cuSLINK: Single-Linkage Agglomerative Clustering on the GPU

In this paper, we propose cuSLINK, a novel and state-of-the-art reformulation of the SLINK algorithm on the GPU which requires only O(Nk) space and uses a parameter k to trade off space and time. We also propose a set of novel and reusable building blocks that compose cuSLINK. These building blocks include highly optimized computational patterns for k-NN graph construction, spanning trees, and dendrogram cluster extraction. We show how we used our primitives to implement cuSLINK end-to-end on the GPU, further enabling a wide range of real-world data mining and machine learning applications that were once intractable. In addition to being a primary computational bottleneck in the popular HDBSCAN algorithm, the impact of our end-to-end cuSLINK algorithm spans a large range of important applications, including cluster analysis in social and computer networks, natural language processing, and computer vision.