Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add ChemFM in leaderboard #8

Merged
merged 1 commit into from
Nov 25, 2024
Merged

add ChemFM in leaderboard #8

merged 1 commit into from
Nov 25, 2024

Conversation

feiyang-cai
Copy link
Contributor

@feiyang-cai feiyang-cai commented Nov 14, 2024

@amva13

This PR adds the ChemFM model to the ADMET Leaderboard. Below are the relevant details:

A. A link to the codes for training the model and running the benchmarks.
The code for training the ChemFM model and running the benchmarks can be found at the following GitHub repository:
https://github.com/TheLuoFengLab/ChemFM/tree/master/finetuning/property_prediction

B. Instructions for replicating your results running these codes.
Instructions for replicating our results are included in the README file within the GitHub repository. Additionally, we have provided links to the model checkpoints. https://github.com/TheLuoFengLab/ChemFM/tree/master/finetuning/property_prediction

C. Description of the hardware used for training the model.
The model was trained on a single H100 GPU machine. However, it is also possible to train the model on a moderate GPU machine.

D. Link to paper to be included on the website
The full paper can be accessed here:
https://arxiv.org/abs/2410.21422

E. Paper authors and developers of the model.
Feiyang Cai, Clemson University

F. The dictionary string output of running the TDC benchmark group evaluations.

{
    'caco2_wang': [0.322, 0.026],
    'bioavailability_ma': [0.715, 0.011],
    'lipophilicity_astrazeneca': [0.460, 0.006],
    'solubility_aqsoldb': [0.725, 0.011],
    'hia_hou': [0.984, 0.004],
    'pgp_broccatelli': [0.931, 0.003],
    'bbb_martins': [0.908, 0.010],
    'ppbr_az': [7.505, 0.073],
    'vdss_lombardo': [0.662, 0.013],
    'cyp2c9_veith': [0.788, 0.005],
    'cyp2d6_veith': [0.704, 0.003],
    'cyp3a4_veith': [0.878, 0.003],
    'cyp2c9_substrate_carbonmangels': [0.414, 0.027],
    'cyp2d6_substrate_carbonmangels': [0.739, 0.024],
    'cyp3a4_substrate_carbonmangels': [0.654, 0.022],
    'half_life_obach': [0.551, 0.020],
    'clearance_hepatocyte_az': [0.495, 0.030],
    'clearance_microsome_az': [0.611, 0.016],
    'ld50_zhu': [0.541, 0.015],
    'herg': [0.848, 0.009],
    'ames': [0.854, 0.007],
    'dili': [0.920, 0.012]
}

P. S.

Fix a result typo for "BaseBoosting KyQVZ6b2" in "LD50_Zhu" dataset.

0.522 -> 0.552; based on the last line in their codes https://github.com/Oloren-AI/OCE-TDC/blob/main/submission_20221216.ipynb

@amva13
Copy link
Member

amva13 commented Nov 15, 2024

@ada-f haven't gotten to look too much yet but just fyi. Might be relevant to you.

@amva13 amva13 merged commit e443fa9 into mims-harvard:main Nov 25, 2024
@amva13
Copy link
Member

amva13 commented Nov 25, 2024

@feiyang-cai merged. Great work!

@feiyang-cai
Copy link
Contributor Author

@amva13 Great! Thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants