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In this paper, we propose feature extraction method for prediction model for at the early stage of diabetic kidney disease (DKD) progression. DKD needs continuous treatment; however, a hospital visit interval of a patient at the early stage of DKD is normally from one month to three months, and this is not a short time period. Therefore it makes difficult to apply sophisticated approaches such as using convolutional neural networks because of the data limitation. The propose method uses with hierarchical clustering that can estimate a suitable interval for grouping inputted sequences. We evaluate the proposed method with a real-EMR dataset that consists of 30,810 patient records and conclude that the proposed method outperforms the baseline methods derived from related work.