Graph Representation Learning (GRL) has become essential for modern graph data mining and learning tasks. GRL aims to capture the graph's structural information and exploit it in combination with node and edge attributes to compute low-dimensional representations. While Graph Neural Networks (GNNs) have been used in state-of-the-art GRL architectures, they have been shown to suffer from over smoothing when many GNN layers need to be stacked. In a different GRL approach, spectral methods based on graph filtering have emerged addressing over smoothing; however, up to now, they employ traditional neural networks that cannot efficiently exploit the structure of graph data. Motivated by this, we propose PointSpectrum, a spectral method that incorporates a set equivariant network to account for a graph's structure. PointSpectrum enhances the efficiency and expressiveness of spectral methods, while it outperforms or competes with state-of-the-art GRL methods. Overall, PointSpectrum addresses over smoothing by employing a graph filter and captures a graph's structure through set equivariance, lying on the intersection of GNNs and spectral methods. Our findings are promising for the benefits and applicability of this architectural shift for spectral methods and GRL.