This paper investigates a novel graph embedding procedure based on simplicial complexes. Inherited from algebraic topology, simplicial complexes are collections of increasing-order simplices (e.g., points, lines, triangles, tetrahedrons) which can be interpreted as possibly meaningful substructures (i.e., information granules) on the top of which an embedding space can be built by means of symbolic histograms. In the embedding space, any Euclidean pattern recognition system can be used, possibly equipped with feature selection capabilities in order to select the most informative symbols. The selected symbols can be analysed by field-experts in order to extract further knowledge about the process to be modelled by the learning system, hence the proposed modelling strategy can be considered as a grey-box. The proposed embedding has been tested on thirty benchmark datasets for graph classification and, further, we propose two real-world applications, namely predicting proteins’ enzymatic function and solubility propensity starting from their 3D structure in order to give an example of the knowledge discovery phase which can be carried out starting from the proposed embedding strategy.