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BanditPAM++: Faster $k$-medoids Clustering

Mo Tiwari · Ryan Kang · Donghyun Lee · Sebastian Thrun · Ilan Shomorony · Martin Zhang

Great Hall & Hall B1+B2 (level 1) #918

Abstract: Clustering is a fundamental task in data science with wide-ranging applications. In $k$-medoids clustering, cluster centers must be actual datapoints and arbitrary distance metrics may be used; these features allow for greater interpretability of the cluster centers and the clustering of exotic objects in $k$-medoids clustering, respectively. $k$-medoids clustering has recently grown in popularity due to the discovery of more efficient $k$-medoids algorithms. In particular, recent research has proposed BanditPAM, a randomized $k$-medoids algorithm with state-of-the-art complexity and clustering accuracy. In this paper, we present BanditPAM++, which accelerates BanditPAM via two algorithmic improvements, and is $O(k)$ faster than BanditPAM in complexity and substantially faster than BanditPAM in wall-clock runtime. First, we demonstrate that BanditPAM has a special structure that allows the reuse of clustering information $\textit{within}$ each iteration. Second, we demonstrate that BanditPAM has additional structure that permits the reuse of information $\textit{across}$ different iterations. These observations inspire our proposed algorithm, BanditPAM++, which returns the same clustering solutions as BanditPAM but often several times faster. For example, on the CIFAR10 dataset, BanditPAM++ returns the same results as BanditPAM but runs over 10$\times$ faster. Finally, we provide a high-performance C++ implementation of BanditPAM++, callable from Python and R, that may be of interest to practitioners at Auxiliary code to reproduce all of our experiments via a one-line script is available at

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