A library for variational Bayesian methods in Julia
Author TuringLang
Popularity
6 Stars
Updated Last
4 Months Ago
Started In
October 2019

A library for variational Bayesian inference in Julia.

At the time of writing (05/02/2020), implementations of the variational inference (VI) interface and some algorithms are implemented in Turing.jl. The idea is to soon separate the VI functionality in Turing.jl out and into this package.

The purpose of this package will then be to provide a common interface together with implementations of standard algorithms and utilities with the goal of ease of use and the ability for other packages, e.g. Turing.jl, to write a light wrapper around AdvancedVI.jl for integration.

As an example, in Turing.jl we support automatic differentiation variational inference (ADVI) but really the only piece of code tied into the Turing.jl is the conversion of a Turing.Model to a logjoint(z) function which computes z ↦ log p(x, z), with x denoting the observations embedded in the Turing.Model. As long as this logjoint(z) method is compatible with some AD framework, e.g. ForwardDiff.jl or Zygote.jl, this is all we need from Turing.jl to be able to perform ADVI!

## [WIP] Interface

• vi: the main interface to the functionality in this package
• vi(model, alg): only used when alg has a default variational posterior which it will provide.
• vi(model, alg, q::VariationalPosterior, θ): q represents the family of variational distributions and θ is the initial parameters "indexing" the starting distribution. This assumes that there exists an implementation Variational.update(q, θ) which returns the variational posterior corresponding to parameters θ.
• vi(model, alg, getq::Function, θ): here getq(θ) is a function returning a VariationalPosterior corresponding to θ.
• optimize!(vo, alg::VariationalInference{AD}, q::VariationalPosterior, model::Model, θ; optimizer = TruncatedADAGrad())
• grad!(vo, alg::VariationalInference, q, model::Model, θ, out, args...)
• Different combinations of variational objectives (vo), VI methods (alg), and variational posteriors (q) might use different gradient estimators. grad! allows us to specify these different behaviors.

## Examples

### Variational Inference

A very simple generative model is the following

μ ~ 𝒩(0, 1)
xᵢ ∼ 𝒩(μ, 1) , ∀i = 1, …, n


where μ and xᵢ are some ℝᵈ vectors and 𝒩 denotes a d-dimensional multivariate Normal distribution.

Given a set of n observations [x₁, …, xₙ] we're interested in finding the distribution p(μ∣x₁, …, xₙ) over the mean μ. We can obtain (an approximation to) this distribution that using AdvancedVI.jl!

First we generate some observations and set up the problem:

julia> using Distributions

julia> d = 2; n = 100;

julia> observations = randn((d, n)); # 100 observations from 2D 𝒩(0, 1)

julia> # Define generative model
#    μ ~ 𝒩(0, 1)
#    xᵢ ∼ 𝒩(μ, 1) , ∀i = 1, …, n
prior(μ) = logpdf(MvNormal(ones(d)), μ)
prior (generic function with 1 method)

julia> likelihood(x, μ) = sum(logpdf(MvNormal(μ, ones(d)), x))
likelihood (generic function with 1 method)

julia> logπ(μ) = likelihood(observations, μ) + prior(μ)
logπ (generic function with 1 method)

julia> logπ(randn(2))  # <= just checking that it works
-311.74132761437653

Now there are mainly two different ways of specifying the approximate posterior (and its family). The first is by providing a mapping from distribution parameters to the distribution θ ↦ q(⋅∣θ):

julia> using DistributionsAD, AdvancedVI

julia> # Using a function z ↦ q(⋅∣z)
getq(θ) = TuringDiagMvNormal(θ[1:d], exp.(θ[d + 1:4]))
getq (generic function with 1 method)

Then we make the choice of algorithm, a subtype of VariationalInference,

julia> # Perform VI
ADVI{AdvancedVI.ForwardDiffAD{40}}(10, 10000)

And finally we can perform VI! The usual inferface is to call vi which behind the scenes takes care of the optimization and returns the resulting variational posterior:

julia> q = vi(logπ, advi, getq, randn(4))
TuringDiagMvNormal{Array{Float64,1},Array{Float64,1}}(m=[0.16282745378074515, 0.15789310089462574], σ=[0.09519377533754399, 0.09273176907111745])

Let's have a look at the resulting ELBO:

julia> AdvancedVI.elbo(advi, q, logπ, 1000)
-287.7866366886285

Unfortunately, the final value of the ELBO is not always a very good diagnostic, though it's an important metric to keep an eye on during training since a decrease in the ELBO means we're going in the right direction. Luckily, this is such a simple problem that we can indeed obtain a closed form solution! Because we're lazy (at least I am), we'll let ConjugatePriors.jl do this for us:

julia> # True posterior
using ConjugatePriors

julia> pri = MvNormal(zeros(2), ones(2));

julia> true_posterior = posterior((pri, pri.Σ), MvNormal, observations)
DiagNormal(
dim: 2
μ: [0.1746546592601148, 0.16457110079543008]
Σ: [0.009900990099009901 0.0; 0.0 0.009900990099009901]
)

Comparing to our variational approximation, this looks pretty good! Worth noting that in this particular case the variational posterior seems to overestimate the variance.

To conclude, let's make a somewhat pretty picture:

julia> using Plots

julia> p_samples = rand(true_posterior, 10_000); q_samples = rand(q, 10_000);

julia> p1 = histogram(p_samples[1, :], label="p"); histogram!(q_samples[1, :], alpha=0.7, label="q")

julia> title!(raw"$\mu_1$")

julia> p2 = histogram(p_samples[2, :], label="p"); histogram!(q_samples[2, :], alpha=0.7, label="q")

julia> title!(raw"$\mu_2$")

julia> plot(p1, p2) ### Simple example: using Advanced.jl to directly minimize the KL-divergence between two distributions p(z) and q(z)

In VI we aim to approximate the true posterior p(z ∣ x) by some approximate variational posterior q(z) by maximizing the ELBO:

ELBO(q) = 𝔼_q[log p(x, z) - log q(z)]


Observe that we can express the ELBO as the negative KL-divergence between p(x, ⋅) and q(⋅):

ELBO(q) = - 𝔼_q[log (q(z) / p(x, z))]
= - KL(q(⋅) || p(x, ⋅))


So if we apply VI to something that isn't an actual posterior, i.e. there's no data involved and we write p(z ∣ x) = p(z), we're really just minimizing the KL-divergence between the distributions.

Therefore, we can try out AdvancedVI.jl real quick by applying using the interface to minimize the KL-divergence between two distributions:

julia> using Distributions, DistributionsAD, AdvancedVI

julia> # Target distribution
p = MvNormal(ones(2))
ZeroMeanDiagNormal(
dim: 2
μ: [0.0, 0.0]
Σ: [1.0 0.0; 0.0 1.0]
)

julia> logπ(z) = logpdf(p, z)
logπ (generic function with 1 method)

julia> # Make a choice of VI algorithm
ADVI{AdvancedVI.ForwardDiffAD{40}}(10, 1000)

Now there are two different ways of specifying the approximate posterior (and its family); the first is by providing a mapping from parameters to distribution θ ↦ q(⋅∣θ):

julia> # Using a function z ↦ q(⋅∣z)
getq(θ) = TuringDiagMvNormal(θ[1:2], exp.(θ[3:4]))
getq (generic function with 1 method)

julia> # Perform VI
q = vi(logπ, advi, getq, randn(4))
┌ Info: [ADVI] Should only be seen once: optimizer created for θ
└   objectid(θ) = 0x5ddb564423896704
TuringDiagMvNormal{Array{Float64,1},Array{Float64,1}}(m=[-0.012691337868985757, -0.0004442434543332919], σ=[1.0334797673569802, 0.9957355128767893])

Or we can check the ELBO (which in this case since, as mentioned, doesn't involve data, is the negative KL-divergence):

julia> AdvancedVI.elbo(advi, q, logπ, 1000)  # empirical estimate
0.08031049170093245

It's worth noting that the actual value of the ELBO doesn't really tell us too much about the quality of fit. In this particular case, because we're directly minimizing the KL-divergence, we can only say something useful if we reach 0, in which case we have obtained the true distribution.

Let's just quickly check the mean-squared error between the log p(z) and log q(z) for a random set of samples from the target p:

julia> zs = rand(p, 100);

julia> mean(abs2, logpdf(q, zs) - logpdf(p, zs))
0.0014889109427524852

## Implementing your own training loop

Sometimes it might be convenient to roll your own training loop rather than using vi(...). Here's some psuedo-code for how one would do that when used together with Turing.jl:

using Turing, AdvancedVI, DiffResults
using Turing: Variational

using ProgressMeter

# Assuming you have an instance of a Turing model (model)

# 1. Create log-joint needed for ELBO evaluation
logπ = Variational.make_logjoint(model)

# 2. Define objective
variational_objective = Variational.ELBO()

# 3. Optimizer

# 4. VI-algorithm

# 5. Variational distribution
function getq(θ)
# ...
end

# 6. [OPTIONAL] Implement convergence criterion
function hasconverged(args...)
# ...
end

# 7. [OPTIONAL] Implement a callback for tracking stats
function callback(args...)
# ...
end

# 8. Train
converged = false
step = 1

prog = ProgressMeter.Progress(num_steps, 1)

while (step ≤ num_steps) && !converged
# 1. Compute gradient and objective value; results are stored in diff_results

# 2. Extract gradient from diff_result

# 3. Apply optimizer, e.g. multiplying by step-size
Δ = apply!(optimizer, θ, ∇)

# 4. Update parameters
@. θ = θ - Δ

# 5. Do whatever analysis you want
callback(args...)

# 6. Update
converged = hasconverged(...) # or something user-defined
step += 1

ProgressMeter.next!(prog)
end

## References

• Jordan, Michael I., Zoubin Ghahramani, Tommi S. Jaakkola, and Lawrence K. Saul. "An introduction to variational methods for graphical models." Machine learning 37, no. 2 (1999): 183-233.
• Blei, David M., Alp Kucukelbir, and Jon D. McAuliffe. "Variational inference: A review for statisticians." Journal of the American statistical Association 112, no. 518 (2017): 859-877.
• Kucukelbir, Alp, Rajesh Ranganath, Andrew Gelman, and David Blei. "Automatic variational inference in Stan." In Advances in Neural Information Processing Systems, pp. 568-576. 2015.
• Salimans, Tim, and David A. Knowles. "Fixed-form variational posterior approximation through stochastic linear regression." Bayesian Analysis 8, no. 4 (2013): 837-882.
• Beal, Matthew James. Variational algorithms for approximate Bayesian inference. 2003.