This library runs code associated with the TrajectoryNet paper
Download code
git clone http://github.com/krishanswamylab/TrajectoryNet.git
Install required packages
pip install -r requirements.txt
This code was tested with python 3.8
Run with
python main.py --dataset EB
To use a custom dataset expose the coordinates and timepoint information according to the SCData
class in dataset.py
[1] Tong, A., Huang, J., Wolf, G., van Dijk, D., and Krishnaswamy, S. TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. In International Conference on Machine Learning, 2020. [arxiv]
If you found this library useful, please consider citing
@inproceedings{tong2020trajectorynet,
title = {TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics},
shorttitle = {{{TrajectoryNet}}},
booktitle = {Proceedings of the 37th International Conference on Machine Learning},
author = {Tong, Alexander and Huang, Jessie and Wolf, Guy and {van Dijk}, David and Krishnaswamy, Smita},
year = {2020}
}