banditpam 1.0.5

BanditPAM: A state-of-the-art, high-performance k-medoids algorithm.

Quickstart

Please see https://github.com/ThrunGroup/BanditPAM#python-quickstart.

Introduction

Clustering algorithms are ubiquitous in modern data science applications. Compared to the commonly used k-means clustering, k-medoids clustering uses the points in the dataset itself – the medoids – as cluster centers and supports arbitrary dissimilarity functions in addition to standard distance metrics. This enables greater interpretability of the cluster centers and the clustering of structured objects. We present BanditPAM, a randomized algorithm inspired by techniques from multi-armed bandits, that scales almost linearly with dataset size and runs significantly faster than prior algorithms while still matching the best prior algorithms in clustering quality. Despite its advantages, k-medoids clustering has been less popular than k-means due to its computational cost. Prior k-medoids algorithms such as PAM and FastPAM scale quadratically in the dataset size in each iterations but they are still significantly slower than k-means, which scales linearly in dataset size in each iteration. This algorithm, BanditPAM, matches k-means in complexity and is significantly faster than prior state-of-the-art.

Details

In this package, we provide a high-performance implementation of BanditPAM, a state-of-the-art k-medoids algorithm. The main contributions of BanditPAM are as follows:

• BanditPAM matches the best prior work in clustering quality but scales as O(nlogn) instead of O(n^2) in each iteration.

• BanditPAM supports arbitrary dissimilarity functions between points – these functions need not even be metrics.

This implementation is written in C++ for performance, but is callable from Python via Python bindings. The algorithm is empirically validated on several large, real-word datasets with a reduction in the number of distance evaluations of up to 200x while returning the same results as prior state-of-the-art. For further details, please see the full paper at https://arxiv.org/abs/2006.06856 and the code at https://github.com/ThrunGroup/BanditPAM/

If you use this software, please cite: Mo Tiwari, Martin Jinye Zhang, James Mayclin, Sebastian Thrun, Chris Piech, Ilan Shomorony. “Bandit-PAM: Almost Linear Time k-medoids Clustering via Multi-Armed Bandits” Advances in Neural Information Processing Systems (NeurIPS) 2020.