The Shape of Attraction in UMAP: Exploring the Embedding Forces in Dimensionality Reduction

Mohammad Tariqul Islam, Jason W. Fleischer

Abstract: Uniform manifold approximation and projection (UMAP) is among the most popular neighbor embedding methods. The method samples pairs of point indices according to similarities in the high-dimensional space, and applies attractive and repulsive forces to their coordinates in the low-dimensional embedding. In this paper, we analyze the forces to reveal their effects on cluster formations and visualization, and compare UMAP to its contemporaries. Repulsion emphasizes differences, controlling cluster boundaries and inter-cluster distance. Attraction is more subtle, as attractive tension between points can manifest simultaneously as attraction and repulsion in the lower-dimensional mapping. This explains the need for learning rate annealing and motivates the different treatments between attractive and repulsive terms. Moreover, by modifying attraction, we improve the consistency of cluster formation under random initialization. Overall, our analysis provides a mechanistic understanding of UMAP and related embedding methods.

Submission Type: Long submission (more than 12 pages of main content)

Code: https://github.com/tariqul-islam/explaining_neighbor_embedding

Assigned Action Editor: ~Dmitry_Kobak2

Submission Number: 7309