# GemNet: Universal Directional Graph Neural Networks for Molecules

arXiv: https://arxiv.org/abs/2106.08903 · HTML: https://mlsanity.com/paper/2106.08903/

## Key facts

- Cited by 343 papers in the map (data through 14 Oct 2026).
- Builds on 39 of its 67 references that are in the map.
- First posted on arXiv 2 Jun 2021.

## Builds on (most cited first, 30 of 39)

- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Group Equivariant Convolutional Networks](https://mlsanity.com/paper/1602.07576/) (2016)
- [Sigmoid-Weighted Linear Units for Neural Network Function Approximation in Reinforcement Learning](https://mlsanity.com/paper/1702.03118/) (2017)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [On the Convergence of Adam and Beyond](https://mlsanity.com/paper/1904.09237/) (2019)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [PointConv: Deep Convolutional Networks on 3D Point Clouds](https://mlsanity.com/paper/1811.07246/) (2018)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Self-Normalizing Neural Networks](https://mlsanity.com/paper/1706.02515/) (2017)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Spherical CNNs](https://mlsanity.com/paper/1801.10130/) (2018)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Provably Powerful Graph Networks](https://mlsanity.com/paper/1905.11136/) (2019)
- [High-Performance Large-Scale Image Recognition Without Normalization](https://mlsanity.com/paper/2102.06171/) (2021)
- [How Does Batch Normalization Help Optimization?](https://mlsanity.com/paper/1805.11604/) (2018)
- [3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data](https://mlsanity.com/paper/1807.02547/) (2018)
- [Cormorant: Covariant Molecular Neural Networks](https://mlsanity.com/paper/1906.04015/) (2019)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Learning SO(3) Equivariant Representations with Spherical CNNs](https://mlsanity.com/paper/1711.06721/) (2017)
- [Generalizing Convolutional Neural Networks for Equivariance to Lie Groups on Arbitrary Continuous Data](https://mlsanity.com/paper/2002.12880/) (2020)
- [The Open Catalyst 2020 (OC20) Dataset and Community Challenges](https://mlsanity.com/paper/2010.09990/) (2020)
- [A General Theory of Equivariant CNNs on Homogeneous Spaces](https://mlsanity.com/paper/1811.02017/) (2018)
- [Generalization and Representational Limits of Graph Neural Networks](https://mlsanity.com/paper/2002.06157/) (2020)
- [Clebsch-Gordan Nets: a Fully Fourier Space Spherical Convolutional Neural Network](https://mlsanity.com/paper/1806.09231/) (2018)
- [On the Universality of Invariant Networks](https://mlsanity.com/paper/1901.09342/) (2019)
- [Universal approximations of invariant maps by neural networks](https://mlsanity.com/paper/1804.10306/) (2018)
- [Lorentz Group Equivariant Neural Network for Particle Physics](https://mlsanity.com/paper/2006.04780/) (2020)
- [Expressive Power of Invariant and Equivariant Graph Neural Networks](https://mlsanity.com/paper/2006.15646/) (2020)

## Built on by (most cited first, 30 of 343)

- [MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields](https://mlsanity.com/paper/2206.07697/) (2022)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Learning Local Equivariant Representations for Large-Scale Atomistic Dynamics](https://mlsanity.com/paper/2204.05249/) (2022)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations](https://mlsanity.com/paper/2306.12059/) (2023)
- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [Frame Averaging for Invariant and Equivariant Network Design](https://mlsanity.com/paper/2110.03336/) (2021)
- [Protein Representation Learning by Geometric Structure Pretraining](https://mlsanity.com/paper/2203.06125/) (2022)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Equivariant flow matching](https://mlsanity.com/paper/2306.15030/) (2023)
- [Scalars are universal: Equivariant machine learning, structured like classical physics](https://mlsanity.com/paper/2106.06610/) (2021)
- [Pre-training via Denoising for Molecular Property Prediction](https://mlsanity.com/paper/2206.00133/) (2022)
- [Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs](https://mlsanity.com/paper/2302.03655/) (2023)
- [Generating 3D Molecules for Target Protein Binding](https://mlsanity.com/paper/2204.09410/) (2022)
- [The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials](https://mlsanity.com/paper/2205.06643/) (2022)
- [MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation](https://mlsanity.com/paper/2302.09048/) (2023)
- [MatterGen: a generative model for inorganic materials design](https://mlsanity.com/paper/2312.03687/) (2023)
- [The Open Catalyst 2022 (OC22) Dataset and Challenges for Oxide Electrocatalysts](https://mlsanity.com/paper/2206.08917/) (2022)
- [Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations](https://mlsanity.com/paper/2210.07237/) (2022)
- [On the Expressive Power of Geometric Graph Neural Networks](https://mlsanity.com/paper/2301.09308/) (2023)
- [Periodic Graph Transformers for Crystal Material Property Prediction](https://mlsanity.com/paper/2209.11807/) (2022)
- [Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction](https://mlsanity.com/paper/2502.12147/) (2025)
- [Attending to Graph Transformers](https://mlsanity.com/paper/2302.04181/) (2023)
- [FAENet: Frame Averaging Equivariant GNN for Materials Modeling](https://mlsanity.com/paper/2305.05577/) (2023)
- [ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs](https://mlsanity.com/paper/2206.08515/) (2022)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems](https://mlsanity.com/paper/2312.07511/) (2023)
- [MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design](https://mlsanity.com/paper/2203.14500/) (2022)

## Abstract (arXiv)

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes for this task, overtaking classical methods based on fixed molecular kernels. However, they still appear very limited from a theoretical perspective, since regular GNNs cannot distinguish certain types of graphs. In this work we close this gap between theory and practice. We show that GNNs with spherical representations are indeed universal approximators for predictions that are invariant to translation, and equivariant to permutation and rotation. We then discretize such GNNs via directed edge embeddings and two-hop message passing, and incorporate multiple structural improvements to arrive at the geometric message passing neural network (GemNet). We demonstrate the benefits of the proposed changes in multiple ablation studies. GemNet outperforms previous models on the COLL, MD17, and OC20 datasets by 34%, 41%, and 20%, respectively, and performs especially well on the most challenging molecules. Our implementation is available online.