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Jiangsu University

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EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

Aug 13, 2026

This work addresses the limitations of existing graph neural network–based methods for RNA–protein interaction prediction, which rely on predefined meta-paths or homogeneous graphs and thus exhibit poor generalization under data sparsity and cold-start scenarios. To overcome these challenges, the authors propose EGRL, a novel framework that implicitly learns meta-paths to automatically capture semantic relationships in heterogeneous graphs. EGRL integrates a multi-relational attention mechanism with a learnable soft edge generator, enabling effective modeling of cold-start nodes. The framework jointly optimizes the primary interaction prediction task alongside an auxiliary graph structure generation task. Extensive experiments on four benchmark datasets demonstrate that EGRL significantly outperforms current state-of-the-art methods, achieving an AUROC of 0.867 and an AUPR of 0.861 in cold-start settings—improvements of 8.6% and 5.0%, respectively.

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EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

Aug 13, 2026

This work addresses the limitations of existing graph neural network–based methods for RNA–protein interaction prediction, which rely on predefined meta-paths or homogeneous graphs and thus exhibit poor generalization under data sparsity and cold-start scenarios. To overcome these challenges, the authors propose EGRL, a novel framework that implicitly learns meta-paths to automatically capture semantic relationships in heterogeneous graphs. EGRL integrates a multi-relational attention mechanism with a learnable soft edge generator, enabling effective modeling of cold-start nodes. The framework jointly optimizes the primary interaction prediction task alongside an auxiliary graph structure generation task. Extensive experiments on four benchmark datasets demonstrate that EGRL significantly outperforms current state-of-the-art methods, achieving an AUROC of 0.867 and an AUPR of 0.861 in cold-start settings—improvements of 8.6% and 5.0%, respectively.

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