FIG. 3.

Comparison of the estimated and true off-diagonal rate matrix elements for a trajectory of length N = 10⁷ simulated from the process in Fig. 1 with a time step of 1. The true non-zero elements of K are well-estimated, as shown in the right portion of the plot; here, error bars are small enough to be fully obscured by point markers. On the other hand, the estimator spuriously estimates non-zero rates between many of the states which are not connected in the underlying process. However, the 95% confidence intervals for these spurious rates each overlap with zero.