Some Questions about amap about graphretro HOT 3 CLOSED

Thanks in advance!

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I just find that using the raw data for training transformer without canonicalizing the SMILES will have impressive preformance, but i can not find out the problem

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The products are first canonicalized (following the scipt here), and the atom mapping is set to the canonical order, and the reactants are remapped post this step.

The information leakage is not a problem, since I tested the edit prediction performance with the old (data with leakage), and new (post canonicalization) and they were the same. The predicted edits should be invariant to the order, which the tests confirmed.

In the synthon completion step though, how you do the atom mapping determines what order the fragments are generated in, and you should try to maintain the same atom mapping routine for training and testing.

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