Diffusion-Strings

Repo of the code for the paper Probing the Geometry of Diffusion Models with the String Method

BioEmu notebook

notebooks/bioemu_chignolin_dynamic_se3.ipynb shows how to wrap a pretrained BioEmu model as coupled SE(3) drift and score fields, initialize a string from BioEmu samples, run the finite-temperature dynamic string method, and export PDB/XTC trajectories.

From the repository root, launch it in the environment that contains both BioEmu and this package:

conda activate diffusion-strings
jupyter lab notebooks/bioemu_chignolin_dynamic_se3.ipynb

The first run may download BioEmu model and embedding assets. A CUDA GPU is strongly recommended.