Parametric nonlinear dimensionality reduction using kernel t-SNE

Abstract Novel non-parametric dimensionality reduction techniques such as t-distributed stochastic neighbor embedding (t-SNE) lead to a powerful and flexible visualization of high-dimensional data. One drawback of non-parametric techniques is their lack of an explicit out-of-sample extension. In this contribution, we propose an efficient extension of t-SNE to a parametric framework, kernel t-SNE, which preserves the flexibility of basic t-SNE, but enables explicit out-of-sample extensions. We test the ability of kernel t-SNE in comparison to standard t-SNE for benchmark data sets, in particular addressing the generalization ability of the mapping for novel data. In the context of large data sets, this procedure enables us to train a mapping for a fixed size subset only, mapping all data afterwards in linear time. We demonstrate that this technique yields satisfactory results also for large data sets provided missing information due to the small size of the subset is accounted for by auxiliary information such as class labels, which can be integrated into kernel t-SNE based on the Fisher information.