Pseudo-Observation Parametrisations

Project.toml

@@ -1,7 +1,7 @@
 name = "ApproximateGPs"
 uuid = "298c2ebc-0411-48ad-af38-99e88101b606"
 authors = ["JuliaGaussianProcesses Team"]
-version = "0.3.4"
+version = "0.3.5"
 
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"

docs/src/userguide.md

@@ -46,31 +46,9 @@ The approximate posterior constructed above will be a very poor approximation, s
 ```julia
 elbo(SparseVariationalApproximation(fz, q), fx, y)
 ```
-A detailed example of how to carry out such optimisation is given in [Regression: Sparse Variational Gaussian Process for Stochastic Optimisation with Flux.jl](@ref). For an example of non-conjugate inference, see [Classification: Sparse Variational Approximation for Non-Conjugate Likelihoods with Optim's L-BFGS](@ref).
 
 # Available Parametrizations
 
-Two parametrizations of `q(u)` are presently available: [`Centered`](@ref) and [`NonCentered`](@ref).
-The `Centered` parametrization expresses `q(u)` directly in terms of its mean and covariance.
-The `NonCentered` parametrization instead parametrizes the mean and covariance of
-`ε := cholesky(cov(u)).U' \ (u - mean(u))`.
-These parametrizations are also known respectively as "Unwhitened" and "Whitened".
-
-The choice of parametrization can have a substantial impact on the time it takes for ELBO
-optimization to converge, and which parametrization is better in a particular situation is
-not generally obvious.
-That being said, the `NonCentered` parametrization often converges in fewer iterations, so it is the default --
-it is what is used in all of the examples above.
-
-If you require a particular parametrization, simply use the 3-argument version of the
-approximation constructor:
-```julia
-SparseVariationalApproximation(Centered(), fz, q)
-SparseVariationalApproximation(NonCentered(), fz, q)
-```
-
-For a general discussion around these two parametrizations, see e.g. [^Gorinova].
-For a GP-specific discussion, see e.g. section 3.4 of [^Paciorek].
-
-[^Gorinova]: Gorinova, Maria and Moore, Dave and Hoffman, Matthew [Automatic Reparameterisation of Probabilistic Programs](http://proceedings.mlr.press/v119/gorinova20a)
-[^Paciorek]: [Paciorek, Christopher Joseph. Nonstationary Gaussian processes for regression and spatial modelling. Diss. Carnegie Mellon University, 2003.](https://www.stat.berkeley.edu/~paciorek/diss/paciorek-thesis.pdf)
+There are various ways to parametrise the approximate posterior.
+See [The Various Pseudo-Point Approximation Parametrisations](@ref) for more info and
+worked examples.

examples/d-sparse-parametrisations/Project.toml

@@ -0,0 +1,17 @@
+[deps]
+AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
+ApproximateGPs = "298c2ebc-0411-48ad-af38-99e88101b606"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
+Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
+ParameterHandling = "2412ca09-6db7-441c-8e3a-88d5709968c5"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"

examples/d-sparse-parametrisations/script.jl

@@ -0,0 +1,171 @@
+# # The Various Pseudo-Point Approximation Parametrisations
+#
+# ### Note to the reader
+# At the time of writing (March 2021) the best way to parametrise the approximate posterior
+# remains a surprisingly active area of research.
+# If you are reading this and feel that it has become outdated, or was incorrect in the
+# first instance, it would be greatly appreciated if you could open an issue to discuss.
+# 
+#
+# ## Introduction
+#
+# This example examines the various ways in which this package supports parametrising the
+# approximate posterior when utilising sparse approximations.
+# 
+# All sparse (a.k.a. pseudo-point) approximations in this package utilise an approximate
+# posterior over a GP ``f`` of the form
+# ```math
+# q(f) = q(\mathbf{u}) \, p(f_{\neq \mathbf{u}} | \mathbf{u}) 
+# ```
+# where samples from ``f`` are functions mapping ``\mathcal{X} \to \mathbb{R}``,
+# ``\mathbf{u} := f(\mathbf{z})``, ``\mathbf{z} \in \mathcal{X}^M`` are the pseudo-inputs,
+# and ``f_{\neq \mathbf{u}}`` denotes ``f`` at all indices other than those in
+# ``\mathbf{z}``.[^Titsias]
+# ``\mathbf{u} := q(f(\mathbf{z}))`` is generally restricted to be a multivariate Gaussian, to which end ApproximateGPs presently offers four parametrisations:
+# 1. Centered ("Unwhitened"): ``q(\mathbf{u}) = \mathcal{N}(\mathbf{m}, \mathbf{C})``, ``\quad \mathbf{m} \in \mathbb{R}^M`` and positive-definite ``\mathbf{C} \in \mathbb{R}^{M \times M}``,
+# 1. Non-Centered ("Whitened"): ``q(\mathbf{u}) = \mathcal{N}(\mathbf{L} \mathbf{m}, \mathbf{L} \mathbf{C} \mathbf{T}^\top)``, ``\quad \mathbf{L} \mathbf{L}^\top = \text{cov}(\mathbf{u})``,
+# 1. Pseudo-Observation: ``q(\mathbf{u}) \propto p(\mathbf{u}) \, \mathcal{N}(\hat{\mathbf{y}}; \mathbf{u}, \hat{\mathbf{S}})``, ``\quad \hat{\mathbf{y}} \in \mathbb{R}^M`` and positive-definite ``\hat{\mathbf{S}} \in \mathbb{R}^{M \times M}``,
+# 1. Decoupled Pseudo-Observation: ``q(\mathbf{u}) \propto p(\mathbf{u}) \, \mathcal{N}(\hat{\mathbf{y}}; f(\mathbf{v}), \hat{\mathbf{S}})``, ``\quad \hat{\mathbf{y}} \in \mathbb{R}^R``, ``\hat{\mathbf{S}} \in \mathbb{R}^{R \times R}`` is positive-definite and diagonal, and ``\mathbf{v} \in \mathcal{X}^R``.
+#
+# The choice of parametrization can have a substantial impact on the time it takes for ELBO
+# optimization to converge, and which parametrization is better in a particular situation is
+# not generally obvious.
+# That being said, the `NonCentered` parametrization often converges in fewer iterations
+# than the `Centered`, and is widely used, so it is the default.
+#
+# For a general discussion around the centered vs non-centered, see e.g. [^Gorinova].
+# For a GP-specific discussion, see e.g. section 3.4 of [^Paciorek].
+
+# ## Setup
+
+using AbstractGPs
+using ApproximateGPs
+using CairoMakie
+using Distributions
+using Images
+using KernelFunctions
+using LinearAlgebra
+using Optim
+using Random
+using Zygote
+
+# A simple GP with inputs on the reals.
+f = GP(SEKernel());
+N = 100;
+x = range(-3.0, 3.0; length=N);
+
+# Generate some observations.
+Σ = Diagonal(fill(0.1, N));
+y = rand(Xoshiro(123456), f(x, Σ));
+
+# Use a handful of pseudo-points.
+M = 10;
+z = range(-3.5, 3.5; length=M);
+
+# Other misc. constants that we'll need later:
+x_pred = range(-5.0, 5.0; length=300);
+jitter = 1e-9;
+
+# ## The Relationship Between Parametrisations
+#
+# Much of the time, one can convert between the different parametrisations to obtain
+# equivalent ``q(\mathbf{u})``, for a given set of hyperparameters.
+# If it's unclear from the above how these parametrisations relate to one another, the
+# following should help to crystalise the relationship.
+#
+# ### Centered vs Non-Centered
+#
+# Both the `Centered` and `NonCentered` parametrisations are specified by a mean vector `m`
+# and covariance matrix `C`, but in slightly different ways.
+# The `Centered` parametrisation interprets `m` and `C` as the mean and covariance of
+# ``q(\mathbf{u})`` directly, while the `NonCentered` parametrisation inteprets them as the
+# mean and covariance of the approximate posterior over
+# `ε := cholesky(cov(u)).U' \ (u - mean(u))`.
+#
+# To see this, consider the following non-centered approximate posterior:
+fz = f(z, jitter);
+qu_non_centered = MvNormal(randn(M), Matrix{Float64}(I, M, M));
+non_centered_approx = SparseVariationalApproximation(NonCentered(), fz, qu_non_centered);
+
+# The equivalent centered parametrisation can be found by multiplying the parameters of
+# `qu_non_centered` by the Cholesky factor of the prior covariance:
+L = cholesky(Symmetric(cov(fz))).L;
+qu_centered = MvNormal(L * mean(qu_non_centered), L * cov(qu_non_centered) * L');
+centered_approx = SparseVariationalApproximation(Centered(), fz, qu_centered);
+
+# We can gain some confidence that they're actually the same by querying the approximate
+# posterior statistics at some new locations:
+q_non_centered = posterior(non_centered_approx)
+q_centered = posterior(centered_approx)
+@assert mean(q_non_centered(x_pred)) ≈ mean(q_centered(x_pred))
+@assert cov(q_non_centered(x_pred)) ≈ cov(q_centered(x_pred))
+
+# ### Pseudo-Observation vs Centered
+#
+# The relationship between these two parametrisations is only slightly more complicated.
+# Consider the following pseudo-observation parametrisation of the approximate posterior:
+ŷ = randn(M);
+Ŝ = Matrix{Float64}(I, M, M);
+pseudo_obs_approx = PseudoObsSparseVariationalApproximation(f, z, Ŝ, ŷ);
+q_pseudo_obs = posterior(pseudo_obs_approx);
+
+# The corresponding centered approximation is given via the usual Gaussian conditioning
+# formulae:
+C = cov(fz);
+C_centered = C - C * (cholesky(Symmetric(C + Ŝ)) \ C);
+m_centered = mean(fz) + C / cholesky(Symmetric(C + Ŝ)) * (ŷ - mean(fz));
+qu_centered = MvNormal(m_centered, Symmetric(C_centered));
+centered_approx = SparseVariationalApproximation(Centered(), fz, qu_centered);
+q_centered = posterior(centered_approx);
+
+# Again, we can gain some confidence that they're the same by comparing the posterior
+# marginal statistics.
+@assert mean(q_pseudo_obs(x_pred)) ≈ mean(q_centered(x_pred))
+@assert cov(q_pseudo_obs(x_pred)) ≈ cov(q_centered(x_pred))
+
+# While it's always possible to find an approximation using the centered parametrisation
+# which is equivalent to a given pseudo-observation parametrisation, the converse is not
+# true.
+# That is, for a given `C = cov(fz)` and particular choice of covariance matrix `Ĉ` in a
+# centered parametrisation, it may not be the case that there exists a positive-definite
+# pseudo-observation covariance matrix `Ŝ` such that ``\hat{C} = C - C (C + \hat{S})^{-1} C``.
+#
+# However, ths is not necessarily a problem: if the likelihood used in the model is
+# log-concave then the optimal choice for `Ĉ` can always be represented using this
+# pseudo-observation parametrisation.
+# Even when this is not the case, it is not guaruanteed to be the case that the optimal
+# choice for `q(u)` lives outside of the family of distributions which can be expressed
+# within the pseudo-observation family.
+
+#
+# ### Decoupled Pseudo-Observation vs Non-Centered
+#
+# The relationship here is the most delicate, due to the restriction that
+# ``\hat{\mathbf{S}}`` must be diagonal.
+# This approximation achieves the optimal approximate posterior when the choice of
+# pseudo observational data (``\hat{y}``, ``\hat{\mathbf{S}}``, and ``\mathbf{v}``) equal
+# the original observational data.
+# When the original observational data involves a non-Gaussian likelihood, this
+# approximation family can still obtain the optimal approximate posterior provided that
+# ``\mathbf{v}`` lines up with the inputs associated with the original data, ``\mathbf{x}``.
+#
+# To see this, consider the pseudo-observation approximation which makes use of the
+# original observational data (generated at the top of this example):
+decoupled_approx = PseudoObsSparseVariationalApproximation(f, z, Σ, x, y);
+decoupled_posterior = posterior(decoupled_approx);
+
+# We can get the optimal pseudo-point approximation using standard functionality:
+optimal_approx_post = posterior(VFE(f(z, jitter)), f(x, Σ), y);
+
+# The marginal statistics agree:
+@assert mean(optimal_approx_post(x_pred)) ≈ mean(decoupled_posterior(x_pred))
+@assert cov(optimal_approx_post(x_pred)) ≈ cov(decoupled_posterior(x_pred))
+
+# The reason to think that this parametrisation will do something sensible is this property.
+# Obviously when ``\mathbf{v} \neq \mathbf{x}`` the optimal approximate posterior cannot be
+# recovered, however, when the hope is that there exists a small pseudo-dataset which gets
+# close to the optimum.
+
+# [^Titsias]: Titsias, M. K. [Variational learning of inducing variables in sparse Gaussian processes](https://proceedings.mlr.press/v5/titsias09a.html)
+# [^Gorinova]: Gorinova, Maria and Moore, Dave and Hoffman, Matthew [Automatic Reparameterisation of Probabilistic Programs](http://proceedings.mlr.press/v119/gorinova20a)
+# [^Paciorek]: [Paciorek, Christopher Joseph. Nonstationary Gaussian processes for regression and spatial modelling. Diss. Carnegie Mellon University, 2003.](https://www.stat.berkeley.edu/~paciorek/diss/paciorek-thesis.pdf)

src/ApproximateGPs.jl

@@ -15,7 +15,8 @@ include("SparseVariationalApproximationModule.jl")
     SparseVariationalApproximation, Centered, NonCentered
 @reexport using .SparseVariationalApproximationModule:
     DefaultQuadrature, Analytic, GaussHermite, MonteCarlo
-
+@reexport using .SparseVariationalApproximationModule:
+    PseudoObsSparseVariationalApproximation, ObsCovLikelihood, DecoupledObsCovLikelihood
 include("LaplaceApproximationModule.jl")
 @reexport using .LaplaceApproximationModule: LaplaceApproximation
 @reexport using .LaplaceApproximationModule: