About the number of interactions and the substructure dimension

[SakuraRiven]

About the number of interactions and the substructure dimension

[YifanDengWHU]

Hi.
For question 1:
Yes, it's right. In fact, drugA-drugB is the same as drugB-drugA in this project, we just delete half of interactions to reduce the replication. However, if you try to use Knowledge Graph, the order will make a difference. It means (drugA,relation,drugB) is different from (drugB,relation,drugA). We need to determine the order with dependency relationship.
For question 2:
The original fingerprint is 881 dimension. We perform encoding again toward the results of the 881 dimension again so it results in 583. You can have a look on the table "drug" and column "smile". The maximum number is 881.

[SakuraRiven]

If we want to reproduce the results in your paper or develop our own method, should the dataset keep 37264 in this repo or aug to 74528? But the latter may cause a different split and test set ...

[YifanDengWHU]

I think you should keep 37264, because it may be easier for the model to predict (drugB,drugA) if (drugA,drugB) already exists in the training set. This will lead to false high accuracy.

[SakuraRiven]

OK, understand. Thanks for your answer~