Tess Smidt

YuQing Xie, Ameya Daigavane, Mit Kotak et al. · mit

$E(3)$-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.

Teddy Koker, Mit Kotak, Tess Smidt · mit

Foundation models for materials modeling are advancing quickly, but their training remains expensive, often placing state-of-the-art methods out of reach for many research groups. We introduce Nequix, a compact E(3)-equivariant potential that pairs a simplified NequIP design with modern training practices, including equivariant root-mean-square layer normalization and the Muon optimizer, to retain accuracy while substantially reducing compute requirements. Nequix has 700K parameters and was trained in 100 A100 GPU-hours. On the Matbench-Discovery and MDR Phonon benchmarks, Nequix ranks third overall while requiring a 20 times lower training cost than most other methods, and it delivers two orders of magnitude faster inference speed than the current top-ranked model. We release model weights and fully reproducible codebase at https://github.com/atomicarchitects/nequix.

Chuin Wei Tan, Marc L. Descoteaux, Mit Kotak et al. · mit

Machine learning interatomic potentials, particularly those based on deep equivariant neural networks, have demonstrated state-of-the-art accuracy and computational efficiency in atomistic modeling tasks like molecular dynamics and high-throughput screening. The size of datasets and demands of downstream workflows are growing rapidly, making robust and scalable software essential. This work presents a major overhaul of the NequIP framework focusing on multi-node parallelism, computational performance, and extensibility. The redesigned framework supports distributed training on large datasets and removes barriers preventing full utilization of the PyTorch 2.0 compiler at train time. We demonstrate this acceleration in a case study by training Allegro models on the SPICE 2 dataset of organic molecular systems. For inference, we introduce the first end-to-end infrastructure that uses the PyTorch Ahead-of-Time Inductor compiler for machine learning interatomic potentials. Additionally, we implement a custom kernel for the Allegro model's most expensive operation, the tensor product. Together, these advancements speed up molecular dynamics calculations on system sizes of practical relevance by up to a factor of 18.

Xuan Zhang, Limei Wang, Jacob Helwig et al. · cambridge, mit

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

Yi-Lun Liao, Brandon Wood, Abhishek Das et al. · meta-ai

Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace $SO(3)$ convolutions with eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements -- attention re-normalization, separable $S^2$ activation and separable layer normalization. Putting this all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on large-scale OC20 dataset by up to $9\%$ on forces, $4\%$ on energies, offers better speed-accuracy trade-offs, and $2\times$ reduction in DFT calculations needed for computing adsorption energies. Additionally, EquiformerV2 trained on only OC22 dataset outperforms GemNet-OC trained on both OC20 and OC22 datasets, achieving much better data efficiency. Finally, we compare EquiformerV2 with Equiformer on QM9 and OC20 S2EF-2M datasets to better understand the performance gain brought by higher degrees.

Yi-Lun Liao, Tess Smidt

Despite their widespread success in various domains, Transformer networks have yet to perform well across datasets in the domain of 3D atomistic graphs such as molecules even when 3D-related inductive biases like translational invariance and rotational equivariance are considered. In this paper, we demonstrate that Transformers can generalize well to 3D atomistic graphs and present Equiformer, a graph neural network leveraging the strength of Transformer architectures and incorporating SE(3)/E(3)-equivariant features based on irreducible representations (irreps). First, we propose a simple and effective architecture by only replacing original operations in Transformers with their equivariant counterparts and including tensor products. Using equivariant operations enables encoding equivariant information in channels of irreps features without complicating graph structures. With minimal modifications to Transformers, this architecture has already achieved strong empirical results. Second, we propose a novel attention mechanism called equivariant graph attention, which improves upon typical attention in Transformers through replacing dot product attention with multi-layer perceptron attention and including non-linear message passing. With these two innovations, Equiformer achieves competitive results to previous models on QM9, MD17 and OC20 datasets.

Mario Geiger, Tess Smidt

We present e3nn, a generalized framework for creating E(3) equivariant trainable functions, also known as Euclidean neural networks. e3nn naturally operates on geometry and geometric tensors that describe systems in 3D and transform predictably under a change of coordinate system. The core of e3nn are equivariant operations such as the TensorProduct class or the spherical harmonics functions that can be composed to create more complex modules such as convolutions and attention mechanisms. These core operations of e3nn can be used to efficiently articulate Tensor Field Networks, 3D Steerable CNNs, Clebsch-Gordan Networks, SE(3) Transformers and other E(3) equivariant networks.

Ameya Daigavane, Arthur Kosmala, Miles Cranmer et al. · cambridge

Machine learning has become increasingly popular for efficiently modelling the dynamics of complex physical systems, demonstrating a capability to learn effective models for dynamics which ignore redundant degrees of freedom. Learned simulators typically predict the evolution of the system in a step-by-step manner with numerical integration techniques. However, such models often suffer from instability over long roll-outs due to the accumulation of both estimation and integration error at each prediction step. Here, we propose an alternative construction for learned physical simulators that are inspired by the concept of action-angle coordinates from classical mechanics for describing integrable systems. We propose Action-Angle Networks, which learn a nonlinear transformation from input coordinates to the action-angle space, where evolution of the system is linear. Unlike traditional learned simulators, Action-Angle Networks do not employ any higher-order numerical integration methods, making them extremely efficient at modelling the dynamics of integrable physical systems.

Ameya Daigavane, Song Kim, Mario Geiger et al.

We present Symphony, an $E(3)$-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree $E(3)$-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

YuQing Xie, Ameya Daigavane, Mit Kotak et al. · mit

$E(3)$-equivariant neural networks have proven to be effective in a wide range of 3D modeling tasks. A fundamental operation of such networks is the tensor product, which allows interaction between different feature types. Because this operation scales poorly, there has been considerable work towards accelerating this interaction. However, recently \citet{xieprice} have pointed out that most speedups come from a reduction in expressivity rather than true algorithmic improvements on computing Clebsch-Gordan tensor products. A modification of Gaunt tensor product \citep{gaunt} can give a true asymptotic speedup but is incomplete and misses many interactions. In this work, we provide the first complete algorithm which truly provides asymptotic benefits Clebsch-Gordan tensor products. For full CGTP, our algorithm brings runtime complexity from the naive $O(L^6)$ to $O(L^4\log^2 L)$, close to the lower bound of $O(L^4)$. We first show how generalizing fast Fourier based convolution naturally leads to the previously proposed Gaunt tensor product \citep{gaunt}. To remedy antisymmetry issues, we generalize from scalar signals to irrep valued signals, giving us tensor spherical harmonics. We prove a generalized Gaunt formula for the tensor harmonics. Finally, we show that we only need up to vector valued signals to recover the missing interactions of Gaunt tensor product.

Allan dos Santos Costa, Ilan Mitnikov, Mario Geiger et al.

Three-dimensional native states of natural proteins display recurring and hierarchical patterns. Yet, traditional graph-based modeling of protein structures is often limited to operate within a single fine-grained resolution, and lacks hourglass neural architectures to learn those high-level building blocks. We narrow this gap by introducing Ophiuchus, an SO(3)-equivariant coarse-graining model that efficiently operates on all-atom protein structures. Our model departs from current approaches that employ graph modeling, instead focusing on local convolutional coarsening to model sequence-motif interactions with efficient time complexity in protein length. We measure the reconstruction capabilities of Ophiuchus across different compression rates, and compare it to existing models. We examine the learned latent space and demonstrate its utility through conformational interpolation. Finally, we leverage denoising diffusion probabilistic models (DDPM) in the latent space to efficiently sample protein structures. Our experiments demonstrate Ophiuchus to be a scalable basis for efficient protein modeling and generation.

Elyssa Hofgard, Rui Wang, Robin Walters et al.

3D Euclidean symmetry equivariant neural networks have demonstrated notable success in modeling complex physical systems. We introduce a framework for relaxed $E(3)$ graph equivariant neural networks that can learn and represent symmetry breaking within continuous groups. Building on the existing e3nn framework, we propose the use of relaxed weights to allow for controlled symmetry breaking. We show empirically that these relaxed weights learn the correct amount of symmetry breaking.

Teddy Koker, Abhijeet Gangan, Mit Kotak et al.

Many materials properties depend on higher-order derivatives of the potential energy surface, yet machine learned interatomic potentials (MLIPs) trained with standard a standard loss on energy, force, and stress errors can exhibit error in curvature, degrading the prediction of vibrational properties. We introduce phonon fine-tuning (PFT), which directly supervises second-order force constants of materials by matching MLIP energy Hessians to DFT-computed force constants from finite displacement phonon calculations. To scale to large supercells, PFT stochastically samples Hessian columns and computes the loss with a single Hessian-vector product. We also use a simple co-training scheme to incorporate upstream data to mitigate catastrophic forgetting. On the MDR Phonon benchmark, PFT improves Nequix MP (trained on Materials Project) by 55% on average across phonon thermodynamic properties and achieves state-of-the-art performance among models trained on Materials Project trajectories. PFT also generalizes to improve properties beyond second-derivatives, improving thermal conductivity predictions that rely on third-order derivatives of the potential energy.

YuQing Xie, Tess Smidt

Equivariant neural networks (ENNs) have been shown to be extremely effective in applications involving underlying symmetries. By construction ENNs cannot produce lower symmetry outputs given a higher symmetry input. However, symmetry breaking occurs in many physical systems and we may obtain a less symmetric stable state from an initial highly symmetric one. Hence, it is imperative that we understand how to systematically break symmetry in ENNs. In this work, we propose a novel symmetry breaking framework that is fully equivariant and is the first which fully addresses spontaneous symmetry breaking. We emphasize that our approach is general and applicable to equivariance under any group. To achieve this, we introduce the idea of symmetry breaking sets (SBS). Rather than redesign existing networks, we design sets of symmetry breaking objects which we feed into our network based on the symmetry of our inputs and outputs. We show there is a natural way to define equivariance on these sets, which gives an additional constraint. Minimizing the size of these sets equates to data efficiency. We prove that minimizing these sets translates to a well studied group theory problem, and tabulate solutions to this problem for the point groups. Finally, we provide some examples of symmetry breaking to demonstrate how our approach works in practice. The code for these examples is available at \url{https://github.com/atomicarchitects/equivariant-SBS}.

Yi-Lun Liao, Alexander J. Hoffman, Sabrina C. Shen et al.

As $SE(3)$-equivariant graph neural networks mature as a core tool for 3D atomistic modeling, improving their efficiency, expressivity, and physical consistency has become a central challenge for large-scale applications. In this work, we introduce EquiformerV3, the third generation of the $SE(3)$-equivariant graph attention Transformer, designed to advance all three dimensions: efficiency, expressivity, and generality. Building on EquiformerV2, we have the following three key advances. First, we optimize the software implementation, achieving $1.75\times$ speedup. Second, we introduce simple and effective modifications to EquiformerV2, including equivariant merged layer normalization, improved feedforward network hyper-parameters, and attention with smooth radius cutoff. Third, we propose SwiGLU-$S^2$ activations to incorporate many-body interactions for better theoretical expressivity and to preserve strict equivariance while reducing the complexity of sampling $S^2$ grids. Together, SwiGLU-$S^2$ activations and smooth-cutoff attention enable accurate modeling of smoothly varying potential energy surfaces (PES), generalizing EquiformerV3 to tasks requiring energy-conserving simulations and higher-order derivatives of PES. With these improvements, EquiformerV3 trained with the auxiliary task of denoising non-equilibrium structures (DeNS) achieves state-of-the-art results on OC20, OMat24, and Matbench Discovery.

Derek Lim, Joshua Robinson, Lingxiao Zhao et al.

We introduce SignNet and BasisNet -- new neural architectures that are invariant to two key symmetries displayed by eigenvectors: (i) sign flips, since if $v$ is an eigenvector then so is $-v$; and (ii) more general basis symmetries, which occur in higher dimensional eigenspaces with infinitely many choices of basis eigenvectors. We prove that under certain conditions our networks are universal, i.e., they can approximate any continuous function of eigenvectors with the desired invariances. When used with Laplacian eigenvectors, our networks are provably more expressive than existing spectral methods on graphs; for instance, they subsume all spectral graph convolutions, certain spectral graph invariants, and previously proposed graph positional encodings as special cases. Experiments show that our networks significantly outperform existing baselines on molecular graph regression, learning expressive graph representations, and learning neural fields on triangle meshes. Our code is available at https://github.com/cptq/SignNet-BasisNet .

Allan dos Santos Costa, Ilan Mitnikov, Franco Pellegrini et al.

Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of protein motion, its computational toll hinders its use in practice. To address this challenge, multiple deep learning models for reproducing and accelerating MD have been proposed drawing on transport-based generative methods. However, existing work focuses on generation through transport of samples from prior distributions, that can often be distant from the data manifold. The recently proposed framework of stochastic interpolants, instead, enables transport between arbitrary distribution endpoints. Building upon this work, we introduce EquiJump, a transferable SO(3)-equivariant model that bridges all-atom protein dynamics simulation time steps directly. Our approach unifies diverse sampling methods and is benchmarked against existing models on trajectory data of fast folding proteins. EquiJump achieves state-of-the-art results on dynamics simulation with a transferable model on all of the fast folding proteins.

Julia Balla, Siddharth Mishra-Sharma, Carolina Cuesta-Lazaro et al.

Efficiently processing structured point cloud data while preserving multiscale information is a key challenge across domains, from graphics to atomistic modeling. Using a curated dataset of simulated galaxy positions and properties, represented as point clouds, we benchmark the ability of graph neural networks to simultaneously capture local clustering environments and long-range correlations. Given the homogeneous and isotropic nature of the Universe, the data exhibits a high degree of symmetry. We therefore focus on evaluating the performance of Euclidean symmetry-preserving ($E(3)$-equivariant) graph neural networks, showing that they can outperform non-equivariant counterparts and domain-specific information extraction techniques in downstream performance as well as simulation-efficiency. However, we find that current architectures fail to capture information from long-range correlations as effectively as domain-specific baselines, motivating future work on architectures better suited for extracting long-range information.

Allan dos Santos Costa, Manvitha Ponnapati, Dana Rubin et al.

Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular motion, but its high-resolution temporal evolution comes at significant computational cost, limiting its applicability to timescales of biological relevance. Deep learning approaches have emerged as promising solutions to overcome these computational limitations by learning to predict long-timescale dynamics. However, generalizable kinetics models for proteins remain largely unexplored, and the fundamental limits of achievable acceleration while preserving dynamical accuracy are poorly understood. In this work, we fill this gap with DeepJump, an Euclidean-Equivariant Flow Matching-based model for predicting protein conformational dynamics across multiple temporal scales. We train DeepJump on trajectories of the diverse proteins of mdCATH, systematically studying our model's performance in generalizing to long-term dynamics of fast-folding proteins and characterizing the trade-off between computational acceleration and prediction accuracy. We demonstrate the application of DeepJump to ab initio folding, showcasing prediction of folding pathways and native states. Our results demonstrate that DeepJump achieves significant $\approx$1000$\times$ computational acceleration while effectively recovering long-timescale dynamics, providing a stepping stone for enabling routine simulation of proteins.

Ameya Daigavane, YuQing Xie, Bodhi P. Vani et al.

Diffusion models are a popular class of generative models trained to reverse a noising process starting from a target data distribution. Training a diffusion model consists of learning how to denoise noisy samples at different noise levels. When training diffusion models for point clouds such as molecules and proteins, there is often no canonical orientation that can be assigned. To capture this symmetry, the true data samples are often augmented by transforming them with random rotations sampled uniformly over $SO(3)$. Then, the denoised predictions are often rotationally aligned via the Kabsch-Umeyama algorithm to the ground truth samples before computing the loss. However, the effect of this alignment step has not been well studied. Here, we show that the optimal denoiser can be expressed in terms of a matrix Fisher distribution over $SO(3)$. Alignment corresponds to sampling the mode of this distribution, and turns out to be the zeroth order approximation for small noise levels, explaining its effectiveness. We build on this perspective to derive better approximators to the optimal denoiser in the limit of small noise. Our experiments highlight that alignment is often a `good enough' approximation for the noise levels that matter most for training diffusion models.

Hannah Lawrence, Elyssa Hofgard, Vasco Portilheiro et al.

Symmetry-aware methods for machine learning, such as data augmentation and equivariant architectures, encourage correct model behavior on all transformations (e.g. rotations or permutations) of the original dataset. These methods can improve generalization and sample efficiency, under the assumption that the transformed datapoints are highly probable, or "important", under the test distribution. In this work, we develop a method for critically evaluating this assumption. In particular, we propose a metric to quantify the amount of anisotropy, or symmetry-breaking, in a dataset, via a two-sample neural classifier test that distinguishes between the original dataset and its randomly augmented equivalent. We validate our metric on synthetic datasets, and then use it to uncover surprisingly high degrees of alignment in several benchmark point cloud datasets. We show theoretically that distributional symmetry-breaking can actually prevent invariant methods from performing optimally even when the underlying labels are truly invariant, as we show for invariant ridge regression in the infinite feature limit. Empirically, we find that the implication for symmetry-aware methods is dataset-dependent: equivariant methods still impart benefits on some anisotropic datasets, but not others. Overall, these findings suggest that understanding equivariance -- both when it works, and why -- may require rethinking symmetry biases in the data.

Julia Balla, Jeremiah Bailey, Ali Backour et al.

The immense computational cost of simulating turbulence has motivated the use of machine learning approaches for super-resolving turbulent flows. A central challenge is ensuring that learned models respect physical symmetries, such as rotational equivariance. We show that standard convolutional neural networks (CNNs) can partially acquire this symmetry without explicit augmentation or specialized architectures, as turbulence itself provides implicit rotational augmentation in both time and space. Using 3D channel-flow subdomains with differing anisotropy, we find that models trained on more isotropic mid-plane data achieve lower equivariance error than those trained on boundary layer data, and that greater temporal or spatial sampling further reduces this error. We show a distinct scale-dependence of equivariance error that occurs regardless of dataset anisotropy that is consistent with Kolmogorov's local isotropy hypothesis. These results clarify when rotational symmetry must be explicitly incorporated into learning algorithms and when it can be obtained directly from turbulence, enabling more efficient and symmetry-aware super-resolution.

YuQing Xie, Tess Smidt

Equivariant neural networks have proven to be effective for tasks with known underlying symmetries. However, optimizing equivariant networks can be tricky and best training practices are less established than for standard networks. In particular, recent works have found small training benefits from relaxing equivariance constraints. This raises the question: do equivariance constraints introduce fundamental obstacles to optimization? Or do they simply require different hyperparameter tuning? In this work, we investigate this question through a theoretical analysis of the loss landscape geometry. We focus on networks built using permutation representations, which we can view as a subset of unconstrained MLPs. Importantly, we show that the parameter symmetries of the unconstrained model has nontrivial effects on the loss landscape of the equivariant subspace and under certain conditions can provably prevent learning of the global minima. Further, we empirically demonstrate in such cases, relaxing to an unconstrained MLP can sometimes solve the issue. Interestingly, the weights eventually found via relaxation corresponds to a different choice of group representation in the hidden layer. From this, we draw 3 key takeaways. (1) By viewing the unconstrained version of an architecture, we can uncover hidden parameter symmetries which were broken by choice of constraint enforcement (2) Hidden symmetries give important insights on loss landscapes and can induce critical points and even minima (3) Hidden symmetry induced minima can sometimes be escaped by constraint relaxation and we observe the network jumps to a different choice of constraint enforcement. Effective equivariance relaxation may require rethinking the fixed choice of group representation in the hidden layers.

Yi-Lun Liao, Tess Smidt, Muhammed Shuaibi et al.

Understanding the interactions of atoms such as forces in 3D atomistic systems is fundamental to many applications like molecular dynamics and catalyst design. However, simulating these interactions requires compute-intensive ab initio calculations and thus results in limited data for training neural networks. In this paper, we propose to use denoising non-equilibrium structures (DeNS) as an auxiliary task to better leverage training data and improve performance. For training with DeNS, we first corrupt a 3D structure by adding noise to its 3D coordinates and then predict the noise. Different from previous works on denoising, which are limited to equilibrium structures, the proposed method generalizes denoising to a much larger set of non-equilibrium structures. The main difference is that a non-equilibrium structure does not correspond to local energy minima and has non-zero forces, and therefore it can have many possible atomic positions compared to an equilibrium structure. This makes denoising non-equilibrium structures an ill-posed problem since the target of denoising is not uniquely defined. Our key insight is to additionally encode the forces of the original non-equilibrium structure to specify which non-equilibrium structure we are denoising. Concretely, given a corrupted non-equilibrium structure and the forces of the original one, we predict the non-equilibrium structure satisfying the input forces instead of any arbitrary structures. Since DeNS requires encoding forces, DeNS favors equivariant networks, which can easily incorporate forces and other higher-order tensors in node embeddings. We study the effectiveness of training equivariant networks with DeNS on OC20, OC22 and MD17 datasets and demonstrate that DeNS can achieve new state-of-the-art results on OC20 and OC22 and significantly improve training efficiency on MD17.

Ilyes Batatia, Mario Geiger, Jose Munoz et al.

Reductive Lie Groups, such as the orthogonal groups, the Lorentz group, or the unitary groups, play essential roles across scientific fields as diverse as high energy physics, quantum mechanics, quantum chromodynamics, molecular dynamics, computer vision, and imaging. In this paper, we present a general Equivariant Neural Network architecture capable of respecting the symmetries of the finite-dimensional representations of any reductive Lie Group G. Our approach generalizes the successful ACE and MACE architectures for atomistic point clouds to any data equivariant to a reductive Lie group action. We also introduce the lie-nn software library, which provides all the necessary tools to develop and implement such general G-equivariant neural networks. It implements routines for the reduction of generic tensor products of representations into irreducible representations, making it easy to apply our architecture to a wide range of problems and groups. The generality and performance of our approach are demonstrated by applying it to the tasks of top quark decay tagging (Lorentz group) and shape recognition (orthogonal group).

Wujie Wang, Minkai Xu, Chen Cai et al.

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes accurate backmapping, i.e., restoring fine-grained (FG) coordinates from CG coordinates, a long-standing challenge. Inspired by the recent progress in generative models and equivariant networks, we propose a novel model that rigorously embeds the vital probabilistic nature and geometric consistency requirements of the backmapping transformation. Our model encodes the FG uncertainties into an invariant latent space and decodes them back to FG geometries via equivariant convolutions. To standardize the evaluation of this domain, we provide three comprehensive benchmarks based on molecular dynamics trajectories. Experiments show that our approach always recovers more realistic structures and outperforms existing data-driven methods with a significant margin.

Alice Gatti, Zhixiong Hu, Tess Smidt et al.

We present a graph bisection and partitioning algorithm based on graph neural networks. For each node in the graph, the network outputs probabilities for each of the partitions. The graph neural network consists of two modules: an embedding phase and a partitioning phase. The embedding phase is trained first by minimizing a loss function inspired by spectral graph theory. The partitioning module is trained through a loss function that corresponds to the expected value of the normalized cut. Both parts of the neural network rely on SAGE convolutional layers and graph coarsening using heavy edge matching. The multilevel structure of the neural network is inspired by the multigrid algorithm. Our approach generalizes very well to bigger graphs and has partition quality comparable to METIS, Scotch and spectral partitioning, with shorter runtime compared to METIS and spectral partitioning.

Oliver T. Unke, Mihail Bogojeski, Michael Gastegger et al.

Machine learning has enabled the prediction of quantum chemical properties with high accuracy and efficiency, allowing to bypass computationally costly ab initio calculations. Instead of training on a fixed set of properties, more recent approaches attempt to learn the electronic wavefunction (or density) as a central quantity of atomistic systems, from which all other observables can be derived. This is complicated by the fact that wavefunctions transform non-trivially under molecular rotations, which makes them a challenging prediction target. To solve this issue, we introduce general SE(3)-equivariant operations and building blocks for constructing deep learning architectures for geometric point cloud data and apply them to reconstruct wavefunctions of atomistic systems with unprecedented accuracy. Our model achieves speedups of over three orders of magnitude compared to ab initio methods and reduces prediction errors by up to two orders of magnitude compared to the previous state-of-the-art. This accuracy makes it possible to derive properties such as energies and forces directly from the wavefunction in an end-to-end manner. We demonstrate the potential of our approach in a transfer learning application, where a model trained on low accuracy reference wavefunctions implicitly learns to correct for electronic many-body interactions from observables computed at a higher level of theory. Such machine-learned wavefunction surrogates pave the way towards novel semi-empirical methods, offering resolution at an electronic level while drastically decreasing computational cost. Additionally, the predicted wavefunctions can serve as initial guess in conventional ab initio methods, decreasing the number of iterations required to arrive at a converged solution, thus leading to significant speedups without any loss of accuracy or robustness.

Alice Gatti, Zhixiong Hu, Tess Smidt et al.

We present a novel method for graph partitioning, based on reinforcement learning and graph convolutional neural networks. Our approach is to recursively partition coarser representations of a given graph. The neural network is implemented using SAGE graph convolution layers, and trained using an advantage actor critic (A2C) agent. We present two variants, one for finding an edge separator that minimizes the normalized cut or quotient cut, and one that finds a small vertex separator. The vertex separators are then used to construct a nested dissection ordering to permute a sparse matrix so that its triangular factorization will incur less fill-in. The partitioning quality is compared with partitions obtained using METIS and SCOTCH, and the nested dissection ordering is evaluated in the sparse solver SuperLU. Our results show that the proposed method achieves similar partitioning quality as METIS and SCOTCH. Furthermore, the method generalizes across different classes of graphs, and works well on a variety of graphs from the SuiteSparse sparse matrix collection.

Nathaniel Thomas, Tess Smidt, Steven Kearnes et al.

We introduce tensor field neural networks, which are locally equivariant to 3D rotations, translations, and permutations of points at every layer. 3D rotation equivariance removes the need for data augmentation to identify features in arbitrary orientations. Our network uses filters built from spherical harmonics; due to the mathematical consequences of this filter choice, each layer accepts as input (and guarantees as output) scalars, vectors, and higher-order tensors, in the geometric sense of these terms. We demonstrate the capabilities of tensor field networks with tasks in geometry, physics, and chemistry.