Gaussian Process Latent Variable Model

In a previous tutorial, we have discussed latent variable models, in particular probabilistic principal component analysis (pPCA). Here, we show how we can extend the mapping provided by pPCA to non-linear mappings between input and output. For more details about the Gaussian Process Latent Variable Model (GPLVM), we refer the reader to the original publication and a further extension.

In short, the GPVLM is a dimensionality reduction technique that allows us to embed a high-dimensional dataset in a lower-dimensional embedding. Importantly, it provides the advantage that the linear mappings from the embedded space can be non-linearised through the use of Gaussian Processes.

Let's start by loading some dependencies.

using Turing
using AbstractGPs
using FillArrays
using LaTeXStrings
using Plots
using RDatasets
using ReverseDiff
using StatsBase

using LinearAlgebra
using Random

Random.seed!(1789);

We demonstrate the GPLVM with a very small dataset: Fisher's Iris data set. This is mostly for reasons of run time, so the tutorial can be run quickly. As you will see, one of the major drawbacks of using GPs is their speed, although this is an active area of research. We will briefly touch on some ways to speed things up at the end of this tutorial. We transform the original data with non-linear operations in order to demonstrate the power of GPs to work on non-linear relationships, while keeping the problem reasonably small.

data = dataset("datasets", "iris")
species = data[!, "Species"]
index = shuffle(1:150)
# we extract the four measured quantities,
# so the dimension of the data is only d=4 for this toy example
dat = Matrix(data[index, 1:4])
labels = data[index, "Species"]

# non-linearize data to demonstrate ability of GPs to deal with non-linearity
dat[:, 1] = 0.5 * dat[:, 1] .^ 2 + 0.1 * dat[:, 1] .^ 3
dat[:, 2] = dat[:, 2] .^ 3 + 0.2 * dat[:, 2] .^ 4
dat[:, 3] = 0.1 * exp.(dat[:, 3]) - 0.2 * dat[:, 3] .^ 2
dat[:, 4] = 0.5 * log.(dat[:, 4]) .^ 2 + 0.01 * dat[:, 3] .^ 5

# normalize data
dt = fit(ZScoreTransform, dat; dims=1);
StatsBase.transform!(dt, dat);

We will start out by demonstrating the basic similarity between pPCA (see the tutorial on this topic) and the GPLVM model. Indeed, pPCA is basically equivalent to running the GPLVM model with an automatic relevance determination (ARD) linear kernel.

First, we re-introduce the pPCA model (see the tutorial on pPCA for details)

@model function pPCA(x)
    # Dimensionality of the problem.
    N, D = size(x)
    # latent variable z
    z ~ filldist(Normal(), D, N)
    # weights/loadings W
    w ~ filldist(Normal(), D, D)
    mu = (w * z)'
    for d in 1:D
        x[:, d] ~ MvNormal(mu[:, d], I)
    end
    return nothing
end;

We define two different kernels, a simple linear kernel with an Automatic Relevance Determination transform and a squared exponential kernel.

linear_kernel(α) = LinearKernel() ∘ ARDTransform(α)
sekernel(α, σ) = σ * SqExponentialKernel() ∘ ARDTransform(α);

And here is the GPLVM model. We create separate models for the two types of kernel.

@model function GPLVM_linear(Y, K)
    # Dimensionality of the problem.
    N, D = size(Y)
    # K is the dimension of the latent space
    @assert K <= D
    noise = 1e-3

    # Priors
    α ~ MvLogNormal(MvNormal(Zeros(K), I))
    Z ~ filldist(Normal(), K, N)
    mu ~ filldist(Normal(), N)

    gp = GP(linear_kernel(α))
    gpz = gp(ColVecs(Z), noise)
    Y ~ filldist(MvNormal(mu, cov(gpz)), D)

    return nothing
end;

@model function GPLVM(Y, K)
    # Dimensionality of the problem.
    N, D = size(Y)
    # K is the dimension of the latent space
    @assert K <= D
    noise = 1e-3

    # Priors
    α ~ MvLogNormal(MvNormal(Zeros(K), I))
    σ ~ LogNormal(0.0, 1.0)
    Z ~ filldist(Normal(), K, N)
    mu ~ filldist(Normal(), N)

    gp = GP(sekernel(α, σ))
    gpz = gp(ColVecs(Z), noise)
    Y ~ filldist(MvNormal(mu, cov(gpz)), D)

    return nothing
end;

# Standard GPs don't scale very well in n, so we use a small subsample for the purpose of this tutorial
n_data = 40
# number of features to use from dataset
n_features = 4
# latent dimension for GP case
ndim = 4;

ppca = pPCA(dat[1:n_data, 1:n_features])
chain_ppca = sample(ppca, NUTS{Turing.ReverseDiffAD{true}}(), 1000);

# we extract the posterior mean estimates of the parameters from the chain
z_mean = reshape(mean(group(chain_ppca, :z))[:, 2], (n_features, n_data))
scatter(z_mean[1, :], z_mean[2, :]; group=labels[1:n_data], xlabel=L"z_1", ylabel=L"z_2")

We can see that the pPCA fails to distinguish the groups. In particular, the setosa species is not clearly separated from versicolor and virginica. This is due to the non-linearities that we introduced, as without them the two groups can be clearly distinguished using pPCA (see the pPCA tutorial).

Let's try the same with our linear kernel GPLVM model.

gplvm_linear = GPLVM_linear(dat[1:n_data, 1:n_features], ndim)
chain_linear = sample(gplvm_linear, NUTS{Turing.ReverseDiffAD{true}}(), 500);

# we extract the posterior mean estimates of the parameters from the chain
z_mean = reshape(mean(group(chain_linear, :Z))[:, 2], (n_features, n_data))
alpha_mean = mean(group(chain_linear, :α))[:, 2]

alpha1, alpha2 = partialsortperm(alpha_mean, 1:2; rev=true)
scatter(
    z_mean[alpha1, :],
    z_mean[alpha2, :];
    group=labels[1:n_data],
    xlabel=L"z_{\mathrm{ard}_1}",
    ylabel=L"z_{\mathrm{ard}_2}",
)

We can see that similar to the pPCA case, the linear kernel GPLVM fails to distinguish between the two groups (setosa on the one hand, and virginica and verticolor on the other).

Finally, we demonstrate that by changing the kernel to a non-linear function, we are able to separate the data again.

gplvm = GPLVM(dat[1:n_data, 1:n_features], ndim)
chain_gplvm = sample(gplvm, NUTS{Turing.ReverseDiffAD{true}}(), 500);

# we extract the posterior mean estimates of the parameters from the chain
z_mean = reshape(mean(group(chain_gplvm, :Z))[:, 2], (ndim, n_data))
alpha_mean = mean(group(chain_gplvm, :α))[:, 2]

alpha1, alpha2 = partialsortperm(alpha_mean, 1:2; rev=true)
scatter(
    z_mean[alpha1, :],
    z_mean[alpha2, :];
    group=labels[1:n_data],
    xlabel=L"z_{\mathrm{ard}_1}",
    ylabel=L"z_{\mathrm{ard}_2}",
)

let
    @assert abs(
        mean(z_mean[alpha1, labels[1:n_data] .== "setosa"]) -
        mean(z_mean[alpha1, labels[1:n_data] .!= "setosa"]),
    ) > 1
end

Now, the split between the two groups is visible again.

Appendix

These tutorials are a part of the TuringTutorials repository, found at: https://github.com/TuringLang/TuringTutorials.

To locally run this tutorial, do the following commands:

using TuringTutorials
TuringTutorials.weave("12-gaussian-process", "12_gaussian-process.jmd")

Computer Information:

Julia Version 1.9.2
Commit e4ee485e909 (2023-07-05 09:39 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 128 × AMD EPYC 7502 32-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver2)
  Threads: 1 on 16 virtual cores
Environment:
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⌅ [214eeab7] fzf_jll v0.29.0+0
  [a4ae2306] libaom_jll v3.4.0+0
  [0ac62f75] libass_jll v0.15.1+0
  [f638f0a6] libfdk_aac_jll v2.0.2+0
  [b53b4c65] libpng_jll v1.6.38+0
  [f27f6e37] libvorbis_jll v1.3.7+1
  [1270edf5] x264_jll v2021.5.5+0
  [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.3
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.9.2
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics v1.9.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.0.5+0
  [deac9b47] LibCURL_jll v7.84.0+0
  [29816b5a] LibSSH2_jll v1.10.2+0
  [c8ffd9c3] MbedTLS_jll v2.28.2+0
  [14a3606d] MozillaCACerts_jll v2022.10.11
  [4536629a] OpenBLAS_jll v0.3.21+4
  [05823500] OpenLibm_jll v0.8.1+0
  [efcefdf7] PCRE2_jll v10.42.0+0
  [bea87d4a] SuiteSparse_jll v5.10.1+6
  [83775a58] Zlib_jll v1.2.13+0
  [8e850b90] libblastrampoline_jll v5.8.0+0
  [8e850ede] nghttp2_jll v1.48.0+0
  [3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`