MOTGNN: Interpretable Graph Neural Networks for Multi-Omics Disease Classification

2025/08/10 by Yang, Tiantian, Chen, Zhiqian
#62R07 #FOS: Biological sciences #FOS: Computer and information sciences #Genomics (q-bio.GN) #Machine Learning (cs.LG) #Machine Learning (stat.ML)

paper · doi:10.48550/arxiv.2508.07465

Abstract

Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality and complex interactions among omics layers present major challenges for predictive modeling. We propose Multi-Omics integration with Tree-generated Graph Neural Network (MOTGNN), a novel and interpretable framework for binary disease classification. MOTGNN employs eXtreme Gradient Boosting (XGBoost) to perform omics-specific supervised graph construction, followed by modality-specific Graph Neural Networks (GNNs) for hierarchical representation learning, and a deep feedforward network for cross-omics integration. On three real-world disease datasets, MOTGNN outperforms state-of-the-art baselines by 5-10% in accuracy, ROC-AUC, and F1-score, and remains robust to severe class imbalance (e.g., 87.2% vs. 33.4% F1 on imbalanced data). The model maintains computational efficiency through sparse graphs (2.1-2.8 edges per node) and provides built-in interpretability, revealing both top-ranked biomarkers and the relative contributions of each omics modality. These results highlight MOTGNN's potential to improve both predictive accuracy and interpretability in multi-omics disease modeling.

Citations

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