Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein

This is the code used to produce the experiments for STORIES.

• spacetime/: the source code for the package at the time of writing
• scripts/: contains the code to train and evaluate the model
  • evaluate.sh: commands used to train the model on a SLURM cluster using Hydra and Weights&Biases
  • train.sh: commands used to evaluate the model on a SLURM cluster using Hydra and Weights&Biases
  • configs/: configuration files for datasets, scripts, and GPUs
• notebooks/: Jupyter notebooks for preprocessing and plotting
  • preprocess_*.ipynb: Preprocessing scripts
  • vis_runs.ipynb: Scripts to generate plots in Fig 2.B
  • *_matching.ipynb: Scripts to generate plots in Fig 2.C
  • blender_render.py: Script to generate the 3D plots, to be used in Blender
  • fig3.ipynb: Script to generate the plots in Fig. 3
  • fig4.ipynb: Script to generate the plots in Fig. 4