Frontiers in Molecular Biosciences (Jun 2023)
SMG-BERT: integrating stereoscopic information and chemical representation for molecular property prediction
Abstract
Molecular property prediction is a crucial task in various fields and has recently garnered significant attention. To achieve accurate and fast prediction of molecular properties, machine learning (ML) models have been widely employed due to their superior performance compared to traditional methods by trial and error. However, most of the existing ML models that do not incorporate 3D molecular information are still in need of improvement, as they are mostly poor at differentiating stereoisomers of certain types, particularly chiral ones. Also,routine featurization methods using only incomplete features are hard to obtain explicable molecular representations. In this paper, we propose the Stereo Molecular Graph BERT (SMG-BERT) by integrating the 3D space geometric parameters, 2D topological information, and 1D SMILES string into the self-attention-based BERT model. In addition, nuclear magnetic resonance (NMR) spectroscopy results and bond dissociation energy (BDE) are integrated as extra atomic and bond features to improve the model’s performance and interpretability analysis. The comprehensive integration of 1D, 2D, and 3D information could establish a unified and unambiguous molecular characterization system to distinguish conformations, such as chiral molecules. Intuitively integrated chemical information enables the model to possess interpretability that is consistent with chemical logic. Experimental results on 12 benchmark molecular datasets show that SMG-BERT consistently outperforms existing methods. At the same time, the experimental results demonstrate that SMG-BERT is generalizable and reliable.
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