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Mark van der Wilk

Publications and source records attributed to Mark van der Wilk.

At least 19 recordsLinked to original sources
arXiv2026

Use What You Know: Causal Foundation Models with Partial Graphs

Estimating causal quantities traditionally relies on bespoke estimators tailored to specific assumptions. Recently proposed Causal Foundation Models (CFMs) promise a more unified approach by amortising causal discovery and inference in a single step. However, in their current state, they do not allow for the incorporation of any domain knowledge, which can lead to suboptimal predictions. We bridge this gap by introducing methods to condition CFMs on causal information, such as the causal graph or more readily available ancestral information. When access to complete causal graph information is too strict a requirement, our approach also effectively leverages partial causal information. We systematically evaluate conditioning strategies and find that injecting learnable biases into the attention mechanism, together with a graph-convolutional encoder, is a highly effective method to utilise full and partial causal information. Our experiments show that this conditioning allows a general-purpose CFM to match the performance of specialised models trained on specific causal structures. Overall, our approach addresses a central hurdle on the path towards all-in-one causal foundation models: the capability to answer causal queries in a data-driven manner while effectively leveraging any amount of domain expertise.

cs.LG↗
arXiv2026

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.

cs.LG↗
arXiv2026

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.

math.OC↗
arXiv2026

Symmetry Guarantees Statistic Recovery in Variational Inference

Variational inference (VI) is a central tool in modern machine learning, used to approximate an intractable target density by optimising over a tractable family of distributions. As the variational family cannot typically represent the target exactly, guarantees on the quality of the resulting approximation are crucial for understanding which of its properties VI can faithfully capture. Recent work has identified instances in which symmetries of the target and the variational family enable the recovery of certain statistics, even under model misspecification. However, these guarantees are inherently problem-specific and offer little insight into the fundamental mechanism by which symmetry forces statistic recovery. In this paper, we overcome this limitation by developing a general theory of symmetry-induced statistic recovery in variational inference. First, we characterise when variational minimisers inherit the symmetries of the target and establish conditions under which these pin down identifiable statistics. Second, we unify existing results by showing that previously known statistic recovery guarantees in location-scale families arise as special cases of our theory. Third, we apply our framework to distributions on the sphere to obtain novel guarantees for directional statistics in von Mises-Fisher families. Together, these results provide a modular blueprint for deriving new recovery guarantees for VI in a broad range of symmetry settings.

stat.ML↗
arXiv2026

Inverse-Free Sparse Variational Gaussian Processes

Gaussian processes (GPs) offer appealing properties but are costly to train at scale. Sparse variational GP (SVGP) approximations reduce cost yet still rely on Cholesky decompositions of kernel matrices, ill-suited to low-precision, massively parallel hardware. While one can construct valid variational bounds that rely only on matrix multiplications (matmuls) via an auxiliary matrix parameter, optimising them with off-the-shelf first-order methods is challenging. We make the inverse-free approach practical by proposing a better-conditioned bound and deriving a matmul-only natural-gradient update for the auxiliary parameter, markedly improving stability and convergence. We further provide simple heuristics, such as step-size schedules and stopping criteria, that make the overall optimisation routine fit seamlessly into existing workflows. Across regression and classification benchmarks, we demonstrate that our method 1) serves as a drop-in replacement in SVGP-based models (e.g., deep GPs), 2) recovers similar performance to traditional methods, and 3) can be faster than baselines when well tuned.

stat.ML↗
arXiv2026

The relative value of interventional and observational samples in Bayesian Causal Linear Gaussian Models

We investigate the asymptotic properties of Bayesian bivariate causal discovery for Gaussian Linear Structural Equation Models (SEMs) with heteroscedastic noise. We demonstrate that with purely observational data, the posterior distribution over the models fails to consistently identify the true causal structure - a consequence of the fundamental non-identifiability within the Markov Equivalence Class. Specifically, if the true generating mechanism corresponds to a connected graph (A -> B or B -> A), the asymptotic behavior of the posterior is given by the ratio between the prior on the true model and the push-forward prior of the alternative. In contrast, for the independence model, we establish that the posterior concentrates at a stochastic polynomial rate of O_p(n^{-1/2}). To resolve this non-identifiability, we incorporate m interventional samples and characterize the concentration rates as a function of the observational-to-total sample ratio, η. We identify a sharp concentration dichotomy: while the independence graph maintains a polynomial O_p(N^{-1/2}) rate (where N = n+m), connected graphs undergo a phase transition to exponentially fast convergence. This highlights an exponential relative importance between the two data types, as altering the amount of one data type directly changes the exponent governing the concentration speed. We derive explicit formulae for the exponential decay rates and provide precise conditions under which mixing observational and interventional data optimizes concentration speed. Finally, our theoretical findings are validated through empirical simulations in Bayesian Gaussian equivalent (BGe)-style prior specifications offering a principled foundation for experimental design in Bayesian causal discovery.

math.ST↗
arXiv2026

A Distributed Gaussian Process Model for Multi-Robot Mapping

We propose DistGP: a multi-robot learning method for collaborative learning of a global function using only local experience and computation. We utilise a sparse Gaussian process (GP) model with a factorisation that mirrors the multi-robot structure of the task, and admits distributed training via Gaussian belief propagation (GBP). Our loopy model outperforms Tree-Structured GPs \cite{bui2014tree} and can be trained online and in settings with dynamic connectivity. We show that such distributed, asynchronous training can reach the same performance as a centralised, batch-trained model, albeit with slower convergence. Last, we compare to DiNNO \cite{yu2022dinno}, a distributed neural network (NN) optimiser, and find DistGP achieves superior accuracy, is more robust to sparse communication and is better able to learn continually.

cs.RO↗
arXiv2026

Estimating Interventional Distributions with Uncertain Causal Graphs through Meta-Learning

In scientific domains -- from biology to the social sciences -- many questions boil down to \textit{What effect will we observe if we intervene on a particular variable?} If the causal relationships (e.g.~a causal graph) are known, it is possible to estimate the intervention distributions. In the absence of this domain knowledge, the causal structure must be discovered from the available observational data. However, observational data are often compatible with multiple causal graphs, making methods that commit to a single structure prone to overconfidence. A principled way to manage this structural uncertainty is via Bayesian inference, which averages over a posterior distribution on possible causal structures and functional mechanisms. Unfortunately, the number of causal structures grows super-exponentially with the number of nodes in the graph, making computations intractable. We propose to circumvent these challenges by using meta-learning to create an end-to-end model: the Model-Averaged Causal Estimation Transformer Neural Process (MACE-TNP). The model is trained to predict the Bayesian model-averaged interventional posterior distribution, and its end-to-end nature bypasses the need for expensive calculations. Empirically, we demonstrate that MACE-TNP outperforms strong Bayesian baselines. Our work establishes meta-learning as a flexible and scalable paradigm for approximating complex Bayesian causal inference, that can be scaled to increasingly challenging settings in the future.

cs.LG↗
arXiv2025

Adjusting Model Size in Continual Gaussian Processes: How Big is Big Enough?

Many machine learning models require setting a parameter that controls their size before training, e.g. number of neurons in DNNs, or inducing points in GPs. Increasing capacity typically improves performance until all the information from the dataset is captured. After this point, computational cost keeps increasing, without improved performance. This leads to the question "How big is big enough?" We investigate this problem for Gaussian processes (single-layer neural networks) in continual learning. Here, data becomes available incrementally, and the final dataset size will therefore not be known before training, preventing the use of heuristics for setting a fixed model size. We develop a method to automatically adjust model size while maintaining near-optimal performance. Our experimental procedure follows the constraint that any hyperparameters must be set without seeing dataset properties, and we show that our method performs well across diverse datasets without the need to adjust its hyperparameter, showing it requires less tuning than others.

stat.ML↗
arXiv2025

Rethinking Aleatoric and Epistemic Uncertainty

The ideas of aleatoric and epistemic uncertainty are widely used to reason about the probabilistic predictions of machine-learning models. We identify incoherence in existing discussions of these ideas and suggest this stems from the aleatoric-epistemic view being insufficiently expressive to capture all the distinct quantities that researchers are interested in. To address this we present a decision-theoretic perspective that relates rigorous notions of uncertainty, predictive performance and statistical dispersion in data. This serves to support clearer thinking as the field moves forward. Additionally we provide insights into popular information-theoretic quantities, showing they can be poor estimators of what they are often purported to measure, while also explaining how they can still be useful in guiding data acquisition.

cs.LG↗
arXiv2025

Continuous Bayesian Model Selection for Multivariate Causal Discovery

Current causal discovery approaches require restrictive model assumptions in the absence of interventional data to ensure structure identifiability. These assumptions often do not hold in real-world applications leading to a loss of guarantees and poor performance in practice. Recent work has shown that, in the bivariate case, Bayesian model selection can greatly improve performance by exchanging restrictive modelling for more flexible assumptions, at the cost of a small probability of making an error. Our work shows that this approach is useful in the important multivariate case as well. We propose a scalable algorithm leveraging a continuous relaxation of the discrete model selection problem. Specifically, we employ the Causal Gaussian Process Conditional Density Estimator (CGP-CDE) as a Bayesian non-parametric model, using its hyperparameters to construct an adjacency matrix. This matrix is then optimised using the marginal likelihood and an acyclicity regulariser, giving the maximum a posteriori causal graph. We demonstrate the competitiveness of our approach, showing it is advantageous to perform multivariate causal discovery without infeasible assumptions using Bayesian model selection.

stat.ML↗
arXiv2025

SynDaCaTE: A Synthetic Dataset For Evaluating Part-Whole Hierarchical Inference

Learning to infer object representations, and in particular part-whole hierarchies, has been the focus of extensive research in computer vision, in pursuit of improving data efficiency, systematic generalisation, and robustness. Models which are \emph{designed} to infer part-whole hierarchies, often referred to as capsule networks, are typically trained end-to-end on supervised tasks such as object classification, in which case it is difficult to evaluate whether such a model \emph{actually} learns to infer part-whole hierarchies, as claimed. To address this difficulty, we present a SYNthetic DAtaset for CApsule Testing and Evaluation, abbreviated as SynDaCaTE, and establish its utility by (1) demonstrating the precise bottleneck in a prominent existing capsule model, and (2) demonstrating that permutation-equivariant self-attention is highly effective for parts-to-wholes inference, which motivates future directions for designing effective inductive biases for computer vision.

cs.CV↗
arXiv2025

PSyDUCK: Training-Free Steganography for Latent Diffusion

Recent advances in generative AI have opened promising avenues for steganography, which can securely protect sensitive information for individuals operating in hostile environments, such as journalists, activists, and whistleblowers. However, existing methods for generative steganography have significant limitations, particularly in scalability and their dependence on retraining diffusion models. We introduce PSyDUCK, a training-free, model-agnostic steganography framework specifically designed for latent diffusion models. PSyDUCK leverages controlled divergence and local mixing within the latent denoising process, enabling high-capacity, secure message embedding without compromising visual fidelity. Our method dynamically adapts embedding strength to balance accuracy and detectability, significantly improving upon existing pixel-space approaches. Crucially, PSyDUCK extends generative steganography to latent-space video diffusion models, surpassing previous methods in both encoding capacity and robustness. Extensive experiments demonstrate PSyDUCK's superiority over state-of-the-art techniques, achieving higher transmission accuracy and lower detectability rates across diverse image and video datasets. By overcoming the key challenges associated with latent diffusion model architectures, PSyDUCK sets a new standard for generative steganography, paving the way for scalable, real-world steganographic applications.

cs.LG↗
arXiv2025

A Meta-Learning Approach to Bayesian Causal Discovery

Discovering a unique causal structure is difficult due to both inherent identifiability issues, and the consequences of finite data. As such, uncertainty over causal structures, such as those obtained from a Bayesian posterior, are often necessary for downstream tasks. Finding an accurate approximation to this posterior is challenging, due to the large number of possible causal graphs, as well as the difficulty in the subproblem of finding posteriors over the functional relationships of the causal edges. Recent works have used meta-learning to view the problem of estimating the maximum a-posteriori causal graph as supervised learning. Yet, these methods are limited when estimating the full posterior as they fail to encode key properties of the posterior, such as correlation between edges and permutation equivariance with respect to nodes. Further, these methods also cannot reliably sample from the posterior over causal structures. To address these limitations, we propose a Bayesian meta learning model that allows for sampling causal structures from the posterior and encodes these key properties. We compare our meta-Bayesian causal discovery against existing Bayesian causal discovery methods, demonstrating the advantages of directly learning a posterior over causal structure.

cs.LG↗
arXiv2025

Turbulence: Systematically and Automatically Testing Instruction-Tuned Large Language Models for Code

We present a method for systematically evaluating the correctness and robustness of instruction-tuned large language models (LLMs) for code generation via a new benchmark, Turbulence. Turbulence consists of a large set of natural language $\textit{question templates}$, each of which is a programming problem, parameterised so that it can be asked in many different forms. Each question template has an associated $\textit{test oracle}$ that judges whether a code solution returned by an LLM is correct. Thus, from a single question template, it is possible to ask an LLM a $\textit{neighbourhood}$ of very similar programming questions, and assess the correctness of the result returned for each question. This allows gaps in an LLM's code generation abilities to be identified, including $\textit{anomalies}$ where the LLM correctly solves $\textit{almost all}$ questions in a neighbourhood but fails for particular parameter instantiations. We present experiments against five LLMs from OpenAI, Cohere and Meta, each at two temperature configurations. Our findings show that, across the board, Turbulence is able to reveal gaps in LLM reasoning ability. This goes beyond merely highlighting that LLMs sometimes produce wrong code (which is no surprise): by systematically identifying cases where LLMs are able to solve some problems in a neighbourhood but do not manage to generalise to solve the whole neighbourhood, our method is effective at highlighting $\textit{robustness}$ issues. We present data and examples that shed light on the kinds of mistakes that LLMs make when they return incorrect code results.

cs.SE↗
arXiv2024

System-Aware Neural ODE Processes for Few-Shot Bayesian Optimization

We consider the problem of optimizing initial conditions and termination time in dynamical systems governed by unknown ordinary differential equations (ODEs), where evaluating different initial conditions is costly and the state's value can not be measured in real-time but only with a delay while the measuring device processes the sample. To identify the optimal conditions in limited trials, we introduce a few-shot Bayesian Optimization (BO) framework based on the system's prior information. At the core of our approach is the System-Aware Neural ODE Processes (SANODEP), an extension of Neural ODE Processes (NODEP) designed to meta-learn ODE systems from multiple trajectories using a novel context embedding block. We further develop a two-stage BO framework to effectively incorporate search space constraints, enabling efficient optimization of both initial conditions and observation timings. We conduct extensive experiments showcasing SANODEP's potential for few-shot BO within dynamical systems. We also explore SANODEP's adaptability to varying levels of prior information, highlighting the trade-off between prior flexibility and model fitting accuracy.

cs.LG↗
arXiv2024

Transition Constrained Bayesian Optimization via Markov Decision Processes

Bayesian optimization is a methodology to optimize black-box functions. Traditionally, it focuses on the setting where you can arbitrarily query the search space. However, many real-life problems do not offer this flexibility; in particular, the search space of the next query may depend on previous ones. Example challenges arise in the physical sciences in the form of local movement constraints, required monotonicity in certain variables, and transitions influencing the accuracy of measurements. Altogether, such transition constraints necessitate a form of planning. This work extends classical Bayesian optimization via the framework of Markov Decision Processes. We iteratively solve a tractable linearization of our utility function using reinforcement learning to obtain a policy that plans ahead for the entire horizon. This is a parallel to the optimization of an acquisition function in policy space. The resulting policy is potentially history-dependent and non-Markovian. We showcase applications in chemical reactor optimization, informative path planning, machine calibration, and other synthetic examples.

cs.LG↗
arXiv2024

Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic Assays

With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments workflow to make this development feasible. By combining a transfer learning surrogate model with Bayesian optimization, we show how the total number of experiments can be reduced by sharing information between optimization tasks. We demonstrate the reduction in the number of experiments using data from the development of DNA competitors for use in an amplification-based diagnostic assay. We use cross-validation to compare the predictive accuracy of different transfer learning models, and then compare the performance of the models for both single objective and penalized optimization tasks.

q-bio.QM↗