用机器学习势能模型生成分子3D结构,提升属性预测效果。
Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials
- 用大规模数据训练机器学习势能模型预测能量与受力。
- 生成的近似3D结构虽未达DFT精度,但优于未优化结构。
- 适合需要快速获取分子构型的化学/材料研发人员。
精确的分子属性预测依赖于3D几何结构,通常需通过高成本的密度泛函理论(DFT)获得。本文仅依赖机器学习势能(MLIP)模型来生成分子几何结构。我们首先构建了一个包含350万分子和3亿个快照的大规模分子弛豫数据集。随后,使用监督学习训练预训练的MLIP模型,以给定3D结构预测能量和力。训练完成后,这些模型可用于显式或隐式地获取几何结构:一方面,可通过几何优化获得近似低能3D结构,尽管其化学精度或收敛性未能持续达到DFT水平,但仍显著优于非弛豫结构;另一方面,可基于已松弛结构进行几何微调以缓解偏差,进一步提升下游预测性能。此外,当存在真实3D结构时,可直接微调预训练模型用于属性预测。结果表明,基于弛豫数据训练的MLIP模型能学习可迁移的分子表示,从而提升下游分子属性预测,并提供实用但近似的分子构型,助力属性预测。代码开源:https://github.com/divelab/AIRS/
原文摘要 · Abstract (English)
Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/
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