gibbs_normal
will take the arguments that were given in the macro - hence mu
and Σ
.
# Use a stable RNG for replicability reasons
rng = StableRNG(123)
# Create some parameters
mu = rand(rng, MultivariateNormal(30*randn(rng, 3), I))
Σ = rand(rng, Wishart(4, diagm(ones(3))))
# Define initial values
initial_values = Dict(:x => mu[1], :y => mu[2:end])
# Create a sampler
sampler = gibbs_normal(initial_values, mu, Σ)
After creating a sampler, we are now ready to sample. TinyGibbs overwrites the AbstractMCMC.sample methods such that there is one argument less. If the user absolutely wishes to use the AbstractMCMC.sample methods though, they can still do so, by using TinyGibbsModel as the model.
Sampling can either be done for a single chain, or for multiple chains. In the latter case, sampling of the multiple chains can also make use of parallelization.
# Sampling a single chain of 1000 draws and saving it as a MCMCChains.Chains type
chain_single = sample(rng, sampler, 1_000; chain_type=MCMCChains.Chains)
# Same as above, but this time saving draws as a dictionary of tensors
# The last dimensions follow the following rules
# 1. The last dimension of each tensor refers to the chain
# 2. The second to last dimension refers to the draws
# 3. The remaining dimensions are the dimensions of the sampled object, i.e. two dimensional for covariance matrices
chain_single_dict = sample(rng, sampler, 1_000; chain_type=Dict)
To make use of parallel sampling, we can use any of AbstractMCMCs methods. Here I will choose MCMCThreads()
# Sampling 4 chains each having 1000 draws in parallel
chain_parallel = sample(rng, sampler, MCMCThreads(), 1_000, 4; chain_type=MCMCChains.Chains)
chain_parallel_dict = sample(rng, sampler, MCMCThreads(), 1_000, 4; chain_type=Dict)
We can then use these draws like any other Bayesian draws. For example, we can just plot the draws using MCMCChains interface
using StatsPlots
plot(chain_parallel)
We can also compare the Gibbs sampled distribution for x
with the theoretical marginal distribution
histogram(chain_parallel[:x]; normalize=:pdf, legend=:none)
plot!(minimum(chain_parallel[:x]):0.01:maximum(chain_parallel[:x]), x->pdf(Normal(mu[1], sqrt(Σ[1, 1])), x); color=:red, linewidth=2)
Current Shortcomings / Potential next steps
- TinyGibbs does not currently support the use of MH or HMC within Gibbs. A natrual next step would be to make this possible
- TinyGibbs does not currently support keeping track of any other quantities than those that are being sampled. This can be changed if the need ever comes up. A hack around this would also be to have a deterministic distribution.
TODOS
- Documentation