We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing a novel method which converts molecular geometries into SE(3)-invariant 1D discrete sequences. Our method consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with our proposed method, various LMs excel in molecular geometry generation, especially in controlled generation tasks. Our code has been released as part of the AIRS library (https://github.com/divelab/AIRS/).

SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks whose CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single shared parameter set without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

We consider using deep neural networks to solve time-dependent partial differential equations (PDEs), where multi-scale processing is crucial for modeling complex, time-evolving dynamics. While the U-Net architecture with skip connections is commonly used by prior studies to enable multi-scale processing, our analysis shows that the need for features to evolve across layers results in temporally misaligned features in skip connections, which limits the model’s performance. To address this limitation, we propose SineNet, consisting of multiple sequentially connected U-shaped network blocks, referred to as waves. In SineNet, high-resolution features are evolved progressively through multiple stages, thereby reducing the amount of misalignment within each stage. We furthermore analyze the role of skip connections in enabling both parallel and sequential processing of multi-scale information. Our method is rigorously tested on multiple PDE datasets, including the Navier-Stokes equations and shallow water equations, showcasing the advantages of our proposed approach over conventional U-Nets with a comparable parameter budget. We further demonstrate that increasing the number of waves in SineNet while maintaining the same number of parameters leads to a monotonically improved performance. The results highlight the effectiveness of SineNet and the potential of our approach in advancing the state-of-the-art in neural PDE solver design. Our code is available as part of AIRS (https://github.com/divelab/AIRS).

We consider achieving equivariance in machine learning systems via frame averaging. Current frame averaging methods involve a costly sum over large frames or rely on sampling-based approaches that only yield approximate equivariance. Here, we propose Minimal Frame Averaging (MFA), a mathematical framework for constructing provably minimal frames that are exactly equivariant. The general foundations of MFA also allow us to extend frame averaging to more groups than previously considered, including the Lorentz group for describing symmetries in space-time, and the unitary group for complex-valued domains. Results demonstrate the efficiency and effectiveness of encoding symmetries via MFA across a diverse range of tasks, including $n$-body simulation, top tagging in collider physics, and relaxed energy prediction. Our code is available at https://github.com/divelab/MFA.

We study property prediction for crystal materials. A crystal structure consists of a minimal unit cell that is repeated infinitely in 3D space. How to accurately represent such repetitive structures in machine learning models remains unresolved. Current methods construct graphs by establishing edges only between nearby nodes, thereby failing to faithfully capture infinite repeating patterns and distant interatomic interactions. In this work, we propose several innovations to overcome these limitations. First, we propose to model physics-principled interatomic potentials directly instead of only using distances as in many existing methods. These potentials include the Coulomb potential, London dispersion potential, and Pauli repulsion potential. Second, we model the complete set of potentials among all atoms, instead of only between nearby atoms as in existing methods. This is enabled by our approximations of infinite potential summations with provable error bounds. We further develop efficient algorithms to compute the approximations. Finally, we propose to incorporate our computations of complete interatomic potentials into message passing neural networks for representation learning. We perform experiments on the JARVIS and Materials Project benchmarks for evaluation. Results show that the use of interatomic potentials and complete interatomic potentials leads to consistent performance improvements with reasonable computational costs. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Many real-world data can be modeled as 3D graphs, but learning representations that incorporates 3D information completely and efficiently is challenging. Existing methods either use partial 3D information, or suffer from excessive computational cost. To incorporate 3D information completely and efficiently, we propose a novel message passing scheme that operates within 1-hop neighborhood. Our method guarantees full completeness of 3D information on 3D graphs by achieving global and local completeness. Notably, we propose the important rotation angles to fulfill global completeness. Additionally, we show that our method is orders of magnitude faster than prior methods. We provide rigorous proof of completeness and analysis of time complexity for our methods. As molecules are in essence quantum systems, we build the \underline{com}plete and \underline{e}fficient graph neural network (ComENet) by combing quantum inspired basis functions and the proposed message passing scheme. Experimental results demonstrate the capability and efficiency of ComENet, especially on real-world datasets that are large in both numbers and sizes of graphs. Our code is publicly available as part of the DIG library (\url{https://github.com/divelab/DIG}).

We consider representation learning on periodic graphs encoding crystal materials. Different from regular graphs, periodic graphs consist of a minimum unit cell repeating itself on a regular lattice in 3D space. How to effectively encode these periodic structures poses unique challenges not present in regular graph representation learning. In addition to being E(3) invariant, periodic graph representations need to be periodic invariant. That is, the learned representations should be invariant to shifts of cell boundaries as they are artificially imposed. Furthermore, the periodic repeating patterns need to be captured explicitly as lattices of different sizes and orientations may correspond to different materials. In this work, we propose a transformer architecture, known as Matformer, for periodic graph representation learning. Our Matformer is designed to be invariant to periodicity and can capture repeating patterns explicitly. In particular, Matformer encodes periodic patterns by efficient use of geometric distances between the same atoms in neighboring cells. Experimental results on multiple common benchmark datasets show that our Matformer outperforms baseline methods consistently. In addition, our results demonstrate the importance of periodic invariance and explicit repeating pattern encoding for crystal representation learning. Our code is publicly available at https://github.com/YKQ98/Matformer.