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For the kernel K-mean cluster method is run in an implicit feature space, the initial and iterative cluster centers cannot be defined explicitly. Against the deficiency of the initial cluster centers selected in the original space discretionarily in the existing methods, this paper proposes a new method for ensuring the clustering center that virtual clustering centers are defined in the feature space by the original classification as the initial cluster centers and the iteration clustering centers are ensured by the further virtual classification. The improved method is used for fault diagnosis of roller bearing that achieves a good cluster and diagnosis result, which demonstrates the effectiveness of the proposed method.