DQHTFI: Dynamic-Query Hypergraph Transformer for Fine-Grained Drug–Target Interaction and Affinity Prediction

Drug–target interaction prediction and binding affinity prediction are two key tasks in drug discovery and drug repurposing. Although deep learning methods have made significant progress, existing models typically rely on global representations of drugs and proteins, making it difficult to adequately model fine-grained interactions between their local units. Fixed multimodal fusion strategies also struggle to dynamically adjust the contributions of different modalities for different drug–target combinations. To address these issues, we propose DQHTFI, a fine-grained interaction prediction framework for drug–target interaction classification and binding affinity regression. DQHTFI employs BRICS fragments and Pfam functional domains as the basic interaction units and jointly learns semantic and structural representations. We design a dynamic-query hypergraph Transformer framework in which hyperedges are constructed among the multimodal features of fragment–domain pairs. Dynamic queries are generated from the cross-conditioned features of fragment–domain pairs to adaptively adjust the contribution of each modality, thereby modeling higher-order interactions between local units. Our proposed model achieves competitive results on multiple benchmark datasets.