Extended Data Fig. 10: Effect of the number of neighbors used in the UMAP representation during the exploration phase.
From: MiLoPYP: self-supervised molecular pattern mining and particle localization in situ
Panels show changes in the UMAP representation as a function of the number of neighbors (10, 40 and 80). Results are shown for EMPIAR-10304, EMPIAR-10453 and EMPIAR-10987. The use of fewer neighbors reveals finer local structure while the use of more neighbors captures the overall structure with some loss of fine local structure. However, the full vector representation for each sub-volume remains unchanged, as UMAP only serves as a post-processing dimensionality reduction technique for the purpose of visualization.
