Predicting the potential associations between circRNA and drug sensitivity using a multisource feature-based approach

Abstract

The unique non-coding RNA molecule known as circular RNA (circRNA) is distinguished from conventional linear RNA by having a longer half-life, greater degree of conservation and inherent solidity. Extensive research has demonstrated the profound impact of circRNA expression on cellular drug sensitivity and therapeutic efficacy. There is an immediate need for the creation of efficient computational techniques to anticipate the potential correlations between circRNA and drug sensitivity, as classical biological research approaches are time-consuming and costly. In this work, we introduce a novel deep learning model called SNMGCDA, which aims to forecast the relationships between circRNA and drug sensitivity. SNMGCDA incorporates a diverse range of similarity networks, enabling the derivation of feature vectors for circRNAs and drugs using three distinct calculation methods. First, we utilize a sparse autoencoder for the extraction of drug characteristics. Subsequently, the application of non-negative matrix factorization (NMF) enables the identification of relationships between circRNAs and drugs based on their shared features. Additionally, the multi-head graph attention network is employed to capture the characteristics of circRNAs. After acquiring the characteristics from these three separate components, we combine them to form a unified and inclusive feature vector for each cluster of circRNA and drug. Finally, the relevant feature vectors and labels are inputted into a multilayer perceptron (MLP) to make predictions. The outcomes of the experiment, obtained through 5-fold cross-validation (5-fold CV) and 10-fold cross-validation (10-fold CV), demonstrate SNMGCDA outperforms five other state-of-art methods in terms of performance. Additionally, the majority of case studies have predominantly confirmed newly discovered correlations by SNMGCDA, thereby emphasizing its reliability in predicting potential relationships between circRNAs and drugs.