They did something that I always wanted to do which is to put a neural network between the data and the variables from which you construct a (diffusion kernel) transfer operator. You can then optimize the encoding to produce the largest possible timescale separation.
Spectral maps for slow collective variables
Most recent reference
May 25, 2026
Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles