Publications

Structure-informed Language Models Are Protein Designers
Zaixiang Zheng*, Yifan Deng*, Dongyu Xue, Yi Zhou, Fei Ye, Quanquan Gu
Proc. of the 40 th International Conference on Machine Learning (ICML), Hawaii, USA, 2023 [URL]

Improved drug–target interaction prediction with intermolecular graph transformer
Siyuan Liu, Yusong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu, Tong Wang
Briefings in Bioinformatics br/> [code] [URL]

META-DDIE: predicting drug–drug interaction events with few-shot learning
Yifan Deng, Yang Qiu, Xinran Xu, Shichao Liu, Zhongfei Zhang, Shanfeng Zhu, Wen Zhang
Briefings in Bioinformatics
[code] [URL]

A multimodal deep learning framework for predicting drug-drug interaction events
Yifan Deng, Xinran Xu, Yang Qiu, Jingbo Xia, Wen Zhang, and Shichao Liu
Bioinformatics
[code] [URL]

Enhancing drug-drug interaction prediction using deep attention neural networks
Shichao Liu, Yang Zhang, Yuxin Cui, Yang Qiu, Yifan Deng, Zhongfei Mark Zhang, Wen Zhang IEEE/ACM Transactions on Computational Biology and Bioinformatics [URL]

A Comprehensive Review of Computational Methods for Drug-drug Interaction Detection
Yang Qiu, Yang Zhang, Yifan Deng, Shichao Liu and Wen Zhang
IEEE/ACM Transactions on Computational Biology and Bioinformatics
[URL]