Visualizing Uncertainty in Non-linear Projections with Ensembles

Abstract

Widely used non-linear dimensionality reduction (NLDR) methods such as UMAP and t-SNE are stochastic--repeated runs on the same data can produce different low-dimensional projections. In this paper, we explore two problems related to projection variability: on some datasets clusters, structure, and outliers may change run-to-run, and on others projections can be extremely stable when overfitting noise. To address the first problem, we propose visualizing the median of multiple NLDR outputs rather than relying on individual projections. To address the second, we perturb input data before creating consensus embeddings. We find that taking the median of multiple projections performs comparably to individual runs on multiple quality metrics, while increasing perturbation emphasizes global over local structure. We show through a set of exploratory visualizations that even relatively simple ensemble presentations can be used to better communicate the reliability of projection patterns.