Shufang Xie

66 papers A* 16A 1Journal 40Unranked 9
YearRankTypeTitle / Venue / Authors
2026 J jnl
Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization.
CoRR
Zequn Liu, Kehan Wu, Shufang Xie, Zekun Guo, Wei Zhang, Tao Qin, Renhe Liu, Yingce Xia
2025 J jnl
MIN: Multi-Channel Interaction Network for Drug-Target Interaction With Protein Distillation.
IEEE Trans. Comput. Biol. Bioinform.
Shuqi Li, Shufang Xie, Hongda Sun, Yuhan Chen, Tao Qin, Tianjun Ke, Rui Yan
2025 J jnl
MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design.
CoRR
Wei Zhang, Zekun Guo, Yingce Xia, Peiran Jin, Shufang Xie, Tao Qin, Xiang-Yang Li
2025 J jnl
NatureLM: Deciphering the Language of Nature for Scientific Discovery.
CoRR
Yingce Xia, Peiran Jin, Shufang Xie, Liang He, Chuan Cao, Renqian Luo, Guoqing Liu, Yue Wang, Zequn Liu, Yuan-Jyue Chen, Zekun Guo, Yeqi Bai, Pan Deng, Yaosen Min, Ziheng Lu, Hongxia Hao, Han Yang, Jielan Li, Chang Liu, Jia Zhang, Jianwei Zhu, Kehan Wu, Wei Zhang, Kaiyuan Gao, Qizhi Pei, Qian Wang, Xixian Liu, Yanting Li, Houtian Zhu, Yeqing Lu, Mingqian Ma, Zun Wang, Tian Xie, Krzysztof Maziarz, Marwin H. S. Segler, Zhao Yang, Zilong Chen, Yu Shi, Shuxin Zheng, Lijun Wu, Chen Hu, Peggy Dai, Tie-Yan Liu, Haiguang Liu, Tao Qin
2025 J jnl
Trust Region Preference Approximation: A simple and stable reinforcement learning algorithm for LLM reasoning.
CoRR
Xuerui Su, Shufang Xie, Guoqing Liu, Yingce Xia, Renqian Luo, Peiran Jin, Zhiming Ma, Yue Wang, Zun Wang, Yuting Liu
2024 A* conf
An Analysis and Mitigation of the Reversal Curse.
EMNLP
Ang Lv, Kaiyi Zhang, Shufang Xie, Quan Tu, Yuhan Chen, Ji-Rong Wen, Rui Yan
2024 — conf
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning.
ACL (Findings)
Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
2024 J jnl
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning.
CoRR
Qizhi Pei, Lijun Wu, Kaiyuan Gao, Xiaozhuan Liang, Yin Fang, Jinhua Zhu, Shufang Xie, Tao Qin, Rui Yan
2024 A conf
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors.
CIKM
Qizhi Pei, Lijun Wu, Zhenyu He, Jinhua Zhu, Yingce Xia, Shufang Xie, Rui Yan
2024 J jnl
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors.
CoRR
Qizhi Pei, Lijun Wu, Zhenyu He, Jinhua Zhu, Yingce Xia, Shufang Xie, Rui Yan
2024 — conf
Learning to Generate Style-Specific Adapters for Stylized Dialogue Generation.
NLPCC (1)
Jinpeng Li, Yuhan Chen, Pengfei Wu, Yingce Xia, Shufang Xie, Dongyan Zhao, Rui Yan
2024 J jnl
MIN: Multi-channel Interaction Network for Drug-Target Interaction with Protein Distillation.
CoRR
Shuqi Li, Shufang Xie, Hongda Sun, Yuhan Chen, Tao Qin, Tianjun Ke, Rui Yan
2024 J jnl
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation.
CoRR
Liang He, Peiran Jin, Yaosen Min, Shufang Xie, Lijun Wu, Tao Qin, Xiaozhuan Liang, Kaiyuan Gao, Yuliang Jiang, Tie-Yan Liu
2024 J jnl
YuLan: An Open-source Large Language Model.
CoRR
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
2023 J jnl
Are We Falling in a Middle-Intelligence Trap? An Analysis and Mitigation of the Reversal Curse.
CoRR
Ang Lv, Kaiyi Zhang, Shufang Xie, Quan Tu, Yuhan Chen, Ji-Rong Wen, Rui Yan
2023 J jnl
Breaking the barriers of data scarcity in drug-target affinity prediction.
Briefings Bioinform.
Qizhi Pei, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Haiguang Liu, Tie-Yan Liu, Rui Yan
2023 A* conf
De Novo Molecular Generation via Connection-aware Motif Mining.
ICLR
Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu
2023 J jnl
De Novo Molecular Generation via Connection-aware Motif Mining.
CoRR
Zijie Geng, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Jie Wang, Yongdong Zhang, Feng Wu, Tie-Yan Liu
2023 A* conf
Dual-view Molecular Pre-training.
KDD
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu
2023 — conf
Envisioning Future from the Past: Hierarchical Duality Learning for Multi-Turn Dialogue Generation.
ACL (1)
Ang Lv, Jinpeng Li, Shufang Xie, Rui Yan
2023 — conf
Extract and Attend: Improving Entity Translation in Neural Machine Translation.
ACL (Findings)
Zixin Zeng, Rui Wang, Yichong Leng, Junliang Guo, Shufang Xie, Xu Tan, Tao Qin, Tie-Yan Liu
2023 A* conf
FABind: Fast and Accurate Protein-Ligand Binding.
NeurIPS
Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan
2023 J jnl
FABind: Fast and Accurate Protein-Ligand Binding.
CoRR
Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan
2023 — conf
MolXPT: Wrapping Molecules with Text for Generative Pre-training.
ACL (2)
Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu
2023 J jnl
MolXPT: Wrapping Molecules with Text for Generative Pre-training.
CoRR
Zequn Liu, Wei Zhang, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Ming Zhang, Tie-Yan Liu
2023 A* conf
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design.
KDD
Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu
2023 J jnl
R2-DDI: relation-aware feature refinement for drug-drug interaction prediction.
Briefings Bioinform.
Jiacheng Lin, Lijun Wu, Jinhua Zhu, Xiaobo Liang, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu
2023 J jnl
Re-evaluating Retrosynthesis Algorithms with Syntheseus.
CoRR
Krzysztof Maziarz, Austin Tripp, Guoqing Liu, Megan Stanley, Shufang Xie, Piotr Gainski, Philipp Seidl, Marwin H. S. Segler
2023 J jnl
ResiDual: Transformer with Dual Residual Connections.
CoRR
Shufang Xie, Huishuai Zhang, Junliang Guo, Xu Tan, Jiang Bian, Hany Hassan Awadalla, Arul Menezes, Tao Qin, Rui Yan
2023 A* conf
Retrosynthesis Prediction with Local Template Retrieval.
AAAI
Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin
2023 J jnl
Retrosynthesis Prediction with Local Template Retrieval.
CoRR
Shufang Xie, Rui Yan, Junliang Guo, Yingce Xia, Lijun Wu, Tao Qin
2023 A* conf
Retrosynthetic Planning with Dual Value Networks.
ICML
Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin H. S. Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu
2023 J jnl
Retrosynthetic Planning with Dual Value Networks.
CoRR
Guoqing Liu, Di Xue, Shufang Xie, Yingce Xia, Austin Tripp, Krzysztof Maziarz, Marwin H. S. Segler, Tao Qin, Zongzhang Zhang, Tie-Yan Liu
2023 — conf
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization.
ACL (1)
Griffin Adams, Bichlien Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
2023 J jnl
What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization.
CoRR
Griffin Adams, Bichlien H. Nguyen, Jake Smith, Yingce Xia, Shufang Xie, Anna Ostropolets, Budhaditya Deb, Yuan-Jyue Chen, Tristan Naumann, Noémie Elhadad
2023 A* conf
𝒪-GNN: incorporating ring priors into molecular modeling.
ICLR
Jinhua Zhu, Kehan Wu, Bohan Wang, Yingce Xia, Shufang Xie, Qi Meng, Lijun Wu, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
2022 J jnl
A study of BERT for context-aware neural machine translation.
Mach. Learn.
Xueqing Wu, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin
2022 J jnl
Back translation for molecule generation.
Bioinform.
Yang Fan, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Tao Qin
2022 J jnl
Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations.
CoRR
Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan Awadalla
2022 — conf
Building Multilingual Machine Translation Systems That Serve Arbitrary XY Translations.
NAACL-HLT
Akiko Eriguchi, Shufang Xie, Tao Qin, Hany Hassan
2022 A* conf
Debiased, Longitudinal and Coordinated Drug Recommendation through Multi-Visit Clinic Records.
NeurIPS
Hongda Sun, Shufang Xie, Shuqi Li, Yuhan Chen, Ji-Rong Wen, Rui Yan
2022 J jnl
Direct Molecular Conformation Generation.
CoRR
Jinhua Zhu, Yingce Xia, Chang Liu, Lijun Wu, Shufang Xie, Tong Wang, Yusong Wang, Wengang Zhou, Tao Qin, Houqiang Li, Tie-Yan Liu
2022 J jnl
Direct Molecular Conformation Generation.
Trans. Mach. Learn. Res.
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
2022 J jnl
Discovering drug-target interaction knowledge from biomedical literature.
Bioinform.
Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Tao Qin, Tie-Yan Liu
2022 J jnl
End-to-end entity-aware neural machine translation.
Mach. Learn.
Shufang Xie, Yingce Xia, Lijun Wu, Yiqing Huang, Yang Fan, Tao Qin
2022 J jnl
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design.
CoRR
Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Tianbo Peng, Yingce Xia, Liang He, Shufang Xie, Tao Qin, Haiguang Liu, Kun He, Tie-Yan Liu
2022 A* conf
RetroGraph: Retrosynthetic Planning with Graph Search.
KDD
Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin
2022 J jnl
RetroGraph: Retrosynthetic Planning with Graph Search.
CoRR
Shufang Xie, Rui Yan, Peng Han, Yingce Xia, Lijun Wu, Chenjuan Guo, Bin Yang, Tao Qin
2022 J jnl
SMT-DTA: Improving Drug-Target Affinity Prediction with Semi-supervised Multi-task Training.
CoRR
Qizhi Pei, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Haiguang Liu, Tie-Yan Liu
2022 J jnl
SPRoBERTa: protein embedding learning with local fragment modeling.
Briefings Bioinform.
Lijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie, Tao Qin, Tie-Yan Liu
2022 J jnl
Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design.
CoRR
Kehan Wu, Yingce Xia, Yang Fan, Pan Deng, Haiguang Liu, Lijun Wu, Shufang Xie, Tong Wang, Tao Qin, Tie-Yan Liu
2022 A* conf
Target-Side Input Augmentation for Sequence to Sequence Generation.
ICLR
Shufang Xie, Ang Lv, Yingce Xia, Lijun Wu, Tao Qin, Tie-Yan Liu, Rui Yan
2022 A* conf
Unified 2D and 3D Pre-Training of Molecular Representations.
KDD
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
2022 J jnl
Unified 2D and 3D Pre-Training of Molecular Representations.
CoRR
Jinhua Zhu, Yingce Xia, Lijun Wu, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
2021 J jnl
Discovering Drug-Target Interaction Knowledge from Biomedical Literature.
CoRR
Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Wanxiang Che, Tao Qin, Tie-Yan Liu
2021 A* conf
IOT: Instance-wise Layer Reordering for Transformer Structures.
ICLR
Jinhua Zhu, Lijun Wu, Yingce Xia, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
2021 J jnl
IOT: Instance-wise Layer Reordering for Transformer Structures.
CoRR
Jinhua Zhu, Lijun Wu, Yingce Xia, Shufang Xie, Tao Qin, Wengang Zhou, Houqiang Li, Tie-Yan Liu
2021 A* conf
Learning to Reweight with Deep Interactions.
AAAI
Yang Fan, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Xiang-Yang Li
2021 A* conf
Temporally Correlated Task Scheduling for Sequence Learning.
ICML
Xueqing Wu, Lewen Wang, Yingce Xia, Weiqing Liu, Lijun Wu, Shufang Xie, Tao Qin, Tie-Yan Liu
2021 — conf
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost.
NAACL-HLT
Zhen Wu, Lijun Wu, Qi Meng, Yingce Xia, Shufang Xie, Tao Qin, Xinyu Dai, Tie-Yan Liu
2021 J jnl
UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost.
CoRR
Zhen Wu, Lijun Wu, Qi Meng, Yingce Xia, Shufang Xie, Tao Qin, Xinyu Dai, Tie-Yan Liu
2021 — conf
mixSeq: A Simple Data Augmentation Methodfor Neural Machine Translation.
IWSLT
Xueqing Wu, Yingce Xia, Jinhua Zhu, Lijun Wu, Shufang Xie, Yang Fan, Tao Qin
2020 J jnl
Learn to Use Future Information in Simultaneous Translation.
CoRR
Xueqing Wu, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Tie-Yan Liu
2020 J jnl
Learning to Teach with Deep Interactions.
CoRR
Yang Fan, Yingce Xia, Lijun Wu, Shufang Xie, Weiqing Liu, Jiang Bian, Tao Qin, Xiang-Yang Li, Tie-Yan Liu
2020 J jnl
Multi-branch Attentive Transformer.
CoRR
Yang Fan, Shufang Xie, Yingce Xia, Lijun Wu, Tao Qin, Xiang-Yang Li, Tie-Yan Liu
2020 A* conf
Sequence Generation with Mixed Representations.
ICML
Lijun Wu, Shufang Xie, Yingce Xia, Yang Fan, Jian-Huang Lai, Tao Qin, Tie-Yan Liu