Multi-task learning for predicting synergistic drug combinations based on auto-encoding multi-relational graphs

Combinatorial drug therapy is a promising approach for treating complex diseases by combining drugs with synergistic effects. However, predicting effective drug combinations is challenging due to the complexity of biological systems and the limited understanding of pathophysiological mechanisms and drug targets. In this paper, we proposed a computational framework called VGAETF (Variational Graph Autoencoder Tensor Decomposition), which leveraged multi-relational graph to model complex relation-ships between entities in biological systems and predicted disease-related synergistic drug combinations in an end-to-end manner. In the computational experiments, VGAETF achieved high performances (AUROC [the area under receiver operating characteristic] = 0.9767, AUPR [the area under precision -recall] = 0.9660), outperforming other compared methods. Moreover, case studies further demonstrated the effectiveness of VGAETF in identifying potential disease-related synergistic drug combinations.