This is a python pipeline for training an autoencoder for the paper:

Shao-Chun Lee, Y Z, "Interpretation of autoencoder-learned collective variables using Morse–Smale complex and sublevelset persistent homology: An application on molecular trajectories", J. Chem. Phys. 160, 144104 (2024) DOI: https://doi.org/10.1063/5.0191446

Please cite this paper if you use this pipeline.