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We introduce a new approach to the problem of overlapping clustering. The main idea is to formulate overlapping clustering as an optimization problem in which each data point is mapped to a small set of labels, representing membership to different clusters. The objective is to find a mapping so that the distances between data points agree as much as possible with distances taken over their label sets. To define distances between label sets, we consider two measures: a set-intersection indicator function and the Jaccard coefficient. To solve the main optimization problem we propose a local-search algorithm. The iterative step of our algorithm requires solving non-trivial optimization sub problems, which, for the measures of set-intersection and Jaccard, we solve using a greedy method and non-negative least squares, respectively. Since our frameworks uses pair wise similarities of objects as the input, it lends itself naturally to the task of clustering structured objects for which feature vectors can be difficult to obtain. As a proof of concept we show how easily our framework can be applied in two different complex application domains. Firstly, we develop overlapping clustering of animal trajectories, obtaining zoologically meaningful results. Secondly, we apply our framework for overlapping clustering of proteins based on pair wise similarities of amino acid sequences, outperforming the of state-of-the-art method in matching a ground truth taxonomy.