ADMET Benchmark Group

ADMET is one of the cornerstones for small molecule drug discovery, where it defines the drug's efficacy and toxicity's profile. Thus, a machine learning model that can accurately predict all of the ADMET properties given the drug's structural information is highly valuable. We select 22 ADMET datasets from TDC's collection and formulate it as a benchmark group. To access, type:

from tdc import BenchmarkGroup
group = BenchmarkGroup(name = 'ADMET_Group', path = 'data/')
predictions = {}

for benchmark in group:
    name = benchmark['name']
    train_val, test = benchmark['train_val'], benchmark['test']
    ## --- train your model --- ##
    predictions[name] = y_pred_test

group.evaluate(predictions)
# {'caco2_wang': {'mae': 4.328}, 'hia_hou': {'roc-auc': 0.802}, ...}

Follow the instruction on how to use the BenchmarkGroup class and for other useful functions to facilitate your model building.

For every dataset, we use scaffold split and hold out 20% for test set. The evaluation metrics are selected given the following criteria:

• For binary classification:
• AUROC is used when the number of positive and negative samples are close.
• AUPRC is used when the number of positive samples are much smaller than negative samples.
• For regression:
• MAE is used for majority of benchmarks.
• Spearman's correlation coefficient is used for benchmarks that depend on factors beyond the chemical structure.

We encourage submissions that reports results for the entire benchmark group. Still, we welcome and accept submissions that report partial results, for example, for just one of the five ADMET categories.

Absorption

Absorption measures how a drug travels from the site of administration to site of action.

Summary

Leaderboard

: The higher the better. : The lower the better. : Click to sort models for specific benchmark column.

Distribution

Drug distribution refers to how drug moves to and from the various tissues of the body and the amount of drugs in the tissues.

Summary

Leaderboard

: The higher the better. : The lower the better. : Click to sort models for specific benchmark column.

Metabolism

Drug metabolism measures how specialized enzymatic systems breakdown the drugs and it determines the duration and intensity of a drug's action.

Summary

Leaderboard

: The higher the better. : The lower the better. : Click to sort models for specific benchmark column.

Excretion

Drug excretion is the removal of drugs from the body using various different routes of excretion, including urine, bile, sweat, saliva, tears, milk, and stool.

Summary

Leaderboard

: The higher the better. : The lower the better. : Click to sort models for specific benchmark column.

Toxicity

Toxicity measures how much damage a drug could cause to organisms.

Summary

Leaderboard

: The higher the better. : The lower the better. : Click to sort models for specific benchmark column.