MinkaiXu / GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
MIT License
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m_{ij} notation in GNN architecture #17

Closed CaptainCuong closed 1 year ago

CaptainCuong commented 2 years ago

Hi Minkai Xu,

I think there is a flaw in your mathematical notation for GNN, Equation 5 and 6 in particular. I found that the notations m_{ij} in equation 5 and 6 are not the same. m_{ij} in equation 5 and m_{ij} in equation 6

MinkaiXu commented 2 years ago

Here in practice we just use one layer of GFN after the graph encoders. For the final output, we only need $x$, so actually the two lines you quoted are all corresponding to Eq.5, with Eq.6 skipped since we don't need updated node embedding.