Calibrating dimension reduction hyperparameters in the presence of noise
Fig 14
Trustworthiness vs. n_neighbors for UMAP (scRNA-seq).
UMAP outputs were calculated with varying n_neighbors values. Local performance was measured via trustworthiness. The trustworthiness-maximizing n_neighbors was 190 when comparing against the original data, while the trustworthiness-maximizing n_neighbors was 300 when comparing against just the signal.