Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations

LncRNAs are intermediate molecules that participate in the most diverse biological processes in humans, such as gene expression control and X-chromosome inactivation. Numerous researches have associated lncRNAs with a wide range of diseases, such as breast cancer, leukemia, and many other conditions. In this work, we propose a graph-based method named PANDA. This method treats the prediction of new associations between lncRNAs and diseases as a link prediction problem in a graph. We start by building a heterogeneous graph that contains the known associations between lncRNAs and diseases and additional information such as gene expression levels and symptoms of diseases. We then use a Graph Auto-encoder to learn the representation of the nodes' features and edges, finally applying a Neural Network to predict potentially interesting novel edges. The experimental results indicate that PANDA achieved a 0.976 AUC-ROC, surpassing state-of-the-art methods for the same problem, showing that PANDA could be a promising approach to generate embeddings to predict potentially novel lncRNA-disease associations.