XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties

• Published in: Journal of chemical information and modeling 2021-06, Vol.61 (6), p.2697-2705
• Main Authors: Deng, Daiguo, Chen, Xiaowei, Zhang, Ruochi, Lei, Zengrong, Wang, Xiaojian, Zhou, Fengfeng
• Format: Article
• Language: English
• Subjects: Algorithms; Chemical Information; Convolution; Feature extraction; Graph neural networks; Machine learning; Message passing; Molecular properties; Neural networks; Prediction models; Side effects; Source code; Training
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.0c01489

Determining the properties of chemical molecules is essential for screening candidates similar to a specific drug. These candidate molecules are further evaluated for their target binding affinities, side effects, target missing probabilities, etc. Conventional machine learning algorithms demonstrated satisfying prediction accuracies of molecular properties. A molecule cannot be directly loaded into a machine learning model, and a set of engineered features needs to be designed and calculated from a molecule. Such hand-crafted features rely heavily on the experiences of the investigating researchers. The concept of graph neural networks (GNNs) was recently introduced to describe the chemical molecules. The features may be automatically and objectively extracted from the molecules through various types of GNNs, e.g., GCN (graph convolution network), GGNN (gated graph neural network), DMPNN (directed message passing neural network), etc. However, the training of a stable GNN model requires a huge number of training samples and a large amount of computing power, compared with the conventional machine learning strategies. This study proposed the integrated framework XGraphBoost to extract the features using a GNN and build an accurate prediction model of molecular properties using the classifier XGBoost. The proposed framework XGraphBoost fully inherits the merits of the GNN-based automatic molecular feature extraction and XGBoost-based accurate prediction performance. Both classification and regression problems were evaluated using the framework XGraphBoost. The experimental results strongly suggest that XGraphBoost may facilitate the efficient and accurate predictions of various molecular properties. The source code is freely available to academic users at https://github.com/chenxiaowei-vincent/XGraphBoost.git.