Interpretation of autoencoder-learned collective variables using Morse–Smale complex and sublevelset persistent homology: An application on molecular trajectories

Abstract

Dimensionality reduction often serves as the first step toward a minimalist understanding of physical systems as well as the accelerated simulations of them. In particular, neural network-based nonlinear dimensionality reduction methods, such as autoencoders, have shown promising outcomes in uncovering collective variables (CVs). However, the physical meaning of these CVs remains largely elusive. In this work, we constructed a framework that (1) determines the optimal number of CVs needed to capture the essential molecular motions using an ensemble of hierarchical autoencoders and (2) provides topology-based interpretations to the autoencoder-learned CVs with Morse–Smale complex and sublevelset persistent homology. This approach was exemplified using a series of n-alkanes and can be regarded as a general, explainable nonlinear dimensionality reduction method.