Protocols for RNA-RNA Interaction Dataset Construction and Model Training

Protocols are central to the Methods in Molecular Biology series, enabling reproducibility and practical adoption of computational techniques. For RNA-RNA interaction (RRI) prediction, standardized protocols are essential due to the heterogeneity of data sources, preprocessing steps, and modeling choices. This chapter presents step-by-step protocols for constructing RRI datasets, generating negative samples, extracting sequence and structural features, training deep learning models, and evaluating performance through reproducible, standardized workflows. The protocols are modular and adaptable, supporting sequence-based, structure-aware, and graph-based models. By following these procedures, researchers can build robust, Findable, Accessible, Interoperable, and Reusable (FAIR)-aligned RRI prediction pipelines suitable for both academic research and clinical applications.