Yuheng Chen 陈宇恒

Research

I am interested in spatial transcriptomics and spatial omics, cell segmentation and cell-type annotation, probabilistic modeling and optimal transport, and LLM agents for scientific data analysis.

Publications

• CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics
  Yuheng Chen, Yuyao Liu, Zhiwei Wang, Yeqin Zeng, Zitong Chao, Peiqi Jiang, Hao Chen, Jiguang Wang, Jiashun Xiao, Can Yang
  Nature Computational Science, 2026
  paper / code

  Combines stained tissue images, spatial transcriptomics and single-cell references to segment cells and annotate cell types jointly. Validated on Xenium, Visium HD, MERFISH and Stereo-seq.

• STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis
  Yuheng Chen, Shi Han, Zitong Chao, Yuyao Liu, Fan Zhang, Hao Chen, Jiguang Wang, Jiashun Xiao, Can Yang
  bioRxiv, 2026
  preprint / code / PyPI / demo

  A multi-agent system that plans, runs and explains spatial transcriptomics analyses from natural-language requests, alongside a shared tissue viewer. Benchmarked on 3 platforms and 11 categories of analysis tasks.

• Accurate and scalable decontamination of imaging-based spatial transcriptomics via optimal transport
  Yuheng Chen*, Yuyao Liu*, Zitong Chao, Shi Han, Yeqin Zeng, Baichen Yu, Fan Zhang, Angela Ruohao Wu, Jiguang Wang, Hao Chen, Jiashun Xiao, Can Yang
  bioRxiv, 2026

  CellDot uses optimal transport to decide whether each molecule should be kept, reassigned to another cell or removed as background, correcting errors from segmentation and transcript spillover.

• Mapping cell-type-specific spatial gene programs uncovers tissue architecture and microenvironment organization
  Yeqin Zeng, Zhiwei Wang, Yuyao Liu, Yuheng Chen, Jiguang Wang, Hao Chen, Can Yang
  Nature Communications, 2026
• NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics
  Xinyi Yu, Xiaomeng Wan, Leqi Tian, Yuheng Chen, Yuyao Liu, Tianwei Yu, Can Yang, Jiashun Xiao
  Nature Cell Biology, 2026 (in press)
• Hierarchical distribution matching enables comprehensive characterization of common and condition-specific cell niches in spatial omics data
  Yuyao Liu, Jiashun Xiao, Xiaoheng Ma, Xiaomeng Wan, Peiqi Jiang, Zhiwei Wang, Yuheng Chen, Can Yang
  bioRxiv, 2026
• OceanMind: A multi-agent AI system for ocean diagnosis
  Fan Zhang, Weicong Cheng, Yuheng Chen, Hiuseut Kung, Ying Zhang, Aixi Han, Quanjia Zhong, Can Yang, Jianping Gan
  arXiv:2610.03780, 2026
• Generative atlasing in universal gene expression space defines cell types and microenvironment spectra during disease progression
  Xiaomeng Wan, Lei Yu, Yuheng Chen, Jiashun Xiao, Mu He, Can Yang, Angela Ruohao Wu
  Research Square, 2026
• A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
  Zhiwei Wang, Yeqin Zeng, Ziyue Tan, Yuheng Chen, Xinrui Huang, Hongyu Zhao, Zhixiang Lin, Can Yang
  PNAS, 122(46), e2503952122, 2025
• UCS: A Unified Approach to Cell Segmentation for Subcellular Spatial Transcriptomics
  Yuheng Chen, Xin Xu, Xiaomeng Wan, Jiashun Xiao, Can Yang
  Small Methods, 9(5), 2400975, 2025
  paper / code

* Equal contribution

Education

2023 – present

PhD in Data Science, Department of Mathematics, HKUST
Advisor: Prof. Can Yang

2019 – 2023

BSc in Statistics, Sun Yat-sen University