Insight mixed deep neural network architectures for molecular representation

Abstract

Learning molecular representation is a crucial task in the field of drug discovery, particularly for various specific applications such as predicting molecular properties. Current methods are mainly based on deep neural network models, such as convolutional neural networks (CNN), recurrent neural networks (RNN), graph neural networks (GNN) and their mixed models. However, these neural network models mentioned above do not provide detailed explanations for the ability to learn molecular representations and why such experimental results occurred. In this paper, we aim to compare the performance of these models in predicting molecular properties based on molecular representation, and give more insight into deep neural network architectures for specific molecular tasks. Our experimental results demonstrate that the graph neural network can obtain superior performance on the regression tasks, while the mixed deep neural network models show better performance on the classification tasks. Ablation study also gives more explanation and analysis to the experimental results.

Keywords

• Deep neural network
• Graph neural network
• Molecular representation
• Molecular property prediction