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Graph partitioning has been studied in the discipline between computer science and applied mathematics. It is a technique to distribute the whole graph data as a disjoint subset to a different device. The minimum graph partition problem with respect to an independence system of a graph has been studied in this paper. The considered independence system consists of one of the independent sets defined by Boutin. We solve the minimum partition problem in path graphs, cycle graphs, and wheel graphs. We supply a relation of twin vertices of a graph with its independence system. We see that a maximal independent set is not always a minimal set in some situations. We also provide realizations about the maximum cardinality of a minimum partition of the independence system. Furthermore, we study the comparison of the metric dimension problem of a graph with the minimum partition problem of that graph.