Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866911811564994560 |
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| author | Song, Yuxuan Gong, Jingjing Qu, Yanru Zhou, Hao Zheng, Mingyue Liu, Jingjing Ma, Wei-Ying |
| author_facet | Song, Yuxuan Gong, Jingjing Qu, Yanru Zhou, Hao Zheng, Mingyue Liu, Jingjing Ma, Wei-Ying |
| contents | Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance). |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_15441 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Song, Yuxuan Gong, Jingjing Qu, Yanru Zhou, Hao Zheng, Mingyue Liu, Jingjing Ma, Wei-Ying Chemical Physics Artificial Intelligence Machine Learning Biomolecules Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance). |
| title | Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks |
| topic | Chemical Physics Artificial Intelligence Machine Learning Biomolecules |
| url | https://arxiv.org/abs/2403.15441 |