A merged molecular representation learning for molecular properties prediction with a web-based service

Abstract

Abstract Deep learning has brought a dramatic development in molecular property prediction that is crucial in the field of drug discovery using various representations such as fingerprints, SMILES, and graphs. In particular, SMILES is used in various deep learning models via character-based approaches. However, SMILES has a limitation in that it is hard to reflect chemical properties. In this paper, we propose a new self-supervised method to learn SMILES and chemical contexts of molecules simultaneously in pre-training the Transformer. The key of our model is learning structures with adjacency matrix embedding and learning logics that can infer descriptors via Quantitative Estimation of Drug-likeness prediction in pre-training. As a result, our method improves the generalization of the data and achieves the best average performance by benchmarking downstream tasks. Moreover, we develop a web-based fine-tuning service to utilize our model on various tasks.