Well I couldn't understand what your task was when you didn't say what it was until now.

Other than that, skimming through the paper it quite clearly says the following:

> Our present results do not indicate our procedure can generalize to motifs that are not present in the training set

Because what they're doing doesn't generalize, I think the starting assumptions (that there will be imprevements with a larger model) are wrong, and so the question is unnecessary... The issue is with the method or the data, they do not elaborate more than that.