# A standard transformer and attention with linear biases for molecular conformer generation

arXiv: https://arxiv.org/abs/2506.19834 · HTML: https://mlsanity.com/paper/2506.19834/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 39 of its 50 references that are in the map.
- First posted on arXiv 24 Jun 2025.

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

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [MLP-Mixer: An all-MLP Architecture for Vision](https://mlsanity.com/paper/2105.01601/) (2021)
- [Cascaded Diffusion Models for High Fidelity Image Generation](https://mlsanity.com/paper/2106.15282/) (2021)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Perceiver IO: A General Architecture for Structured Inputs & Outputs](https://mlsanity.com/paper/2107.14795/) (2021)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (2020)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [Torsional Diffusion for Molecular Conformer Generation](https://mlsanity.com/paper/2206.01729/) (2022)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [On the Importance of Noise Scheduling for Diffusion Models](https://mlsanity.com/paper/2301.10972/) (2023)
- [On Embeddings for Numerical Features in Tabular Deep Learning](https://mlsanity.com/paper/2203.05556/) (2022)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [Learning Gradient Fields for Molecular Conformation Generation](https://mlsanity.com/paper/2105.03902/) (2021)
- [Graph Inductive Biases in Transformers without Message Passing](https://mlsanity.com/paper/2305.17589/) (2023)
- [GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles](https://mlsanity.com/paper/2106.07802/) (2021)
- [Transformer for Graphs: An Overview from Architecture Perspective](https://mlsanity.com/paper/2202.08455/) (2022)
- [Molecular geometry prediction using a deep generative graph neural network](https://mlsanity.com/paper/1904.00314/) (2019)
- [Learning Neural Generative Dynamics for Molecular Conformation Generation](https://mlsanity.com/paper/2102.10240/) (2021)
- [Memory Transformer](https://mlsanity.com/paper/2006.11527/) (2020)
- [A Generative Model for Molecular Distance Geometry](https://mlsanity.com/paper/1909.11459/) (2019)

## Abstract (arXiv)

Sampling low-energy molecular conformations, spatial arrangements of atoms in a molecule, is a critical task for many different calculations performed in the drug discovery and optimization process. Numerous specialized equivariant networks have been designed to generate molecular conformations from 2D molecular graphs. Recently, non-equivariant transformer models have emerged as a viable alternative due to their capability to scale to improve generalization. However, the concern has been that non-equivariant models require a large model size to compensate the lack of equivariant bias. In this paper, we demonstrate that a well-chosen positional encoding effectively addresses these size limitations. A standard transformer model incorporating relative positional encoding for molecular graphs when scaled to 25 million parameters surpasses the current state-of-the-art non-equivariant base model with 64 million parameters on the GEOM-DRUGS benchmark. We implemented relative positional encoding as a negative attention bias that linearly increases with the shortest path distances between graph nodes at varying slopes for different attention heads, similar to ALiBi, a widely adopted relative positional encoding technique in the NLP domain. This architecture has the potential to serve as a foundation for a novel class of generative models for molecular conformations.