Toward drug-miRNA resistance association prediction by positional encoding graph neural network and multi-channel neural network

•We propose a novel computational method named DMR-PEG, which can precisely predict the resistance associations between the drugs and miRNAs.•We design a positional encoding neural network with layer attention that considers both the potential information in the miRNA-drug resistance heterogeneous network and the specific characteristics (properties) of drugs and miRNAs.•We construct a multi-channel neural network that models various sophisticated relations and synthesizes the predictions from different perspectives effectively.•We conduct comprehensive experiments to compare DMR-PEG with the most state-of-the-art methods (where DMR-PEG achieves the most competitive results), discuss the robustness and sensitivity, validate the effectiveness of components in our proposed model, and finally testify its practical value in real-world data. Drug discovery is a costly and time-consuming process, and most drugs exert therapeutic efficacy by targeting specific proteins. However, there are a large number of proteins that are not targeted by any drug. Recently, miRNA-based therapeutics are becoming increasingly important, since miRNA can regulate the expressions of specific genes and affect a variety of human diseases. Therefore, it is of great significance to study the associations between miRNAs and drugs to enable drug discovery and disease treatment. In this work, we propose a novel method named DMR-PEG, which facilitates drug-miRNA resistance association (DMRA) prediction by leveraging positional encoding graph neural network with layer attention (LAPEG) and multi-channel neural network (MNN). LAPEG considers both the potential information in the miRNA-drug resistance heterogeneous network and the specific characteristics of entities (i.e., drugs and miRNAs) to learn favorable representations of drugs and miRNAs. And MNN models various sophisticated relations and synthesizes the predictions from different perspectives effectively. In the comprehensive experiments, DMR-PEG achieves the area under the precision-recall curve (AUPR) score of 0.2793 and the area under the receiver-operating characteristic curve (AUC) score of 0.9475, which outperforms the most state-of-the-art methods. Further experimental results show that our proposed method has good robustness and stability. The ablation study demonstrates each component in DMR-PEG is essential for drug-miRNA drug resistance association prediction. And real-world case study presents that DMR-PEG is promising for