Bayesian optimisation (BO) is widely used to optimise stochastic black box functions. While most BO approaches focus on optimising conditional expectations, many applications require risk-averse strategies and alternative criteria accounting for the distribution tails need to be considered. In this paper, we propose new variational models for Bayesian quantile and expectile regression that are well-suited for heteroscedastic noise settings. Our models consist of two latent Gaussian processes accounting respectively for the conditional quantile (or expectile) and the scale parameter of an asymmetric likelihood functions. Furthermore, we propose two BO strategies based on max-value entropy search and Thompson sampling, that are tailored to such models and that can accommodate large batches of points. Contrary to existing BO approaches for risk-averse optimisation, our strategies can directly optimise for the quantile and expectile, without requiring replicating observations or assuming a parametric form for the noise. As illustrated in the experimental section, the proposed approach clearly outperforms the state of the art in the heteroscedastic, non-Gaussian case.

Gaussian processes are a versatile framework for learning unknown functions in a manner that permits one to utilize prior information about their properties. Although many different Gaussian process models are readily available when the input space is Euclidean, the choice is much more limited for Gaussian processes whose input space is an undirected graph. In this work, we leverage the stochastic partial differential equation characterization of Matérn Gaussian processes—a widely-used model class in the Euclidean setting—to study their analog for undirected graphs. We show that the resulting Gaussian processes inherit various attractive properties of their Euclidean and Riemannian analogs and provide techniques that allow them to be trained using standard methods, such as inducing points. This enables graph Matérn Gaussian processes to be employed in mini-batch and non-conjugate settings, thereby making them more accessible to practitioners and easier to deploy within larger learning frameworks.

In the univariate setting, using the kernel spectral representation is an appealing approach for generating stationary covariance functions. However, performing the same task for multiple-output Gaussian processes is substantially more challenging. We demonstrate that current approaches to modelling cross-covariances with a spectral mixture kernel possess a critical blind spot. Pairs of highly correlated (or highly anti-correlated) processes are not reproducible, aside from the special case when their spectral densities are of identical shape. We present a solution to this issue by replacing the conventional Gaussian components of a spectral mixture with block components of finite bandwidth (i.e. rectangular step functions). The proposed family of kernel represents the first multi-output generalisation of the spectral mixture kernel that can approximate any stationary multi-output kernel to arbitrary precision.

Neural networks and Gaussian processes are complementary in their strengths and weaknesses. Having a better understanding of their relationship comes with the promise to make each method benefit from the strengths of the other. In this work, we establish an equivalence between the forward passes of neural networks and (deep) sparse Gaussian process models. The theory we develop is based on interpreting activation functions as interdomain inducing features through a rigorous analysis of the interplay between activation functions and kernels. This results in models that can either be seen as neural networks with improved uncertainty prediction or deep Gaussian processes with increased prediction accuracy. These claims are supported by experimental results on regression and classification datasets.

Kernel selection plays a central role in determining the performance of Gaussian Process (GP) models, as the chosen kernel determines both the inductive biases and prior support of functions under the GP prior. This work addresses the challenge of constructing custom kernel functions for high-dimensional GP regression models. Drawing inspiration from recent progress in deep learning, we introduce a novel approach named KITT: Kernel Identification Through Transformers. KITT exploits a transformer-based architecture to generate kernel recommendations in under 0.1 seconds, which is several orders of magnitude faster than conventional kernel search algorithms. We train our model using synthetic data generated from priors over a vocabulary of known kernels. By exploiting the nature of the self-attention mechanism, KITT is able to process datasets with inputs of arbitrary dimension. We demonstrate that kernels chosen by KITT yield strong performance over a diverse collection of regression benchmarks.

The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression patterns and levels. Since the post-transcriptional regulation of Drosophila depends on spatiotemporal interactions between mRNAs and gap proteins, proper physically-inspired stochastic models are required to study the link between both quantities. Previous research attempts have shown that using Gaussian processes (GPs) and differential equations lead to promising predictions when analysing regulatory networks. Here we aim at further investigating two types of physically-inspired GP models based on a reaction-diffusion equation where the main difference lies in where the prior is placed. While one of them has been studied previously using protein data only, the other is novel and yields a simple approach requiring only the differentiation of kernel functions. In contrast to other stochastic frameworks, discretising the spatial space is not required here. Both GP models are tested under different conditions depending on the availability of gap gene mRNA expression data. Finally, their performances are assessed on a high-resolution dataset describing the blastoderm stage of the early embryo of Drosophila melanogaster

The use of Gaussian process models is typically limited to datasets with a few tens of thousands of observations due to their complexity and memory footprint.The two most commonly used methods to overcome this limitation are 1) the variational sparse approximation which relies on inducing points and 2) the state-space equivalent formulation of Gaussian processes which can be seen as exploiting some sparsity in the precision matrix.In this work, we propose to take the best of both worlds: we show that the inducing point framework is still valid for state space models and that it can bring further computational and memory savings. Furthermore, we provide the natural gradient formulation for the proposed variational parameterisation.Finally, this work makes it possible to use the state-space formulation inside deep Gaussian process models as illustrated in one of the experiments.

We introduce a new class of inter-domain variational Gaussian processes (GP) where data is mapped onto the unit hypersphere in order to use spherical harmonic representations. Our inference scheme is comparable to variational Fourier features, but it does not suffer from the curse of dimensionality, and leads to diagonal covariance matrices between inducing variables. This enables a speed-up in inference, because it bypasses the need to invert large covariance matrices. Our experiments show that our model is able to fit a regression model for a dataset with 6 million entries two orders of magnitude faster compared to standard sparse GPs, while retaining state of the art accuracy. We also demonstrate competitive performance on classification with non-conjugate likelihoods.

Banded matrices can be used as precision matrices in several models including linear state-space models, some Gaussian processes, and Gaussian Markov random fields. The aim of the paper is to make modern inference methods (such as variational inference or gradient-based sampling) available for Gaussian models with banded precision. We show that this can efficiently be achieved by equipping an automatic differentiation framework, such as TensorFlow or PyTorch, with some linear algebra operators dedicated to banded matrices. This paper studies the algorithmic aspects of the required operators, details their reverse-mode derivatives, and show that their complexity is linear in the number of observations.

Gaussian process (GP) modulated Cox processes are widely used to model point patterns. Existing approaches require a mapping (link function) between the unconstrained GP and the positive intensity function. This commonly yields solutions that do not have a closed form or that are restricted to specific covariance functions. We introduce a novel finite approximation of GP-modulated Cox processes where positiveness conditions can be imposed directly on the GP, with no restrictions on the covariance function. Our approach can also ensure other types of inequality constraints (e.g. monotonicity, convexity), resulting in more versatile models that can be used for other classes of point processes (e.g. renewal processes). We demonstrate on both synthetic and real-world data that our framework accurately infers the intensity functions. Where monotonicity is a feature of the process, our ability to include this in the inference improves results.