SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

BACKGROUND: Numerous studies on discovering the roles of long non-coding RNAs (lncRNAs) in the occurrence, development and prognosis progresses of various human diseases have drawn substantial attentions. Since only a tiny portion of lncRNA-disease associations have been properly annotated, an increasing number of computational methods have been proposed for predicting potential lncRNA-disease associations. However, traditional predicting models lack the ability to precisely extract features of biomolecules, it is urgent to find a model which can identify potential lncRNA-disease associations with both efficiency and accuracy. RESULTS: In this study, we proposed a novel model, SVDNVLDA, which gained the linear and non-linear features of lncRNAs and diseases with Singular Value Decomposition (SVD) and node2vec methods respectively. The integrated features were constructed from connecting the linear and non-linear features of each entity, which could effectively enhance the semantics contained in ultimate representations. And an XGBoost classifier was employed for identifying potential lncRNA-disease associations eventually. CONCLUSIONS: We propose a novel model to predict lncRNA-disease associations. This model is expected to identify potential relationships between lncRNAs and diseases and further explore the disease mechanisms at the lncRNA molecular level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04457-1.