/Amiya

The coupled GNN model for reconstructing spatial metabolomics from spatial transcriptomics. Project named as CHIMERA, nick name Amiya. Based on pyg.

Primary LanguagePythonMIT LicenseMIT

Amiya

The coupled GNN model for reconstructing spatial metabolomics from spatial transcriptomics. Project named as CHIMERA, nick name Amiya. Based on pyg.

Notes for Xiantong

  • This project is based on Saturn.
  • Since we haven't packaged the CHIMERA, the file paths in these scripts should be changed according to your own working env.
  • If you have any problem building your working env, you can use my conda env under the following path /fs/home/liuzhaoyang/biosoft/mambaforge/envs/MS. But don't directly install any new packages in my env.
  • If you want to test the model, start from a small data size.
  • codes are under \Amiya, where *_pre for pre-training; *_fine for fine-tuning; _ablation for ablation experiments. _L denotes the training used Lightning framework.