arXiv:2503.09101v4 Announce Type: replace-cross
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.
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