Predicting new drug indications based on double variational autoencoders

Experimental drug development is costly, complex, and time-consuming, and the number of drugs that have been put into application treatment is small. The identification of drug-disease correlations can provide important information for drug discovery and drug repurposing. Computational drug repurposing is an important and effective method that can be used to determine novel treatments for diseases. In recent years, an increasing number of large databases have been utilized for biological data research, particularly in the fields of drugs and diseases. Consequently, researchers have begun to explore the application of deep neural networks in biological data development. One particularly promising method for unsupervised learning is the deep generative model, with the variational autoencoder (VAE) being among the mainstream models. Here, we propose a drug indication prediction algorithm called DIDVAE (predicting new drug indications based on double variational autoencoders), which generates new data by learning the latent variable distribution of known data to achieve the goal of predicting drug-disease associations. In the experiment, we compared the DIDVAE algorithm with the BBNR, DrugNet, MBiRW and DRRS algorithms on a unified dataset. The comprehensive experimental results show that, compared with these prediction algorithms, the DIDVAE algorithm provides an overall improved prediction. In addition, further analysis and verification of the predicted unknown drug-disease association also proved the practicality of the method.

Automated summary

Drug development is expensive, complex, and time-consuming, and the number of drugs put into application is limited. Identifying drug-disease correlations can provide valuable information for drug discovery and repurposing. Computational drug repurposing, specifically the application of deep neural networks, has become a popular and effective method for predicting novel treatments for diseases. This study proposes a drug indication prediction algorithm called DIDVAE, which utilizes double variational autoencoders to generate new data and predict drug-disease associations. Experimental results demonstrate that the DIDVAE algorithm outperforms other prediction algorithms and the predicted drug-disease associations have been practically validated.