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Brooks Paige

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21 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

Effects of Dropout on Performance in Long-range Graph Learning Tasks

Jasraj Singh
Keyue Jiang
Brooks Paige
Laura Toni

Message Passing Neural Networks (MPNNs) are a class of Graph Neural Networks (GNNs) that propagate information across the graph via local neighborhoods. The scheme gives rise to two key challenges: over-smoothing and over-squashing. While several Dropout-style algorithms, such as DropEdge and DropMessage, have successfully addressed over-smoothing, their impact on over-squashing remains largely unexplored. This represents a critical gap in the literature, as failure to mitigate over-squashing would make these methods unsuitable for long-range tasks – the intended use case of deep MPNNs. In this work, we study the aforementioned algorithms, and closely related edge-dropping algorithms – DropNode, DropAgg and DropGNN – in the context of over-squashing. We present theoretical results showing that DropEdge-variants reduce sensitivity between distant nodes, limiting their suitability for long-range tasks. To address this, we introduce DropSens, a sensitivity-aware variant of DropEdge, which is developed following the message-passing scheme of GCN. DropSens explicitly controls the proportion of information lost due to edge-dropping, thereby increasing sensitivity to distant nodes despite dropping the same number of edges. Our experiments on long-range synthetic and real-world datasets confirm the predicted limitations of existing edge-dropping and feature-dropping methods. Moreover, DropSens with GCN consistently outperforms graph rewiring techniques designed to mitigate over-squashing, suggesting that simple, targeted modifications can substantially improve a model’s ability to capture long-range interactions. Our conclusions highlight the need to re-evaluate and re-design existing methods for training deep GNNs, with a renewed focus on modelling long-range interactions. The code for reproducing the results in our this work is available at https: //github. com/ignasa007/Dropout-Effects-GNNs.

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ICML Conference 2025 Conference Paper

Right Now, Wrong Then: Non-Stationary Direct Preference Optimization under Preference Drift

Seongho Son
William Bankes
Sayak Ray Chowdhury
Brooks Paige
Ilija Bogunovic

Current Large Language Model (LLM) preference optimization algorithms do not account for temporal preference drift, which can lead to severe misalignment. To address this limitation, we propose Non-Stationary Direct Preference Optimisation (NS-DPO) that models time-dependent reward functions with a Dynamic Bradley-Terry model. NS-DPO proposes a computationally efficient solution by introducing only a single discount parameter in the loss function, which is used for exponential weighting that proportionally focuses learning on more time-relevant datapoints. We theoretically analyze the convergence of NS-DPO in a general setting where the exact nature of the preference drift is not known, providing upper bounds on the estimation error and regret caused by non-stationary preferences. Finally, we demonstrate the effectiveness of NS-DPO for fine-tuning LLMs under drifting preferences. Using scenarios where various levels of preference drift is introduced, with popular LLM reward models and datasets, we show that NS-DPO fine-tuned LLMs remain robust under non-stationarity, significantly outperforming baseline algorithms that ignore temporal preference changes, without sacrificing performance in stationary cases.

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NeurIPS Conference 2024 Conference Paper

Analysing the Generalisation and Reliability of Steering Vectors

Daniel Tan
David Chanin
Aengus Lynch
Brooks Paige
Dimitrios Kanoulas
Adrià Garriga-Alonso
Robert Kirk

Steering vectors (SVs) are a new approach to efficiently adjust language model behaviour at inference time by intervening on intermediate model activations. They have shown promise in terms of improving both capabilities and model alignment. However, the reliability and generalisation properties of this approach are unknown. In this work, we rigorously investigate these properties, and show that steering vectors have substantial limitations both in- and out-of-distribution. In-distribution, steerability is highly variable across different inputs. Depending on the concept, spurious biases can substantially contribute to how effective steering is for each input, presenting a challenge for the widespread use of steering vectors. Out-of-distribution, while steering vectors often generalise well, for several concepts they are brittle to reasonable changes in the prompt, resulting in them failing to generalise well. Overall, our findings show that while steering can work well in the right circumstances, there remain many technical difficulties of applying steering vectors to guide models' behaviour at scale.

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NeurIPS Conference 2024 Conference Paper

AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction

Chu'nan Liu
Lilian Denzler
Yihong Chen
Andrew Martin
Brooks Paige

Epitope identification is vital for antibody design yet challenging due to the inherent variability in antibodies. While many deep learning methods have been developed for general protein binding site prediction tasks, whether they work for epitope prediction remains an understudied research question. The challenge is also heightened by the lack of a consistent evaluation pipeline with sufficient dataset size and epitope diversity. We introduce a filtered antibody-antigen complex structure dataset, AsEP (Antibody-specific Epitope Prediction). AsEP is the largest of its kind and provides clustered epitope groups, allowing the community to develop and test novel epitope prediction methods and evaluate their generalisability. AsEP comes with an easy-to-use interface in Python and pre-built graph representations of each antibody-antigen complex while also supporting customizable embedding methods. Using this new dataset, we benchmark several representative general protein-binding site prediction methods and find that their performances fall short of expectations for epitope prediction. To address this, we propose a novel method, WALLE, which leverages both unstructured modeling from protein language models and structural modeling from graph neural networks. WALLE demonstrate up to 3-10X performance improvement over the baseline methods. Our empirical findings suggest that epitope prediction benefits from combining sequential features provided by language models with geometrical information from graph representations. This provides a guideline for future epitope prediction method design. In addition, we reformulate the task as bipartite link prediction, allowing convenient model performance attribution and interpretability. We open source our data and code at https: //github. com/biochunan/AsEP-dataset.

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ICML Conference 2024 Conference Paper

Diffusive Gibbs Sampling

Wenlin Chen
Mingtian Zhang
Brooks Paige
José Miguel Hernández-Lobato
David Barber

The inadequate mixing of conventional Markov Chain Monte Carlo (MCMC) methods for multi-modal distributions presents a significant challenge in practical applications such as Bayesian inference and molecular dynamics. Addressing this, we propose Diffusive Gibbs Sampling (DiGS), an innovative family of sampling methods designed for effective sampling from distributions characterized by distant and disconnected modes. DiGS integrates recent developments in diffusion models, leveraging Gaussian convolution to create an auxiliary noisy distribution that bridges isolated modes in the original space and applying Gibbs sampling to alternately draw samples from both spaces. A novel Metropolis-within-Gibbs scheme is proposed to enhance mixing in the denoising sampling step. DiGS exhibits a better mixing property for sampling multi-modal distributions than state-of-the-art methods such as parallel tempering, attaining substantially improved performance across various tasks, including mixtures of Gaussians, Bayesian neural networks and molecular dynamics.

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ICML Conference 2024 Conference Paper

Gaussian Processes on Cellular Complexes

Mathieu Alain
So Takao
Brooks Paige
Marc Peter Deisenroth

In recent years, there has been considerable interest in developing machine learning models on graphs to account for topological inductive biases. In particular, recent attention has been given to Gaussian processes on such structures since they can additionally account for uncertainty. However, graphs are limited to modelling relations between two vertices. In this paper, we go beyond this dyadic setting and consider polyadic relations that include interactions between vertices, edges and one of their generalisations, known as cells. Specifically, we propose Gaussian processes on cellular complexes, a generalisation of graphs that captures interactions between these higher-order cells. One of our key contributions is the derivation of two novel kernels, one that generalises the graph Matérn kernel and one that additionally mixes information of different cell types.

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NeurIPS Conference 2023 Conference Paper

Moment Matching Denoising Gibbs Sampling

Mingtian Zhang
Alex Hawkins-Hooker
Brooks Paige
David Barber

Energy-Based Models (EBMs) offer a versatile framework for modelling complex data distributions. However, training and sampling from EBMs continue to pose significant challenges. The widely-used Denoising Score Matching (DSM) method for scalable EBM training suffers from inconsistency issues, causing the energy model to learn a noisy data distribution. In this work, we propose an efficient sampling framework: (pseudo)-Gibbs sampling with moment matching, which enables effective sampling from the underlying clean model when given a noisy model that has been well-trained via DSM. We explore the benefits of our approach compared to related methods and demonstrate how to scale the method to high-dimensional datasets.

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ICLR Conference 2021 Conference Paper

Relating by Contrasting: A Data-efficient Framework for Multimodal Generative Models

Yuge Shi
Brooks Paige
Philip H. S. Torr
N. Siddharth 0001

Multimodal learning for generative models often refers to the learning of abstract concepts from the commonality of information in multiple modalities, such as vision and language. While it has proven effective for learning generalisable representations, the training of such models often requires a large amount of related multimodal data that shares commonality, which can be expensive to come by. To mitigate this, we develop a novel contrastive framework for generative model learning, allowing us to train the model not just by the commonality between modalities, but by the distinction between "related" and "unrelated" multimodal data. We show in experiments that our method enables data-efficient multimodal learning on challenging datasets for various multimodal VAE models. We also show that under our proposed framework, the generative model can accurately identify related samples from unrelated ones, making it possible to make use of the plentiful unlabeled, unpaired multimodal data.

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NeurIPS Conference 2020 Conference Paper

Barking up the right tree: an approach to search over molecule synthesis DAGs

John Bradshaw
Brooks Paige
Matt J. Kusner
Marwin Segler
José Miguel Hernández-Lobato

When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple building blocks can be recursively combined through chemical reactions to create more complicated molecules of interest. In contrast, many current deep generative models for molecules ignore synthesizability. We therefore propose a deep generative model that better represents the real world process, by directly outputting molecule synthesis DAGs. We argue that this provides sensible inductive biases, ensuring that our model searches over the same chemical space that chemists would also have access to, as well as interoperability. We show that our approach is able to model chemical space well, producing a wide range of diverse molecules, and allows for unconstrained optimization of an inherently constrained problem: maximize certain chemical properties such that discovered molecules are synthesizable.

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NeurIPS Conference 2020 Conference Paper

Goal-directed Generation of Discrete Structures with Conditional Generative Models

Amina Mollaysa
Brooks Paige
Alexandros Kalousis

Despite recent advances, goal-directed generation of structured discrete data remains challenging. For problems such as program synthesis (generating source code) and materials design (generating molecules), finding examples which satisfy desired constraints or exhibit desired properties is difficult. In practice, expensive heuristic search or reinforcement learning algorithms are often employed. In this paper, we investigate the use of conditional generative models which directly attack this inverse problem, by modeling the distribution of discrete structures given properties of interest. Unfortunately, the maximum likelihood training of such models often fails with the samples from the generative model inadequately respecting the input properties. To address this, we introduce a novel approach to directly optimize a reinforcement learning objective, maximizing an expected reward. We avoid high-variance score-function estimators that would otherwise be required by sampling from an approximation to the normalized rewards, allowing simple Monte Carlo estimation of model gradients. We test our methodology on two tasks: generating molecules with user-defined properties and identifying short python expressions which evaluate to a given target value. In both cases, we find improvements over maximum likelihood estimation and other baselines.

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NeurIPS Conference 2019 Conference Paper

A Model to Search for Synthesizable Molecules

John Bradshaw
Brooks Paige
Matt Kusner
Marwin Segler
José Miguel Hernández-Lobato

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees that the molecules can actually be synthesized in practice. We propose a new molecule generation model, mirroring a more realistic real-world process, where (a) reactants are selected, and (b) combined to form more complex molecules. More specifically, our generative model proposes a bag of initial reactants (selected from a pool of commercially-available molecules) and uses a reaction model to predict how they react together to generate new molecules. We first show that the model can generate diverse, valid and unique molecules due to the useful inductive biases of modeling reactions. Furthermore, our model allows chemists to interrogate not only the properties of the generated molecules but also the feasibility of the synthesis routes. We conclude by using our model to solve retrosynthesis problems, predicting a set of reactants that can produce a target product.

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TIST Journal 2019 Journal Article

Take a Look Around

Stephen Law
Brooks Paige
Chris Russell

When an individual purchases a home, they simultaneously purchase its structural features, its accessibility to work, and the neighborhood amenities. Some amenities, such as air quality, are measurable while others, such as the prestige or the visual impression of a neighborhood, are difficult to quantify. Despite the well-known impacts intangible housing features have on house prices, limited attention has been given to systematically quantifying these difficult to measure amenities. Two issues have led to this neglect. Not only do few quantitative methods exist that can measure the urban environment, but that the collection of such data is both costly and subjective. We show that street image and satellite image data can capture these urban qualities and improve the estimation of house prices. We propose a pipeline that uses a deep neural network model to automatically extract visual features from images to estimate house prices in London, UK. We make use of traditional housing features such as age, size, and accessibility as well as visual features from Google Street View images and Bing aerial images in estimating the house price model. We find encouraging results where learning to characterize the urban quality of a neighborhood improves house price prediction, even when generalizing to previously unseen London boroughs. We explore the use of non-linear vs. linear methods to fuse these cues with conventional models of house pricing, and show how the interpretability of linear models allows us to directly extract proxy variables for visual desirability of neighborhoods that are both of interest in their own right, and could be used as inputs to other econometric methods. This is particularly valuable as once the network has been trained with the training data, it can be applied elsewhere, allowing us to generate vivid dense maps of the visual appeal of London streets.

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NeurIPS Conference 2019 Conference Paper

Variational Mixture-of-Experts Autoencoders for Multi-Modal Deep Generative Models

Yuge Shi
Siddharth N
Brooks Paige
Philip Torr

Learning generative models that span multiple data modalities, such as vision and language, is often motivated by the desire to learn more useful, generalisable representations that faithfully capture common underlying factors between the modalities. In this work, we characterise successful learning of such models as the fulfilment of four criteria: i) implicit latent decomposition into shared and private subspaces, ii) coherent joint generation over all modalities, iii) coherent cross-generation across individual modalities, and iv) improved model learning for individual modalities through multi-modal integration. Here, we propose a mixture-of-experts multi-modal variational autoencoder (MMVAE) for learning of generative models on different sets of modalities, including a challenging image language dataset, and demonstrate its ability to satisfy all four criteria, both qualitatively and quantitatively.

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ICML Conference 2017 Conference Paper

Grammar Variational Autoencoder

Matt J. Kusner
Brooks Paige
José Miguel Hernández-Lobato

Deep generative models have been wildly successful at learning coherent latent representations for continuous data such as natural images, artwork, and audio. However, generative modeling of discrete data such as arithmetic expressions and molecular structures still poses significant challenges. Crucially, state-of-the-art methods often produce outputs that are not valid. We make the key observation that frequently, discrete data can be represented as a parse tree from a context-free grammar. We propose a variational autoencoder which directly encodes from and decodes to these parse trees, ensuring the generated outputs are always syntactically valid. Surprisingly, we show that not only does our model more often generate valid outputs, it also learns a more coherent latent space in which nearby points decode to similar discrete outputs. We demonstrate the effectiveness of our learned models by showing their improved performance in Bayesian optimization for symbolic regression and molecule generation.

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NeurIPS Conference 2017 Conference Paper

Learning Disentangled Representations with Semi-Supervised Deep Generative Models

Siddharth N
Brooks Paige
Jan-Willem van de Meent
Alban Desmaison
Noah Goodman
Pushmeet Kohli
Frank Wood
Philip Torr

Variational autoencoders (VAEs) learn representations of data by jointly training a probabilistic encoder and decoder network. Typically these models encode all features of the data into a single variable. Here we are interested in learning disentangled representations that encode distinct aspects of the data into separate variables. We propose to learn such representations using model architectures that generalise from standard VAEs, employing a general graphical model structure in the encoder and decoder. This allows us to train partially-specified models that make relatively strong assumptions about a subset of interpretable variables and rely on the flexibility of neural networks to learn representations for the remaining variables. We further define a general objective for semi-supervised learning in this model class, which can be approximated using an importance sampling procedure. We evaluate our framework's ability to learn disentangled representations, both by qualitative exploration of its generative capacity, and quantitative evaluation of its discriminative ability on a variety of models and datasets.

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ICML Conference 2016 Conference Paper

Inference Networks for Sequential Monte Carlo in Graphical Models

Brooks Paige
Frank Wood

We introduce a new approach for amortizing inference in directed graphical models by learning heuristic approximations to stochastic inverses, designed specifically for use as proposal distributions in sequential Monte Carlo methods. We describe a procedure for constructing and learning a structured neural network which represents an inverse factorization of the graphical model, resulting in a conditional density estimator that takes as input particular values of the observed random variables, and returns an approximation to the distribution of the latent variables. This recognition model can be learned offline, independent from any particular dataset, prior to performing inference. The output of these networks can be used as automatically-learned high-quality proposal distributions to accelerate sequential Monte Carlo across a diverse range of problem settings.

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ICML Conference 2016 Conference Paper

Interacting Particle Markov Chain Monte Carlo

Tom Rainforth
Christian A. Naesseth
Fredrik Lindsten
Brooks Paige
Jan-Willem van de Meent
Arnaud Doucet
Frank Wood

We introduce interacting particle Markov chain Monte Carlo (iPMCMC), a PMCMC method based on an interacting pool of standard and conditional sequential Monte Carlo samplers. Like related methods, iPMCMC is a Markov chain Monte Carlo sampler on an extended space. We present empirical results that show significant improvements in mixing rates relative to both non-interacting PMCMC samplers and a single PMCMC sampler with an equivalent memory and computational budget. An additional advantage of the iPMCMC method is that it is suitable for distributed and multi-core architectures.

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UAI Conference 2016 Conference Paper

Super-Sampling with a Reservoir

Brooks Paige
Dino Sejdinovic
Frank Wood

We introduce an alternative to reservoir sampling, a classic and popular algorithm for drawing a fixed-size subsample from streaming data in a single pass. Rather than draw a random sample, our approach performs an online optimization which aims to select the subset that provides the best overall approximation to the full data set, as judged using a kernel two-sample test. This produces subsets which minimize the worst-case relative error when computing expectations of functions in a specified function class, using just the samples from the subset. Kernel functions are approximated using random Fourier features, and the subset of samples itself is stored in a random projection tree. The resulting algorithm runs in a single pass through the whole data set, and has a per-iteration computational complexity logarithmic in the size of the subset. These “supersamples” subsampled from the full data provide a concise summary, as demonstrated empirically on mixture models and the MNIST dataset.

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ICML Conference 2014 Conference Paper

A Compilation Target for Probabilistic Programming Languages

Brooks Paige
Frank Wood

Forward inference techniques such as sequential Monte Carlo and particle Markov chain Monte Carlo for probabilistic programming can be implemented in any programming language by creative use of standardized operating system functionality including processes, forking, mutexes, and shared memory. Exploiting this we have defined, developed, and tested a probabilistic programming language intermediate representation language we call probabilistic C, which itself can be compiled to machine code by standard compilers and linked to operating system libraries yielding an efficient, scalable, portable probabilistic programming compilation target. This opens up a new hardware and systems research path for optimizing probabilistic programming systems.

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NeurIPS Conference 2014 Conference Paper

Asynchronous Anytime Sequential Monte Carlo

Brooks Paige
Frank Wood
Arnaud Doucet
Yee Whye Teh

We introduce a new sequential Monte Carlo algorithm we call the particle cascade. The particle cascade is an asynchronous, anytime alternative to traditional sequential Monte Carlo algorithms that is amenable to parallel and distributed implementations. It uses no barrier synchronizations which leads to improved particle throughput and memory efficiency. It is an anytime algorithm in the sense that it can be run forever to emit an unbounded number of particles while keeping within a fixed memory budget. We prove that the particle cascade provides an unbiased marginal likelihood estimator which can be straightforwardly plugged into existing pseudo-marginal methods.

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NeurIPS Conference 2013 Conference Paper

Bayesian Inference and Online Experimental Design for Mapping Neural Microcircuits

Ben Shababo
Brooks Paige
Ari Pakman
Liam Paninski

We develop an inference and optimal design procedure for recovering synaptic weights in neural microcircuits. We base our procedure on data from an experiment in which populations of putative presynaptic neurons can be stimulated while a subthreshold recording is made from a single postsynaptic neuron. We present a realistic statistical model which accounts for the main sources of variability in this experiment and allows for large amounts of information about the biological system to be incorporated if available. We then present a simpler model to facilitate online experimental design which entails the use of efficient Bayesian inference. The optimized approach results in equal quality posterior estimates of the synaptic weights in roughly half the number of experimental trials under experimentally realistic conditions, tested on synthetic data generated from the full model.

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