Journal Article

Magicmol: a light-weighted pipeline for drug-like molecule evolution and quick chemical space exploration

Shen, Qing, Lou, Jungang, Chen, Lin

2023

Overview

The flourishment of machine learning and deep learning methods has boosted the development of cheminformatics, especially regarding the application of drug discovery and new material exploration. Lower time and space expenses make it possible for scientists to search the enormous chemical space. Recently, some work combined reinforcement learning strategies with recurrent neural network (RNN)-based models to optimize the property of generated small molecules, which notably improved a batch of critical factors for these candidates. However, a common problem among these RNN-based methods is that several generated molecules have difficulty in synthesizing despite owning higher desired properties such as binding affinity. However, RNN-based framework better reproduces the molecule distribution among the training set than other categories of models during molecule exploration tasks. Thus, to optimize the whole exploration process and make it contribute to the optimization of specified molecules, we devised a light-weighted pipeline called Magicmol; this pipeline has a re-mastered RNN network and utilize SELFIES presentation instead of SMILES. Our backbone model achieved extraordinary performance while reducing the training cost; moreover, we devised reward truncate strategies to eliminate the model collapse problem. Additionally, adopting SELFIES presentation made it possible to combine STONED-SELFIES as a post-processing procedure for specified molecule optimization and quick chemical space exploration.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Analysis / Bioinformatics / Biomedical and Life Sciences / Chemical compounds / Chemical synthesis / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Datasets / De novo drug design / Deep Learning / Discovery and exploration / Drug Design / Drug discovery / Drug Discovery - methods / Exploration / Generative models / Informatics / Learning strategies / Life Sciences / Machine Learning / Methods / Microarrays / Molecular modelling / Neural networks / Neural Networks, Computer / Optimization / Outer space / Recurrent neural networks / Reinforcement learning / Space exploration / Synthetic accessibility / Training / Validity