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Molecular Property Prediction on MoleculeNet BBBP (scaffold)

96.4ROC AUCDumplingGNN
67.59275.07182.5590.029May 29, 2019Aug 1, 2020Oct 6, 2021Dec 10, 2022Feb 14, 2024Apr 19, 2025Jun 24, 2026
Updated 4mo ago

Evaluation results

MethodLinks
DumplingGNN2024.0996.4
KPGT2023.0490.8
SELFormer2023.0490.2
Attentive FP2024.0987.5
MGCN2023.0485
SchNet2023.0484.8
ChemBFN2024.0980.5
DMP(TF+GNN)Model category=Specialist2023.1177.8
MPTr+CIPEBackbone=MPTr, Positional encoding=CIPE2026.0676.6
MolBERT2023.0476.2
SYN-FUSIONfusion_source=Hu et. al2023.0875.5
GraSPNet2026.0274.4
SYN-FUSIONfusion_source=MolCLR2023.0874.2
MolCLRbackbone=GIN2023.0873.9
MolCLR2023.0473.6
APTBase Model=Mole-BERT2023.1173.1
SVM2023.0872.9
MolFMModel category=Specialist2023.1172.9
Uni-MolModel category=Specialist2023.1172.9
MolXPT2024.0972.9
ChemBERTa-22023.0472.8
SimSGT2026.0272.8
BGRL2026.0272.5
GraphLogPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0572.5
Hi-GMAE-GPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0572.5
GraphLoG2026.0672.5
GraphMVP-C2023.0472.4
GEM2023.0472.4
GraphMVP-CModel category=Specialist2023.1172.4
Instruct-GSModel category=LLM Based Generalist2023.1172.4
MolCLR2024.0972.4
Uni-Mol2024.0972.4
GEM2024.0972.2
CP2026.0272.1
GraphMAEPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0572
GraphMAE2026.0672
Mole-BERT2023.1171.9
Mole-BERTPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0571.9
GCN2023.0871.8
GCN2023.0471.8
JOAO2026.0271.8
GraphMAE2026.0271.7
MPTr+RWSEBackbone=MPTr, Positional encoding=RWSE2026.0671.7
GraphMAE22026.0271.6
GraphMAE2Pre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0571.6
GTOT-TuningBackbone=GIN (supervised_contextpred), Strategy=GTOT-Tuning2022.0371.5
RF2023.0871.4
GraphCL2026.0271.4
MPTr+CycleSEBackbone=MPTr, Positional encoding=CycleSE2026.0671.3
D-MPNN2023.0871.2
SimGRACE2023.1171.2
GraphMAE2023.1171.2
SimGRACEPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0571.2
RGCLPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0571.2
D-MPNN2023.0471
D-MPNN2024.0971
Hi-GMAE-FPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0571
G2PT2026.0671
MPTrBackbone=MPTr2026.0670.9
Hu et al.2023.0870.8
Hu et al.2023.0470.8
MolCA(1D)Model category=LLM Based Generalist, Input modality=1D2023.1170.8
GraphMVP2023.1170.8
Mole-BERT2026.0270.8
GraphMVPPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0570.8
AD-GCL2023.1170.7
APTBase Model=EdgePred2023.1170.7
ContextPred2023.1170.6
KV-PLMModel category=Specialist2023.1170.5
MoMuModel category=Specialist2023.1170.5
ADGCL2026.0270.5
Hi-GMAE-GPre-training status=None, Pre-training dataset=N/A, Evaluation protocol=Supervised Learning, Split type=Scaffold-split2024.0570.4
UnifiedMolPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0570.4
JOAOPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0570.2
MolCA(1D + 2D)Model category=LLM Based Generalist, Input modality=1D + 2D2023.1170
BSSBackbone=GIN (supervised_contextpred), Strategy=Fine-tuning strategy2022.0370
G-Contextual2023.1169.9
ChemBERTa v2Model category=Specialist2023.1169.8
StochNormBackbone=GIN (supervised_contextpred), Strategy=Fine-tuning strategy2022.0369.8
Chem-GMNetPre-trained=true, Pre-training Corpus=10M SMILES, Pre-training Task=MLM-10M2026.0569.8
GraphCLModel category=Specialist2023.1169.7
N-Gram RFClassifier=Random Forest2024.0969.7
MGSSL2026.0269.7
GraphCLPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0569.7
AD-GCLPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0569.7
GraphCLPre-training strategy=GraphCL2026.0669.7
ChemBERTa-2Pre-trained=true, Pre-training Corpus=10M SMILES, Pre-training Task=MLM-10M2026.0569.6
GraphMVP2024.0969.5
Infomax2026.0269.2
GraphGPSPre-training status=None, Pre-training dataset=N/A, Evaluation protocol=Supervised Learning, Split type=Scaffold-split2024.0569.2
PretrainGNN2024.0969.1
3D InfoMax2023.1169.1
GINGraph-level pre-training=None, Node-level pre-training=Infomax2019.0568.8
MGSSL2023.1168.8
InfomaxPre-training status=Pre-trained, Pre-training dataset=ZINC15, Evaluation protocol=Fine-tuning, Split type=Scaffold-split2024.0568.8
SSL pre-trainingPre-training strategy=SSL2026.0668.8
GROVER_largeModel scale=large2024.0968.7
GINGraph-level pre-training=Supervised, Node-level pre-training=Context Prediction2019.0568.7
Fine-TuningBackbone=GIN (supervised_contextpred), Strategy=Baseline2022.0368.7
InfoGraph2023.1168.7