MiRformer: a dual-transformer-encoder framework for predicting microRNA-mRNA interactions from paired sequences

MOTIVATION: MicroRNAs (miRNAs) regulate gene expression by binding to target messenger RNAs (mRNAs), inducing translational repression or mRNA degradation. Accurate prediction of miRNA-mRNA interactions and precise localization of binding and cleavage sites are critical for understanding post-transcriptional regulation and for enabling RNA therapeutics. Existing computational methods often rely on handcrafted or indirect features, scale poorly to kilobase-long mRNA sequences, or provide limited interpretability. RESULTS: We present MiRformer, a transformer-based framework that jointly predicts miRNA-mRNA interactions and localizes miRNA binding and cleavage sites directly from raw sequence pairs. MiRformer employs a dual-transformer encoder architecture for miRNA and mRNA sequences and incorporates a sliding-window attention mechanism to efficiently model kilobase-long mRNA contexts while preserving nucleotide-level resolution. Across multiple benchmrks, MiRformer achieves state-of-the-art performance on interaction prediction, binding-site localization, and cleavage-site identification from experimental Human Degradome-seq data. Beyond accuracy, MiRformer provides strong interpretability: attention patterns consistently highlight miRNA seed regions within 500-nt mRNA windows, revealing clear and biologically meaningful interaction signals. When applied to jointly infer binding and cleavage sites across 13k miRNA-mRNA pairs, predicted sites frequently co-localize, supporting a miRNA-mediated degradation mechanism. AVAILABILITY AND IMPLEMENTATION: Python code and datasets are publicly available at https://github.com/li-lab-mcgill/miRformer.