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


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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
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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
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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
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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
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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
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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 /
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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
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Unified Molecular Modeling via Modality Blending


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


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

Preprints


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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
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Unimap: Universal Smiles-graph Representation Learning


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

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