Improving Molecular Modeling with Geometric GNNs: an Empirical Study

Rapid advancements in machine learning (ML) are transforming materials science by significantly speeding up material property calculations. However, the proliferation of ML approaches has made it challenging for scientists to keep up with the most promising techniques. This paper presents an empirical study on Geometric Graph Neural Networks for 3D atomic systems, focusing on the impact of different (1) canonicalization methods, (2) graph creation strategies, and (3) auxiliary tasks, on performance, scalability and symmetry enforcement. Our findings and insights aim to guide researchers in selecting optimal modeling components for molecular modeling tasks.

A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems

Recent advances in computational modelling of atomic systems, spanning molecules, proteins, and materials, represent them as geometric graphs with atoms embedded as nodes in 3D Euclidean space. In these graphs, the geometric attributes transform according to the inherent physical symmetries of 3D atomic systems, including rotations and translations in Euclidean space, as well as node permutations. In recent years, Geometric Graph Neural Networks have emerged as the preferred machine learning architecture powering applications ranging from protein structure prediction to molecular simulations and material generation. Their specificity lies in the inductive biases they leverage -- such as physical symmetries and chemical properties -- to learn informative representations of these geometric graphs. In this opinionated paper, we provide a comprehensive and self-contained overview of the field of Geometric GNNs for 3D atomic systems. We cover fundamental background material and introduce a pedagogical taxonomy of Geometric GNN architectures:(1) invariant networks, (2) equivariant networks in Cartesian basis, (3) equivariant networks in spherical basis, and (4) unconstrained networks. Additionally, we outline key datasets and application areas and suggest future research directions. The objective of this work is to present a structured perspective on the field, making it accessible to newcomers and aiding practitioners in gaining an intuition for its mathematical abstractions.

On the importance of catalyst-adsorbate 3D interactions for relaxed energy predictions

The use of machine learning for material property prediction and discovery has traditionally centered on graph neural networks that incorporate the geometric configuration of all atoms. However, in practice not all this information may be readily available, e.g.~when evaluating the potentially unknown binding of adsorbates to catalyst. In this paper, we investigate whether it is possible to predict a system's relaxed energy in the OC20 dataset while ignoring the relative position of the adsorbate with respect to the electro-catalyst. We consider SchNet, DimeNet++ and FAENet as base architectures and measure the impact of four modifications on model performance: removing edges in the input graph, pooling independent representations, not sharing the backbone weights and using an attention mechanism to propagate non-geometric relative information. We find that while removing binding site information impairs accuracy as expected, modified models are able to predict relaxed energies with remarkably decent MAE. Our work suggests future research directions in accelerated materials discovery where information on reactant configurations can be reduced or altogether omitted.

Crystal-GFN: sampling crystals with desirable properties and constraints

Accelerating material discovery holds the potential to greatly help mitigate the climate crisis. Discovering new solid-state crystals such as electrocatalysts, ionic conductors or photovoltaics can have a crucial impact, for instance, in improving the efficiency of renewable energy production and storage. In this paper, we introduce Crystal-GFlowNet, a generative model of crystal structures that sequentially samples a crystal's composition, space group and lattice parameters. This domain-inspired approach enables the flexible incorporation of physical and geometrical constraints, as well as the use of any available predictive model of a desired property as an objective function. We evaluate the capabilities of Crystal-GFlowNet by using as objective the formation energy of a crystal structure, as predicted by a new proxy model trained on MatBench. The results demonstrate that Crystal-GFlowNet is able to sample diverse crystals with low formation energy.

FAENet: Frame Averaging Equivariant GNN for Materials Modeling

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

PhAST: Physics-Aware, Scalable, and Task-specific GNNs for Accelerated Catalyst Design

Mitigating the climate crisis requires a rapid transition towards lower carbon energy. Catalyst materials play a crucial role in the electrochemical reactions involved in a great number of industrial processes key to this transition, such as renewable energy storage and electrofuel synthesis. To reduce the amount of energy spent on such processes, we must quickly discover more efficient catalysts to drive the electrochemical reactions. Machine learning (ML) holds the potential to efficiently model the properties of materials from large amounts of data, and thus to accelerate electrocatalyst design. The Open Catalyst Project OC20 data set was constructed to that end. However, most existing ML models trained on OC20 are still neither scalable nor accurate enough for practical applications. Here, we propose several task-specific innovations, applicable to most architectures, which increase both computational efficiency and accuracy. In particular, we propose improvements in (1) the graph creation step, (2) atom representations and (3) the energy prediction head. We describe these contributions and evaluate them on several architectures, showing up to 5$\times$ reduction in inference time without sacrificing accuracy.

The eyes and hearts of UAV pilots: observations of physiological responses in real-life scenarios

The drone industry is diversifying and the number of pilots increases rapidly. In this context, flight schools need adapted tools to train pilots, most importantly with regard to their own awareness of their physiological and cognitive limits. In civil and military aviation, pilots can train themselves on realistic simulators to tune their reaction and reflexes, but also to gather data on their piloting behavior and physiological states. It helps them to improve their performances. Opposed to cockpit scenarios, drone teleoperation is conducted outdoor in the field, thus with only limited potential from desktop simulation training. This work aims to provide a solution to gather pilots behavior out in the field and help them increase their performance. We combined advance object detection from a frontal camera to gaze and heart-rate variability measurements. We observed pilots and analyze their behavior over three flight challenges. We believe this tool can support pilots both in their training and in their regular flight tasks. A demonstration video is available on https://www.youtube.com/watch?v=eePhjd2qNiI

Higher-order Clustering and Pooling for Graph Neural Networks

Graph Neural Networks achieve state-of-the-art performance on a plethora of graph classification tasks, especially due to pooling operators, which aggregate learned node embeddings hierarchically into a final graph representation. However, they are not only questioned by recent work showing on par performance with random pooling, but also ignore completely higher-order connectivity patterns. To tackle this issue, we propose HoscPool, a clustering-based graph pooling operator that captures higher-order information hierarchically, leading to richer graph representations. In fact, we learn a probabilistic cluster assignment matrix end-to-end by minimising relaxed formulations of motif spectral clustering in our objective function, and we then extend it to a pooling operator. We evaluate HoscPool on graph classification tasks and its clustering component on graphs with ground-truth community structure, achieving best performance. Lastly, we provide a deep empirical analysis of pooling operators' inner functioning.

GraphSVX: Shapley Value Explanations for Graph Neural Networks

Graph Neural Networks (GNNs) achieve significant performance for various learning tasks on geometric data due to the incorporation of graph structure into the learning of node representations, which renders their comprehension challenging. In this paper, we first propose a unified framework satisfied by most existing GNN explainers. Then, we introduce GraphSVX, a post hoc local model-agnostic explanation method specifically designed for GNNs. GraphSVX is a decomposition technique that captures the "fair" contribution of each feature and node towards the explained prediction by constructing a surrogate model on a perturbed dataset. It extends to graphs and ultimately provides as explanation the Shapley Values from game theory. Experiments on real-world and synthetic datasets demonstrate that GraphSVX achieves state-of-the-art performance compared to baseline models while presenting core theoretical and human-centric properties.

Controllable and contextualised writing tool for novel authors

Complex language models trained on huge text corpora have shown unparalleled text generation capabilities, and thanks to transfer learning, are accessible to a greater number. However, despite recent developments, users are not yet able to fully control particular aspects of the text produced. This is why we propose a finetuned OpenAI GPT-2 model for controllable and contextualised text generation specific to novels. By integrating it into a web-service, we would like to enable authors to write and ask for automatic text generation which is consistent with both previous and next paragraphs. They can specify the genre of their book, the length of the desired text, the entities it should mention and its content via keywords or a short summary. We explore the technical possibilities and limitations around these objectives.