For all approaches, graph edges were determined by a nearest neighbor search limited by a cutoff radius of 6A, retaining up to the 50 nearest neighbors. When computing distances, periodic boundary conditions were taken into consideration.
I was wondering why the specific cutoff radius and neighbors sizes were chosen? Is there any scientific provenance to them and have you experimented with different values, too?
Our nearest neighbor limits were incorporated to help with model efficiency. We ran the following experiment on a literature dataset before arriving at the parameter we felt comfortable with:
More recently, we ran the following experiment exploring the trade-off between max neighbors, cutoff radius, and performance for an identical, small DimeNet++ model. Disclaimer- it’s likely that tuning model hyperparameters for each of these combinations can result in better/worse numbers but hopefully this gives you an idea.