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Yuyan Ni

AMSS, Chinese Academy of Sciences.
AIR, Tsinghua University.

Research Interest: Deep Generative Modeling, AI4Science, Representation Learning

Academic Experience

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Academic

Education

  • 2017/09 – 2021/07. Bachelor, Mathematics and Applied Mathematics, University of Chinese Academy of Sciences (UCAS).
  • 2020/02 – 2020/06. Visiting Student, Mathematics, École Polytechnique Fédérale de Lausanne (EPFL).
  • 2021/03 – 2026/06. Research Intern, ATOM Lab, Institute for AI Industry Research (AIR), Tsinghua University. Academic Supervisor: Prof. Yanyan Lan.
  • 2021/09 – 2026/06. Ph.D., Probability and Statistics, Academy of Mathematics and Systems Science (AMSS), Chinese Academy of Sciences (CAS). Academic Supervisor: Academician Zhi-Ming Ma.
  • 2025/05 – Present. Research Intern, Seed-AI for Science, ByteDance.

Publications

Google Scholar / Semantic Scholar / OpenReview / ResearchGate


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Towards A Universally Transferable Acceleration Method for Density Functional Theory


Zhe Liu, Yuyan Ni, Zhichen Pu, Qiming Sun, Siyuan Liu, Wen Yan
ICLR 2026
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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
Neurips 2025
Paper / Code / Talk / Poster
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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
Neurips 2025
Paper
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Revisiting Sampling Strategies for Molecular Generation


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

  • Reviewer: NeurIPS, ICLR, ICML
  • Talks & Presentations:
    • "AI for Science: Interdisciplinary Research Pathways in Drug Discovery"
      with Prof. Yanyan Lan, Gaoling School of Artificial Intelligence, Renmin University of China
    • "Straight-Line Diffusion Models"
      2025 Beijing International Youth Innovation and Development Forum
    • "Insights from PhD Journey"
      2025 BAAI Conference Talent Exchange Forum (Slides)
    • "Fractional Denoising Pre-Training"
      2024 International Conference on Data Science and Brain-Inspired Intelligence (Slides)
    • Oral Presentation: "Elastic Information Bottleneck"
      2022 Annual Meeting of the Chinese Society for Industrial and Applied Mathematics (CSIAM)

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