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)

BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations. - Qizhi Pei; Wei Zhang; Jinhua Zhu 001; Kehan Wu; Kaiyuan Gao; Lijun Wu 003; Yingce Xia; Rui Yan 001 (EMNLP, 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)

Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models. - Kaiyuan Gao; Sunan He; Zhenyu He 012; Jiacheng Lin; Qizhi Pei; Jie Shao; Wei Zhang (CoRR, 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)

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey. - Qizhi Pei; Lijun Wu 003; Kaiyuan Gao; Jinhua Zhu 001; Yue Wang 017; Zun Wang; Tao Qin 001; Rui Yan 001 (CoRR, 2024)

FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation. - Kaiyuan Gao; Qizhi Pei; Jinhua Zhu 001; Tao Qin 001; Kun He 001; Lijun Wu 003 (CoRR, 2024)

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization. - Qizhi Pei; Lijun Wu 003; Kaiyuan Gao; Jinhua Zhu 001; Rui Yan 001 (CoRR, 2024)

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates. - Kaiyuan Gao; Yusong Wang; Haoxiang Guan; Zun Wang; Qizhi Pei; John E. Hopcroft; Kun He 001; Lijun Wu 003 (CoRR, 2024)

CipherBank: Exploring the Boundary of LLM Reasoning Capabilities through Cryptography Challenge. - Yu Li 006; Qizhi Pei; Mengyuan Sun; Honglin Lin; Chenlin Ming; Xin Gao 001; Jiang Wu; Conghui He; Lijun Wu 003 (ACL (Findings), 2025)

A Strategic Coordination Framework of Small LMs Matches Large LMs in Data Synthesis. - Xin Gao; Qizhi Pei; Zinan Tang; Yu Li; Honglin Lin; Jiang Wu; Lijun Wu; Conghui He (ACL (1), 2025)

LEMMA: Learning from Errors for MatheMatical Advancement in LLMs. - Zhuoshi Pan; Yu Li; Honglin Lin; Qizhi Pei; Zinan Tang; Wei Wu; Chenlin Ming; H. Vicky Zhao; Conghui He; Lijun Wu (ACL (Findings), 2025)

MathFusion: Enhancing Mathematical Problem-solving of LLM through Instruction Fusion. - Qizhi Pei; Lijun Wu 003; Zhuoshi Pan; Yu Li 006; Honglin Lin; Chenlin Ming; Xin Gao 001; Conghui He; Rui Yan 001 (ACL (1), 2025)

3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling. - Qizhi Pei; Rui Yan 001; Kaiyuan Gao; Jinhua Zhu 001; Lijun Wu 003 (ICLR, 2025)

FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation. - Kaiyuan Gao; Qizhi Pei; Gongbo Zhang; Jinhua Zhu 001; Kun He 001; Lijun Wu 003 (KDD (1), 2025)

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)

MetaLadder: Ascending Mathematical Solution Quality via Analogical-Problem Reasoning Transfer. - Honglin Lin; Zhuoshi Pan; Yu Li; Qizhi Pei; Xin Gao; Mengzhang Cai; Conghui He; Lijun Wu (CoRR, 2025)

MathFusion: Enhancing Mathematic Problem-solving of LLM through Instruction Fusion. - Qizhi Pei; Lijun Wu 003; Zhuoshi Pan; Yu Li 006; Honglin Lin; Chenlin Ming; Xin Gao 001; Conghui He; Rui Yan 001 (CoRR, 2025)

A Strategic Coordination Framework of Small LLMs Matches Large LLMs in Data Synthesis. - Xin Gao; Qizhi Pei; Zinan Tang; Yu Li; Honglin Lin; Jiang Wu; Lijun Wu; Conghui He (CoRR, 2025)

CipherBank: Exploring the Boundary of LLM Reasoning Capabilities through Cryptography Challenges. - Yu Li; Qizhi Pei; Mengyuan Sun; Honglin Lin; Chenlin Ming; Xin Gao; Jiang Wu; Conghui He; Lijun Wu (CoRR, 2025)

IDEAL: Data Equilibrium Adaptation for Multi-Capability Language Model Alignment. - Chenlin Ming; Chendi Qu; Mengzhang Cai; Qizhi Pei; Zhuoshi Pan; Yu Li; Xiaoming Duan; Lijun Wu; Conghui He (CoRR, 2025)

REST: Stress Testing Large Reasoning Models by Asking Multiple Problems at Once. - Zhuoshi Pan; Qizhi Pei; Yu Li; Qiyao Sun; Zinan Tang; H. Vicky Zhao; Conghui He; Lijun Wu (CoRR, 2025)