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ORCIDShufang Xie 0003
Person information
- affiliation: Microsoft Research Asia
Other persons with the same name
- Shufang Xie 0001 — Universität der Bundeswehr München, Neubiberg, Germany
- Shufang Xie 0002 — Southeast University, School of Computer Science and Engineering, Nanjing, China
- Shufang Xie 0004 — Hunan Biological And Electromechanical Polytechnic, Changsha, China
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Journal Articles
- 2023
[j7]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)- 2022
- [j6]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) - [j5]Yang Fan, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin:
Back translation for molecule generation. Bioinform. 38(5): 1244-1251 (2022) - [j4]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): 5100-5107 (2022) - [j3]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): 917-935 (2022) - [j2]Shufang Xie, Yingce Xia, Lijun Wu, Yiqing Huang, Yang Fan, Tao Qin:
End-to-end entity-aware neural machine translation. Mach. Learn. 111(3): 1181-1203 (2022) - [j1]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)
Conference and Workshop Papers
- 2024
- [c23]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: 1216-1240 - 2023
- [c22]Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin:
Retrosynthesis Prediction with Local Template Retrieval. AAAI 2023: 5330-5338 - [c21]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: 1606-1616 - [c20]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: 1697-1710 - [c19]Ang Lv, Jinpeng Li, Shufang Xie, Rui Yan:
Envisioning Future from the Past: Hierarchical Duality Learning for Multi-Turn Dialogue Generation. ACL (1) 2023: 7382-7394 - [c18]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: 10520-10542 - [c17]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 - [c16]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 - [c15]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: 22266-22276 - [c14]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: 506-517 - [c13]Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu:
Dual-view Molecular Pre-training. KDD 2023: 3615-3627 - [c12]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 - 2022
- [c11]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 - [c10]Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin:
RetroGraph: Retrosynthetic Planning with Graph Search. KDD 2022: 2120-2129 - [c9]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: 2626-2636 - [c8]Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan:
Building Multilingual Machine Translation Systems That Serve Arbitrary XY Translations. NAACL-HLT 2022: 600-606 - [c7]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 - 2021
- [c6]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: 7385-7393 - [c5]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 - [c4]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: 11274-11284 - [c3]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: 192-197 - [c2]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: 3865-3878 - 2020
- [c1]Lijun Wu, Shufang Xie, Yingce Xia, Yang Fan, Jian-Huang Lai, Tao Qin, Tie-Yan Liu:
Sequence Generation with Mixed Representations. ICML 2020: 10388-10398
Informal and Other Publications
- 2024
- [i25]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 abs/2402.17810 (2024) - [i24]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 abs/2406.19853 (2024) - [i23]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 abs/2407.15202 (2024) - 2023
- [i22]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 abs/2301.13755 (2023) - [i21]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 abs/2302.01129 (2023) - [i20]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 abs/2304.14802 (2023) - [i19]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 abs/2305.07615 (2023) - [i18]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 abs/2305.10688 (2023) - [i17]Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin:
Retrosynthesis Prediction with Local Template Retrieval. CoRR abs/2306.04123 (2023) - [i16]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 abs/2310.06763 (2023) - [i15]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 abs/2310.19796 (2023) - [i14]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 abs/2311.07468 (2023) - 2022
- [i13]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 abs/2202.01356 (2022) - [i12]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 abs/2206.09818 (2022) - [i11]Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin:
RetroGraph: Retrosynthetic Planning with Graph Search. CoRR abs/2206.11477 (2022) - [i10]Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan Awadalla:
Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations. CoRR abs/2206.14982 (2022) - [i9]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 abs/2207.08806 (2022) - [i8]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 abs/2209.06158 (2022) - [i7]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 abs/2211.08406 (2022) - 2021
- [i6]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 abs/2103.03457 (2021) - [i5]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 abs/2104.04946 (2021) - [i4]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 abs/2109.13187 (2021) - 2020
- [i3]Yang Fan, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Xiang-Yang Li, Tie-Yan Liu:
Multi-branch Attentive Transformer. CoRR abs/2006.10270 (2020) - [i2]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 abs/2007.04649 (2020) - [i1]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 abs/2007.05290 (2020)
Coauthor Index
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