Moreover, we utilize amino acid replacement matrices for the diffusion forward process, encoding the biologically meaningful prior knowledge of amino acids from their spatial and sequential neighbors as well as themselves, which reduces the sampling space of the generative process.

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (\textbf{LSE}) and frame transition encoding (\textbf{FTE}). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks.

Graph Neural Networks (GNN) come in many flavors, but should always be either invariant (permutation of the nodes of the input graph does not affect the output) or \emph{equivariant} (permutation of the input permutes the output). In this paper, we consider a specific class of invariant and equivariant networks, for which we prove new universality theorems. More precisely, we consider networks with a single hidden layer, obtained by summing channels formed by applying an equivariant linear operator, a pointwise non-linearity, and either an invariant or equivariant linear output layer. Recently, Maron et al. (2019) showed that by allowing higher-order tensorization inside the network, universal invariant GNNs can be obtained. As a first contribution, we propose an alternative proof of this result, which relies on the Stone-Weierstrass theorem for algebra of real-valued functions. Our main contribution is then an extension of this result to the \emph{equivariant} case, which appears in many practical applications but has been less studied from a theoretical point of view. The proof relies on a new generalized Stone-Weierstrass theorem for algebra of equivariant functions, which is of independent interest. Additionally, unlike many previous works that consider a fixed number of nodes, our results show that a GNN defined by a single set of parameters can approximate uniformly well a function defined on graphs of varying size.

Multi-Agent Reinforcement Learning (MARL) struggles with sample inefficiency and poor generalization [1]. These challenges are partially due to a lack of structure or inductive bias in the neural networks typically used in learning the policy. One such form of structure that is commonly observed in multi-agent scenarios is symmetry. The field of Geometric Deep Learning has developed Equivariant Graph Neural Networks (EGNN) that are equivariant (or symmetric) to rotations, translations, and reflections of nodes. Incorporating equivariance has been shown to improve learning efficiency and decrease error [ 2 ]. In this paper, we demonstrate that EGNNs improve the sample efficiency and generalization in MARL.

Equivariant Graph Neural Networks (GNNs) that incorporate E(3) symmetry have achieved significant success in various scientific applications. As one of the most successful models, EGNN leverages a simple scalarization technique to perform equivariant message passing over only Cartesian vectors (i.e., 1st-degree steerable vectors), enjoying greater efficiency and efficacy compared to equivariant GNNs using higher-degree steerable vectors. This success suggests that higher-degree representations might be unnecessary. In this paper, we disprove this hypothesis by exploring the expressivity of equivariant GNNs on symmetric structures, including $k$-fold rotations and regular polyhedra. We theoretically demonstrate that equivariant GNNs will always degenerate to a zero function if the degree of the output representations is fixed to 1 or other specific values. Based on this theoretical insight, we propose HEGNN, a high-degree version of EGNN to increase the expressivity by incorporating high-degree steerable vectors while maintaining EGNN's efficiency through the scalarization trick. Our extensive experiments demonstrate that HEGNN not only aligns with our theoretical analyses on toy datasets consisting of symmetric structures, but also shows substantial improvements on more complicated datasets such as $N$-body and MD17. Our theoretical findings and empirical results potentially open up new possibilities for the research of equivariant GNNs.

Message-passing has proved to be an effective way to design graph neural networks, as it is able to leverage both permutation equivariance and an inductive bias towards learning local structures in order to achieve good generalization. However, current message-passing architectures have a limited representation power and fail to learn basic topological properties of graphs. We address this problem and propose a powerful and equivariant message-passing framework based on two ideas: first, we propagate a one-hot encoding of the nodes, in addition to the features, in order to learn a local context matrix around each node. This matrix contains rich local information about both features and topology and can eventually be pooled to build node representations. Second, we propose methods for the parametrization of the message and update functions that ensure permutation equivariance. Having a representation that is independent of the specific choice of the one-hot encoding permits inductive reasoning and leads to better generalization properties. Experimentally, our model can predict various graph topological properties on synthetic data more accurately than previous methods and achieves state-of-the-art results on molecular graph regression on the ZINC dataset.

Moreover, we utilize amino acid replacement matrices for the diffusion forward process, encoding the biologically meaningful prior knowledge of amino acids from their spatial and sequential neighbors as well as themselves, which reduces the sampling space of the generative process.

Equivariant Graph Neural Networks (eGNNs) trained on density-functional theory (DFT) data can potentially perform electronic structure prediction at unprecedented scales, enabling investigation of the electronic properties of materials with extended defects, interfaces, or exhibiting disordered phases. However, as interactions between atomic orbitals typically extend over 10+ angstroms, the graph representations required for this task tend to be densely connected, and the memory requirements to perform training and inference on these large structures can exceed the limits of modern GPUs. Here we present a distributed eGNN implementation which leverages direct GPU communication and introduce a partitioning strategy of the input graph to reduce the number of embedding exchanges between GPUs. Our implementation shows strong scaling up to 128 GPUs, and weak scaling up to 512 GPUs with 87% parallel efficiency for structures with 3,000 to 190,000 atoms on the Alps supercomputer.

Multi-Agent Reinforcement Learning (MARL) struggles with sample inefficiency and poor generalization [1]. These challenges are partially due to a lack of structure or inductive bias in the neural networks typically used in learning the policy. One such form of structure that is commonly observed in multi-agent scenarios is symmetry. The field of Geometric Deep Learning has developed Equivariant Graph Neural Networks (EGNN) that are equivariant (or symmetric) to rotations, translations, and reflections of nodes. Incorporating equivariance has been shown to improve learning efficiency and decrease error [ 2 ]. In this paper, we demonstrate that EGNNs improve the sample efficiency and generalization in MARL.

Equivariant Graph Neural Networks (GNNs) that incorporate E(3) symmetry have achieved significant success in various scientific applications. As one of the most successful models, EGNN leverages a simple scalarization technique to perform equivariant message passing over only Cartesian vectors (i.e., 1st-degree steerable vectors), enjoying greater efficiency and efficacy compared to equivariant GNNs using higher-degree steerable vectors. This success suggests that higher-degree representations might be unnecessary. In this paper, we disprove this hypothesis by exploring the expressivity of equivariant GNNs on symmetric structures, including k -fold rotations and regular polyhedra. We theoretically demonstrate that equivariant GNNs will always degenerate to a zero function if the degree of the output representations is fixed to 1 or other specific values.