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Rose-STL-Lab / LIMO

generative model for drug discovery
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table1&2 #14

Closed zhanghan1234 closed 1 year ago

zhanghan1234 commented 1 year ago

python generate_molecules.py --prop penalized_logp generating molecules: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [01:38<00:00, 9.82s/it] 16.639477 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC1CC1 16.639477 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC1CC1 17.468054 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=CCC

python generate_molecules.py --prop qed generating molecules: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [01:35<00:00, 9.54s/it] calculating QED: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10000/10000 [00:14<00:00, 671.45it/s] 0.8635939 CC=CC1=CC1NC(=O)C2CCCCCCCC3=CC=CC=C23 0.8734434 CC=CC1=CC1NC(=O)C2CCCC=CC=CC3=CC=CC=C23 0.88593656 CC=CC1=CC1NC(=O)C2CC=CC=CC=CC3=CC=CC=C23 Hello. This is the result of my run. I did not change the hyperparameter, but directly used the provided code to get the hyperparameter. I didn't train my own VAE model, but instead used the provided VAE.PT and the provided QED.PT. Can you help me check which step I made a mistake.

PeterEckmann1 commented 1 year ago

Hi, sorry for the very late reply! I must have missed your issue when it was first posted. If you're still interested in getting this to work, the first thing I would try would be to set --num_mols 100000, since for logP and QED we used 100,000 compounds for the tables. That will likely get you a lot closer to the results in the paper, but let me know if it's still not close and we can see what else might be going on.

zhanghan1234 commented 1 year ago

Thanks

发自我的iPhone

------------------ Original ------------------ From: PeterEckmann1 @.> Date: Wed,Oct 4,2023 9:49 AM To: Rose-STL-Lab/LIMO @.> Cc: zhanghan1234 @.>, Author @.> Subject: Re: [Rose-STL-Lab/LIMO] table1&2 (Issue #14)

Hi, sorry for the very late reply! I must have missed your issue when it was first posted. If you're still interested in getting this to work, the first thing I would try would be to set --num_mols 100000, since for logP and QED we used 100,000 compounds for the tables. That will likely get you a lot closer to the results in the paper, but let me know if it's still not close and we can see what else might be going on.

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