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Jonathan Godwin

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5 papers

2 author rows

TMLR Journal 2026 Journal Article

Training speedups via batching for geometric learning: an analysis of static and dynamic algorithms

Daniel T. Speckhard
Tim Bechtel
Sebastian Kehl
Jonathan Godwin
Claudia Draxl

Graph neural networks (GNN) have shown promising results for several domains such as materials science, chemistry, and the social sciences. GNN models often contain millions of parameters, and like other neural network (NN) models, are often fed only a fraction of the graphs that make up the training dataset in batches to update model parameters. The effect of batching algorithms on training time and model performance has been thoroughly explored for NNs but not yet for GNNs. We analyze two different batching algorithms for graph-based models, namely static and dynamic batching for two datasets, the QM9 dataset of small molecules and the AFLOW materials database. Our experiments show that changing the batching algorithm can provide up to a 2.7x speedup, but the fastest algorithm depends on the data, model, batch size, hardware, and number of training steps run. Experiments show that for a select number of combinations of batch size, dataset, and model, significant differences in model learning metrics are observed between static and dynamic batching algorithms.

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ICLR Conference 2023 Conference Paper

Pre-training via Denoising for Molecular Property Prediction

Sheheryar Zaidi
Michael Schaarschmidt
James Martens
Hyunjik Kim
Yee Whye Teh
Alvaro Sanchez-Gonzalez
Peter W. Battaglia
Razvan Pascanu

Many important problems involving molecular property prediction from 3D structures have limited data, posing a generalization challenge for neural networks. In this paper, we describe a pre-training technique based on denoising that achieves a new state-of-the-art in molecular property prediction by utilizing large datasets of 3D molecular structures at equilibrium to learn meaningful representations for downstream tasks. Relying on the well-known link between denoising autoencoders and score-matching, we show that the denoising objective corresponds to learning a molecular force field -- arising from approximating the Boltzmann distribution with a mixture of Gaussians -- directly from equilibrium structures. Our experiments demonstrate that using this pre-training objective significantly improves performance on multiple benchmarks, achieving a new state-of-the-art on the majority of targets in the widely used QM9 dataset. Our analysis then provides practical insights into the effects of different factors -- dataset sizes, model size and architecture, and the choice of upstream and downstream datasets -- on pre-training.

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ICLR Conference 2022 Conference Paper

Learned Simulators for Turbulence

Kimberly L. Stachenfeld
Drummond Buschman Fielding
Dmitrii Kochkov
Miles D. Cranmer
Tobias Pfaff
Jonathan Godwin
Can Cui
Shirley Ho

Turbulence simulation with classical numerical solvers requires high-resolution grids to accurately resolve dynamics. Here we train learned simulators at low spatial and temporal resolutions to capture turbulent dynamics generated at high resolution. We show that our proposed model can simulate turbulent dynamics more accurately than classical numerical solvers at the comparably low resolutions across various scientifically relevant metrics. Our model is trained end-to-end from data and is capable of learning a range of challenging chaotic and turbulent dynamics at low resolution, including trajectories generated by the state-of-the-art Athena++ engine. We show that our simpler, general-purpose architecture outperforms various more specialized, turbulence-specific architectures from the learned turbulence simulation literature. In general, we see that learned simulators yield unstable trajectories; however, we show that tuning training noise and temporal downsampling solves this problem. We also find that while generalization beyond the training distribution is a challenge for learned models, training noise, added loss constraints, and dataset augmentation can help. Broadly, we conclude that our learned simulator outperforms traditional solvers run on coarser grids, and emphasize that simple design choices can offer stability and robust generalization.

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ICLR Conference 2022 Conference Paper

Simple GNN Regularisation for 3D Molecular Property Prediction and Beyond

Jonathan Godwin
Michael Schaarschmidt
Alex Gaunt
Alvaro Sanchez-Gonzalez
Yulia Rubanova
Petar Velickovic
James Kirkpatrick
Peter W. Battaglia

In this paper we show that simple noisy regularisation can be an effective way to address oversmoothing. We first argue that regularisers ad-dressing oversmoothing should both penalise node latent similarity and encourage meaningful node representations. From this observation we derive “Noisy Nodes”,a simple technique in which we corrupt the input graph with noise, and add a noise correcting node-level loss. The diverse node level loss encourages latent node diversity, and the denoising objective encourages graph manifold learning. Our regulariser applies well-studied methods in simple, straightforward ways which allow even generic architectures to overcome oversmoothing and achieve state of the art results on quantum chemistry tasks such as QM9 and Open Catalyst, and improve results significantly on Open Graph Benchmark (OGB) datasets. Our results suggest Noisy Nodes can serve as a complementary building block in the GNN toolkit.

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ICML Conference 2020 Conference Paper

Learning to Simulate Complex Physics with Graph Networks

Alvaro Sanchez-Gonzalez
Jonathan Godwin
Tobias Pfaff
Rex Ying
Jure Leskovec
Peter W. Battaglia

Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework—which we term "Graph Network-based Simulators" (GNS)—represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model was robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.

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