Publications

Preprints

• Wenzhuo Tang, Haitao Mao, Danial Dervovic, Ivan Brugere, Saumitra Mishra, Yuying Xie, Jiliang Tang
  Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models [pdf]

• Wenzhuo Tang^*, Renming Liu^*, Hongzhi Wen, Xinnan Dai, Jiayuan Ding, Hang Li, Wenqi Fan, Yuying Xie, Jiliang Tang
  A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models [pdf]

• Hongzhi Wen, Wenzhuo Tang, Wei Jin, Jiayuan Ding, Renming Liu, Feng Shi, Yuying Xie, Jiliang Tang
  Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation [pdf]

• Jiayuan Ding^*, Hongzhi Wen^*, Wenzhuo Tang^*, Renming Liu, Zhaoheng Li, Julian Venegas, Runze Su, Dylan Molho, Wei Jin, Wangyang Zuo, Yixin Wang, Robert Yang, Yuying Xie, Jiliang Tang
  DANCE: A Deep Learning Library and Benchmark for Single-Cell Analysis [pdf]

Conference/Journal Papers

• Haitao Mao^*, Zhikai Chen^*, Wenzhuo Tang, Jianan Zhao, Yao Ma, Tong Zhao, Neil Shah, Mikhail Galkin, Jiliang Tang
  Position: Graph Foundation Models Are Already Here [pdf]
  Forty-first International Conference on Machine Learning (ICML), Spotlight, 2024

• Jiayuan Ding, Julian Venegas, Qiaolin Lu, Yixin Wang, Lidan Wu, Wei Jin, Hongzhi Wen, Renming Liu, Wenzhuo Tang, Zhaoheng Li, Wangyang Zuo, Yi Chang, Yu Leo Lei, View ORCID ProfilePatrick Danaher, Yuying Xie, Jiliang Tang
  SpatialCTD: a large-scale TME spatial transcriptomic dataset to evaluate cell type deconvolution for immuno-oncology [pdf]
  Journal of Computational Biology, 2024

• Hongzhi Wen^*, Wenzhuo Tang^*, Xinnan Dai, Jiayuan Ding, Wei Jin, Yuying Xie, Jiliang Tang
  CellPLM: Pre-training of Cell Language Model Beyond Single Cells [pdf]
  The Twelfth International Conference on Learning Representations (ICLR). 2024.

• Dylan Molho^*, Jiayuan Ding^*, Wenzhuo Tang^*, Zhaoheng Li, Hongzhi Wen, Yixin Wang, Julian Venegas, Wei Jin, Renming Liu, Runze Su, Patrick Danaher, Robert Yang, Yu Leo Lei, Yuying Xie, Jiliang Tang
  Deep Learning in Single-Cell Analysis [pdf]
  ACM Transactions on Intelligent Systems and Technology (2024).

• Wenzhuo Tang^*, Hongzhi Wen^*, Renming Liu^*, Jiayuan Ding, Wei Jin, Yuying Xie, Hui Liu, Jiliang Tang
  Single-Cell Multimodal Prediction via Transformers [pdf] [code]
  In Proceedings of the 32nd ACM International Conference on Information and Knowledge Management (CIKM), 2023