arXiv:2509.20240v1 Announce Type: cross Abstract: Non-coding RNAs (ncRNAs) play pivotal roles in gene expression regulation and the pathogenesis of various diseases. Accurate classification of ncRNAs is essential for functional annotation and disease diagnosis. To address existing limitations in feature extraction depth and multimodal fusion, we propose HGMamba-ncRNA, a HyperGraphMamba-based multichannel adaptive model, which integrates sequence, secondary structure, and optionally available expression features of ncRNAs to enhance classification performance. Specifically, the sequence of ncRNA is modeled using a parallel Multi-scale Convolution and LSTM architecture (MKC-L) to capture both local patterns and long-range dependencies of nucleotides. The structure modality employs a multi-scale graph transformer (MSGraphTransformer) to represent the multi-level topological characteristics of ncRNA secondary structures. The expression modality utilizes a Chebyshev Polynomial-based Kolmogorov-Arnold Network (CPKAN) to effectively model and interpret high-dimensional expression profiles. Finally, by incorporating virtual nodes to facilitate efficient and comprehensive multimodal interaction, HyperGraphMamba is proposed to adaptively align and integrate multichannel heterogeneous modality features. Experiments conducted on three public datasets demonstrate that HGMamba-ncRNA consistently outperforms state-of-the-art methods in terms of accuracy and other metrics. Extensive empirical studies further confirm the model's robustness, effectiveness, and strong transferability, offering a novel and reliable strategy for complex ncRNA functional classification. Code and datasets are available at https://anonymous.4open.science/r/HGMamba-ncRNA-94D0.