is not advisable as changes in hyperparameters can change the physical meaning of the MSM eigenvectors. The commonly used VAMP2 metric when used with the assumption of reversibility can give rise to rankings of MSMs which are inconsistent with the implied timescales. We suggest that this is due to a numerical, rather than theoretical problem. In its place, we suggest using the sum of the square eigenvalues, or other model observables, e.g., t 2 , with bootstrapping in order to estimate uncertainty.