JointAlignmentDeepEmbedding

This repository contains data and saved models associated with our paper:

"JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics"

You can access the data and cached results via the following link:

• Google Drive Folder

Please refer to Jade_dlpfc.py and FastJade_dlpfc.py for running JADE and Fast-JADE respectively.

To reproduce the results presented in our paper from scratch, follow these steps:

• Install Dependencies

  • Run the following command to install all necessary packages:

  pip install -r requirements.txt

• Reproducing Results

  • Open and run the Jupyter notebook Axolotl_Brain.ipynb and Human_DLPFC.ipynb for step-by-step instructions.

For further details, please refer to the accompanying documentation or contact the authors for support.

Enjoy playing around with JADE!

How to cite JADE

Guo, Yuanchuan; Jun S. Liu#; Huimin Cheng#; Ying Ma# (2025). “JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.” NeurIPS 2025