t-distributed stochastic neighbor embedding

t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in a two or three-dimensional map. It is based on Stochastic Neighbor Embedding originally developed by Geoffrey Hinton and Sam Roweis, where Laurens van der Maaten proposed the t-distributed variant. It is a nonlinear dimensionality reduction technique for embedding high-dimensional data for visualization in a low-dimensional space of two or three dimensions. Specifically, it models each high-dimensional object by a two- or three-dimensional point in such a way that similar objects are modeled by nearby points and dissimilar objects are modeled by distant points with high probability.

The t-SNE algorithm comprises two main stages. First, t-SNE constructs a probability distribution over pairs of high-dimensional objects in such a way that similar objects are assigned a higher probability while dissimilar points are assigned a lower probability. Second, t-SNE defines a similar probability distribution over the points in the low-dimensional map, and it minimizes the Kullback–Leibler divergence (KL divergence) between the two distributions with respect to the locations of the points in the map. While the original algorithm uses the Euclidean distance between objects as the base of its similarity metric, this can be changed as appropriate. A Riemannian variant is UMAP.

t-SNE has been used for visualization in a wide range of applications, including genomics, computer security research, natural language processing, music analysis, cancer research, bioinformatics, geological domain interpretation, and biomedical signal processing.

While t-SNE plots often seem to display clusters, the visual clusters can be influenced strongly by the chosen parameterization and therefore a good understanding of the parameters for t-SNE is necessary. Such "clusters" can be shown to even appear in non-clustered data, and thus may be false findings. Interactive exploration may thus be necessary to choose parameters and validate results. It has been demonstrated that t-SNE is often able to recover well-separated clusters, and with special parameter choices, approximates a simple form of spectral clustering.

For a data set with n elements, t-SNE runs in O(n²) time and requires O(n²) space.