DDHMDA: Dual Dynamic Hypergraph Convolution Framework for Human Microbe-Disease Association Prediction
TL;DR
A novel deep learning approach named the Dual Dynamic Hypergraph Convolution Framework for Human Microbe-Disease Association Prediction (DDHMDA) is proposed, which dynamically constructs a dual hypergraph architecture: a differentiable K-means similarity hypergraph to capture intra-modal global clustering patterns, and an attention-based cross-modal interaction hypergraph to model inter-modal interactions synergistically.
Abstract
The human microbiota is essential for maintaining physiological homeostasis, and microbial dysbiosis is increasingly implicated in the pathogenesis of complex diseases. Identifying potential microbe-disease associations (MDAs) can therefore facilitate mechanistic investigation, biomarker discovery, and therapeutic development. However, wet-laboratory validation is costly and time-consuming, while existing computational methods often struggle with sparse association networks and complex nonlinear interactions. We propose a novel deep learning approach named the Dual Dynamic Hypergraph Convolution Framework for Human Microbe-Disease Association Prediction (DDHMDA). Specifically, DDHMDA first utilizes graph convolutional networks to encode local topological features. Subsequently, it dynamically constructs a dual hypergraph architecture: a differentiable K-means similarity hypergraph to capture intra-modal global clustering patterns, and an attention-based cross-modal interaction hypergraph to model inter-modal interactions synergistically. Under leakage-free pair-level five-fold cross-validation (denoted as CV3), DDHMDA achieved AUC/AUPR values of 0.9789 ± 0.0177/0.9843 ± 0.0129 on HMDAD and 0.9651 ± 0.0042/0.9740 ± 0.0031 on Disbiome. DDHMDA also obtained the best overall CV3 performance among the eight evaluated methods. Furthermore, ablation experiments and case studies validate the practical effectiveness of individual modules and the biological interpretability in discovering novel MDAs. Therefore, DDHMDA would be a reliable tool for identifying potential MDAs.