MADGAN:A microbe-disease association prediction model based on generative adversarial networks

Researches have demonstrated that microorganisms are indispensable for the nutrition transportation, growth and development of human bodies, and disorder and imbalance of microbiota may lead to the occurrence of diseases. Therefore, it is crucial to study relationships between microbes and diseases. In this manuscript, we proposed a novel prediction model named MADGAN to infer potential microbe-disease associations by combining biological information of microbes and diseases with the generative adversarial networks. To our knowledge, it is the first attempt to use the generative adversarial network to complete this important task. In MADGAN, we firstly constructed different features for microbes and diseases based on multiple similarity metrics. And then, we further adopted graph convolution neural network (GCN) to derive different features for microbes and diseases automatically. Finally, we trained MADGAN to identify latent microbe-disease associations by games between the generation network and the decision network. Especially, in order to prevent over-smoothing during the model training process, we introduced the cross-level weight distribution structure to enhance the depth of the network based on the idea of residual network. Moreover, in order to validate the performance of MADGAN, we conducted comprehensive experiments and case studies based on databases of HMDAD and Disbiome respectively, and experimental results demonstrated that MADGAN not only achieved satisfactory prediction performances, but also outperformed existing state-of-the-art prediction models.