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Information processing of radiotherapy systems has become an important research area for sophisticated radiation treatment methodology. Geometrically precise delivery of radiotherapy in the thorax and upper abdomen is compromised by respiratory motion during treatment. Accurate prediction of the respiratory motion would be beneficial for improving tumor targeting. However, a wide variety of breathing patterns can make it difficult to predict the breathing motion with explicit models. We proposed a respiratory motion predictor, that is, customized prediction with multiple patient interactions using neural network (CNN). For the preprocedure of prediction for individual patient, we construct the clustering based on breathing patterns of multiple patients using the feature selection metrics that are composed of a variety of breathing features. In the intraprocedure, the proposed CNN used neural networks (NN) for a part of the prediction and the extended Kalman filter (EKF) for a part of the correction. The prediction accuracy of the proposed method was investigated with a variety of prediction time horizons using normalized root mean squared error (NRMSE) values in comparison with the alternate recurrent neural network (RNN). We have also evaluated the prediction accuracy using the marginal value that can be used as the reference value to judge how many signals lie outside the confidence level. The experimental results showed that the proposed CNN can outperform RNN with respect to the prediction accuracy with an improvement of 50%. Categories and Subject Descriptors: J.3 [Computer Applications]: Life and Medical Sciences -- Medical information systems; I.4.4 [Image Processing and Computer Vision] : Restoration -- Kalman filtering General Terms: Algorithms [ABSTRACT FROM AUTHOR]