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Rose-STL-Lab / LIMO

generative model for drug discovery
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table1&2 #14

Closed zhanghan1234 closed 11 months 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 11 months 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 11 months 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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