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EEG pattern recognition is an important part of motor imagery- (MI-) based brain computer interface (BCI) system. Traditional EEG pattern recognition algorithm usually includes two steps, namely, feature extraction and feature classification. In feature extraction, common spatial pattern (CSP) is one of the most frequently used algorithms. However, in order to extract the optimal CSP features, prior knowledge and complex parameter adjustment are often required. Convolutional neural network (CNN) is one of the most popular deep learning models at present. Within CNN, feature learning and pattern classification are carried out simultaneously during the procedure of iterative updating of network parameters; thus, it can remove the complicated manual feature engineering. In this paper, we propose a novel deep learning methodology which can be used for spatial-frequency feature learning and classification of motor imagery EEG. Specifically, a multilayer CNN model is designed according to the spatial-frequency characteristics of MI EEG signals. An experimental study is carried out on two MI EEG datasets (BCI competition III dataset IVa and a self-collected right index finger MI dataset) to validate the effectiveness of our algorithm in comparison with several closely related competing methods. Superior classification performance indicates that our proposed method is a promising pattern recognition algorithm for MI-based BCI system. [ABSTRACT FROM AUTHOR]