An implementation of the Orthogonal Instantaneous Linear Mixing Model (OILMM).
The Python implementation can be found here.
Please refer to the examples directory for basic usage, or below for a very quick intro.
The API broadly follows Stheno.jl's.
f = OILMM(...)constructs an Orthogonal Instantaneous Linear Mixing Model. This object represents a distribution over vector-valued functions -- see the docstring for more info.
f(x)represents f at the input locations x.
logpdf(f(x), y) # compute the log marginal probability of `y` under the model.
rand(rng, f(x)) # sample from `f` at `x`, for random number generator `rng`.
marginals(f(x)) # compute the marginal statistics of `f` at `x`.y should be an AbstractVector{<:Real} of the same length as x.
To perform inference, simply invoke the posterior function:
f_post = posterior(f(x), y)
f_post is then another OILMM that is the posterior distribution. That this works is one of the very convenient properties of the OILMM.
All public functions should have docstrings. If you encounter something that is unclear, please raise an issue so that it can be fixed.
using AbstractGPs
using LinearAlgebra
using OILMMs
using Random
# Specify and construct an OILMM.
p = 10
m = 3
U, s, _ = svd(randn(p, m))
σ² = 0.1
f = OILMM(
[GP(SEKernel()) for _ in 1:m],
U,
Diagonal(s),
Diagonal(rand(m) .+ 0.1),
);
# Sample from the model.
x = MOInput(randn(10), p);
fx = f(x, σ²);
rng = MersenneTwister(123456);
y = rand(rng, fx);
# Compute the logpdf of the data under the model.
logpdf(fx, y)
# Perform posterior inference. This produces another OILMM.
f_post = posterior(fx, y)
# Compute the posterior marginals. We can also use `rand` and `logpdf` as before.
post_marginals = marginals(f_post(x));TemporalGPs.jl makes inference and learning in GPs for time series much more efficient than performing exact inference.
It plays nicely with this package, and can be used to accelerate inference in an OILMM
simply by wrapping each of the base processes using to_sde. See the TemporalGPs.jl docs
for more info on this.
using AbstractGPs
using LinearAlgebra
using OILMMs
using Random
using TemporalGPs
# Specify and construct an OILMM.
p = 10
m = 3
U, s, _ = svd(randn(p, m))
σ² = 0.1
f = OILMM(
[to_sde(GP(Matern52Kernel()), SArrayStorage(Float64)) for _ in 1:m],
U,
Diagonal(s),
Diagonal(rand(m) .+ 0.1),
);
# Sample from the model. LARGE DATA SET!
x = MOInput(RegularSpacing(0.0, 1.0, 1_000_000), p);
fx = f(x, σ²);
rng = MersenneTwister(123456);
y = rand(rng, fx);
# Compute the logpdf of the data under the model.
logpdf(fx, y)
# Perform posterior inference. This produces another OILMM.
f_post = posterior(fx, y)
# Compute the posterior marginals. We can also use `rand` and `logpdf` as before.
post_marginals = marginals(f_post(x));Notice that this example is nearly identical to the one above, because all GP-related packages used utilise the AbstractGPs.jl APIs.
We don't provide a fit+predict interface, instead we rely on external packages to provide something similar that is more flexible. Specifically, we recommend using a mixture of ParameterHandling.jl, Optim.jl or some other general non-linear optimisation package), and Zygote.jl. Below we provide a small example:
# Load GP-related packages.
using AbstractGPs
using OILMMs
using TemporalGPs
# Load standard packages from the Julia ecosystem
using LinearAlgebra
using Optim # Standard optimisation algorithms.
using ParameterHandling # Helper functionality for dealing with model parameters.
using Random
using Zygote # Algorithmic Differentiation
# Specify OILMM parameters as a NamedTuple.
# Utilise orthogonal, and positive from ParameterHandling.jl to constrain appropriately.
p = 2
m = 1
θ_init = (
U = orthogonal(randn(p, m)),
s = positive.(rand(m) .+ 0.1),
σ² = positive(0.1),
)
# Define a function which builds an OILMM, given a NamedTuple of parameters.
function build_oilmm(θ::NamedTuple)
return OILMM(
[to_sde(GP(Matern52Kernel()), SArrayStorage(Float64)) for _ in 1:m],
θ.U,
Diagonal(θ.s),
Diagonal(zeros(m)),
)
end
# Generate some synthetic data to train on.
f = build_oilmm(ParameterHandling.value(θ_init));
const x = MOInput(RegularSpacing(0.0, 0.01, 1_000_000), p);
fx = f(x, 0.1);
rng = MersenneTwister(123456);
const y = rand(rng, fx);
# Define a function which computes the NLML given the parameters.
function objective(θ::NamedTuple)
f = build_oilmm(θ)
return -logpdf(f(x, θ.σ²), y)
end
# Build a version of the objective function which can be used with Optim.jl.
θ_init_flat, unflatten = flatten(θ_init);
unpack(θ::Vector{<:Real}) = ParameterHandling.value(unflatten(θ))
objective(θ::Vector{<:Real}) = objective(unpack(θ))
# Utilise Optim.jl + Zygote.jl to optimise the model parameters.
training_results = Optim.optimize(
objective,
θ -> only(Zygote.gradient(objective, θ)),
θ_init_flat + randn(length(θ_init_flat)), # Add some noise to make learning non-trivial
BFGS(
alphaguess = Optim.LineSearches.InitialStatic(scaled=true),
linesearch = Optim.LineSearches.BackTracking(),
),
Optim.Options(show_trace = true);
inplace=false,
)
# Compute posterior marginals at optimal solution.
θ_opt = unpack(training_results.minimizer)
f = build_oilmm(θ_opt)
f_post = posterior(f(x, θ_opt.σ²), y)
fx = marginals(f_post(x))Please refer to the CITATION.bib file.