Before revision:  Here, we applied the ivis framework as a novel machine learning based dimensionality reduction method originally developed for single-cell datasets for analysis of macromolecular simulations . Compared with other methods, ivis is  superior in constructing Markov state model (MSM), preserving global distance and maintaining similarity between high dimension and low dimension with the least information loss.
After revision:  Here, we applied the ivis framework as a novel machine learning based dimensionality reduction method originally developed for single-cell datasets for analysis of macromolecular simulations . Compared with other methods, ivis is superior in constructing Markov state model (MSM), preserving information of both local and global distances and maintaining similarity between high dimension and low dimension with the least information loss.