Interval-Shared Information Integration and False-Negative Association Reduction in Multi-Source MiRNA-Disease Association Prediction

Numerous studies have demonstrated that microRNAs (miRNAs) play crucial roles in the development and progression of various diseases, making the identification of miRNA-disease association (MDA) essential for understanding human disease etiology. While several computational models have been developed to predict MDAs, challenges persist—particularly the limited consideration of information interactions among multi-source similarities and the presence of “false-negative” associations in the original topology. To address these issues, we propose ISFNMDA, a model designed to infer potential MDAs by leveraging multi-view collaborative learning for feature extraction and optimizing association topology through graph structure momentum contrastive learning. Specifically, multi-source similarities of miRNAs and diseases are mapped into a unified feature space via encoders. The Pearson correlation coefficient is employed to derive pairwise constraints between nodes, facilitating information interactions and constructing interval-shared information constraints. Subsequently, an inference graph learner models the representations to generate an inferred graph topology. By maximizing mutual information between the inferred topology and the original “false-negative” associations through momentum contrastive learning, the model effectively reduces spurious correlations. The final comprehensive representations and optimized graph structure are then used to predict potential MDAs. Experimental results demonstrate that ISFNMDA outperforms existing methods, and case studies further validate its predictive capability.