Noise-Consistent Hypergraph Autoencoder Based on Contrastive Learning for Cancer ceRNA Association Prediction in Complex Biological Regulatory Networks

Competitive endogenous RNA (ceRNA) regulatory networks (CENA) have advanced our understanding of noncoding RNAs’ roles in complex diseases, providing a theoretical basis for disease mechanisms. Existing ceRNA-disease association prediction methods are limited by traditional graph structures’ inability to model long-range dependencies in biological networks. While hypergraph models partially address this, they often fail to effectively handle graph-level and node-level noise, hindering improvements in predictive performance. To address these challenges, we propose a Noise-Consistent hypeRgraph AutoEncoder framework with denoising strategies, termed NCRAE, aimed at achieving robust node embeddings in ceRNA regulatory networks and enabling the precise prediction of cancer-related ceRNA biomarkers. NCRAE employs a multiview contrastive learning strategy, integrating graph-level and node-level corruption with clean feature references to significantly enhance the robustness of hypergraph feature learning. Furthermore, to mitigate potential biases introduced by contrastive learning, NCRAE incorporates a noise consistency loss constraint, dynamically adjusting the weights of each component to further optimize the model’s noise resistance and generalization ability. Combined with hypergraph convolution and Fourier KAN techniques, NCRAE achieves effective node embedding learning. Experiments on cancer-related ceRNA data sets show that NCRAE outperforms existing methods, especially in noisy conditions, demonstrating its robustness and predictive capability. Case studies further illustrate its practical value in cancer biomarker prediction, providing a powerful tool for cancer biomarker discovery.