arXiv subjects

Brooks Paige

Publications and source records attributed to Brooks Paige.

At least 19 recordsLinked to original sources

arXiv2025

Towards Healing the Blindness of Score Matching

Score-based divergences have been widely used in machine learning and statistics applications. Despite their empirical success, a blindness problem has been observed when using these for multi-modal distributions. In this work, we discuss the blindness problem and propose a new family of divergences that can mitigate the blindness problem. We illustrate our proposed divergence in the context of density estimation and report improved performance compared to traditional approaches.

stat.ML↗

arXiv2025

AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking

Accurate prediction of antibody-antigen (Ab-Ag) binding affinity is essential for therapeutic design and vaccine development, yet the performance of current models is limited by noisy experimental labels, heterogeneous assay conditions, and poor generalization across the vast antibody and antigen sequence space. We introduce AbRank, a large-scale benchmark and evaluation framework that reframes affinity prediction as a pairwise ranking problem. AbRank aggregates over 380,000 binding assays from nine heterogeneous sources, spanning diverse antibodies, antigens, and experimental conditions, and introduces standardized data splits that systematically increase distribution shift, from local perturbations such as point mutations to broad generalization across novel antigens and antibodies. To ensure robust supervision, AbRank defines an m-confident ranking framework by filtering out comparisons with marginal affinity differences, focusing training on pairs with at least an m-fold difference in measured binding strength. As a baseline for the benchmark, we introduce WALLE-Affinity, a graph-based approach that integrates protein language model embeddings with structural information to predict pairwise binding preferences. Our benchmarks reveal significant limitations in current methods under realistic generalization settings and demonstrate that ranking-based training improves robustness and transferability. In summary, AbRank offers a robust foundation for machine learning models to generalize across the antibody-antigen space, with direct relevance for scalable, structure-aware antibody therapeutic design.

q-bio.BM↗

arXiv2025

SmilesT5: Domain-specific pretraining for molecular language models

Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in natural language processing have highlighted the capabilities of neural networks to learn complex human language using masked language modelling. These approaches to training large transformer-based deep learning models have also been used to learn the language of molecules, as represented by simplified molecular-input line-entry system (SMILES) strings. Here, we present novel domain-specific text-to-text pretraining tasks that yield improved performance in six classification-based molecular property prediction benchmarks, relative to both traditional likelihood-based training and previously proposed fine-tuning tasks. Through ablation studies, we show that data and computational efficiency can be improved by using these domain-specific pretraining tasks. Finally, the pretrained embeddings from the model can be used as fixed inputs into a downstream machine learning classifier and yield comparable performance to finetuning but with much lower computational overhead.

cs.LG↗

arXiv2025

A study of EHVI vs fixed scalarization for molecule design

Multi-objective Bayesian optimization (MOBO) provides a principled framework for navigating trade-offs in molecular design. However, its empirical advantages over scalarized alternatives remain underexplored. We benchmark a simple Pareto-based MOBO strategy - Expected Hypervolume Improvement (EHVI) - against a simple fixed-weight scalarized baseline using Expected Improvement (EI), under a tightly controlled setup with identical Gaussian Process surrogates and molecular representations. Across three molecular optimization tasks, EHVI consistently outperforms scalarized EI in terms of Pareto front coverage, convergence speed, and chemical diversity. While scalarization encompasses flexible variants - including random or adaptive schemes - our results show that even strong deterministic instantiations can underperform in low-data regimes. These findings offer concrete evidence for the practical advantages of Pareto-aware acquisition in de novo molecular optimization, especially when evaluation budgets are limited and trade-offs are nontrivial.

cs.LG↗

arXiv2025

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

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 that 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 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.

cs.LG↗

arXiv2025

Analyzing the Generalization and Reliability of Steering Vectors

Steering vectors (SVs) have been proposed as an effective approach to 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 technical difficulties of applying steering vectors to guide models' behaviour at scale. Our code is available at https://github.com/dtch1997/steering-bench

cs.LG↗

arXiv2025

Time-varying Factor Augmented Vector Autoregression with Grouped Sparse Autoencoder

Recent economic events, including the global financial crisis and COVID-19 pandemic, have exposed limitations in linear Factor Augmented Vector Autoregressive (FAVAR) models for forecasting and structural analysis. Nonlinear dimension techniques, particularly autoencoders, have emerged as promising alternatives in a FAVAR framework, but challenges remain in identifiability, interpretability, and integration with traditional nonlinear time series methods. We address these challenges through two contributions. First, we introduce a Grouped Sparse autoencoder that employs the Spike-and-Slab Lasso prior, with parameters under this prior being shared across variables of the same economic category, thereby achieving semi-identifiability and enhancing model interpretability. Second, we incorporate time-varying parameters into the VAR component to better capture evolving economic dynamics. Our empirical application to the US economy demonstrates that the Grouped Sparse autoencoder produces more interpretable factors through its parsimonious structure; and its combination with time-varying parameter VAR shows superior performance in both point and density forecasting. Impulse response analysis reveals that monetary policy shocks during recessions generate more moderate responses with higher uncertainty compared to expansionary periods.

stat.ML↗

arXiv2024

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

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.

cs.LG↗

arXiv2024

Gaussian Processes on Cellular Complexes

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.

cs.LG↗

arXiv2024

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

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.

cs.LG↗

arXiv2024

Diffusive Gibbs Sampling

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.

stat.ML↗

arXiv2024

Generative Active Learning for the Search of Small-molecule Protein Binders

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

q-bio.BM↗

arXiv2024

Moment Matching Denoising Gibbs Sampling

Energy-Based Models (EBMs) offer a versatile framework for modeling 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.

stat.ML↗

arXiv2024

Can a Confident Prior Replace a Cold Posterior?

Benchmark datasets used for image classification tend to have very low levels of label noise. When Bayesian neural networks are trained on these datasets, they often underfit, misrepresenting the aleatoric uncertainty of the data. A common solution is to cool the posterior, which improves fit to the training data but is challenging to interpret from a Bayesian perspective. We explore whether posterior tempering can be replaced by a confidence-inducing prior distribution. First, we introduce a "DirClip" prior that is practical to sample and nearly matches the performance of a cold posterior. Second, we introduce a "confidence prior" that directly approximates a cold likelihood in the limit of decreasing temperature but cannot be easily sampled. Lastly, we provide several general insights into confidence-inducing priors, such as when they might diverge and how fine-tuning can mitigate numerical instability.

cs.LG↗

arXiv2022

Simulation Intelligence: Towards a New Generation of Scientific Methods

The original "Seven Motifs" set forth a roadmap of essential methods for the field of scientific computing, where a motif is an algorithmic method that captures a pattern of computation and data movement. We present the "Nine Motifs of Simulation Intelligence", a roadmap for the development and integration of the essential algorithms necessary for a merger of scientific computing, scientific simulation, and artificial intelligence. We call this merger simulation intelligence (SI), for short. We argue the motifs of simulation intelligence are interconnected and interdependent, much like the components within the layers of an operating system. Using this metaphor, we explore the nature of each layer of the simulation intelligence operating system stack (SI-stack) and the motifs therein: (1) Multi-physics and multi-scale modeling; (2) Surrogate modeling and emulation; (3) Simulation-based inference; (4) Causal modeling and inference; (5) Agent-based modeling; (6) Probabilistic programming; (7) Differentiable programming; (8) Open-ended optimization; (9) Machine programming. We believe coordinated efforts between motifs offers immense opportunity to accelerate scientific discovery, from solving inverse problems in synthetic biology and climate science, to directing nuclear energy experiments and predicting emergent behavior in socioeconomic settings. We elaborate on each layer of the SI-stack, detailing the state-of-art methods, presenting examples to highlight challenges and opportunities, and advocating for specific ways to advance the motifs and the synergies from their combinations. Advancing and integrating these technologies can enable a robust and efficient hypothesis-simulation-analysis type of scientific method, which we introduce with several use-cases for human-machine teaming and automated science.

cs.AI↗

arXiv2022

I Don't Need u: Identifiable Non-Linear ICA Without Side Information

In this paper, we investigate the algorithmic stability of unsupervised representation learning with deep generative models, as a function of repeated re-training on the same input data. Algorithms for learning low dimensional linear representations -- for example principal components analysis (PCA), or linear independent components analysis (ICA) -- come with guarantees that they will always reveal the same latent representations (perhaps up to an arbitrary rotation or permutation). Unfortunately, for non-linear representation learning, such as in a variational auto-encoder (VAE) model trained by stochastic gradient descent, we have no such guarantees. Recent work on identifiability in non-linear ICA have introduced a family of deep generative models that have identifiable latent representations, achieved by conditioning on side information (e.g. informative labels). We empirically evaluate the stability of these models under repeated re-estimation of parameters, and compare them to both standard VAEs and deep generative models which learn to cluster in their latent space. Surprisingly, we discover side information is not necessary for algorithmic stability: using standard quantitative measures of identifiability, we find deep generative models with latent clusterings are empirically identifiable to the same degree as models which rely on auxiliary labels. We relate these results to the possibility of identifiable non-linear ICA.

cs.LG↗

arXiv2022

Improving VAE-based Representation Learning

Latent variable models like the Variational Auto-Encoder (VAE) are commonly used to learn representations of images. However, for downstream tasks like semantic classification, the representations learned by VAE are less competitive than other non-latent variable models. This has led to some speculations that latent variable models may be fundamentally unsuitable for representation learning. In this work, we study what properties are required for good representations and how different VAE structure choices could affect the learned properties. We show that by using a decoder that prefers to learn local features, the remaining global features can be well captured by the latent, which significantly improves performance of a downstream classification task. We further apply the proposed model to semi-supervised learning tasks and demonstrate improvements in data efficiency.

stat.ML↗

arXiv2022

Fast and Scalable Spike and Slab Variable Selection in High-Dimensional Gaussian Processes

Variable selection in Gaussian processes (GPs) is typically undertaken by thresholding the inverse lengthscales of automatic relevance determination kernels, but in high-dimensional datasets this approach can be unreliable. A more probabilistically principled alternative is to use spike and slab priors and infer a posterior probability of variable inclusion. However, existing implementations in GPs are very costly to run in both high-dimensional and large-$n$ datasets, or are only suitable for unsupervised settings with specific kernels. As such, we develop a fast and scalable variational inference algorithm for the spike and slab GP that is tractable with arbitrary differentiable kernels. We improve our algorithm's ability to adapt to the sparsity of relevant variables by Bayesian model averaging over hyperparameters, and achieve substantial speed ups using zero temperature posterior restrictions, dropout pruning and nearest neighbour minibatching. In experiments our method consistently outperforms vanilla and sparse variational GPs whilst retaining similar runtimes (even when $n=10^6$) and performs competitively with a spike and slab GP using MCMC but runs up to $1000$ times faster.

stat.ML↗