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In the Intelligent Transportation Systems (ITS), highly accurate traffic flow prediction is considered as key technology to evaluate traffic state of the urban road network. However, due to disturbing from environment, the original traffic flow data may be influenced by noise and finally cause the decline of prediction accuracy. This study design a hybrid prediction model combining Ensemble Empirical Mode Decomposition (EEMD) denoising schemes and classifying learning algorithm based on Fuzzy C-means Neural Network (FCMNN) to improve prediction accuracy. In the model training process, several key parameters in EEMD and FCMNN are determined according to prediction errors based on traffic volume detected from highway network in the Minneapolis city. In the model validation, three widely used indicators for error evaluation are applied to estimate the prediction accuracy of four candidate models under single and multi step, including Artificial Neural Network (ANN), EEMD+ANN, FCMNN and EEMD+FCMNN. The results shown in the case study indicate that the prediction models combined with denoising methods are superior to the models without adopting denoising algorithm. Furthermore, the model using classifying learning method FCMNN can produce higher prediction accuracy than traditional ANN model. In addition, the long-term prediction performance of FCMNN is also much better than that of ANN because that sub-NN system is trained according to each classifying patterns to obtain better optimization effect. Results summarized in this study could be helpful for administration to design managing and controlling strategies according to high prediction accuracy. INDEX TERMS Traffic flow prediction, ensemble empirical mode decomposition, artificial neural network, fuzzy c-means, de-noising algorithm.