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Biometric-based authentication methods have been widely used, for example on portable devices (e.g., Android and iOS devices). However, there are several known limitations in existing authentication methods based on biometrics (e.g., those using facial, iris, and fingerprint). For example, in a healthcare context, a user may be physically incapable of completing the authentication due to his/her medical conditions. Hence, as a complementary authentication mechanism, there have been attempts to also utilize electrocardiogram (ECG). In this work, we propose an ECG authentication system that leverages deep learning. Specifically, to achieve generalization ability, complementary ensemble empirical decomposition (CEEMD) is introduced in our design. Moreover, a 1-D Multi-scale Convolutional Neural Network (1-D MCNN) is implemented to achieve accurate authentication. To evaluate the usability of our proposed approach, we have performed extensive experiments on eight databases, and the findings show that our proposed approach achieves good performance even on abnormal databases and can be adapted for different application environments. In addition, our adopted data from eight public databases requires theoretical statistical treatment for practical applications in real authentication scenarios. [ABSTRACT FROM AUTHOR]