KGNN: Knowledge Graph Neural Network for Drug-Drug Interaction Prediction. - Xuan Lin; Zhe Quan; Zhi-Jie Wang 009; Tengfei Ma 002; Xiangxiang Zeng (IJCAI, 2020)

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning. - Xiangxiang Zeng; Xiang Song 003; Tengfei Ma 002; Xiaoqin Pan; Yadi Zhou; Yuan Hou; Zheng Zhang 001; George Karypis; Feixiong Cheng (CoRR, 2020)

MUFFIN: multi-scale feature fusion for drug-drug interaction prediction. - Yujie Chen; 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; Wen Tao; Dashun Zheng; Xuan Lin; Patrick Cheong-lao Pang; Yiping Liu; Yijun Wang 002; Bosheng Song; Xiangxiang Zeng (CoRR, 2023)

KG-MTL: Knowledge Graph Enhanced Multi-Task Learning for Molecular Interaction. - Tengfei Ma 002; Xuan Lin; Bosheng Song; Philip S. Yu; Xiangxiang Zeng (IEEE Trans. Knowl. Data Eng., 2023)

KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion. - Tengfei Ma 002; Xiang Song 003; Wen Tao; Mufei Li; Jiani Zhang 003; Xiaoqin Pan; Jianxin Lin; Bosheng Song; Xiangxiang Zeng (CoRR, 2024)

Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development. - Tengfei Ma 002; Xuan Lin; Tianle Li; Chaoyi Li; Long Chen; Peng Zhou 011; Xibao Cai; Xinyu Yang; Daojian Zeng; Dong-Sheng Cao 001; Xiangxiang Zeng (CoRR, 2024)

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

Towards Synergistic Path-based Explanations for Knowledge Graph Completion: Exploration and Evaluation. - Tengfei Ma 002; Xiang Song 003; Wen Tao; Mufei Li; Jiani Zhang 003; Xiaoqin Pan; Yijun Wang 002; Bosheng Song; Xiangxiang Zeng (ICLR, 2025)

Predicting Drug-Drug Interaction via Dual-Drug Visual Representation. - Lingxuan Xie; Tengfei Ma 002; Yuqin He; Yiping Liu; Xiangxiang Zeng (J. Chem. Inf. Model., 2025)

AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery. - Yifan Dai; Xuanbai Ren; Tengfei Ma 002; Qipeng Yan; Yiping Liu; Yuansheng Liu; Xiangxiang Zeng (CoRR, 2025)

From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing. - Chengrui Xiang; Tengfei Ma 002; Xiangzheng Fu; Yiping Liu; Bosheng Song; Xiangxiang Zeng (CoRR, 2025)

MolBridge: Atom-Level Joint Graph Refinement for Robust Drug-Drug Interaction Event Prediction. - Xuan Lin; Aocheng Ding; Tengfei Ma 002; Hua Liang; Zhe Quan (CoRR, 2025)

ImageDDI: Image-enhanced molecular motif sequence representation for drug-drug interaction prediction. - Yuqin He; Tengfei Ma 002; Chaoyi Li; Pengsen Ma; Hongxin Xiang; Jianmin Wang 016; Yiping Liu; Bosheng Song; Xiangxiang Zeng (Inf. Fusion, 2026)