E2Former: A Linear-time Efficient and Equivariant Transformer for Scalable Molecular Modeling

• URL: http://arxiv.org/abs/2501.19216v2
• Date: Mon, 03 Feb 2025 18:46:30 GMT
• Title: E2Former: A Linear-time Efficient and Equivariant Transformer for Scalable Molecular Modeling
• Authors: Yunyang Li, Lin Huang, Zhihao Ding, Chu Wang, Xinran Wei, Han Yang, Zun Wang, Chang Liu, Yu Shi, Peiran Jin, Jia Zhang, Mark Gerstein, Tao Qin,
• Abstract summary: We introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv) By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|mathcalE|)$ to $ O(| mathcalV|)$ while preserving both the model's expressive power and rotational equivariance. This development could suggest a promising direction for scalable and efficient molecular modeling.
• Score: 44.75336958712181
• License:
• Abstract: Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tensor products, making them impractical for large-scale systems. To address this limitation, we introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv). By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|\mathcal{E}|)$ to $ O(| \mathcal{V}|)$ while preserving both the model's expressive power and rotational equivariance. We show that this approach achieves a 7x-30x speedup compared to conventional $\mathrm{SO}(3)$ convolutions. Furthermore, our empirical results demonstrate that the derived E2Former mitigates the computational challenges of existing approaches without compromising the ability to capture detailed geometric information. This development could suggest a promising direction for scalable and efficient molecular modeling.

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