Tree-SNE: Hierarchical Clustering and Visualization Using t-SNE

Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a hierarchical clustering and visualization algorithm based on stacked one-dimensional t-SNE embeddings. We also introduce alpha-clustering, which recommends the optimal cluster assignment, without foreknowledge of the number of clusters, based off of the cluster stability across multiple scales. We demonstrate the effectiveness of tree-SNE and alphaclustering on images of handwritten digits, mass cytometry (CyTOF) data from blood cells, and single-cell RNAsequencing (scRNA-seq) data from retinal cells. Furthermore, to demonstrate the validity of the visualization, we use alpha-clustering to obtain unsupervised clustering results competitive with the state of the art on several image data sets. Software is available at https: //github.com/isaacrob/treesne.