Mingze Dong

Yale University.

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I am a PhD student in the Computational Biology and Bioinformatics (CBB) program at Yale University, where I am fortunate to be co-advised by Prof. Yuval Kluger and Prof. Rong Fan. Prior to my PhD, I earned a B.S. in Integrated Science from Peking University with a focus on applied math and biology. I also conducted research in the Lin lab and van Dijk lab. I am currently building better single-cell models at Arc.

I work at the intersection of statistics, deep learning, and computational biology.

selected publications

  1. Nature Methods
    Causal identification of single-cell experimental perturbation effects with CINEMA-OT
    Mingze Dong, Bao Wang, Jessica Wei, and 8 more authors
    Nature Methods, 2023
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  2. Preprint
    Scaling deep identifiable models enables zero-shot characterization of single-cell biological states
    Mingze Dong, Kriti Agrawal, Rong Fan, and 3 more authors
    bioRxiv, 2024
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  3. Nature Commun
    Editor’s Highlight
    SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data
    Mingze Dong, David Su, Harriet Kluger, and 2 more authors
    Nature Communications (Featured Article, <5%), 2025
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  4. Preprint
    Predicting cellular responses to perturbation across diverse contexts with STATE
    Abhinav Adduri, Dhruv Gautam, Beatrice Bevilacqua, and 8 more authors
    bioRxiv, 2025
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  5. Preprint
    Pertpy: an end-to-end framework for perturbation analysis
    Lukas Heumos, Yuge Ji, Lilly May, and 25 more authors
    bioRxiv, 2024
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  6. NeurIPS
    Understanding and enhancing mask-based pretraining towards universal representations
    Mingze Dong, Leda Wang, and Yuval Kluger
    The Thirty-Ninth Annual Conference on Neural Information Processing Systems, 2025
  7. ICML
    Towards Understanding and Reducing Graph Structural Noise for GNNs
    Mingze Dong, and Yuval Kluger
    Proceedings of the 40th International Conference on Machine Learning, 2023
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