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Samuel Stanton

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4 papers

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NeurIPS Conference 2023 Conference Paper

GAUCHE: A Library for Gaussian Processes in Chemistry

Ryan-Rhys Griffiths
Leo Klarner
Henry Moss
Aditya Ravuri
Sang Truong
Yuanqi Du
Samuel Stanton
Gary Tom

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https: //github. com/leojklarner/gauche.

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NeurIPS Conference 2023 Conference Paper

Protein Design with Guided Discrete Diffusion

Nate Gruver
Samuel Stanton
Nathan Frey
Tim G. J. Rudner
Isidro Hotzel
Julien Lafrance-Vanasse
Arvind Rajpal
Kyunghyun Cho

A popular approach to protein design is to combine a generative model with a discriminative model for conditional sampling. The generative model samples plausible sequences while the discriminative model guides a search for sequences with high fitness. Given its broad success in conditional sampling, classifier-guided diffusion modeling is a promising foundation for protein design, leading many to develop guided diffusion models for structure with inverse folding to recover sequences. In this work, we propose diffusioN Optimized Sampling (NOS), a guidance method for discrete diffusion models that follows gradients in the hidden states of the denoising network. NOS makes it possible to perform design directly in sequence space, circumventing significant limitations of structure-based methods, including scarce data and challenging inverse design. Moreover, we use NOS to generalize LaMBO, a Bayesian optimization procedure for sequence design that facilitates multiple objectives and edit-based constraints. The resulting method, LaMBO-2, enables discrete diffusions and stronger performance with limited edits through a novel application of saliency maps. We apply LaMBO-2 to a real-world protein design task, optimizing antibodies for higher expression yield and binding affinity to several therapeutic targets under locality and developability constraints, attaining a 99\% expression rate and 40\% binding rate in exploratory in vitro experiments.

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NeurIPS Conference 2021 Conference Paper

Conditioning Sparse Variational Gaussian Processes for Online Decision-making

Wesley J. Maddox
Samuel Stanton
Andrew G. Wilson

With a principled representation of uncertainty and closed form posterior updates, Gaussian processes (GPs) are a natural choice for online decision making. However, Gaussian processes typically require at least $\mathcal{O}(n^2)$ computations for $n$ training points, limiting their general applicability. Stochastic variational Gaussian processes (SVGPs) can provide scalable inference for a dataset of fixed size, but are difficult to efficiently condition on new data. We propose online variational conditioning (OVC), a procedure for efficiently conditioning SVGPs in an online setting that does not require re-training through the evidence lower bound with the addition of new data. OVC enables the pairing of SVGPs with advanced look-ahead acquisition functions for black-box optimization, even with non-Gaussian likelihoods. We show OVC provides compelling performance in a range of applications including active learning of malaria incidence, and reinforcement learning on MuJoCo simulated robotic control tasks.

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NeurIPS Conference 2021 Conference Paper

Does Knowledge Distillation Really Work?

Samuel Stanton
Pavel Izmailov
Polina Kirichenko
Alexander A. Alemi
Andrew G. Wilson

Knowledge distillation is a popular technique for training a small student network to emulate a larger teacher model, such as an ensemble of networks. We show that while knowledge distillation can improve student generalization, it does not typically work as it is commonly understood: there often remains a surprisingly large discrepancy between the predictive distributions of the teacher and the student, even in cases when the student has the capacity to perfectly match the teacher. We identify difficulties in optimization as a key reason for why the student is unable to match the teacher. We also show how the details of the dataset used for distillation play a role in how closely the student matches the teacher --- and that more closely matching the teacher paradoxically does not always lead to better student generalization.

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