A Hybrid GNN Approach for Improved Molecular Property Prediction.

Abstract

The development of new drugs is a vital effort that has the potential to improve human health, well-being and life expectancy. Molecular property prediction is a crucial step in drug discovery, as it helps to identify potential therapeutic compounds. However, experimental methods for drug development can often be time-consuming and resource-intensive, with a low probability of success. To address such limitations, deep learning (DL) methods have emerged as a viable alternative due to their ability to identify high-discriminating patterns in molecular data. In particular, graph neural networks (GNNs) operate on graph-structured data to identify promising drug candidates with desirable molecular properties. These methods represent molecules as a set of node (atoms) and edge (chemical bonds) features to aggregate local information for molecular graph representation learning. Despite the availability of several GNN frameworks, each approach has its own shortcomings. Although, some GNNs may excel in certain tasks, they may not perform as well in others. In this work, we propose a hybrid approach that incorporates different graph-based methods to combine their strengths and mitigate their limitations to accurately predict molecular properties. The proposed approach consists in a multi-layered hybrid GNN architecture that integrates multiple GNN frameworks to compute graph embeddings for molecular property prediction. Furthermore, we conduct extensive experiments on multiple benchmark datasets to demonstrate that our hybrid approach significantly outperforms the state-of-the-art graph-based models. The data and code scripts to reproduce the results are available in the repository, https://github.com/pedro-quesado/HybridGNN.