A standard transformer and attention with linear biases for molecular conformer generation
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arXiv
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| Natura: | Preprint |
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2025
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| _version_ | 1866916810015637504 |
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| author | Gurev, Viatcheslav Rumbell, Timothy |
| author_facet | Gurev, Viatcheslav Rumbell, Timothy |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_19834 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | A standard transformer and attention with linear biases for molecular conformer generation Gurev, Viatcheslav Rumbell, Timothy Biomolecules Artificial Intelligence Machine Learning 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. |
| title | A standard transformer and attention with linear biases for molecular conformer generation |
| topic | Biomolecules Artificial Intelligence Machine Learning |
| url | https://arxiv.org/abs/2506.19834 |