# DeepChem Equivariant: SE(3)-Equivariant Support in an Open-Source Molecular Machine Learning Library

arXiv: https://arxiv.org/abs/2510.16897 · HTML: https://mlsanity.com/paper/2510.16897/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 17 references that are in the map.
- First posted on arXiv 19 Oct 2025.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [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)
- [Generalizing Convolutional Neural Networks for Equivariance to Lie Groups on Arbitrary Continuous Data](https://mlsanity.com/paper/2002.12880/) (2020)
- [Everything is Connected: Graph Neural Networks](https://mlsanity.com/paper/2301.08210/) (2023)
- [Wavelet Scattering Regression of Quantum Chemical Energies](https://mlsanity.com/paper/1605.04654/) (2016)
- [Graph Neural Networks in Computer Vision -- Architectures, Datasets and Common Approaches](https://mlsanity.com/paper/2212.10207/) (2022)
- [EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions](https://mlsanity.com/paper/2504.04654/) (2025)

## Abstract (arXiv)

Neural networks that incorporate geometric relationships respecting SE(3) group transformations (e.g. rotations and translations) are increasingly important in molecular applications, such as molecular property prediction, protein structure modeling, and materials design. These models, known as SE(3)-equivariant neural networks, ensure outputs transform predictably with input coordinate changes by explicitly encoding spatial atomic positions. Although libraries such as E3NN [4] and SE(3)-TRANSFORMER [3 ] offer powerful implementations, they often require substantial deep learning or mathematical prior knowledge and lack complete training pipelines. We extend DEEPCHEM [ 13] with support for ready-to-use equivariant models, enabling scientists with minimal deep learning background to build, train, and evaluate models, such as SE(3)-Transformer and Tensor Field Networks. Our implementation includes equivariant models, complete training pipelines, and a toolkit of equivariant utilities, supported with comprehensive tests and documentation, to facilitate both application and further development of SE(3)-equivariant models.