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Finding hidden layers in complex networks is an important and a non-trivial problem in modern science. We explore the framework of quantum graphs to determine whether concealed parts of a multi-layer system exist and if so then what is their extent, i.e., how many unknown layers there are. Assuming that all information available is the time evolution of a wave propagation on a single layer of a network it is indeed possible to uncover that which is hidden by merely observing the dynamics. We present evidence on both synthetic and real-world networks that the frequency spectrum of the wave dynamics can express distinct features in the form of additional frequency peaks. These peaks exhibit dependence on the number of layers taking part in the propagation and thus allowing for the extraction of said number. We show that in fact, with sufficient observation time, one can fully reconstruct the row-normalised adjacency matrix spectrum. We compare our propositions to a machine learning approach using a modified, for the purposes of multi-layer systems, wave packet signature method.