A fingerprints based molecular property prediction method using the BERT model

Molecular property prediction (MPP) is vital in drug discovery and drug reposition. Deep learning-based MPP models capture molecular property-related features from various molecule representations. In this paper, we propose a molecule sequence embedding and prediction model facing with MPP task. We pre-trained a bi-directional encoder representations from Transformers (BERT) encoder to obtain the semantic representation of compound fingerprints, called Fingerprints-BERT (FP-BERT), in a self-supervised learning manner. Then, the encoded molecular representation by the FP-BERT is input to the convolutional neural network (CNN) to extract higher-level abstract features, and the predicted properties of the molecule are finally obtained through fully connected layer for distinct classification or regression MPP tasks. Comparison with the baselines shows that the proposed model achieves high prediction performance on all of the classification tasks and regression tasks.