Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge. - Yaosen Min; Shang Liu; Chenyao Lou; Xuefeng Cui (BIBM, 2018)

Homologous Protein Detection. - Xuefeng Cui; Yaosen Min (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

MolCloze: A Unified Cloze-style Self-supervised Molecular Structure Learning Model for Chemical Property Prediction. - Yingheng Wang; Xin Chen; Yaosen Min; Ji Wu 002 (BIBM, 2021)

Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations. - Yingheng Wang; Yaosen Min; Erzhuo Shao; Ji Wu 002 (BIBM, 2021)

Multi-view Graph Contrastive Representation Learning for Drug-Drug Interaction Prediction. - Yingheng Wang; Yaosen Min; Xin Chen; Ji Wu 002 (WWW, 2021)

Predicting the protein-ligand affinity from molecular dynamics trajectories. - Yaosen Min; Ye Wei; Peizhuo Wang; Nian Wu; Stefan Bauer; Shuxin Zheng; Yu Shi; Yingheng Wang; Dan Zhao 004; Ji Wu 002; Jianyang Zeng 001 (CoRR, 2022)

Molecule Generation For Target Protein Binding with Structural Motifs. - Zaixi Zhang; Yaosen Min; Shuxin Zheng; Qi Liu 003 (ICLR, 2023)

Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (CoRR, 2023)

Control Risk for Potential Misuse of Artificial Intelligence in Science. - Jiyan He; Weitao Feng 001; Yaosen Min; Jingwei Yi; Kunsheng Tang; Shuai Li; Jie Zhang 073; Kejiang Chen; Wenbo Zhou; Xing Xie 001; Weiming Zhang 001; Nenghai Yu; et al. (CoRR, 2023)

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)

Predicting equilibrium distributions for molecular systems with deep learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (Nat. Mac. Intell., 2024)

Author Correction: Predicting equilibrium distributions for molecular systems with deep learning. - Shuxin Zheng; Jiyan He; Chang Liu 030; Yu Shi; Ziheng Lu; Weitao Feng 001; Fusong Ju; Jiaxi Wang; Jianwei Zhu; Yaosen Min; He Zhang; Shidi Tang; et al. (Nat. Mac. Intell., 2024)

FragFormer: A Fragment-based Representation Learning Framework for Molecular Property Prediction. - Jiaxi Wang; Yaosen Min; Miao Li 003; Ji Wu 002 (Trans. Mach. Learn. Res., 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)

MIPS: a Multimodal Infinite Polymer Sequence Pre-training Framework for Polymer Property Prediction. - Jiaxi Wang; Yaosen Min; Xun Zhu; Miao Li 003; Ji Wu 002 (CoRR, 2025)