Yes. This problem is of particular importance in drug response prediction, where small molecules are represented as graphs where the atoms are nodes and the bonds are edges. These are difficult to work with because of the variability in the number of nodes.
[1] https://arxiv.org/abs/1509.09292
[2] https://arxiv.org/abs/1603.00856
[3] http://proceedings.mlr.press/v48/niepert16.html
[4] https://persagen.com/files/misc/xu2017seq2seq.pdf (PDF)