Extended Data Fig. 1: Condensing on manifold, reproducibility and run time comparisons.

a, Visualization of toy swiss roll after performing condensation in euclidean space or on diffusion potential. Top: schematic of the movement vectors of each point when run in euclidean space or on diffusion potential for one iteration. Bottom: Visualization of toy swiss roll dataset after several iterations of diffusion condensation, running in both euclidean space and diffusion potential. b, Comparison of diffusion condensation on diffusion potential to diffusion condensation on ambient measurement dimensions on an increasingly noisy stochastic block model to simulate nonlinear noise in a high-dimensional space. In this model, increasing amounts of Gaussian noise were added to the edge weights of the adjacency matrix. c, Pipeline for identifying cellular populations enriched based on clinical variables with Multiscale PHATE and MELD. d, Comparing run time across visualization techniques on increasingly high-dimensional flow cytometry data. e, Visualization of reproduciblity of Multiscale PHATE across two different runs of PBMCs measured by scRNA-seq. Each run was initialized with a different random seed.