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AstraZeneca / chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
https://chemicalx.readthedocs.io
Apache License 2.0
700 stars 89 forks source link

How are the methods implemented outside of the domain they are designed for? #101

Open jasperhyp opened 2 years ago

jasperhyp commented 2 years ago

For example, DeepSynergy and MatchMaker are requiring cell line information, and they are both implemented in the DrugBankDDI & TWOSIDES benchmarks where no cell line information is available at all (and TWOSIDES is even at the patient level), with DS reaching the highest performance among all methods. What then was the "cell line gene expression" component in both methods replaced within those tasks? Also, does this ensure a fair comparison?

jasperhyp commented 2 years ago

I also noticed that all drug features are set to be Morgan FP by design. However, a lot of those models rely on specific features, e.g. SSI-DDI, CASTER both explicitly leverage substructure features. I am not so sure why features are all unified anyways...?