MotRNA: Encoding RNA Motifs via Explicit N-gram Memory

Abstract

RNA motifs and Low-Complexity Repeats (LCRs)—recurrent, conserved sequences of nucleotides—serve as the fundamental vocabulary of RNA structure and biological function. While current RNA foundation models have revolutionized sequence modeling through Transformer architectures, they predominantly prioritize modeling global dependencies within the raw sequence. To address this limitation, we propose MotRNA, a motif-aware RNA language model integrating an Explicit N-gram Memory mechanism. Unlike standard implicit neural modeling, MotRNA employs a conditional memory module to explicitly retrieve and fuse motif embeddings based on input k-mers. This mechanism provides direct access to strictly defined local patterns, complementing the global context modeled by self-attention. We validate MotRNA on large-scale RNA datasets. The model achieves a 9.6% absolute improvement in Masked Language Modeling (MLM) accuracy at a 30% masking ratio compared to state-of-the-art baselines. Notably, MotRNA maintains high robustness under extreme masking ratios, indicating effective biological signal reconstruction from sparse context. Crucially, our analysis reveals that the backbone encoder becomes self-contained post-training: the memory module facilitates the internalization of motif semantics into the model parameters, allowing the backbone to retain performance advantages even when the memory is detached during inference.