Representing molecules as Graph Neural Networks

From the NSF C-CAS Training Series:
Representing molecules as Graph Neural Networks (GNNs) - Zhichun Guo
Further Reading:
The NSF Center for Computer-Assisted Synthesis:
ccas.nd.edu/
For work in the Chawla laboratory group at the University:of Notre Dame
niteshchawla.nd.edu/
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The C-CAS Series of Training videos consist of tutorials created and presented by students and postdocs working in the Center.

[@SamDig]

Thank you for such an intuitive explanation. I have a question, What about the hydrogens on the benzene ring and methyl group?. Is it like those 2 H's represent two types of hydrogen?: N's Hydrogen and C's Hydrogen? Despite Benzene's hydrogen being slightly different than Methyl's hydrogen?

[@anhluongbui2001]

I think the H in benzene and the -CH3 radical are not listed in A (atom set) because it does not affect any reactions with this chemical and C is enough to show in this case. For example, for the C at the top right is -CH3, when the chemical in the reaction with some substance results in NH2-(C6H4)-R then we can simply eliminate C but not Remove C and all three H letters. And similarly, with H in benzene.