GADNN: A graph attention-based method for drug-drug association prediction considering the contribution rate of different types of drug-related features

Abstract

The simultaneous use of multiple drugs, known as drug combinations, is increasingly common in the treatment of complex diseases such as cancer. However, drug-drug interactions (DDIs) caused by the simultaneous use of multiple drugs can lead to unexpected side effects and even death, resulting in high medical costs. Therefore, understanding potential DDI is an essential step in reducing the risk of adverse drug reactions before administering clinical drug compounds. Recently, many machine learning-based methods for DDI prediction have been introduced, but in these methods, no attention is paid to determining the contribution rate of each type of drug feature. Here, a Graph Attention-based Deep Neural Network method called GADNN is proposed to predict DDIs based on considering the influence or contribution rate of different drug-related features. The introduced method consists of two stages. In the first stage, four basic drug datasets, including target, enzyme, infrastructure, and pathway, are used as types of drug features. Using a graph neural network-based method, the embedding vector is generated for each drug based on each dataset separately. In the second stage, the contribution coefficient of each dataset is calculated dynamically through a new graph attention mechanism. Then, the weighted combination of the separate vectors is used to predict the probability of drug-drug interactions using a dense neural network. The experimental results confirmed that the presented innovation has been able to improve the accuracy compared to state-of-the-art methods.

Keywords

• Deep learning
• Drug-drug interaction prediction
• Attention mechanism