clusiVAT: A mixed visual/numerical clustering algorithm for big data

Recent algorithmic and computational improvements have reduced the time it takes to build a minimal spanning tree (MST) for big data sets. In this paper we compare single linkage clustering based on MSTs built with the Filter-Kruskal method to the proposed clusiVAT algorithm, which is based on sampling the data, imaging the sample to estimate the number of clusters, followed by non-iterative extension of the labels to the rest of the big data with the nearest prototype rule. Numerical experiments with both synthetic and real data confirm the theory that clusiVAT produces true single linkage clusters in compact, separated data. We also show that single linkage fails, while clusiVAT finds high quality partitions that match ground truth labels very well. And clusiVAT is fast: it recovers the preferred c = 3 Gaussian clusters in a mixture of 1 million two-dimensional data points with 100% accuracy in 3.1 seconds.