Boosting drug-disease association prediction for drug repositioning via dual-feature extraction and cross-dual-domain decoding

Uncovering new therapeutic uses of existing drugs, drug repositioning offers a fast and cost-effective strategy and holds considerable significance in the realm of drug discovery and development. In recent years, deep learning techniques have emerged as powerful tools in drug repositioning due to their ability to analyze large and complex datasets. However, many existing methods focus on extracting feature information from nearby nodes in the network to represent drugs and diseases, without considering the potential inter-relationships between the features of drugs and diseases, which may lead to inaccurate representations. To address this limitation, we use two features (similarity and association) to capture the potential relationships between the features of drugs and diseases, proposing a Dual-Feature Drug Repositioning Neural Network (DFDRNN) model. DFDRNN uses a self-attention mechanism to extract neighbor features and incorporates two dual-feature extraction modules: the intra-domain dual-feature extraction (IntraDDFE) module for extracting features within a single domain (drugs or diseases) and the inter-domain dual-feature extraction (InterDDFE) module for extracting features across domains. By utilizing these modules, we ensure more appropriate encoding of drugs and diseases. Additionally, a cross-dual-domain decoder is designed to predict drug-disease associations in both domains. Our proposed DFDRNN model outperforms six state-of-the-art methods on four benchmark datasets, achieving an average AUROC of 0.946 and an average AUPR of 0.597. Case studies on two diseases show that the proposed DFDRNN model can be applied in real-world scenarios, demonstrating its significant potential in drug repositioning.