Publications

Journal Papers

• J. Ding^*, R. Liu^*, H. Wen^*, W. Tang^*, et al.
  DANCE: A Deep Learning Library and Benchmark Platform for Single-cell Analysis. [link]
  Genome Biology, 2024.

• D. Molho^*, J. Ding^*, W. Tang^*, et al.
  Deep Learning in Single-Cell Analysis. [pdf]
  ACM Transactions on Intelligent Systems and Technology (ACM TIST), 2024.

• S. Wang, J. Huang, Z. Chen, Y. Song, W. Tang, et al.
  Graph Machine Learning in the Era of Large Language Models (LLMs). [link]
  ACM Transactions on Intelligent Systems and Technology (ACM TIST), 2025.

• J. Ding, J. Venegas, Q. Lu, Y. Wang, W. Jin, H. Wen, R. Liu, W. Tang, et al.
  SpatialCTD: A Large-Scale Tumor Microenvironment Spatial Transcriptomic Dataset to Evaluate Cell Type Deconvolution for Immuno-Oncology. [pdf]
  Journal of Computational Biology, 2024.

Conference Papers

• W. Tang, et al.
  Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models. [pdf]
  NeurIPS, 2025.

• H. Wen^*, W. Tang^*, et al.
  CellPLM: Pre-training of Cell Language Model Beyond Single Cells. [pdf]
  ICLR, 2024.

• H. Mao^*, Z. Chen^*, W. Tang, et al.
  Position: Graph Foundation Models Are Already Here. [pdf]
  ICML (Spotlight), 2024.

• W. Tang^*, H. Wen^*, R. Liu^*, et al.
  Single-Cell Multimodal Prediction via Transformers. [pdf]
  CIKM, 2023.

• H. Li, W. Jin, G. Skenderi, H. Shomer, W. Tang, et al.
  Sub-graph Based Diffusion Model for Link Prediction.
  Learning on Graphs Conference (LoG), 2024.

Preprints

• W. Tang^*, R. Liu^*, et al.
  A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models. [pdf]
  bioRxiv, 2023.

• H. Wen, W. Tang, et al.
  Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Denoising. [pdf]
  arXiv, 2023.

• J. Ding, Z. Xing, Y. Wang, R. Liu, S. Liu, Z. Huang, W. Tang, et al.
  DANCE 2.0: Transforming Single-Cell Analysis from Black Box to Transparent Workflow.
  bioRxiv, 2025.

• Y. Wang^*, J. Ding^*, L. Wu, A. Wardhani, P. Danaher, Q. Lu, H. Wen, W. Tang, et al.
  MEM-GAN: A Pseudo Membrane Generator for Single-cell Imaging in Fluorescent Microscopy.
  bioRxiv, 2023.