Nonlinear embedding algorithms such as stochastic neighbor embedding do dimensionality reduction by optimizing an objective function involving similarities between pairs of input patterns. The result is a low-dimensional projection of each input pattern. A common way to define an out-of-sample mapping is to optimize the objective directly over a parametric mapping of the inputs, such as a neural net. This can be done using the chain rule and a nonlinear optimizer, but is very slow, because the objective involves a quadratic number of terms each dependent on the entire mapping's parameters. Using the method of auxiliary coordinates, we derive a training algorithm that works by alternating steps that train an auxiliary embedding with steps that train the mapping. This has two advantages: 1) The algorithm is universal in that a specific learning algorithm for any choice of embedding and mapping can be constructed by simply reusing existing algorithms for the embedding and for the mapping. A user can then try possible mappings and embeddings with less effort. 2) The algorithm is fast, and it can reuse N-body methods developed for nonlinear embeddings, yielding linear-time iterations.
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