Identifying disease-related microbes based on multi-scale variational graph autoencoder embedding Wasserstein distance

• Published in: BMC biology Vol. 21; no. 1; p. 294
• Main Authors: Zhu, Huan, Hao, Hongxia, Yu, Liang
• Format: Journal Article
• Language: English
• Published: England BioMed Central 20.12.2023; BMC
• Subjects: Ablation; Accuracy; Alzheimer's disease; Bacteria; Colorectal Neoplasms; Crohn's disease; Crohns disease; Embedding; Experiments; Graphical representations; Humans; Medical research; Microbe-disease association; Microorganisms; Neighborhoods; Neoplasms; Neural networks; Neurodegenerative diseases; Performance evaluation; Perturbation; Precision Medicine; Regularization methods; Variational graph autoencoder; Wasserstein distance; XGBoost; Microbe-disease association; Wasserstein distance; Variational graph autoencoder; XGBoost
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-023-01796-8

Enormous clinical and biomedical researches have demonstrated that microbes are crucial to human health. Identifying associations between microbes and diseases can not only reveal potential disease mechanisms, but also facilitate early diagnosis and promote precision medicine. Due to the data perturbation and unsatisfactory latent representation, there is a significant room for improvement. In this work, we proposed a novel framework, Multi-scale Variational Graph AutoEncoder embedding Wasserstein distance (MVGAEW) to predict disease-related microbes, which had the ability to resist data perturbation and effectively generate latent representations for both microbes and diseases from the perspective of distribution. First, we calculated multiple similarities and integrated them through similarity network confusion. Subsequently, we obtained node latent representations by improved variational graph autoencoder. Ultimately, XGBoost classifier was employed to predict potential disease-related microbes. We also introduced multi-order node embedding reconstruction to enhance the representation capacity. We also performed ablation studies to evaluate the contribution of each section of our model. Moreover, we conducted experiments on common drugs and case studies, including Alzheimer's disease, Crohn's disease, and colorectal neoplasms, to validate the effectiveness of our framework. Significantly, our model exceeded other currently state-of-the-art methods, exhibiting a great improvement on the HMDAD database.