Geometry Informed Tokenization of Molecules for Language Model Generation

• URL: http://arxiv.org/abs/2408.10120v1
• Date: Mon, 19 Aug 2024 16:09:59 GMT
• Title: Geometry Informed Tokenization of Molecules for Language Model Generation
• Authors: Xiner Li, Limei Wang, Youzhi Luo, Carl Edwards, Shurui Gui, Yuchao Lin, Heng Ji, Shuiwang Ji,
• Abstract summary: We consider molecule generation in 3D space using language models (LMs) Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. We propose the Geo2Seq, which converts molecular geometries into $SE(3)$-invariant 1D discrete sequences.
• Score: 85.80491667588923
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing the Geo2Seq, which converts molecular geometries into $SE(3)$-invariant 1D discrete sequences. Geo2Seq consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with Geo2Seq, various LMs excel in molecular geometry generation, especially in controlled generation tasks.

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