ci9b00816_si_001.pdf (111.49 kB)
Download file

Costless Performance Improvement in Machine Learning for Graph-Based Molecular Analysis

Download (111.49 kB)
journal contribution
posted on 28.01.2020, 16:36 by Gyoung S. Na, Hyun Woo Kim, Hyunju Chang
Graph neural networks (GNNs) have attracted significant attention from the chemical science community because molecules can be represented as a featured graph. In particular, graph convolutional network (GCN) and its variants have been widely used and have shown a state-of-the-art performance in analyzing molecules, such as molecular label classification, drug discovery, and molecular property prediction. However, in molecular analysis, existing GCNs have two fundamental limitations: (1) information of the molecular scale is distorted and (2) global structures in a molecule are ignored. These limitations can seriously degrade the performance in the machine learning-based molecular analysis because the scale and global structure information of a molecule occasionally have a significant effect on the molecular properties. To overcome the limitations of existing GCNs, we comprehensively analyzed the structure of GCNs and developed a costless solution for the limitations of GCNs. To demonstrate the effectiveness of our solution, extensive experiments were conducted on various benchmark datasets.