# Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling

arXiv: https://arxiv.org/abs/2302.00855 · HTML: https://mlsanity.com/paper/2302.00855/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 26 of its 46 references that are in the map.
- First posted on arXiv 2 Feb 2023.

## Builds on (most cited first, 26 of 26)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Root Mean Square Layer Normalization](https://mlsanity.com/paper/1910.07467/) (2019)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Learning to Simulate Complex Physics with Graph Networks](https://mlsanity.com/paper/2002.09405/) (2020)
- [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)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [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)
- [The Open Catalyst 2020 (OC20) Dataset and Community Challenges](https://mlsanity.com/paper/2010.09990/) (2020)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Benchmarking Graphormer on Large-Scale Molecular Modeling Datasets](https://mlsanity.com/paper/2203.04810/) (2022)
- [ForceNet: A Graph Neural Network for Large-Scale Quantum Calculations](https://mlsanity.com/paper/2103.01436/) (2021)
- [Rotation Invariant Graph Neural Networks using Spin Convolutions](https://mlsanity.com/paper/2106.09575/) (2021)
- [Spherical Channels for Modeling Atomic Interactions](https://mlsanity.com/paper/2206.14331/) (2022)
- [Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures](https://mlsanity.com/paper/2011.07457/) (2020)
- [Heterogeneous Molecular Graph Neural Networks for Predicting Molecule Properties](https://mlsanity.com/paper/2009.12710/) (2020)
- [Equivariant Graph Attention Networks for Molecular Property Prediction](https://mlsanity.com/paper/2202.09891/) (2022)
- [Heterogeneous relational message passing networks for molecular dynamics simulations](https://mlsanity.com/paper/2109.00711/) (2021)

## Built on by (most cited first, 4 of 4)

- [Geometric-Facilitated Denoising Diffusion Model for 3D Molecule Generation](https://mlsanity.com/paper/2401.02683/) (2024)
- [Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers](https://mlsanity.com/paper/2402.04538/) (2024)
- [A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Era](https://mlsanity.com/paper/2604.16586/) (2026)
- [DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins](https://mlsanity.com/paper/2306.13957/) (2023)

## Abstract (arXiv)

Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT calculations. Molecular energy is at least related to atoms, bonds, bond angles, torsion angles, and nonbonding atom pairs. Previous Transformer models only use atoms as inputs which lack explicit modeling of the aforementioned factors. To alleviate this limitation, we propose Moleformer, a novel Transformer architecture that takes nodes (atoms) and edges (bonds and nonbonding atom pairs) as inputs and models the interactions among them using rotational and translational invariant geometry-aware spatial encoding. Proposed spatial encoding calculates relative position information including distances and angles among nodes and edges. We benchmark Moleformer on OC20 and QM9 datasets, and our model achieves state-of-the-art on the initial state to relaxed energy prediction of OC20 and is very competitive in QM9 on predicting quantum chemical properties compared to other Transformer and Graph Neural Network (GNN) methods which proves the effectiveness of the proposed geometry-aware spatial encoding in Moleformer.