Molecule Property Prediction

This page contains benchmarks of popular property prediction models.

We consider both vanilla random split and scaffold-based random split for molecule datasets. The split for train/validation/test sets is 80%:10%:10%. For each model, we evaluate it with 5 random splits and report the mean and the deviation of the performance. We report MAE and R2 metrics for regression datasets, AUROC and AURPC metrics for binary classification datasets.

For datasets containing a lot of tasks, only the first 16 tasks are showed here due to space limitations.

Random Split

QM9

../_images/qm9_mae.png ../_images/qm9_r2.png

QM8

../_images/qm8_mae.png ../_images/qm8_r2.png

BACE

../_images/bace_auroc.png ../_images/bace_auprc.png

BBBP

../_images/bbbp_auroc.png ../_images/bbbp_auprc.png

CEP

../_images/cep_mae.png ../_images/cep_r2.png

HIV

../_images/hiv_auroc.png ../_images/hiv_auprc.png

ClinTox

../_images/clintox_auroc.png ../_images/clintox_auprc.png

ESOL

../_images/esol_mae.png ../_images/esol_r2.png

FreeSolv

../_images/freesolv_mae.png ../_images/freesolv_r2.png

Lipophilicity

../_images/lipophilicity_mae.png ../_images/lipophilicity_r2.png

SIDER

../_images/sider_auroc.png ../_images/sider_auprc.png

Tox21

../_images/tox21_auroc.png ../_images/tox21_auprc.png

ToxCast

../_images/toxcast_auroc.png ../_images/toxcast_auprc.png

MUV

../_images/muv_auroc.png ../_images/muv_auprc.png

Malaria

../_images/malaria_mae.png ../_images/malaria_r2.png

Scaffold Split

QM9

../_images/qm9_scaffold_mae.png ../_images/qm9_scaffold_r2.png

QM8

../_images/qm8_scaffold_mae.png ../_images/qm8_scaffold_r2.png

BACE

../_images/bace_scaffold_auroc.png ../_images/bace_scaffold_auprc.png

BBBP

../_images/bbbp_scaffold_auroc.png ../_images/bbbp_scaffold_auprc.png

CEP

../_images/cep_scaffold_mae.png ../_images/cep_scaffold_r2.png

HIV

../_images/hiv_scaffold_auroc.png ../_images/hiv_scaffold_auprc.png

ClinTox

../_images/clintox_scaffold_auroc.png ../_images/clintox_scaffold_auprc.png

ESOL

../_images/esol_scaffold_mae.png ../_images/esol_scaffold_r2.png

FreeSolv

../_images/freesolv_scaffold_mae.png ../_images/freesolv_scaffold_r2.png

Lipophilicity

../_images/lipophilicity_scaffold_mae.png ../_images/lipophilicity_scaffold_r2.png

SIDER

../_images/sider_scaffold_auroc.png ../_images/sider_scaffold_auprc.png

Tox21

../_images/tox21_scaffold_auroc.png ../_images/tox21_scaffold_auprc.png

ToxCast

../_images/toxcast_scaffold_auroc.png ../_images/toxcast_scaffold_auprc.png

MUV

../_images/muv_scaffold_auroc.png ../_images/muv_scaffold_auprc.png

Malaria

../_images/malaria_scaffold_mae.png ../_images/malaria_scaffold_r2.png