  Dimensionality reduction and manifold learning methods such as t-Distributed
Stochastic Neighbor Embedding (t-SNE) are routinely used to map
high-dimensional data into a 2-dimensional space to visualize and explore the
data. However, two dimensions are typically insufficient to capture all
structure in the data, the salient structure is often already known, and it is
not obvious how to extract the remaining information in a similarly effective
manner. To fill this gap, we introduce \emph{conditional t-SNE} (ct-SNE), a
generalization of t-SNE that discounts prior information from the embedding in
the form of labels. To achieve this, we propose a conditioned version of the
t-SNE objective, obtaining a single, integrated, and elegant method. ct-SNE has
one extra parameter over t-SNE; we investigate its effects and show how to
efficiently optimize the objective. Factoring out prior knowledge allows
complementary structure to be captured in the embedding, providing new
insights. Qualitative and quantitative empirical results on synthetic and
(large) real data show ct-SNE is effective and achieves its goal.
