Probabilistic generative transformer language models for generative design of molecules

Abstract

Self-supervised neural language models have recently found wide applications in the generative design of organic molecules and protein sequences as well as representation learning for downstream structure classification and functional prediction. However, most of the existing deep learning models for molecule design usually require a big dataset and have a black-box architecture, which makes it difficult to interpret their design logic. Here we propose the Generative Molecular Transformer (GMTransformer), a probabilistic neural network model for generative design of molecules. Our model is built on the blank filling language model originally developed for text processing, which has demonstrated unique advantages in learning the “molecules grammars” with high-quality generation, interpretability, and data efficiency. Benchmarked on the MOSES datasets, our models achieve high novelty and Scaf compared to other baselines. The probabilistic generation steps have the potential in tinkering with molecule design due to their capability of recommending how to modify existing molecules with explanation, guided by the learned implicit molecule chemistry. The source code and datasets can be accessed freely at https://github.com/usccolumbia/GMTransformer