DNMDA: Deep Non-negative Matrix Factorization with Multi-level Integration for MiRNA-Drug Interaction Prediction

Yujie Qi, Jiaxin Yang, Yu-An Huang, Zhu-Hong You, Zimai Zhang, Lun Hu, Xi Zhou, Pengwei Hu

Abstract: Numerous studies have demonstrated that the interaction between miRNAs and drugs plays a pivotal role in regulating gene expression and cellular function. Therefore, predicting these interactions is crucial for the development of novel drugs and personalized therapies. Existing methods for predicting miRNA-drug interactions often fail to leverage the full spectrum of molecular and biological features and overlook complex high-dimensional patterns. Deep non-negative matrix factorization (DNMF) addresses these limitations by extracting higher-level representations, thereby enhancing prediction accuracy and robustness. Building on this, this paper proposes a model called DNMDA. In this model, we integrate multiple similarity networks for both miRNAs and drugs and then extract their features through three key modules. Moreover, autoencoders are used to combine various feature sets, allowing for the capture of complementary information and enhancing the model’s capacity for making precise and reliable predictions. The resulting features are consolidated into a unified feature vector for each miRNA-drug pair. Ultimately, these feature vectors and their associated labels are provided to the classifier for training. To verify the predictions, a five-fold cross-validation was conducted. The five-fold cross-validation demonstrated a clear advantage in DNMDA’s metrics, underscoring its reliability in predicting potential miRNA-drug interactions. This claim is further supported by the predictive results section in the paper, offering concrete evidence of DNMDA’s efficacy in this field.