The k-means algorithm is arguably the most popular nonparametric clustering method but cannot generally be applied to datasets with incomplete records. The usual practice then is to either impute missing values under an assumed missing-completelyat-random mechanism or to ignore the incomplete records, and apply the algorithm on the resulting dataset. We develop an efficient version of the k-means algorithm that allows for clustering in the presence of incomplete records. Our extension is called kmmeans and reduces to the k-means algorithm when all records are complete. We also provide initialization strategies for our algorithm and methods to estimate the number of groups in the dataset. Illustrations and simulations demonstrate the efficacy of our approach in a variety of settings and patterns of missing data. Our methods are also applied to the analysis of activation images obtained from a functional Magnetic Resonance Imaging experiment.
Index TermsAMELIA, CARP, FMRI, IMPUTATION, JUMP STATISTIC, k-MEANS++, k-POD, MICE, SOFT CONSTRAINTS, SDSS arXiv:1802.08363v2 [stat.ML] 8 Sep 2018 algorithm using partial distances. However, the repeated application of k-means at every iteration is computationally expensive. The literature is also sparse on estimating the number of groups K for data with incomplete records. This paper develops an efficient k-means-type clustering algorithm called k m -means that accommodates incomplete records and generalizes the algorithm of [38] that is popular in the statistical literature and software. Expressions for the objective function and its changes following the cluster reassignment of an observation play central roles in our generalization of the [38] algorithm. Section II also provides an initialization strategy for k m -means and an adaptation of the jump statistic [39] for estimating the number of groups. Section III comprehensively evaluates our methodology through a series of large-scale simulation experiments for datasets of different clustering complexities, sizes, numbers of groups, and with different missingness mechanisms and proportions. Section IV uses our methods to find the types of activated cerebral regions from several singletask functional Magnetic Resonance Imaging (fMRI) experiments. We conclude with some discussion in Section V. This paper also has an online supplement having additional illustrations on performance evaluations and other preliminary data analysis. Figures in the supplement referred to in this paper have the prefix "S-".