When do I use QM9Dataset v2? about hermnet

[thu-wangz17]

Sorry for my late answer. QM9Dataset was implemented according to the implements in torch_geometic. The differences between v1 and v2 are the different edge_index. In v1, the edge index is the chemical bond obtained from rdkit, while those in v2 is based on a cutoff radius. Thus the number of edge_index in v2 is more than those in v1. The results in our work were based on the first one, and v2 is just provided for interests.

[thu-wangz17]

I want to add that the edge_index based on cutoff radius should be more make sense in principle. Although you can add the information of chemical bonds in v1, the interactions between some atoms must be modelled by stacking multi message passing layers. While the method which is based on distance will link these pairs directly. It may be more obvious in the condition of protein folding, i.e. the two terminations of a chain may be close after folding, while the link of bond could not refleck these interactions unless stacking more message passing layers.

[thu-wangz17]

If you have no questions, I will close the issue.