Modeling Single Cell Trajectory Using Forward-Backward Stochastic Differential Equations

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.