Preserving Continuous Symmetry in Discrete Spaces: Geometric-Aware Quantization for SO(3)-Equivariant GNNs

SO(3) equivariant graph neural networks have become the dominant paradigm for atomistic foundation models, achieving high accuracy and data efficiency by building rotational symmetry directly into the architecture. Yet the computational cost of their higher-order tensor operations creates a tough trade-off between model accuracy and inference efficiency. In this paper, we propose a structural pruning method for SO(3) equivariant atomistic foundation models to bridge this accuracy-efficiency gap. The pruning is applied along the channel and order dimensions, with each irreducible representation kept or removed as a complete block, thereby retaining SO(3) equivariance. Starting from a large checkpoint, the pruned model substantially reduces the inference cost while retaining higher accuracy than an independently trained small model. The pruned MACE-MP model outperforms the official from-scratch trained small model on 7 of 9 metrics on the Matbench Discovery leaderboard. In terms of efficiency, compressed MACE-MP and MACE-OFF models contain 1.5$\times$ to 4$\times$ fewer parameters and require 2.5$\times$ to 4$\times$ less pre-training compute than training a small model from scratch. For downstream applications, fine-tuning the pruned model reduces energy and force errors by 70.1% and 34.4% compared to training task-specific models from scratch across eight representative downstream datasets. We demonstrate that the method generalizes to other SO(3) equivariant architectures (SevenNet, eSCN) and can be combined with quantization and knowledge distillation for further gains.

Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes. We present GEqTrain, a configuration-driven framework that separates dataset semantics, model composition, and training objectives. Raw data are mapped to typed node-, edge-, and graph-level fields, while model stacks, losses, and training workflows are assembled declaratively through Hydra configurations. A shared equivariant backbone and training infrastructure can therefore be retargeted to a new task primarily through configuration. We demonstrate this flexibility on three different problems handled within one software stack: coarse-grained-to-atomistic backmapping of biomolecular systems, prediction of NMR chemical shifts in molecular solids, and equivariant generative modeling. Our aim is not to surpass individually optimized task-specific systems, but to show that a shared representation and training infrastructure can achieve competitive accuracy across qualitatively different tasks at the cost of a configuration change. We further introduce GEqDiff, a generative extension based on equivariant flow matching. GEqDiff treats user-defined equivariant fields as first-class generation targets, jointly transporting Cartesian positions and non-scalar node fields spanning representations up to l=3 within a single equivariant flow. We validate this capability on a controlled synthetic benchmark inspired by protein secondary-structure motifs, showing that fields with heterogeneous transformation properties can be reconstructed jointly and with high fidelity. By reducing the software overhead of moving between predictive and generative, scalar and tensorial settings, GEqTrain aims to make equivariant modeling more reproducible, extensible, and reusable.

Gaussian processes (GPs) provide principled probabilistic predictions while encoding prior knowledge, including equivariances. Yet, their use in large-scale scientific problems is limited by computational cost. Equivariant neural networks are common but typically lack the uncertainty quantification offered by GPs, which is valuable in applications such as molecular research. High-dimensional inputs and large symmetry groups further demand scalability. We establish results pertaining to the interplay of GP equivariance and conditioning and leverage them to obtain equivariant sparse GPs through suitable mean functions and covariance kernels. We instantiate this framework with a flexible class of integration-free equivariant kernels, yielding scalable and data-efficient GP inference. In particular, we introduce triply scalable equivariant Gaussian processes. We employ equivariant sparse variational Gaussian processes for $\mathrm{SO}(2)$-equivariant vector fields and molecular property prediction. Alongside the SVGP, we develop a matrix-free equivariant full-GP implementation that combines an exact Kronecker reduction with preconditioned conjugate-gradient solves, enabling fast and scalable evaluation of the full joint predictive density. We further compare different approaches for selecting inducing points in the equivariant sparse GP models. Our test cases include synthetic $\mathrm{SO}(2)$-equivariant fields as well as the prediction of electric dipole moments of N-methylformamide based on quantum chemistry simulations, achieving accurate, uncertainty-aware predictions at a fraction of the computational cost of classical GP inference.