Measuring and Decomposing Mode Separation via the Canonical Diffusion

Mode separation, namely how sharply a distribution fragments into barrier-separated clusters, is a fundamental geometric property of densities, difficult to quantify in high dimensions. It is structurally distinct from dispersion, yet existing tools fall short: differential entropy rises with spread regardless of fragmentation, PCA orders directions by variance regardless of barriers, and mutual information requires a mixture decomposition one usually does not have. We measure mode separation through a single stochastic process intrinsic to the density: a unique reversible diffusion with f as its stationary distribution and constant scalar diffusion coefficient. We extract two readouts from its autocovariance matrix: SSA (Sum of Squared Autocorrelations), a scalar barrier-sensitive measure; and DA (Dominant Autocorrelation directions), linear projections ordered by metastability rather than variance. Under an isotropic-Gaussian null, we derive a closed-form spectrum for the empirical autocovariance that generalizes Marchenko--Pastur, with an analytic upper edge that selects the lag at which DA is read off. Both readouts use only samples and a score function, scaling to high dimensions through pretrained score-based generative models via Tweedie's identity. We apply our framework to three settings: (i) synthetic Gaussian mixtures, where SSA tracks mutual information; (ii) SDXL text-to-image generations, where SSA and DA capture structure that entropy and PCA miss; and (iii) molecular dynamics of alanine dipeptide, where DA recovers the known slow backbone dihedrals from static samples alone.