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Projection ambiguities of t-SNE. A two-dimensional dataset (a) was first transformed into eight dimensions (see §2) and then projected back into two dimensions using t-SNE ((b–d) three different runs of t-SNE). Point colours are the same in all subfigures. For these parameter settings (perplexity = 30) originally connected clusters may be separated into disconnected subsets. Similar effects are also seen in the presence of noise (see the electronic supplementary material).
