Shufang Xie

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 55

Top Topics

Machine Translation

Nearest Neighbor

Biomedical Literature

Top Venues

Publications

Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning. ACL (Findings) (2024)
Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning. CoRR (2024)
Yutao Zhu, Kun Zhou, Kelong Mao, Wentong Chen, Yiding Sun, Zhipeng Chen, Qian Cao, Yihan Wu, Yushuo Chen, Feng Wang, Lei Zhang, Junyi Li, Xiaolei Wang, Lei Wang, Beichen Zhang, Zican Dong, Xiaoxue Cheng, Yuhan Chen, Xinyu Tang, Yupeng Hou, Qiangqiang Ren, Xincheng Pang, Shufang Xie, Wayne Xin Zhao, Zhicheng Dou, Jiaxin Mao, Yankai Lin, Ruihua Song, Jun Xu, Xu Chen, Rui Yan, Zhewei Wei, Di Hu, Wenbing Huang, Ze-Feng Gao, Yueguo Chen, Weizheng Lu, Ji-Rong Wen
YuLan: An Open-source Large Language Model. CoRR (2024)
Qizhi Pei, Lijun Wu, Zhenyu He, Jinhua Zhu, Yingce Xia, Shufang Xie, Rui Yan
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors. CoRR (2024)
Ang Lv, Jinpeng Li, Shufang Xie, Rui Yan
Envisioning Future from the Past: Hierarchical Duality Learning for Multi-Turn Dialogue Generation. ACL (1) (2023)
Griffin Adams, Bichlien H. Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization. CoRR (2023)
Zixin Zeng, Rui Wang, Yichong Leng, Junliang Guo, Shufang Xie, Xu Tan, Tao Qin, Tie-Yan Liu
Extract and Attend: Improving Entity Translation in Neural Machine Translation. ACL (Findings) (2023)
Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu
De Novo Molecular Generation via Connection-aware Motif Mining. CoRR (2023)
Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu
MolXPT: Wrapping Molecules with Text for Generative Pre-training. CoRR (2023)
Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu
De Novo Molecular Generation via Connection-aware Motif Mining. ICLR (2023)
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu
Dual-view Molecular Pre-training. KDD (2023)
Ang Lv, Kaiyi Zhang, Shufang Xie, Quan Tu, Yuhan Chen, Ji-Rong Wen, Rui Yan
Are We Falling in a Middle-Intelligence Trap? An Analysis and Mitigation of the Reversal Curse. CoRR (2023)
Krzysztof Maziarz, Austin Tripp, Guoqing Liu, Megan Stanley, Shufang Xie, Piotr Gainski, Philipp Seidl, Marwin H. S. Segler
Re-evaluating Retrosynthesis Algorithms with Syntheseus. CoRR (2023)
Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin
Retrosynthesis Prediction with Local Template Retrieval. AAAI (2023)
Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu
MolXPT: Wrapping Molecules with Text for Generative Pre-training. ACL (2) (2023)
Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization. ACL (1) (2023)
Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design. KDD (2023)
Jiacheng Lin, Lijun Wu, Jinhua Zhu, Xiaobo Liang, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu
R2-DDI: relation-aware feature refinement for drug-drug interaction prediction. Briefings Bioinform. 24 (1) (2023)
Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan
FABind: Fast and Accurate Protein-Ligand Binding. NeurIPS (2023)
Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin H. S. Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu
Retrosynthetic Planning with Dual Value Networks. ICML (2023)
Jinhua Zhu, Kehan Wu, Bohan Wang, Yingce Xia, Shufang Xie, Qi Meng, Lijun Wu, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
𝒪-GNN: incorporating ring priors into molecular modeling. ICLR (2023)
Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin H. S. Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu
Retrosynthetic Planning with Dual Value Networks. CoRR (2023)
Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan
FABind: Fast and Accurate Protein-Ligand Binding. CoRR (2023)
Shufang Xie, Huishuai Zhang, Junliang Guo, Xu Tan, Jiang Bian, Hany Hassan Awadalla, Arul Menezes, Tao Qin, Rui Yan
ResiDual: Transformer with Dual Residual Connections. CoRR (2023)
Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin
Retrosynthesis Prediction with Local Template Retrieval. CoRR (2023)
Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design. CoRR (2022)
Xueqing Wu, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin
A study of BERT for context-aware neural machine translation. Mach. Learn. 111 (3) (2022)
Hongda Sun, Shufang Xie, Shuqi Li, Yuhan Chen, Ji-Rong Wen, Rui Yan
Debiased, Longitudinal and Coordinated Drug Recommendation through Multi-Visit Clinic Records. NeurIPS (2022)
Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan Awadalla
Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations. CoRR (2022)
Qizhi Pei, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Haiguang Liu, Tie-Yan Liu
SMT-DTA: Improving Drug-Target Affinity Prediction with Semi-supervised Multi-task Training. CoRR (2022)
Shufang Xie, Ang Lv, Yingce Xia, Lijun Wu, Tao Qin, Tie-Yan Liu, Rui Yan
Target-Side Input Augmentation for Sequence to Sequence Generation. ICLR (2022)
Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin
RetroGraph: Retrosynthetic Planning with Graph Search. KDD (2022)
Yang Fan, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin
Back translation for molecule generation. Bioinform. 38 (5) (2022)
Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Tong Wang, Yusong Wang, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu
Direct Molecular Conformation Generation. CoRR (2022)
Lijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu
SPRoBERTa: protein embedding learning with local fragment modeling. Briefings Bioinform. 23 (6) (2022)
Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Tao Qin, Tie-Yan Liu
Discovering drug-target interaction knowledge from biomedical literature. Bioinform. 38 (22) (2022)
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
Unified 2D and 3D Pre-Training of Molecular Representations. CoRR (2022)
Shufang Xie, Yingce Xia, Lijun Wu, Yiqing Huang, Yang Fan, Tao Qin
End-to-end entity-aware neural machine translation. Mach. Learn. 111 (3) (2022)
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
Unified 2D and 3D Pre-Training of Molecular Representations. KDD (2022)
Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Yusong Wang, Tong Wang, Tao Qin, Wengang Zhou, Houqiang Li, Haiguang Liu, Tie-Yan Liu
Direct Molecular Conformation Generation. Trans. Mach. Learn. Res. 2022 (2022)
Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin
RetroGraph: Retrosynthetic Planning with Graph Search. CoRR (2022)
Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan
Building Multilingual Machine Translation Systems That Serve Arbitrary XY Translations. NAACL-HLT (2022)
Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu
Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design. CoRR (2022)
Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Wanxiang Che, Tao Qin, Tie-Yan Liu
Discovering Drug-Target Interaction Knowledge from Biomedical Literature. CoRR (2021)
Jinhua Zhu, Lijun Wu, Yingce Xia, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
IOT: Instance-wise Layer Reordering for Transformer Structures. ICLR (2021)
Xueqing Wu, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Yang Fan, Tao Qin
mixSeq: A Simple Data Augmentation Methodfor Neural Machine Translation. IWSLT (2021)
Zhen Wu, Lijun Wu, Qi Meng, Yingce Xia, Shufang Xie, Tao Qin, Xinyu Dai, Tie-Yan Liu
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost. CoRR (2021)
Jinhua Zhu, Lijun Wu, Yingce Xia, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
IOT: Instance-wise Layer Reordering for Transformer Structures. CoRR (2021)
Zhen Wu, Lijun Wu, Qi Meng, Yingce Xia, Shufang Xie, Tao Qin, Xinyu Dai, Tie-Yan Liu
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost. NAACL-HLT (2021)
Yang Fan, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Xiang-Yang Li
Learning to Reweight with Deep Interactions. AAAI (2021)
Xueqing Wu, Lewen Wang, Yingce Xia, Weiqing Liu, Lijun Wu, Shufang Xie, Tao Qin, Tie-Yan Liu
Temporally Correlated Task Scheduling for Sequence Learning. ICML (2021)
Yang Fan, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Xiang-Yang Li, Tie-Yan Liu
Multi-branch Attentive Transformer. CoRR (2020)
Xueqing Wu, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Tie-Yan Liu
Learn to Use Future Information in Simultaneous Translation. CoRR (2020)
Lijun Wu, Shufang Xie, Yingce Xia, Yang Fan, Jian-Huang Lai, Tao Qin, Tie-Yan Liu
Sequence Generation with Mixed Representations. ICML (2020)
Yang Fan, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Xiang-Yang Li, Tie-Yan Liu
Learning to Teach with Deep Interactions. CoRR (2020)