MOTIVATION: In recent years, protein language models (pLMs) and graph neural networks (GNNs) have demonstrated powerful expressive and reasoning capabilities in modeling protein-RNA/DNA interactions. However, existing methods, which use simple graphs to describe the relationships between residues, struggle to effectively capture the high-order, multi-body residue interactions present in protein-nucleic acid complex structures. In fact, spatially continuous but sequence-wise discontinuous residues often cooperatively determine nucleic acid binding capacity. RESULTS: In this study, we present IKANbind, a computational approach that combines hypergraph representation learning and interpretable Kolmogorov-Arnold Networks (KANs), for identifying nucleic acid binding residues (NBRs) in proteins. By combining the advantages of pLM, hypergraph neural networks and symbolic KAN, IKANbind outperforms existing methods on multiple NBR benchmark datasets. We also demonstrated that the pLM used in IKANbind can implicitly learn the physicochemical properties of binding residues, such as charge and hydrophobicity. In addition, the symbolic KAN, which uses a unique weighted mechanism of decomposable basis functions, can accurately identify the features with the greatest contribution to NBR recognition. We found that polarity and charge make greater contributions to NBR prediction than other physicochemical properties or evolutionary information. Finally, IKANbind achieves promising performance when extended to other ligand-binding residue prediction tasks. AVAILABILITY AND IMPLEMENTATION: IKANbind is freely available at https://github.com/yangfengzhuguet/IKANBind.

A recommendation system is of vital importance in delivering personalization services, which often brings continuous dual improvement in user experience and organization revenue. However, the data of one single organization may not be enough to build an accurate recommendation model for inactive or new cold-start users. Moreover, due to the recent regulatory restrictions on user privacy and data security, as well as the commercial conflicts, the raw data in different organizations cannot be merged to alleviate the scarcity issue in training a model. In order to learn users’ preferences from such cross-silo data of different organizations and then provide recommendations to the cold-start users, we propose a novel federated learning framework, i.e., federated cross-organization recommendation ecosystem (FedCORE). Specifically, we first focus on the ecosystem problem of cross-organization federated recommendation, including cooperation patterns and privacy protection. For the former, we propose a privacy-aware collaborative training and inference algorithm. For the latter, we define four levels of privacy leakage and propose some methods for protecting the privacy. We then conduct extensive experiments on three real-world datasets and two seminal recommendation models to study the impact of cooperation in our proposed ecosystem and the effectiveness of privacy protection.