Academic Experience

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Academic

Education

2017/09 to 2021/07. Bachelor Student, majored in Mathematics and Applied Mathematics, at University of Chinese Academy of Sciences (UCAS).
2020/02 to 2020/06. Visiting Student, majored in Mathematics, at Ecole Polytechnique Federale de Lausanne (EPFL).
2021/03 till now. Research Intern, at ATOM Lab, Institute of AI Industry Research (AIR), Tsinghua University. Academic Supervisor: Prof. Yanyan Lan.
2025/05 till now. Research Intern, at Seed-AI for Science, ByteDance.
2021/09 till now. PhD Candidate, majored in Probability and Statistics, at Academy of Mathematics and Systems Science (AMSS), Chinese Academy of Sciences (CAS). Academic Supervisor: Academician Zhi-Ming Ma.

Publications

Google Scholar / Semantic Scholar / OpenReview / ResearchGate

Straight-Line Diffusion Model for Efficient 3D Molecular Generation

Yuyan Ni*, Shikun Feng*, Haohan Chi, Bowen Zheng, Huan-ang Gao, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan, *Equal Contribution
GenBio workshop, ICML 2025
Paper / Code / Talk / Poster

Revisiting Sampling Strategies for Molecular Generation

Yuyan Ni, Shikun Feng, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan
GenBio workshop, ICML 2025
Arxiv

FIGRDock: Fast Interaction-Guided Regression for Flexible Docking

Shikun Feng, Bicheng Lin, Yuanhuan Mo, Yuyan Ni, Wenyu Zhu, Bowen Gao, Wei-Ying Ma, Haitao Li, Yanyan Lan
GenBio workshop, ICML 2025

UniGEM: A Unified Approach to Generation and Property Prediction for Molecules

Shikun Feng*, Yuyan Ni*, Yan Lu, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan, *Equal Contribution
ICLR 2025
Arxiv / Paper / Code / Poster / Media-1 / Media-2

Pre-training with fractional denoising to enhance molecular property prediction

Yuyan Ni*, Shikun Feng*, Xin Hong, Yuancheng Sun, Wei-Ying Ma, Zhi-Ming Ma, Qiwei Ye, Yanyan Lan, *Equal Contribution
Nat. Mach. Intell. (2024)
Paper / Arxiv / Code / Slides / Media-1 / Media-2 / Media-3

Beyond Efficiency: Molecular Data Pruning for Enhanced Generalization

Dingshuo Chen, Zhixun Li, Yuyan Ni, Guibin Zhang, Ding Wang, Qiang Liu, Shu Wu, Jeffrey Xu Yu, Liang Wang
NeurIPS 2024
Paper

UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning

Shikun Feng*, Yuyan Ni*, Minghao Li, Yanwen Huang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan, *Equal Contribution
ICML 2024
Paper / Poster / Media-1 / Media-2

Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion

Bowen Gao, Minsi Ren, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma, Wei-Ying Ma, Yanyan Lan
ICML 2024
Paper

Sliced Denoising: A Physics-Informed Molecular Pre-Training Method

Yuyan Ni*, Shikun Feng*, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan, *Equal Contribution
ICLR 2024
OpenReview / Code / Poster / Slides / Media

Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment

Bowen Gao, Yinjun Jia, Yuanle Mo, Yuyan Ni, Weiying Ma, Zhiming Ma, Yanyan Lan
ICLR 2024
Paper / Code

Unified Molecular Modeling via Modality Blending

Qiying Yu, Yudi Zhang, Yuyan Ni, Shikun Feng, Yanyan Lan, Hao Zhou, Jingjing Liu
ICLR 2024
Paper / Code

Fractional denoising for 3d molecular pre-training

Shikun Feng*, Yuyan Ni*, Yanyan Lan, Zhi-Ming Ma, Wei-Ying Ma, *Equal Contribution
ICML 2023
Paper / Code / Poster / Talk_5min / Talk_15min

Elastic Information Bottleneck

Yuyan Ni, Yanyan Lan, Ao Liu, Zhiming Ma
Mathematics 10 (18), 3352, 2022
Paper / Code

Preprints

Straight-Line Diffusion Model for Efficient 3D Molecular Generation

Yuyan Ni*, Shikun Feng*, Haohan Chi, Bowen Zheng, Huan-ang Gao, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan, *Equal Contribution
2025
Paper / Code

FIGRDock: Fast Interaction-Guided Regression for Flexible Docking

Shikun Feng, Bicheng Lin, Yuanhuan Mo, Yuyan Ni, Wenyu Zhu, Bowen Gao, Wei-Ying Ma, Haitao Li, Yanyan Lan
2025
Paper / Code

Unimap: Universal Smiles-graph Representation Learning

Shikun Feng, Lixin Yang, Yanwen Huang, Yuyan Ni, Weiying Ma, Yanyan Lan
2023
Paper / Code

Contextual Molecule Representation Learning from Chemical Reaction Knowledge

Han Tang, Shikun Feng, Bicheng Lin, Yuyan Ni, JIngjing Liu, Wei-Ying Ma, Yanyan Lan
2023
Paper / Code

Service

Reviewer: NeurIPS 2024, ICLR 2025, NeurIPS 2025.
Talks:

Oral presentation at the 2025 BAAI Conference Talent Exchange Forum. (Slides)
Oral presentation at the 2024 International Conference on Data Science and Brain-Inspired Intelligence. (Slides)
Oral presentation at the annual meeting of the Chinese Society for Industrial and Applied Mathematics (CSIAM) in 2022 for the paper "Elastic Information Bottleneck".