admet-prediction

ADMET Prediction

Predict comprehensive ADMET properties for drug candidate molecules using GraphMVP ensemble models.

When to Use

• User asks to predict ADMET properties for a molecule
• User provides a drug candidate and wants safety assessment
• User needs blood-brain barrier penetration prediction
• User wants to evaluate toxicity (LD50) or side effects (SIDER)
• User requests pharmacokinetic properties (half-life, Caco-2)

Workflow

Step 1: Load Molecule

Create molecule from SMILES string.

from open_biomed.data import Molecule
molecule = Molecule.from_smiles("CC(=O)OC1=CC=CC=C1C(=O)O")  # Aspirin

Step 2: Build ADMET Pipeline

Initialize ensemble pipeline with all GraphMVP checkpoints.

from open_biomed.core.pipeline import InferencePipeline, EnsemblePipeline

pipelines = {
    "BBBP": InferencePipeline(
        task="molecule_property_prediction", model="graphmvp",
        model_ckpt="./checkpoints/server/graphmvp-BBBP.ckpt",
        additional_config="./configs/dataset/bbbp.yaml", device="cuda:0"),
    "SIDER": InferencePipeline(
        task="molecule_property_prediction", model="graphmvp",
        model_ckpt="./checkpoints/server/graphmvp-SIDER.ckpt",
        additional_config="./configs/dataset/sider.yaml", device="cuda:0"),
    # See examples/basic_example.py for full pipeline setup
}
pipeline = EnsemblePipeline(pipelines)

Step 3: Run Predictions

Execute predictions for each ADMET property.

# BBB penetration
bbb_result = pipeline.run(molecule=molecule, task="BBBP")

# Side effects (27 categories)
sider_result = pipeline.run(molecule=molecule, task="SIDER")

# Regression properties
caco2_result = pipeline.run(molecule=molecule, task="caco2_wang")
half_life_result = pipeline.run(molecule=molecule, task="half_life_obach")
ld50_result = pipeline.run(molecule=molecule, task="ld50_zhu")

Expected Outputs

Task	Output Type	Description
BBBP	float [0-1]	Probability of BBB penetration
SIDER	list[27 floats]	Side effect probabilities per category
caco2_wang	float	Log permeability (cm/s)
half_life_obach	float	Log half-life (hours)
ld50_zhu	float	Log LD50 (mg/kg)