Modeling Single Cell Trajectory Using Forward-Backward Stochastic Differential Equations
February 3, 2024 ยท View on GitHub
Research Project by Kevin Zhang Preprint paper avaiable on bioarxiv
Dependency
- numpy
- pandas
- sklearn
- matplotlib
- seaborn
- pytorch
- pot
Instructions
The repository is able to train 4 different models.
- TrajectoryNet by (Tong, 2020)
- Waddingtong-OT by (Schiebinger, 2019)
- Stationary-OT by (Zhang, 2021)
- FBSDE (preprint)
To train the model, run the workflow_single.py file. To perform parameter tuning using validation, run the workflow_valid.py file. To summarize the performance from simulations, run the workflow_eval.py file.