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yuyangw / MolCLR

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.
MIT License
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Benchmark splits #2

Closed MarieOestreich closed 2 years ago

MarieOestreich commented 2 years ago

Hi, I have got another question: Would you mind providing the seed for splitting the benchmarking datasets (or the splits themselves)? And also: Did you run all the benchmarkings of the other models on your paper yourself or did you gather the results from the corresponding papers (Table1 and Table2)?

Thanks!

yuyangw commented 2 years ago

Hi,

  1. All the benchmarks from MoleculeNet (except for QM9) are split by scaffold, which gives you a deterministic split for each database, unlike random splitting. For QM9, we didn't pick a specific seed for splitting. Each individual run uses a different random seed.
  2. We borrow the results from other literature if available and run experiments on our side otherwise.

Best