Author willtebbutt
1 Star
Updated Last
4 Months Ago
Started In
March 2021


Build Status Coverage Code Style: Blue ColPrac: Contributor's Guide on Collaborative Practices for Community Packages

This is an implementation of [1]. It utilises the AbstractGPs.jl interface, so should play nicely with any AbstractGP, including those from Stheno.jl and TemporalGPs.jl. No attempt has been made to make this implementation work for anything other than Gaussian processes.

Example Usage

Approximate inference and learning in a GP under an Exponential likelihood. This is primarily handled using the build_latent_gp function, which produces a LatentGP specifying this model when provided with kernel parameters. ParameterHandling.jl is used to handle the book-keeping associated with the model parameters.

using AbstractGPs
using ConjugateComputationVI
using Distributions
using Optim
using ParameterHandling
using Plots
using Random
using RDatasets
using StatsFuns
using Zygote

using ConjugateComputationVI: GaussHermiteQuadrature, UnivariateFactorisedLikelihood

# Specify the model parameters.
θ_init = (scale=positive(1.9), stretch=positive(0.8));
θ_init_flat, unflatten = ParameterHandling.flatten(θ_init);

# Specify the model.
# A core requirement of this package is that you are able to provide a function mapping
# from your model parameters to a `LatentGP`.
function build_latent_gp::AbstractVector{<:Real})
    return build_latent_gp(ParameterHandling.value(unflatten(θ)))
function build_latent_gp::NamedTuple)
    gp = GP.scale * AbstractGPs.transform(SEKernel(), θ.stretch))
    lik = UnivariateFactorisedLikelihood(f -> Exponential(exp(f)))
    return LatentGP(gp, lik, 1e-9)

# Specify inputs and generate some synthetic outputs.
x = range(-5.0, 5.0; length=100);
y = rand(build_latent_gp(θ_init_flat)(x)).y;

# Attempt to recover the kernel parameters used when generating the data.
# Add some noise to the initialisation to make this more interesting.
# We specify that the reconstruction term in the ELBO is to be approximated using
# Gauss-Hermite quadrature with 10 points.
f_approx_post, results_summary = ConjugateComputationVI.optimize_elbo(
    θ_init_flat + randn(length(θ_init_flat)),
        alphaguess = Optim.LineSearches.InitialStatic(scaled=true),
        linesearch = Optim.LineSearches.BackTracking(),
        show_trace = true,

# Compute approx. posterior CIs using Monte Carlo.
function approx_post_95_CI(x::AbstractVector, N::Int)
    samples = map(marginals(f_approx_post(x, 1e-6))) do latent_marginal
        f = rand(latent_marginal, N)
        return rand.(Exponential.(exp.(f)))
    return quantile.(samples, Ref((0.025, 0.5, 0.975)))

x_pr = range(-6.0, 6.0; length=250);
qs = approx_post_95_CI(x_pr, 10_000);

# Plot the predictions.
p1 = plot(
    x_pr, getindex.(qs, 1);
    fillrange=getindex.(qs, 3),
    label="95% CI",
scatter!(p1, x, y; markersize=2, label="Observations");

p2 = plot(
    f_approx_post(x_pr, 1e-6);
    ribbon_scale=3, color=:blue, label="approx posterior latent",
sampleplot!(f_approx_post(x_pr, 1e-6), 10; color=:blue);

plot(p1, p2; layout=(2, 1))

See the examples directory for more.


This approximation does not presently play nicely with pseudo-point approximations. That would be an interesting research direction.


[1] - Khan, Mohammad, and Wu Lin. "Conjugate-computation variational inference: Converting variational inference in non-conjugate models to inferences in conjugate models." Artificial Intelligence and Statistics. PMLR, 2017.

Used By Packages

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