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Accurate traffic speed forecasting is one of the most critical tasks in proactive traffic management and the deployment of advanced traveler information systems. This paper proposes a hybrid forecasting approach named DeepEnsemble by integrating the three‐dimensional convolutional neural network (3D CNN) with ensemble empirical mode decomposition (EEMD). There are four steps in this hybrid approach. First, EEMD is adopted to decompose the complex traffic speed time series data with noise into several intrinsic mode functions (IMFs) and a residue. Second, a three‐dimensional tensor is established and fed into 3D CNN for prediction. Third, the output of 3D CNN prediction is obtained by a linear combination of the results of all components. Finally, the 3D CNN prediction output, external features, and historical features are fused to predict the network‐wide traffic speed simultaneously. The proposed DeepEnsemble approach is tested on the three‐month traffic speed series data of a real‐world large‐scale urban expressway network with 308 traffic flow detectors in Beijing, China. The experimental results indicate that DeepEnsemble outperforms the state‐of‐the‐art network‐wide traffic speed forecasting models. 3D CNN learns temporal, spatial, and depth information better than 2D CNN. Moreover, forecasting accuracy can be improved by employing EEMD. DeepEnsemble is a promising model with scalability and portability for network‐wide traffic speed prediction and can be further extended to conduct traffic status monitoring and congestion mitigation strategies. [ABSTRACT FROM AUTHOR]