VAE-GANMDA: A microbe-drug association prediction model integrating variational autoencoders and generative adversarial networks

Abstract

Traditional biological experimental methods typically require weeks or even months of experimentation, and the cost of each experiment can reach hundreds or even thousands of dollars, which is quite expensive and time-consuming. To address this, a model called VAE-GANMDA, which integrates variational autoencoders (VAE) and generative adversarial networks (GAN) for predicting microbe-drug associations, has been proposed. Firstly, a heterogeneous network of microbes and drugs is established to enrich the association information. Secondly, by fusing VAE and GAN, the model learns the manifold distribution of data through association features, obtaining nonlinear manifold features. Furthermore, the VAE generation module is improved by integrating the Convolutional Block Attention Module (CBAM) and Gaussian kernel function, enhancing the smooth perception of manifold features, thus endowing VAE with stronger feature extraction capabilities. Then, singular value decomposition (SVD) technique is employed to extract linear features of the data. Finally, by combining linear and nonlinear features, the k-means++ algorithm is used to select balanced and high-quality negative samples for training the MLP classifier. Through performance evaluation, the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC) of VAE-GANMDA reach 0.9724 and 0.9635 respectively, outperforming classical machine learning methods and the majority of deep learning methods. Case studies demonstrate that VAE-GANMDA accurately predicts candidate drugs related to SARS-CoV-2 and candidate microbes related to ciprofloxacin.