Ke Ni

Ke Ni

he/him

Applied Scientist at Amazon. The Joint CMU–Pitt Ph.D. Program in Computational Biology (CPCB). I work on multimodal models, LLMs, computer vision, and AI for science.

Publications

First / Co-first / Corresponding Author

  1. Ke Ni, et al. (in review, Nature Communications). LivecellX: A Scalable Deep Learning Framework for Single-Cell Object-Oriented Analysis. BioRxiv.
  2. Ke Ni, et al. (in preparation). LivecellAction: Guiding Spatiotemporal Deep Learning Models for Precise Detection of Rare Single-Cell Actions.
  3. Zehua Zeng, Sichao Yu, Ke Ni (co-first authors), Yan Zhang, Ukyeon Shin, Cinlong Huang, Natalie Cao, Jonathan Weissman, Jianhua Xing, Xiaojie Qiu. (in review, Nature Protocols). Predictive Modeling of Single Cell Transcriptomic Dynamics with Dynamo.
  4. Ke Ni, William Yang Wang. (2017). Learning to Explain Non-standard English. ACL-IJCNLP 2017 (Oral, Taipei).

Co-authored Papers

  1. Xiaoqi Wu, Xueying Zhan, Wen Li, Junhao Wu, Xin Huang, Ke Ni, Min Xu. (2026). Score-Based Matching with Target Guidance for Cryo-EM Denoising. Accepted by ECCV 2026.
  2. Huidong Su, Caicai Zhang, Frank Qingyun Wang, Chun Hing She, Xinxin Chen, Xiao Dang, Yao Lei, Ke Ni, Zewei Xiong, Danqing Yin, Xingtian Yang, Hong Feng, Philip H Li, Wanling Yang. (2025). OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.
  3. Danqing Yin, Zhongmin Zhang, Xinci Liu, Ke Ni, Huidong Su, Nicolas Lin Li, Hongyu Dong, Qiuchen Zhao, Xinyi Lin, Luyi Tian, Ye Meng, Joshua W. K. Ho. (2025). AtlasAgent: Vision Language Model and Agent-guided Framework for Evaluation of Atlas-scale Single-cell Integration. BioRxiv.
  4. Yuhao Chen, Yan Zhang, Jiaqi Gan, Ke Ni, Ming Chen, Ivet Bahar, Jianhua Xing. (2025). GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells. Nature Communications.
  5. Sophia Hu, Yong Lu, Gaohan Yu, Zhiqian Zheng, Weikang Wang, Ke Ni, Amitava Giri, Jingyu Zhang, Yan Zhang, Kazuhide Watanabe, Guang Yao, Jianhua Xing. (2025). Epithelial-Mesenchymal Transition Couples with Cell Cycle Arrest at Various Stages. BioRxiv.
  6. Yanshuo Chen, Xidong Wu, Ke Ni, Haoran Hu, Molin Yue, Wei Chen, Heng Huang. (in submission). Robust and Accurate Doublet Detection of Single-Cell Sequencing Data via Maximizing Area Under Precision-Recall Curve. BioRxiv.
  7. Weikang Wang, Ke Ni, et al. (2024). Transiently Increased Coordination in Gene Regulation During Cell Phenotypic Transitions. PRX Life.
  8. Yan Zhang, Xiaojie Qiu, Ke Ni, Jonathan Weissman, Ivet Bahar, Jianhua Xing. (2023). Graph-Dynamo: Learning stochastic cellular state transition dynamics from single-cell data. BioRxiv.
  9. Yanshuo Chen, Zhengmian Hu, Ke Ni, Site Feng, Wei Chen, Heng Huang. Inferring Single-Cell RNA Kinetics from Various Biological Priors. BioRxiv.
  10. Jason Xiaotian Dou, Minxue Jia, Nika Zaslavsky, Mark Ebeid, Runxue Bao, Shiyi Zhang, Ke Ni, Paul Pu Liang, Haiyi Mao, Zhi-Hong Mao, et al. (2022). Cell Representation Learning. NeurIPS LMRL Workshop.