arXiv subjects

Jack Simons

Publications and source records attributed to Jack Simons.

4 recordsLinked to original sources

arXiv2026

How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models

Foundation models for protein structure prediction remain unreliable on certain targets. External oracles can flag and correct these failures, but biological oracles are expensive, making oracle budget a critical constraint. Existing guidance methods, such as FK-steering, DPO, and Best K-of-N sampling, differ in how they spend this budget, yet no systematic comparison exists to guide method selection. To bridge this gap, we benchmark these methods alongside the recently proposed Optimisation Over Outputs (O3), which applies off-the-shelf optimisers within a generative model's latent subspace. We extend the usage of O3 to protein structure prediction models. Overall, our work provides the first practical reference for oracle budget-aware guidance. Our evaluation on two protein targets, calmodulin (1CLL) and E. coli aspartate transcarbamoylase (9EEH), reveals that no single method consistently dominates across all budgets and oracles. Specifically, O3 proves most effective at low oracle budgets, while FK-steering and DPO demonstrate improved performance as the budget increases. We distil these findings into actionable recommendations for practitioners operating under real-world oracle-budget constraints.

cs.AI↗

arXiv2025

Sample-Efficient Optimisation over the Outputs of Generative Models

Modern generative AI models, such as diffusion and flow matching models, can sample from rich data distributions. However, many applications, especially in science and engineering, require more than drawing samples from the model distribution: they require searching within this distribution for samples that optimise task-specific criteria. In this work, we propose O3 (Optimisation Over the Outputs of Generative Models), a method for sample-efficient black-box optimisation over continuous-variable diffusion and flow-matching models. O3 is built around surrogate latent spaces: low-dimensional Euclidean embeddings that can be extracted from a generative model without additional training. The resulting representations have controllable dimensionality and support the direct application of standard optimisation algorithms. We show, on image and protein design tasks, that surrogate-space optimisation finds substantially higher-scoring samples than standard sampling or optimisation in the original latent space. Our method is model- and optimiser-agnostic, incurs negligible additional cost over standard generation, and requires no retraining or fine-tuning of the generative model.

stat.ML↗

arXiv2023

Minimizing $f$-Divergences by Interpolating Velocity Fields

Many machine learning problems can be seen as approximating a \textit{target} distribution using a \textit{particle} distribution by minimizing their statistical discrepancy. Wasserstein Gradient Flow can move particles along a path that minimizes the $f$-divergence between the target and particle distributions. To move particles, we need to calculate the corresponding velocity fields derived from a density ratio function between these two distributions. Previous works estimated such density ratio functions and then differentiated the estimated ratios. These approaches may suffer from overfitting, leading to a less accurate estimate of the velocity fields. Inspired by non-parametric curve fitting, we directly estimate these velocity fields using interpolation techniques. We prove that our estimators are consistent under mild conditions. We validate their effectiveness using novel applications on domain adaptation and missing data imputation.

stat.ML↗

arXiv2022

Sequential Neural Score Estimation: Likelihood-Free Inference with Conditional Score Based Diffusion Models

We introduce Sequential Neural Posterior Score Estimation (SNPSE), a score-based method for Bayesian inference in simulator-based models. Our method, inspired by the remarkable success of score-based methods in generative modelling, leverages conditional score-based diffusion models to generate samples from the posterior distribution of interest. The model is trained using an objective function which directly estimates the score of the posterior. We embed the model into a sequential training procedure, which guides simulations using the current approximation of the posterior at the observation of interest, thereby reducing the simulation cost. We also introduce several alternative sequential approaches, and discuss their relative merits. We then validate our method, as well as its amortised, non-sequential, variant on several numerical examples, demonstrating comparable or superior performance to existing state-of-the-art methods such as Sequential Neural Posterior Estimation (SNPE).

stat.ML↗