- Quick intro
- Density estimation
- Kernels
- Using state filtering
- On lattice observations
- On manifolds
- By variational inference
- With inducing variables
- By variational inference with inducing variables
- With vector output
- Deep
- Approximation with dropout
- For dimension reduction
- Readings
- Implementations
- Geostat Framework
- References

Gaussian random fields
are stochastic processes/fields with jointly Gaussian
distributions of observations.
While “Gaussian process regression” is not wrong *per se*, there is a common convention in stochastic process theory (and also in pedagogy) to use *process* to talk about some notionally time-indexed process and *field* to talk about ones that have a some space-like index without a presumption of an arrow of time.
This leads to much confusion, because Gaussian *field* regression is what we usually want to talk about here. Gaussian processes do not presume an arrow of time.
Although they can use one.
Regardless, hereafter I’ll use “field” and “process” interchangeably.

In machine learning, Gaussian fields are used often as a means of regression or classification, since it is fairly easy to conditionalize a Gaussian field on data and produce a posterior distribution over functions. They provide nonparametric method of inferring regression functions, with a conveniently Bayesian interpretation and reasonably elegant learning and inference steps. I would further add that this is the crystal meth of machine learning methods, in terms of the addictiveness, and of the passion of the people who use it.

The central trick is using a clever union of
Hilbert spaces and probability
to give a probabilistic interpretation of
functional regression as a kind of
nonparametric Bayesian posterior inference via
representer theorems
where one gets posterior distributions over functions.
Regression using Gaussian processes is common
e.g. spatial statistics
where it arises as *kriging*.
Cressie (1990) traces a history of this idea via Matheron (1963a), to works of Krige (1951).

This web site aims to provide an overview of resources concerned with probabilistic modeling, inference and learning based on Gaussian processes. Although Gaussian processes have a long history in the field of statistics, they seem to have been employed extensively only in niche areas. With the advent of kernel machines in the machine learning community, models based on Gaussian processes have become commonplace for problems of regression (kriging) and classification as well as a host of more specialized applications.

I’ve not been enthusiastic about these in the past. It’s nice to have a principled nonparametric Bayesian formalism, but it has always seemed pointless having a formalism that is so computationally demanding that people don’t try to use more than a thousand data points, or spend most of a paper working out how to approximate this simple elegant model with a complex messy model.

However, perhaps I should be persuaded by tricks such as AutoGP (Krauth et al. 2016) which breaks some computational deadlocks by clever use of inducing variables and variational approximation to produce a compressed representation of the data with tractable inference and model selection, including kernel selection, and doing the whole thing in many dimensions simultaneously. There are other clever tricks like this one, e.g (Saatçi 2012) shows how to use a lattice structure for observations to make computation cheap.

## Quick intro

I am not the right guy to provide the canonical introduction, because it already exists. Specifically, the canonical introduction is Rasmussen and Williams (2006). But here is a quick simple special case sufficient to start from.

We work with a centred (i.e. mean-zero) process, in which case for every finite set \(\mathbf{f}:=\{f(t_k);k=1,\dots,K\}\) of realisations of that process, the joint distribution is centred Gaussian,

\[\begin{aligned}
\mathbf{f}(t)
&\sim \operatorname{GP}\left(0, \kappa(t, t';\mathbf{\theta})\right)
\\
p(\mathbf{f}) &=(2\pi )^{-{\frac {K}{2}}}\det({\boldsymbol {\mathrm{K} }})^{-{\frac {1}{2}}}\,e^{-{\frac{1}{2}}\mathbf {f}^{\!{\mathsf {T}}}{\boldsymbol {\mathrm{K} }}^{-1}\mathbf {f}}\\
&=\mathcal{N}(\mathbf{f};\mathbf{0},\textrm{K}).
\end{aligned}\]
where \(\mathrm{K}\) is the sample covariance matrix defined such that its
entries are given by \(\mathrm{K}_{jk}=\kappa(t_j,t_k).\)
In this case, we are specifying *only* the second moments and this is giving us
all the remaining properties of the process.
That is, the unobserved, continuous random function \(f\) generates realisations
\(\mathbf{f}\in\mathbb{R}^T\)
at a discrete times \(\mathbf{t}=t_1,t_2,\dots,t_T.\)

Now,

\[\begin{aligned} f(t) &\sim \operatorname{GP}\left(0, \kappa(t, t';\mathbf{\theta})\right) & \text{Prior} \\ \mathbf{y}|\mathbf{f} &\sim \prod_{k=1}^{T} p\left(y_{k} | f\left(t_{k}\right)\right) & \text{Likelihood} \end{aligned}\]

To begin with these will form a lattice \(\mathbf{t}=1,2,\dots,T.\)

We allow that the observations may be distinct from the realisations in that the realisations may be observed with some noise. The observation noise will be Gaussian also, in the sense that

\[ y=f(\mathbf{x})+\epsilon,\]

where

\[ \epsilon \sim \mathcal{N}\left(0, \sigma_{y}^{2}\right) \]

We refer to the set of observations as \(\mathbf{y}\in\mathbb{R}^T\). The data includes observations and coordinates, and is written \(\mathcal{D}:=\{(t_k, y_k)\}_{k=1,2,\dots,T}\).

The main insight is that the Gaussian prior is conjugate to the Gaussian likelihood, which means that the posterior distributions are also Gaussian. (Although it will no longer be centred.)

We can find a likelihood for the latent functions given the observations by considering the joint distribution

\[ \begin{aligned} \left(\begin{array}{c}{\mathbf{y}} \\ {\mathbf{f}}\end{array}\right) \sim \mathcal{N}\left(\mathbf{0},\left(\begin{array}{cc}{\mathbf{K}_{y}} & {\mathbf{K}} \\ {\mathbf{K}^{T}} & {\mathbf{K}_{\mathbf{f}}}\end{array}\right)\right) \end{aligned} \]

## Density estimation

Can I infer a density using these? Yes. One popular method is apparently the logistic Gaussian process. (Tokdar 2007; Lenk 2003)

## Kernels

a.k.a. covariance models.

GP regression models are kernel machines. As such covariance kernels are the parameters. More or less. One can also parameterise with a mean function, but let us ignore that detail for now because usually we do not use them.

## Using state filtering

When one dimension of the input vector can be interpreted as a time dimension we are Kalman filtering Gaussian Processes, which has benefits in terms of speed.

## On lattice observations

## On manifolds

I would like to read Terenin on GPs on Manifolds who also makes a suggsetive connection to SDEs, which is the filtering GPs trick again.

## By variational inference

🏗

## With inducing variables

“Sparse GP”. See Quiñonero-Candela and Rasmussen (2005). 🏗

## By variational inference with inducing variables

See GP factoring.

## With vector output

## Approximation with dropout

See NN ensembles.

## For dimension reduction

e.g. GP-LVM (N. Lawrence 2005). 🏗

## Readings

This lecture by the late David Mackay is probably good; the man could talk.

There is also a well-illustrated and elementary introduction by Yuge Shi.

## Implementations

I think that GPy is a common default choice in python and GPFlow, for example, has attempted to follow its API. For another value of default, scikit-learn has a GP implementation. Moreover, many generic bayesian inference toolkits support GP models generically.

All things being equal I want better-than-generic support for GP models. Making them go fast can be a subtle business, and there are all kind of fancy bells and whistles I would generally like to support, such as inducing point methods and sparse variational inference.

## Geostat Framework

This Framework was created within the PhD project of Sebastian Müller at the Computational Hydrosystems Department at the UFZ Leipzig.

### GPy

GPy originates in GP-urdaddy Neil Lawrence’s lab. It is well-tested and featureful. However it is also crufty and confusing and slow It predates some modern autodiff technology and rolls its own, in opaque ways. It is best regarded as a kind of reference implementation but maybe not used in practice.

### Stheno

Stheno seems to be popular for Julia and also comes in an alternative flavour, python stheno. AugmentedGaussianProcess.jl by Théo Galy-Fajou looks nice and has sparse approximation plus some nice variational approx tricks.

It seems to be sponsored by Invenia as a by-product of their main business. They write excellent GP tutorials, e.g. Scaling multi-output Gaussian process models with exact inference.

### GPyTorch

have you used gpytorch? Its the bomb it is truly amazing. This tutorial is well worth the 15 minutes it takes. Crank up the training and testing set datasize to 10000 and it is a breeze I have tried GPy, GPflow and tensorflow in the past and they would struggle

### GPFlow

GPflow (using tensorflow). The GPflow docs includes the following clarification of its genealogy.

GPflow has origins in GPy…, and much of the interface is intentionally similar for continuity (though some parts of the interface may diverge in future). GPflow has a rather different remit from GPy though:

- GPflow leverages TensorFlow for faster/bigger computation
- GPflow has much less code than GPy, mostly because all gradient computation is handled by TensorFlow.
- GPflow focusses on variational inference and MCMC — there is no expectation propagation or Laplace approximation.
- GPflow does not have any plotting functionality.

It practice is is faster than GPy but does seem any easier or less confusing to implement tricky stuff in.

### Misc python

There are additionally several GP models in the pytorch-based pyro. PyMC3. ladax is a jax-based one. George is another python GP regression that claims to handle big data at the cost of lots of C++.

### Stan

Bayes workhorse Stan can do Gaussian Process regression just like almost everything else; see Michael Betancourt’s blog, 1. 2. 3.

### AutoGP

autogp (also using tensorflow) incpororates much fancy GP technology at once.

### scikit-learn

The current scikit-learn has basic Gaussian processes, and an introduction.

Gaussian Processes (GP) are a generic supervised learning method designed to solve regression and probabilistic classification problems.

The advantages of Gaussian processes are:

- The prediction interpolates the observations (at least for regular kernels).
- The prediction is probabilistic (Gaussian) so that one can compute empirical confidence intervals and decide based on those if one should refit (online fitting, adaptive fitting) the prediction in some region of interest.
- Versatile: different kernels can be specified. Common kernels are provided, but it is also possible to specify custom kernels.
The disadvantages of Gaussian processes include:

- They are not sparse, i.e., they use the whole samples/features information to perform the prediction.
- They lose efficiency in high dimensional spaces — namely when the number of features exceeds a few dozens.

This description disposes me against using this implementation, because it has at best imprecision and at worst mistakes in the disadvantages section.

The first point is *strictly* correct, but not useful, in that sparse approximate GPs is a whole industry, and this is a statement about their implementation missing a commonly-used approximate inference method rather than a problem with the family of methods per se.
The second is just wrong, unless I have misunderstood something.
Cost scaling should be linear in the dimension of the feature space, as with all other kernel methods.
As such scaling costs due to dimensionality of the features is negligible compared to scaling costs of the number of data points, AFAICT.
Naïve inference is \(\mathcal{O}(DN^3)\) for \(N\) observations and \(D\) features.
Dimensionality cost is no worse than linear regression for prediction and superior for training, although other models that have a linear complexity in sample dimension escape without such a warning.

### Misc julia

A comparison of some options is done by Théo Galy-Fajou.

So… It’s easy enough to be bikeshedded is the message I’m getting here. There is an attempt at unifying the julia ecosystem in this area via AbstractGPs and other tools in JuliaGaussianProcesses organisation, e.g. KernelFunctions.jl.

### MATLAB

Should mention the various matlab/scilab options.

GPStuff is one for MATLAB/Octave that I have seen around the place.

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