A promising approach to overcome the various shortcomings of password systems is the use of biometric authentication, in particular the use of electroencephalogram (EEG) data. In this paper, we propose a subject-independent learning method for EEG-based biometrics using Hilbert spectrograms of the data. The proposed neural network architecture treats the spectrogram as a collection of one-dimensional series and applies one-dimensional dilated convolutions over them, and a multi-similarity loss was used as the loss function for subject-independent learning. The architecture was tested on the publicly available PhysioNet EEG Motor Movement/Imagery Dataset (PEEGMIMDB) with a 14.63% Equal Error Rate (EER) achieved. The proposed approach’s main advantages are subject independence and suitability for interpretation via created spectrograms and the integrated gradients method.