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Xiaoxin Du

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EAAI Journal 2025 Journal Article

Predicting potential microbe-disease associations based on heterogeneous graph attention network and deep sparse autoencoder

Bo Wang
Wenlong Zhao
Xiaoxin Du
Jianfei Zhang
Chunyu Zhang
Liping Wang
Yang He

Identifying potential associations between microbes and diseases is crucial for explaining disease pathogenesis and designing targeted therapeutic strategies. Basic biological experiments for microbe-disease association (MDA) prediction are costly, time-consuming, and labor-intensive, whereas computational methods can effectively complement traditional biological experiments. We propose a computational framework called graph attention convolutional deep sparse autoencoder microbe-disease association (GCDSAEMDA) to predict unknown MDAs. First, we calculate the semantic similarity and Gaussian interaction profile (GIP) similarity of diseases, as well as the functional similarity and GIP similarity of microbes, and integrate these similarity matrices to construct a heterogeneous graph. Next, a multi-head dynamic graph attention mechanism is employed to extract low-order features of microbe and disease nodes in the heterogeneous graph, while multiple convolutional neural networks with different kernels aggregate and concatenate these low-order features to form new high-order representations. Third, we apply a cosine distance-based k-means clustering to select reliable negative samples and use a deep sparse autoencoder to extract high-order features of microbe-disease pairs. Finally, an ensemble Light Gradient Boosting Machine (LightGBM) algorithm is used to predict potential MDAs. GCDSAEMDA was compared to four state-of-the-art MDA models on the Human Microbe-Disease Association Database (HMDAD) and Disbiome databases and validated through five-fold cross-validation on diseases, microbes, and microbe-disease pairs. Results indicate that GCDSAEMDA outperforms the other four models in MDA prediction. Additionally, case studies demonstrate the robust predictive capability of GCDSAEMDA. The source code and datasets for GCDSAEMDA are available at https: //github. com/chenyunmolu/GCDSAEMDA.

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AIIM Journal 2025 Journal Article

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

Bo Wang
Yang He
Xiaoxin Du
Lei Zhu
Junqi Wang
Tongxuan Wang

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.

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