# Geometric Deep Learning on Molecular Representations

arXiv: https://arxiv.org/abs/2107.12375 · HTML: https://mlsanity.com/paper/2107.12375/

## Key facts

- Cited by 113 papers in the map (data through 14 Oct 2026).
- Builds on 85 of its 209 references that are in the map.
- First posted on arXiv 26 Jul 2021.

## Builds on (most cited first, 30 of 85)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [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)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Conditional Generative Adversarial Nets](https://mlsanity.com/paper/1411.1784/) (2014)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Group Equivariant Convolutional Networks](https://mlsanity.com/paper/1602.07576/) (2016)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Learning Mesh-Based Simulation with Graph Networks](https://mlsanity.com/paper/2010.03409/) (2020)
- [Deep Learning in Neural Networks: An Overview](https://mlsanity.com/paper/1404.7828/) (2014)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Interaction Networks for Learning about Objects, Relations and Physics](https://mlsanity.com/paper/1612.00222/) (2016)
- [Geometric deep learning on graphs and manifolds using mixture model CNNs](https://mlsanity.com/paper/1611.08402/) (2016)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)

## Built on by (most cited first, 30 of 113)

- [Structure-based Drug Design with Equivariant Diffusion Models](https://mlsanity.com/paper/2210.13695/) (2022)
- [Graph neural networks for materials science and chemistry](https://mlsanity.com/paper/2208.09481/) (2022)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [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)
- [GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2109.11730/) (2021)
- [Efficient Evolutionary Search Over Chemical Space with Large Language Models](https://mlsanity.com/paper/2406.16976/) (2024)
- [A new perspective on building efficient and expressive 3D equivariant graph neural networks](https://mlsanity.com/paper/2304.04757/) (2023)
- [Structure-based drug design with geometric deep learning](https://mlsanity.com/paper/2210.11250/) (2022)
- [Enabling Efficient Equivariant Operations in the Fourier Basis via Gaunt Tensor Products](https://mlsanity.com/paper/2401.10216/) (2024)
- [A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material](https://mlsanity.com/paper/2304.01565/) (2023)
- [ACMP: Allen-Cahn Message Passing with Attractive and Repulsive Forces for Graph Neural Networks](https://mlsanity.com/paper/2206.05437/) (2022)
- [A graphon-signal analysis of graph neural networks](https://mlsanity.com/paper/2305.15987/) (2023)
- [A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications](https://mlsanity.com/paper/2403.00485/) (2024)
- [Interpretable Geometric Deep Learning via Learnable Randomness Injection](https://mlsanity.com/paper/2210.16966/) (2022)
- [Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials](https://mlsanity.com/paper/2306.09375/) (2023)
- [LLaMo: Large Language Model-based Molecular Graph Assistant](https://mlsanity.com/paper/2411.00871/) (2024)
- [Graph Neural Networks for Molecules](https://mlsanity.com/paper/2209.05582/) (2022)
- [Controllable Data Generation by Deep Learning: A Review](https://mlsanity.com/paper/2207.09542/) (2022)
- [Beyond Euclid: An Illustrated Guide to Modern Machine Learning with Geometric, Topological, and Algebraic Structures](https://mlsanity.com/paper/2407.09468/) (2024)
- [A General Theory of Correct, Incorrect, and Extrinsic Equivariance](https://mlsanity.com/paper/2303.04745/) (2023)
- [Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning](https://mlsanity.com/paper/2306.01474/) (2023)
- [Learning Long Sequences in Spiking Neural Networks](https://mlsanity.com/paper/2401.00955/) (2023)
- [Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks](https://mlsanity.com/paper/2212.03447/) (2022)
- [Molecular geometric deep learning](https://mlsanity.com/paper/2306.15065/) (2023)
- [FlowGNN: A Dataflow Architecture for Real-Time Workload-Agnostic Graph Neural Network Inference](https://mlsanity.com/paper/2204.13103/) (2022)
- [Denoise Pretraining on Nonequilibrium Molecules for Accurate and Transferable Neural Potentials](https://mlsanity.com/paper/2303.02216/) (2023)
- [From Generalist to Specialist: A Survey of Large Language Models for Chemistry](https://mlsanity.com/paper/2412.19994/) (2024)
- [Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity](https://mlsanity.com/paper/2502.01171/) (2025)

## Abstract (arXiv)

Geometric deep learning (GDL), which is based on neural network architectures that incorporate and process symmetry information, has emerged as a recent paradigm in artificial intelligence. GDL bears particular promise in molecular modeling applications, in which various molecular representations with different symmetry properties and levels of abstraction exist. This review provides a structured and harmonized overview of molecular GDL, highlighting its applications in drug discovery, chemical synthesis prediction, and quantum chemistry. Emphasis is placed on the relevance of the learned molecular features and their complementarity to well-established molecular descriptors. This review provides an overview of current challenges and opportunities, and presents a forecast of the future of GDL for molecular sciences.