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kexinhuang12345 / MolTrans

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa880/5929692
BSD 3-Clause "New" or "Revised" License
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Baseline model implementation #13

Closed hyojin0912 closed 3 years ago

hyojin0912 commented 3 years ago

Hello, I saw your two great paper MolTrans and DeepPurpose. According to MolTrans you compared MolTrans with DeepConv-DTI, GNN-CPI etc.

These baseline models are implemented in DeepPurpose? For example, is the DeepConv-DTI model implemented as Drug Encodings=Morgan, Target Encodings=CNN?

If it is right, plz tell me baseline model - Encodings mapping table. If it is false, could you provide baseline model implementation?

kexinhuang12345 commented 3 years ago

Hi, the only fully reproduced model is DeepDTA - CNN + CNN. The other should have similar performances if you adjust the hyperparameters in the DeepPurpose (e.g. DeepConv-DTI would be Morgan + CNN). However, in the MolTrans paper, we use the author implementations, which you can find in the original authors provided repo.