3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction. - Haohuai He; Guanxing Chen; Calvin Yu-Chian Chen (Briefings Bioinform., 2022)

3D graph neural network with few-shot learning for predicting drug-drug interactions in scaffold-based cold start scenario. - Qiujie Lv; Jun Zhou; Ziduo Yang; Haohuai He; Calvin Yu-Chian Chen (Neural Networks, 2023)

Integrating sequence and graph information for enhanced drug-target affinity prediction. - Haohuai He; Guanxing Chen; Calvin Yu-Chian Chen (Sci. China Inf. Sci., 2024)

GINCM-DTA: A graph isomorphic network with protein contact map representation for potential use against COVID-19 and Omicron subvariants BQ.1, BQ.1.1, XBB.1.5, XBB.1.16. - Guanxing Chen; Haohuai He; Lu Zhao; Qiujie Lv; Calvin Yu-Chian Chen (Expert Syst. Appl., 2024)

MFAE: Multilevel Feature Aggregation Enhanced Drug-Target Affinity Prediction for Drug Repurposing Against Colorectal Cancer. - Guanxing Chen; Haohuai He; Calvin Yu-Chian Chen (Adv. Intell. Syst., 2024)

Dual modality feature fused neural network integrating binding site information for drug target affinity prediction. - Haohuai He; Guanxing Chen; Zhenchao Tang; Calvin Yu-Chian Chen (npj Digit. Medicine, 2025)

Modal-NexT: Towards unified heterogeneous cellular data integration. - Zhenchao Tang; Guanxing Chen; Shouzhi Chen; Haohuai He; Jiehui Huang; Tiejun Dong; Jun Zhou; Lu Zhao; Linlin You; Calvin Yu-Chian Chen (Inf. Fusion, 2026)