Multi-view Graph Learning Framework with Spectral Encoding and Sparse Cross-Attention for miRNA-Drug Association Prediction.

Abstract

Chemoresistance is a major contributor to cancer treatment failure, and microRNAs (miRNAs) play a critical role in mediating this resistance by regulating gene expression. Therefore, identifying miRNA-drug associations is of great significance for advancing cancer therapy. However, existing computational models face significant challenges, including heterogeneous feature integration and data sparsity. To overcome these limitations, we propose a novel Multi-view Graph Learning Framework with Spectral Encoding and Sparse Cross-Attention (MVGSCA) for predicting miRNA-drug associations. The model constructs node features based on miRNA sequence similarity and drug SMILES similarity. Then it builds two distinct graphs: a gene-mediated functional graph from miRNA-drug target interactions and an association-guided structural graph from known miRNA-drug associations. These two graphs are linearly combined to produce a collaborative feature representation. To capture both local and global topological features, the model applies local power filtering and global heat kernel diffusion, followed by spectral encoding via Poisson-Charlier polynomial approximation to enhance the feature representation. Furthermore, a sparse cross-attention mechanism is introduced to dynamically weight and integrate heterogeneous features from multiple sources. On a benchmark dataset with 8,720 associations, MVGSCA achieves an AUC of 96.32% and an AUPR of 95.69% under five-fold cross-validation, significantly outperforming six state-of-the-art methods. Experimental results show that MVGSCA effectively integrates heterogeneous biological information and achieves superior prediction performance, offering valuable insights into cancer resistance mechanisms and supporting drug discovery efforts.