Sequence Generation with Mixed Representations. - Lijun Wu 003; Shufang Xie 003; Yingce Xia; Yang Fan; Jian-Huang Lai; Tao Qin 001; Tie-Yan Liu (ICML, 2020)

Multi-branch Attentive Transformer. - Yang Fan; Shufang Xie 003; Yingce Xia; Lijun Wu 003; Tao Qin 001; Xiang-Yang Li 001; Tie-Yan Liu (CoRR, 2020)

Learning to Teach with Deep Interactions. - Yang Fan; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Weiqing Liu; Jiang Bian 002; Tao Qin 001; Xiang-Yang Li 001; Tie-Yan Liu (CoRR, 2020)

Learn to Use Future Information in Simultaneous Translation. - Xueqing Wu 001; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Weiqing Liu; Jiang Bian 002; Tao Qin 001; Tie-Yan Liu (CoRR, 2020)

Learning to Reweight with Deep Interactions. - Yang Fan; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Weiqing Liu; Jiang Bian 002; Tao Qin 001; Xiang-Yang Li 001 (AAAI, 2021)

IOT: Instance-wise Layer Reordering for Transformer Structures. - Jinhua Zhu 001; Lijun Wu 003; Yingce Xia; Shufang Xie 003; Tao Qin 001; Wengang Zhou 001; Houqiang Li; Tie-Yan Liu (ICLR, 2021)

Temporally Correlated Task Scheduling for Sequence Learning. - Xueqing Wu 001; Lewen Wang; Yingce Xia; Weiqing Liu; Lijun Wu 003; Shufang Xie 003; Tao Qin 001; Tie-Yan Liu (ICML, 2021)

mixSeq: A Simple Data Augmentation Methodfor Neural Machine Translation. - Xueqing Wu 001; Yingce Xia; Jinhua Zhu 001; Lijun Wu 003; Shufang Xie 003; Yang Fan; Tao Qin 001 (IWSLT, 2021)

UniDrop: A Simple yet Effective Technique to Improve Transformer without Extra Cost. - Zhen Wu 002; Lijun Wu 003; Qi Meng; Yingce Xia; Shufang Xie 003; Tao Qin 001; Xinyu Dai; Tie-Yan Liu (NAACL-HLT, 2021)

Discovering Drug-Target Interaction Knowledge from Biomedical Literature. - Yutai Hou; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Yang Fan; Jinhua Zhu 001; Wanxiang Che; Tao Qin 001; Tie-Yan Liu (CoRR, 2021)

Target-Side Input Augmentation for Sequence to Sequence Generation. - Shufang Xie 003; Ang Lv; Yingce Xia; Lijun Wu 003; Tao Qin 001; Tie-Yan Liu; Rui Yan 001 (ICLR, 2022)

RetroGraph: Retrosynthetic Planning with Graph Search. - Shufang Xie 003; Rui Yan 001; Peng Han 005; Yingce Xia; Lijun Wu 003; Chenjuan Guo; Bin Yang 002; Tao Qin 001 (KDD, 2022)

Unified 2D and 3D Pre-Training of Molecular Representations. - Jinhua Zhu 001; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Tao Qin 001; Wengang Zhou 001; Houqiang Li; Tie-Yan Liu (KDD, 2022)

Building Multilingual Machine Translation Systems That Serve Arbitrary XY Translations. - Akiko Eriguchi; Shufang Xie 003; Tao Qin 001; Hany Hassan (NAACL-HLT, 2022)

Debiased, Longitudinal and Coordinated Drug Recommendation through Multi-Visit Clinic Records. - Hongda Sun 001; Shufang Xie 003; Shuqi Li; Yuhan Chen 001; Ji-Rong Wen; Rui Yan 001 (NeurIPS, 2022)

SPRoBERTa: protein embedding learning with local fragment modeling. - Lijun Wu 003; Chengcan Yin; Jinhua Zhu 001; Zhen Wu 002; Liang He 010; Yingce Xia; Shufang Xie 003; Tao Qin 001; Tie-Yan Liu (Briefings Bioinform., 2022)

Back translation for molecule generation. - Yang Fan; Yingce Xia; Jinhua Zhu 001; Lijun Wu 003; Shufang Xie 003; Tao Qin 001 (Bioinform., 2022)

Direct Molecular Conformation Generation. - Jinhua Zhu 001; Yingce Xia; Chang Liu 030; Lijun Wu 003; Shufang Xie 003; Tong Wang 014; Yusong Wang; Wengang Zhou 001; Tao Qin 001; Houqiang Li; Tie-Yan Liu (CoRR, 2022)

SMT-DTA: Improving Drug-Target Affinity Prediction with Semi-supervised Multi-task Training. - Qizhi Pei; Lijun Wu 003; Jinhua Zhu 001; Yingce Xia; Shufang Xie 003; Tao Qin 001; Haiguang Liu; Tie-Yan Liu (CoRR, 2022)

Building Multilingual Machine Translation Systems That Serve Arbitrary X-Y Translations. - Akiko Eriguchi; Shufang Xie 003; Tao Qin 001; Hany Hassan Awadalla (CoRR, 2022)

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design. - Kehan Wu; Yingce Xia; Yang Fan; Pan Deng; Haiguang Liu; Lijun Wu 003; Shufang Xie 003; Tong Wang 014; Tao Qin 001; Tie-Yan Liu (CoRR, 2022)

Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design. - Kaiyuan Gao; Lijun Wu 003; Jinhua Zhu 001; Tianbo Peng; Yingce Xia; Liang He 010; Shufang Xie 003; Tao Qin 001; Haiguang Liu; Kun He 001; Tie-Yan Liu (CoRR, 2022)

A study of BERT for context-aware neural machine translation. - Xueqing Wu 001; Yingce Xia; Jinhua Zhu 001; Lijun Wu 003; Shufang Xie 003; Tao Qin 001 (Mach. Learn., 2022)

End-to-end entity-aware neural machine translation. - Shufang Xie 003; Yingce Xia; Lijun Wu 003; Yiqing Huang; Yang Fan; Tao Qin 001 (Mach. Learn., 2022)

Direct Molecular Conformation Generation. - Jinhua Zhu 001; Yingce Xia; Chang Liu 030; Lijun Wu 003; Shufang Xie 003; Yusong Wang; Tong Wang 014; Tao Qin 001; Wengang Zhou 001; Houqiang Li; Haiguang Liu; Tie-Yan Liu (Trans. Mach. Learn. Res., 2022)

Discovering drug-target interaction knowledge from biomedical literature. - Yutai Hou; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Yang Fan; Jinhua Zhu 001; Tao Qin 001; Tie-Yan Liu (Bioinform., 2022)

Retrosynthesis Prediction with Local Template Retrieval. - Shufang Xie 003; Rui Yan 001; Junliang Guo; Yingce Xia; Lijun Wu 003; Tao Qin 001 (AAAI, 2023)

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization. - Griffin Adams; Bichlien Nguyen; Jake Smith; Yingce Xia; Shufang Xie 003; Anna Ostropolets; Budhaditya Deb; Yuan-Jyue Chen; Tristan Naumann; Noémie Elhadad (ACL (1), 2023)

MolXPT: Wrapping Molecules with Text for Generative Pre-training. - Zequn Liu; Wei Zhang; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Tao Qin 001; Ming Zhang 004; Tie-Yan Liu (ACL (2), 2023)

Envisioning Future from the Past: Hierarchical Duality Learning for Multi-Turn Dialogue Generation. - Ang Lv; Jinpeng Li 003; Shufang Xie 003; Rui Yan 001 (ACL (1), 2023)

Extract and Attend: Improving Entity Translation in Neural Machine Translation. - Zixin Zeng; Rui Wang 028; Yichong Leng; Junliang Guo; Shufang Xie 003; Xu Tan 003; Tao Qin 001; Tie-Yan Liu (ACL (Findings), 2023)

De Novo Molecular Generation via Connection-aware Motif Mining. - Zijie Geng; Shufang Xie 003; Yingce Xia; Lijun Wu 003; Tao Qin 001; Jie Wang 005; Yongdong Zhang 001; Feng Wu 001; Tie-Yan Liu (ICLR, 2023)

𝒪-GNN: incorporating ring priors into molecular modeling. - Jinhua Zhu 001; Kehan Wu; Bohan Wang; Yingce Xia; Shufang Xie 003; Qi Meng; Lijun Wu 003; Tao Qin 001; Wengang Zhou 001; Houqiang Li; Tie-Yan Liu (ICLR, 2023)

Retrosynthetic Planning with Dual Value Networks. - Guoqing Liu; Di Xue; Shufang Xie 003; Yingce Xia; Austin Tripp; Krzysztof Maziarz; Marwin H. S. Segler; Tao Qin 001; Zongzhang Zhang; Tie-Yan Liu (ICML, 2023)

Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design. - Kaiyuan Gao; Lijun Wu 003; Jinhua Zhu 001; Tianbo Peng; Yingce Xia; Liang He 010; Shufang Xie 003; Tao Qin 001; Haiguang Liu; Kun He 001; Tie-Yan Liu (KDD, 2023)

Dual-view Molecular Pre-training. - Jinhua Zhu 001; Yingce Xia; Lijun Wu 003; Shufang Xie 003; Wengang Zhou 001; Tao Qin 001; Houqiang Li; Tie-Yan Liu (KDD, 2023)

FABind: Fast and Accurate Protein-Ligand Binding. - Qizhi Pei; Kaiyuan Gao; Lijun Wu 003; Jinhua Zhu 001; Yingce Xia; Shufang Xie 003; Tao Qin 001; Kun He 001; Tie-Yan Liu; Rui Yan 001 (NeurIPS, 2023)

ResiDual: Transformer with Dual Residual Connections. - Shufang Xie 003; Huishuai Zhang; Junliang Guo; Xu Tan 003; Jiang Bian 002; Hany Hassan Awadalla; Arul Menezes; Tao Qin 001; Rui Yan 001 (CoRR, 2023)

Re-evaluating Retrosynthesis Algorithms with Syntheseus. - Krzysztof Maziarz; Austin Tripp; Guoqing Liu; Megan Stanley; Shufang Xie 003; Piotr Gainski; Philipp Seidl; Marwin H. S. Segler (CoRR, 2023)

Are We Falling in a Middle-Intelligence Trap? An Analysis and Mitigation of the Reversal Curse. - Ang Lv; Kaiyi Zhang; Shufang Xie 003; Quan Tu; Yuhan Chen 001; Ji-Rong Wen; Rui Yan 001 (CoRR, 2023)

R2-DDI: relation-aware feature refinement for drug-drug interaction prediction. - Jiacheng Lin; Lijun Wu 003; Jinhua Zhu 001; Xiaobo Liang; Yingce Xia; Shufang Xie 003; Tao Qin 001; Tie-Yan Liu (Briefings Bioinform., 2023)

Breaking the barriers of data scarcity in drug-target affinity prediction. - Qizhi Pei; Lijun Wu 003; Jinhua Zhu 001; Yingce Xia; Shufang Xie 003; Tao Qin 001; Haiguang Liu; Tie-Yan Liu; Rui Yan 001 (Briefings Bioinform., 2023)

BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning. - Qizhi Pei; Lijun Wu 003; Kaiyuan Gao; Xiaozhuan Liang; Yin Fang; Jinhua Zhu 001; Shufang Xie 003; Tao Qin 001; Rui Yan 001 (ACL (Findings), 2024)

Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors. - Qizhi Pei; Lijun Wu 003; Zhenyu He 012; Jinhua Zhu 001; Yingce Xia; Shufang Xie 003; Rui Yan 001 (CIKM, 2024)

An Analysis and Mitigation of the Reversal Curse. - Ang Lv; Kaiyi Zhang; Shufang Xie 003; Quan Tu; Yuhan Chen 001; Ji-Rong Wen; Rui Yan 001 (EMNLP, 2024)

Learning to Generate Style-Specific Adapters for Stylized Dialogue Generation. - Jinpeng Li 003; Yuhan Chen 001; Pengfei Wu 003; Yingce Xia; Shufang Xie 003; Dongyan Zhao 001; Rui Yan 001 (NLPCC (1), 2024)

YuLan: An Open-source Large Language Model. - Yutao Zhu 001; Kun Zhou 002; Kelong Mao; Wentong Chen; Yiding Sun; Zhipeng Chen 001; Qian Cao 001; Yihan Wu; Yushuo Chen; Feng Wang; Lei Zhang; Junyi Li; et al. (CoRR, 2024)

SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation. - Liang He 010; Peiran Jin; Yaosen Min; Shufang Xie 003; Lijun Wu 003; Tao Qin 001; Xiaozhuan Liang; Kaiyuan Gao; Yuliang Jiang; Tie-Yan Liu (CoRR, 2024)

MIN: Multi-channel Interaction Network for Drug-Target Interaction with Protein Distillation. - Shuqi Li; Shufang Xie 003; Hongda Sun 001; Yuhan Chen 001; Tao Qin 001; Tianjun Ke; Rui Yan 001 (CoRR, 2024)

NatureLM: Deciphering the Language of Nature for Scientific Discovery. - Yingce Xia; Peiran Jin; Shufang Xie 003; Liang He 010; Chuan Cao; Renqian Luo; Guoqing Liu; Yue Wang 017; Zequn Liu; Yuan-Jyue Chen; Zekun Guo; Yeqi Bai; et al. (CoRR, 2025)

Trust Region Preference Approximation: A simple and stable reinforcement learning algorithm for LLM reasoning. - Xuerui Su; Shufang Xie 003; Guoqing Liu; Yingce Xia; Renqian Luo; Peiran Jin; Zhiming Ma; Yue Wang 017; Zun Wang; Yuting Liu 002 (CoRR, 2025)