Molecule generation for drug design: A graph learning perspective
Nianzu Yang, Huaijin Wu, Kaipeng Zeng, Yang Li, Siyuan Bao, Junchi Yan
Abstract
• This survey offers a comprehensive overview of state-of-the-art methods in molecule design, particularly focusing on 2D de novo molecule generation models. • We categorize these methods into three distinct groups: i) all-at-once, ii) fragment-based, and iii) node-by-node. • Additionally, we introduce some key public datasets and outline the commonly used evaluation metrics for both the generation and optimization of molecules. • In the end, we discuss the existing challenges in this field and suggest potential directions for future research. Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the pharmaceutical industry. Our survey offers a comprehensive overview of state-of-the-art methods in molecule design, particularly focusing on de novo drug design, which incorporates (deep) graph learning techniques. We categorize these methods into three distinct groups: i) all-at-once, ii) fragment-based , and iii) node-by-node . Additionally, we introduce some key public datasets and outline the commonly used evaluation metrics for both the generation and optimization of molecules. In the end, we discuss the existing challenges in this field and suggest potential directions for future research.