Calibrating dimension reduction hyperparameters in the presence of noise
Fig 10
Trustworthiness vs. perplexity for r = 5 (scRNA-seq).
t-SNE outputs were calculated with varying perplexities. Local performance was measured via trustworthiness. The trustworthiness-maximizing perplexity was 40 when comparing against the original data, while the trustworthiness-maximizing perplexity was 120 when comparing against just the signal.