diff --git a/tutorials/12-gaussian-process-latent-variable-model/12_gaussian-process-latent-variable-model.jmd b/tutorials/12-gaussian-process-latent-variable-model/12_gaussian-process-latent-variable-model.jmd new file mode 100644 index 000000000..907deab6c --- /dev/null +++ b/tutorials/12-gaussian-process-latent-variable-model/12_gaussian-process-latent-variable-model.jmd @@ -0,0 +1,306 @@ +--- +title: Gaussian Process Latent Variable Model +permalink: /:collection/:name/ +redirect_from: tutorials/12-gaussian-process-latent-variable-model/ +--- + +# 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](https://jmlr.org/papers/v6/lawrence05a.html) and a [further extension](http://proceedings.mlr.press/v9/titsias10a/titsias10a.pdf). + +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. +```julia +using Turing +using AbstractGPs, KernelFunctions, Random, Plots + +using LinearAlgebra +using VegaLite, DataFrames, StatsPlots, StatsBase +using RDatasets + +Random.seed!(1789); +``` + +We demonstrate the GPLVM with a very small dataset: [Fisher's Iris data set](https://en.wikipedia.org/wiki/Iris_flower_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. + +```julia +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) +```julia +@model function pPCA(x, ::Type{TV} = Array{Float64}) where {TV} + # 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 +end; +``` + + +We define two different kernels, a simple linear kernel with an Automatic Relevance Determination transform and a +squared exponential kernel. +```julia +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. +```julia +@model function GPLVM_linear(Y, K=4,::Type{T} = Float64) where {T} + + # 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) + + kernel = linear_kernel(α) + + gp = GP(mu, kernel) + cv = cov(gp(ColVecs(Z), noise)) + Y ~ filldist(MvNormal(mu, cv), D) +end; + +@model function GPLVM(Y, K=4,::Type{T} = Float64) where {T} + + # 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) + + kernel = sekernel(α, σ) + + gp = GP(mu, kernel) + cv = cov(gp(ColVecs(Z), noise)) + Y ~ filldist(MvNormal(mu, cv), D) +end; +``` + +```julia +# 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; +``` + +```julia +ppca = pPCA(dat[1:n_data, 1:n_features]) +chain_ppca = sample(ppca, NUTS(), 1000); +``` + +```julia +# we extract the posterior mean estimates of the parameters from the chain +w = reshape(mean(group(chain_ppca, :w))[:, 2], (n_features,n_features)) +z = reshape(mean(group(chain_ppca, :z))[:, 2], (n_features, n_data)) +X = w * z + +df_pre = DataFrame(z', :auto) +rename!(df_pre, Symbol.( ["z"*string(i) for i in collect(1:n_features)])) +df_pre[!,:type] = labels[1:n_data] +p_ppca = df_pre |> @vlplot(:point, x=:z1, y=:z2, color="type:n") +``` + +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. +```julia +gplvm_linear = GPLVM_linear(dat[1:n_data, 1:n_features], ndim) + +chain_linear = sample(gplvm_linear, NUTS(), 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] +``` + +```julia +df_gplvm_linear = DataFrame(z_mean', :auto) +rename!(df_gplvm_linear, Symbol.( ["z"*string(i) for i in collect(1:ndim)])) +df_gplvm_linear[!,:sample] = 1:n_data +df_gplvm_linear[!,:labels] = labels[1:n_data] +alpha_indices = sortperm(alpha_mean, rev=true)[1:2] +println(alpha_indices) +df_gplvm_linear[!,:ard1] = z_mean[alpha_indices[1], :] +df_gplvm_linear[!,:ard2] = z_mean[alpha_indices[2], :] + +p_linear = df_gplvm_linear |> @vlplot(:point, x=:ard1, y=:ard2, color="labels:n") +p_linear +``` +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. +```julia +gplvm = GPLVM(dat[1:n_data, 1:n_features], ndim) + +chain_gplvm = sample(gplvm, NUTS(), 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] +``` + +```julia +df_gplvm = DataFrame(z_mean', :auto) +rename!(df_gplvm, Symbol.( ["z"*string(i) for i in collect(1:ndim)])) +df_gplvm[!,:sample] = 1:n_data +df_gplvm[!,:labels] = labels[1:n_data] +alpha_indices = sortperm(alpha_mean, rev=true)[1:2] +println(alpha_indices) +df_gplvm[!,:ard1] = z_mean[alpha_indices[1], :] +df_gplvm[!,:ard2] = z_mean[alpha_indices[2], :] + +p_gplvm = df_gplvm |> @vlplot(:point, x=:ard1, y=:ard2, color="labels:n") +p_gplvm +``` + + +```julia; echo=false +let + @assert abs(mean(z_mean[alpha_indices[1], labels[1:n_data] .== "setosa"]) - mean(z_mean[alpha_indices[1], labels[1:n_data] .!= "setosa"])) > 1.4 +end +``` + +Now, the split between the two groups is visible again. + +### Speeding up inference + +Gaussian processes tend to be slow, as they naively require operations in the order of $O(n^3)$. +Here, we demonstrate a simple speedup using the Stheno library. +Speeding up Gaussian process inference is an active area of research. + +```julia +using Stheno +@model function GPLVM_sparse(Y, K,::Type{T} = Float64) where {T} + + # Dimensionality of the problem. + N, D = size(Y) + # dimension of latent space + @assert K <= D + # number of inducing points + n_inducing = 25 + noise = 1e-3 + + # Priors + α ~ MvLogNormal(MvNormal(zeros(K), I)) + σ ~ LogNormal(1.0, 1.0) + Z ~ filldist(Normal(), K, N) + mu ~ filldist(Normal(), N) + + kernel = σ * SqExponentialKernel() ∘ ARDTransform(α) + + ## Standard + # gpc = GPC() + # f = Stheno.wrap(GP(kernel), gpc) + # gp = f(ColVecs(Z), noise) + # Y ~ filldist(gp, D) + + ## SPARSE GP + # xu = reshape(repeat(locations, K), :, K) # inducing points + # xu = reshape(repeat(collect(range(-2.0, 2.0; length=20)), K), :, K) # inducing points + lbound = minimum(Y) + 1e-6 + ubound = maximum(Y) - 1e-6 + # locations ~ filldist(Uniform(lbound, ubound), n_inducing) + # locations = [-2., -1.5 -1., -0.5, -0.25, 0.25, 0.5, 1., 2.] + # locations = collect(LinRange(lbound, ubound, n_inducing)) + locations = quantile(vec(Y), LinRange(0.01, 0.99, n_inducing)) + xu = reshape(locations, 1, :) + gp = Stheno.wrap(GP(kernel), GPC()) + fobs = gp(ColVecs(Z), noise) + finducing = gp(xu, 1e-12) + sfgp = SparseFiniteGP(fobs, finducing) + cv = cov(sfgp.fobs) + Y ~ filldist(MvNormal(mu, cv), D) + +end +``` + +```julia +n_data = 50 +gplvm_sparse = GPLVM_sparse(dat[1:n_data, :], ndim) + +chain_gplvm_sparse = sample(gplvm_sparse, NUTS(), 500) +# we extract the posterior mean estimates of the parameters from the chain +z_mean = reshape(mean(group(chain_gplvm_sparse, :Z))[:, 2], (ndim, n_data)) +alpha_mean = mean(group(chain_gplvm_sparse, :α))[:, 2] +``` + +```julia +df_gplvm_sparse = DataFrame(z_mean', :auto) +rename!(df_gplvm_sparse, Symbol.( ["z"*string(i) for i in collect(1:ndim)])) +df_gplvm_sparse[!,:sample] = 1:n_data +df_gplvm_sparse[!,:labels] = labels[1:n_data] +alpha_indices = sortperm(alpha_mean, rev=true)[1:2] +df_gplvm_sparse[!,:ard1] = z_mean[alpha_indices[1], :] +df_gplvm_sparse[!,:ard2] = z_mean[alpha_indices[2], :] +p_sparse = df_gplvm_sparse |> @vlplot(:point, x=:ard1, y=:ard2, color="labels:n") +p_sparse +``` + +Comparing the runtime, between the two versions, we can observe a clear speed-up with the sparse version. + +```julia; echo=false +let + @assert abs(mean(z_mean[alpha_indices[1], labels[1:n_data] .== "setosa"]) - mean(z_mean[alpha_indices[1], labels[1:n_data] .!= "setosa"])) > 1.0 + + @assert abs(mean(z_mean[alpha_indices[2], labels[1:n_data] .== "setosa"]) - mean(z_mean[alpha_indices[2], labels[1:n_data] .!= "setosa"])) > 0.1 +end +``` + +```julia, echo=false, skip="notebook" +if isdefined(Main, :TuringTutorials) + Main.TuringTutorials.tutorial_footer(WEAVE_ARGS[:folder], WEAVE_ARGS[:file]) +end +``` diff --git a/tutorials/12-gaussian-process-latent-variable-model/Manifest.toml b/tutorials/12-gaussian-process-latent-variable-model/Manifest.toml new file mode 100644 index 000000000..903b69a77 --- /dev/null +++ b/tutorials/12-gaussian-process-latent-variable-model/Manifest.toml @@ -0,0 +1,1740 @@ +# This file is machine-generated - editing it directly is not advised + +[[AbstractFFTs]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.0.1" + +[[AbstractGPs]] +deps = ["ChainRulesCore", "Distributions", "FillArrays", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +git-tree-sha1 = 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b/tutorials/12-gaussian-process-latent-variable-model/Project.toml @@ -0,0 +1,16 @@ +[deps] +AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" +Stheno = "8188c328-b5d6-583d-959b-9690869a5511" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" +VegaLite = "112f6efa-9a02-5b7d-90c0-432ed331239a" +Weave = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"