AMDE: a novel attention-mechanism-based multidimensional feature encoder for drug–drug interaction prediction

Abstract

Abstract The properties of the drug may be altered by the combination, which may cause unexpected drug–drug interactions (DDIs). Prediction of DDIs provides combination strategies of drugs for systematic and effective treatment. In most of deep learning-based methods for predicting DDI, encoded information about the drugs is insufficient in some extent, which limits the performances of DDIs prediction. In this work, we propose a novel attention-mechanism-based multidimensional feature encoder for DDIs prediction, namely attention-based multidimensional feature encoder (AMDE). Specifically, in AMDE, we encode drug features from multiple dimensions, including information from both Simplified Molecular-Input Line-Entry System sequence and atomic graph of the drug. Data experiments are conducted on DDI data set selected from Drugbank, involving a total of 34 282 DDI relationships with 17 141 positive DDI samples and 17 141 negative samples. Experimental results show that our AMDE performs better than some state-of-the-art baseline methods, including Random Forest, One-Dimension Convolutional Neural Networks, DeepDrug, Long Short-Term Memory, Seq2seq, Deepconv, DeepDDI, Graph Attention Networks and Knowledge Graph Neural Networks. In practice, we select a set of 150 drugs with 3723 DDIs, which are never appeared in training, validation and test sets. AMDE performs well in DDIs prediction task, with AUROC and AUPRC 0.981 and 0.975. As well, we use Torasemide (DB00214) as an example and predict the most likely drug to interact with it. The top 15 scores all have been reported with clear interactions in literatures.