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Mark van der Wilk

Mark van der Wilk contributes to research discovery and scholarly infrastructure.

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preprint2026arXiv

Meta-learning for sample-efficient Bayesian optimisation of fed-batch processes

The optimisation of fed-batch (bio)chemical process recipes is subject to inherent, underlying, and unmeasurable fluctuations across batches, whose trajectories are difficult to model and costly to measure. Bayesian Optimisation (BayesOpt) is a powerful tool for sampling and optimisation of expensive-to-measure functions. Gaussian Processes (GPs), the surrogate models used in BayesOpt, are static, forecast poorly, and lack generalisation across experiments, limiting their applicability to time-varying batch processes with stochastic parameters, i.e., process fluctuations. This work investigates System-Aware Neural ODE Processes (SANODEP) as a meta-learning model to overcome the limitations of GPs and increase few-shot optimisation performance in BayesOpt. Using a penicillin batch production case study, we find that SANODEP outperforms GP-based BayesOpt in the low-data regime, resulting in improved objectives when few experimental runs are performed. These improvements are observed in both on- and off-distribution batches, highlighting the generalisation capabilities of SANODEP. Using this approach, batch process operators can accelerate the initial optimisation steps in BayesOpt by deploying meta-learning or optimise the process with fewer experiments when the experimental cost is high.

preprint2026arXiv

The Neural Tangent Kernel for Classification

In wide neural networks, the Neural Tangent Kernel (NTK) remains approximately constant during training, providing a powerful theoretical tool for studying training dynamics, generalization, and connections to kernel methods. However, this theory is largely restricted to regression losses. It was previously thought that training on a classification loss, or more generally losses involving nonlinear output transformations, breaks this property, leading to divergent logits and a breakdown of the linearization. In this paper, we extend NTK theory to classification by identifying conditions under which wide neural networks remain in the lazy training regime. We show that parameter-space regularization ensures a constant NTK during training for cross-entropy loss, while in the absence of regularization the regime is recovered when targets are non-degenerate, i.e. when all classes have strictly positive probability. Under these conditions, training is well-approximated by the linearized model, yielding an explicit characterization of the solution in terms of the NTK. We further analyze the distribution of trained predictors induced by random initialization and relate this notion of model uncertainty to Bayesian methods.

preprint2023arXiv

SnAKe: Bayesian Optimization with Pathwise Exploration

Bayesian Optimization is a very effective tool for optimizing expensive black-box functions. Inspired by applications developing and characterizing reaction chemistry using droplet microfluidic reactors, we consider a novel setting where the expense of evaluating the function can increase significantly when making large input changes between iterations. We further assume we are working asynchronously, meaning we have to select new queries before evaluating previous experiments. This paper investigates the problem and introduces 'Sequential Bayesian Optimization via Adaptive Connecting Samples' (SnAKe), which provides a solution by considering large batches of queries and preemptively building optimization paths that minimize input costs. We investigate some convergence properties and empirically show that the algorithm is able to achieve regret similar to classical Bayesian Optimization algorithms in both synchronous and asynchronous settings, while reducing input costs significantly. We show the method is robust to the choice of its single hyper-parameter and provide a parameter-free alternative.

preprint2022arXiv

Bayesian Neural Network Priors Revisited

Isotropic Gaussian priors are the de facto standard for modern Bayesian neural network inference. However, it is unclear whether these priors accurately reflect our true beliefs about the weight distributions or give optimal performance. To find better priors, we study summary statistics of neural network weights in networks trained using stochastic gradient descent (SGD). We find that convolutional neural network (CNN) and ResNet weights display strong spatial correlations, while fully connected networks (FCNNs) display heavy-tailed weight distributions. We show that building these observations into priors can lead to improved performance on a variety of image classification datasets. Surprisingly, these priors mitigate the cold posterior effect in FCNNs, but slightly increase the cold posterior effect in ResNets.

preprint2022arXiv

Last Layer Marginal Likelihood for Invariance Learning

Data augmentation is often used to incorporate inductive biases into models. Traditionally, these are hand-crafted and tuned with cross validation. The Bayesian paradigm for model selection provides a path towards end-to-end learning of invariances using only the training data, by optimising the marginal likelihood. Computing the marginal likelihood is hard for neural networks, but success with tractable approaches that compute the marginal likelihood for the last layer only raises the question of whether this convenient approach might be employed for learning invariances. We show partial success on standard benchmarks, in the low-data regime and on a medical imaging dataset by designing a custom optimisation routine. Introducing a new lower bound to the marginal likelihood allows us to perform inference for a larger class of likelihood functions than before. On the other hand, we demonstrate failure modes on the CIFAR10 dataset, where the last layer approximation is not sufficient due to the increased complexity of our neural network. Our results indicate that once more sophisticated approximations become available the marginal likelihood is a promising approach for invariance learning in neural networks.

preprint2022arXiv

Learning Invariant Weights in Neural Networks

Assumptions about invariances or symmetries in data can significantly increase the predictive power of statistical models. Many commonly used models in machine learning are constraint to respect certain symmetries in the data, such as translation equivariance in convolutional neural networks, and incorporation of new symmetry types is actively being studied. Yet, efforts to learn such invariances from the data itself remains an open research problem. It has been shown that marginal likelihood offers a principled way to learn invariances in Gaussian Processes. We propose a weight-space equivalent to this approach, by minimizing a lower bound on the marginal likelihood to learn invariances in neural networks resulting in naturally higher performing models.

preprint2022arXiv

Memory Safe Computations with XLA Compiler

Software packages like TensorFlow and PyTorch are designed to support linear algebra operations, and their speed and usability determine their success. However, by prioritising speed, they often neglect memory requirements. As a consequence, the implementations of memory-intensive algorithms that are convenient in terms of software design can often not be run for large problems due to memory overflows. Memory-efficient solutions require complex programming approaches with significant logic outside the computational framework. This impairs the adoption and use of such algorithms. To address this, we developed an XLA compiler extension that adjusts the computational data-flow representation of an algorithm according to a user-specified memory limit. We show that k-nearest neighbour and sparse Gaussian process regression methods can be run at a much larger scale on a single device, where standard implementations would have failed. Our approach leads to better use of hardware resources. We believe that further focus on removing memory constraints at a compiler level will widen the range of machine learning methods that can be developed in the future.

preprint2021arXiv

Capsule Networks -- A Probabilistic Perspective

'Capsule' models try to explicitly represent the poses of objects, enforcing a linear relationship between an object's pose and that of its constituent parts. This modelling assumption should lead to robustness to viewpoint changes since the sub-object/super-object relationships are invariant to the poses of the object. We describe a probabilistic generative model which encodes such capsule assumptions, clearly separating the generative parts of the model from the inference mechanisms. With a variational bound we explore the properties of the generative model independently of the approximate inference scheme, and gain insights into failures of the capsule assumptions and inference amortisation. We experimentally demonstrate the applicability of our unified objective, and demonstrate the use of test time optimisation to solve problems inherent to amortised inference in our model.

preprint2021arXiv

Tighter Bounds on the Log Marginal Likelihood of Gaussian Process Regression Using Conjugate Gradients

We propose a lower bound on the log marginal likelihood of Gaussian process regression models that can be computed without matrix factorisation of the full kernel matrix. We show that approximate maximum likelihood learning of model parameters by maximising our lower bound retains many of the sparse variational approach benefits while reducing the bias introduced into parameter learning. The basis of our bound is a more careful analysis of the log-determinant term appearing in the log marginal likelihood, as well as using the method of conjugate gradients to derive tight lower bounds on the term involving a quadratic form. Our approach is a step forward in unifying methods relying on lower bound maximisation (e.g. variational methods) and iterative approaches based on conjugate gradients for training Gaussian processes. In experiments, we show improved predictive performance with our model for a comparable amount of training time compared to other conjugate gradient based approaches.

preprint2020arXiv

A Framework for Interdomain and Multioutput Gaussian Processes

One obstacle to the use of Gaussian processes (GPs) in large-scale problems, and as a component in deep learning system, is the need for bespoke derivations and implementations for small variations in the model or inference. In order to improve the utility of GPs we need a modular system that allows rapid implementation and testing, as seen in the neural network community. We present a mathematical and software framework for scalable approximate inference in GPs, which combines interdomain approximations and multiple outputs. Our framework, implemented in GPflow, provides a unified interface for many existing multioutput models, as well as more recent convolutional structures. This simplifies the creation of deep models with GPs, and we hope that this work will encourage more interest in this approach.

preprint2020arXiv

Bayesian Image Classification with Deep Convolutional Gaussian Processes

In decision-making systems, it is important to have classifiers that have calibrated uncertainties, with an optimisation objective that can be used for automated model selection and training. Gaussian processes (GPs) provide uncertainty estimates and a marginal likelihood objective, but their weak inductive biases lead to inferior accuracy. This has limited their applicability in certain tasks (e.g. image classification). We propose a translation-insensitive convolutional kernel, which relaxes the translation invariance constraint imposed by previous convolutional GPs. We show how we can use the marginal likelihood to learn the degree of insensitivity. We also reformulate GP image-to-image convolutional mappings as multi-output GPs, leading to deep convolutional GPs. We show experimentally that our new kernel improves performance in both single-layer and deep models. We also demonstrate that our fully Bayesian approach improves on dropout-based Bayesian deep learning methods in terms of uncertainty and marginal likelihood estimates.

preprint2020arXiv

Convergence of Sparse Variational Inference in Gaussian Processes Regression

Gaussian processes are distributions over functions that are versatile and mathematically convenient priors in Bayesian modelling. However, their use is often impeded for data with large numbers of observations, $N$, due to the cubic (in $N$) cost of matrix operations used in exact inference. Many solutions have been proposed that rely on $M \ll N$ inducing variables to form an approximation at a cost of $\mathcal{O}(NM^2)$. While the computational cost appears linear in $N$, the true complexity depends on how $M$ must scale with $N$ to ensure a certain quality of the approximation. In this work, we investigate upper and lower bounds on how $M$ needs to grow with $N$ to ensure high quality approximations. We show that we can make the KL-divergence between the approximate model and the exact posterior arbitrarily small for a Gaussian-noise regression model with $M\ll N$. Specifically, for the popular squared exponential kernel and $D$-dimensional Gaussian distributed covariates, $M=\mathcal{O}((\log N)^D)$ suffice and a method with an overall computational cost of $\mathcal{O}(N(\log N)^{2D}(\log\log N)^2)$ can be used to perform inference.

preprint2020arXiv

On the Benefits of Invariance in Neural Networks

Many real world data analysis problems exhibit invariant structure, and models that take advantage of this structure have shown impressive empirical performance, particularly in deep learning. While the literature contains a variety of methods to incorporate invariance into models, theoretical understanding is poor and there is no way to assess when one method should be preferred over another. In this work, we analyze the benefits and limitations of two widely used approaches in deep learning in the presence of invariance: data augmentation and feature averaging. We prove that training with data augmentation leads to better estimates of risk and gradients thereof, and we provide a PAC-Bayes generalization bound for models trained with data augmentation. We also show that compared to data augmentation, feature averaging reduces generalization error when used with convex losses, and tightens PAC-Bayes bounds. We provide empirical support of these theoretical results, including a demonstration of why generalization may not improve by training with data augmentation: the `learned invariance' fails outside of the training distribution.

preprint2020arXiv

Variational Orthogonal Features

Sparse stochastic variational inference allows Gaussian process models to be applied to large datasets. The per iteration computational cost of inference with this method is $\mathcal{O}(\tilde{N}M^2+M^3),$ where $\tilde{N}$ is the number of points in a minibatch and $M$ is the number of `inducing features', which determine the expressiveness of the variational family. Several recent works have shown that for certain priors, features can be defined that remove the $\mathcal{O}(M^3)$ cost of computing a minibatch estimate of an evidence lower bound (ELBO). This represents a significant computational savings when $M\gg \tilde{N}$. We present a construction of features for any stationary prior kernel that allow for computation of an unbiased estimator to the ELBO using $T$ Monte Carlo samples in $\mathcal{O}(\tilde{N}T+M^2T)$ and in $\mathcal{O}(\tilde{N}T+MT)$ with an additional approximation. We analyze the impact of this additional approximation on inference quality.

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