The division of the dataset into peptides and proteins based on a 60-AA cutoff (8) seems arbitrary. Indeed, training GIN models on a combined training set of the peptides plus the proteins produced essentially the same results, see Table . It is true that longer peptides (where all AAs have more than four nearest neighbors) could in theory benefit from a deeper neural network, but this investigation was unable to identify more successful models employing a higher number of layers to study only the protein dataset. The most likely reason is that deep networks require more data to avoid overfitting to a small dataset. In addition, the presence of very low and very high pI values within the protein dataset raises the question of experimental accuracy, as pH measurements typically lose accuracy at very high or low pH.