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High‐dimensional metastable molecular dynamics (MD) can often be characterised by a few features of the system, that is, collective variables (CVs). Thanks to the rapid advance in the area of machine learning and deep learning, various deep learning‐based CV identification techniques have been developed in recent years, allowing accurate modelling and efficient simulation of complex molecular systems. In this paper, we look at two different categories of deep learning‐based approaches for finding CVs, either by computing leading eigenfunctions of transfer operator associated to the underlying dynamics, or by learning an autoencoder via minimisation of reconstruction error. We present a concise overview of the mathematics behind these two approaches and conduct a comparative numerical study of these two approaches on illustrative examples. [ABSTRACT FROM AUTHOR]