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Over the past few years, the processing of motor imagery (MI) electroencephalography (EEG) signals has been attracted for developing brain-computer interface (BCI) applications, since feature extraction and classification of these signals are extremely difficult due to the inherent complexity and tendency to artifact properties of them. The BCI systems can provide a direct interaction pathway/channel between the brain and a peripheral device, hence the MI EEG-based BCI systems seem crucial to control external devices for patients suffering from motor disabilities. The current study presents a semi-supervised model based on three-stage feature extraction and machine learning algorithms for MI EEG signal classification in order to improve the classification accuracy with smaller number of deep features for distinguishing right- and left-hand MI tasks. Stockwell transform is employed at the first phase of the proposed feature extraction method to generate two-dimensional time–frequency maps (TFMs) from one-dimensional EEG signals. Next, the convolutional neural network (CNN) is applied to find deep feature sets from TFMs. Then, the semi-supervised discriminant analysis (SDA) is utilized to minimize the number of descriptors. Finally, the performance of five classifiers, including support vector machine, discriminant analysis, k-nearest neighbor, decision tree, random forest, and the fusion of them are compared. The hyperparameters of SDA and mentioned classifiers are optimized by Bayesian optimization to maximize the accuracy. The presented model is validated using BCI competition II dataset III and BCI competition IV dataset 2b. The performance metrics of the proposed method indicate its efficiency for classifying MI EEG signals. [ABSTRACT FROM AUTHOR]