MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. - Yujie Chen 002; Tengfei Ma 002; Xixi Yang; Jianmin Wang 016; Bosheng Song; Xiangxiang Zeng (Bioinform., 2021)

Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph. - Tengfei Ma 002; Yujie Chen 002; Wen Tao; Dashun Zheng; Xuan Lin; Patrick Cheong-Iao Pang; Yiping Liu; Yijun Wang 002; Bosheng Song; Xiangxiang Zeng (CoRR, 2023)

S2DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion. - Tengfei Ma 002; Yujie Chen 002; Liang Wang; Xuan Lin; Bosheng Song; Xiangxiang Zeng (CoRR, 2024)

Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction. - Tengfei Ma 002; Yujie Chen 002; Wen Tao; Dashun Zheng; Xuan Lin; Patrick Cheong-Iao Pang; Yiping Liu; Yijun Wang 002; Longyue Wang; Bosheng Song; Xiangxiang Zeng; Philip S. Yu (IEEE Trans. Knowl. Data Eng., 2024)

S²DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion. - Tengfei Ma 002; Yujie Chen 002; Liang Wang; Xuan Lin; Bosheng Song; Xiangxiang Zeng (AAAI, 2025)

Self-supervised Blending Structural Context of Visual Molecules for Robust Drug Interaction Prediction. - Tengfei Ma 002; Kun Chen; Yongsheng Zang; Yujie Chen 002; Xuanbai Ren; Bosheng Song; Hongxin Xiang; Yiping Liu; Xiangxiang Zeng (NeurIPS, 2025)

TRACE: Transformation-Aware Graph Refinement for Reaction Condition Prediction. - Yujie Chen 002; Tengfei Ma 002; Yuansheng Liu; Leyi Wei; Shu Wu; Dongsheng Cao 001; Yiping Liu; Xiangxiang Zeng (AAAI, 2026)

Enhancing Retrosynthesis Prediction with Distillation Learning. - Yiping Liu; Zhou Yu; Jiayi Zhang; Yujie Chen 002; Shu Wu; Leyi Wei; Xiangxiang Zeng; Yuyan Han; Yuansheng Liu (J. Chem. Inf. Model., 2026)

SpecX: A Large-Scale Benchmark for Multi-Modal Spectroscopy and Cross-Paradigm Evaluation. - Chengrui Xiang; Tengfei Ma 002; Yujie Chen 002; Tong Wang 014; Haowen Chen; Xiangxiang Zeng (CoRR, 2026)