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.
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

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 / 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 / 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 / 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

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.
Talks:

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