Molecule Property Prediction on MoleculeNet (scaffold split) Suite
80BBBPMolXPT
Evaluation Results
| Method | Links | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| MolXPT2023.10 | 80 | 77.1 | 95.3 | 78.1 | 88.4 | 71.7 | 81.9 | — | — | |
| MolXPTFinetuning=prompt-based2023.05 | 80 | 77.1 | 95.3 | 78.1 | 88.4 | 71.7 | 81.9 | — | — | |
| BioT52023.10 | 77.7 | 77.9 | 95.4 | 81 | 89.4 | 73.2 | 82.4 | — | — | |
| DeMolSplit=scaffold splitting, Seeds=102026.02 | 75.1 | 80.9 | 92.6 | 81.2 | 89 | 68.4 | 79.96 | 69.3 | 82.5 | |
| SMA-1.6MDomain Agnostic=true, Dataset Size=1.6M2024.02 | 75 | — | — | 78.9 | 84.3 | — | — | — | — | |
| KV-PLM2023.10 | 74.6 | 72.7 | — | 74 | — | 61.5 | — | — | — | |
| KV-PLM2023.05 | 74.6 | 72.7 | — | 74 | — | 61.5 | — | — | — | |
| ChemBERTa-2 MTR-5MPre-training Objective=MTR, Parameters=5M, Domain Agnostic=false2024.02 | 74.2 | — | — | — | 73.4 | — | — | — | — | |
| TRIDENT (M-M)Variant=M-M2025.06 | 73.95 | 79.36 | 95.41 | 81.63 | 82.39 | 63.64 | 78.46 | 67.8 | 83.51 | |
| Atomas2025.06 | 73.72 | 77.88 | 93.16 | 80.55 | 83.14 | 64.4 | 77.01 | 66.94 | 76.3 | |
| LEMONSplit=scaffold splitting, Seeds=102026.02 | 73.7 | 77.5 | 85.9 | 79.3 | 87.8 | 64.3 | 76.62 | 65.1 | 79.4 | |
| ChemBERTa-2 MTR-10MPre-training Objective=MTR, Parameters=10M, Domain Agnostic=false2024.02 | 73.3 | — | — | — | 78.3 | — | — | — | — | |
| TRIDENT (M-S)Variant=M-S2025.06 | 73.14 | 78.23 | 95.75 | 79.64 | 84.19 | 64.62 | 78.28 | 67.79 | 82.88 | |
| MoleBlendSplit=scaffold splitting, Seeds=102026.02 | 73 | 77.8 | 87.6 | 79 | 83.7 | 64.9 | 76.16 | 66.1 | 77.2 | |
| Uni-Mol-20MDomain Agnostic=false2024.02 | 72.9 | — | — | 80.8 | 85.7 | — | — | — | — | |
| MolFM2025.06 | 72.9 | 77.2 | 79.7 | 78.8 | 83.9 | 64.2 | 74.64 | 64.4 | 76 | |
| Uni-MolSplit=scaffold splitting, Seeds=102026.02 | 72.9 | 79.6 | 91.9 | 80.8 | 85.7 | 65.9 | 78.63 | 69.6 | 82.1 | |
| ChemBERTa-2 MTR-77MPre-training Objective=MTR, Parameters=77M, Domain Agnostic=false2024.02 | 72.8 | — | — | — | 79.9 | — | — | — | — | |
| GraphMVP2023.10 | 72.4 | 75.9 | 79.1 | 77 | 81.2 | 63.9 | 74.9 | — | — | |
| GEM2023.10 | 72.4 | 78.1 | 90.1 | 80.6 | 85.6 | 67.2 | 79 | — | — | |
| GraphMVP2023.05 | 72.4 | 75.9 | 79.1 | 77 | 81.2 | 63.9 | 74.9 | — | — | |
| GEM2023.05 | 72.4 | 78.1 | 90.1 | 80.6 | 85.6 | 67.2 | 79 | — | — | |
| GEMSplit=scaffold splitting, Seeds=102026.02 | 72.4 | 78.1 | 90.1 | 80.6 | 85.6 | 67.2 | 78.18 | 69.2 | 81.7 | |
| Random Masking-1.6MDomain Agnostic=true, Dataset Size=1.6M2024.02 | 72.3 | — | — | 76.5 | 79.8 | — | — | — | — | |
| MolCLR2023.10 | 72.2 | 75 | 91.2 | 78.1 | 82.4 | 58.9 | 76.3 | — | — | |
| GraphMAESplit=scaffold splitting, Seeds=102026.02 | 72 | 75.5 | 82.3 | 77.2 | 83.1 | 60.3 | 73.85 | 64.1 | 76.3 | |
| Mole-BERTSplit=scaffold splitting, Seeds=102026.02 | 71.9 | 76.8 | 78.9 | 78.2 | 80.8 | 62.8 | 74.04 | 64.3 | 78.6 | |
| MoleculeSDESplit=scaffold splitting, Seeds=102026.02 | 71.8 | 76.8 | 87 | 78.8 | 79.5 | 60.8 | 75.07 | 65 | 80.9 | |
| GalformerSplit=scaffold splitting, Seeds=102026.02 | 71.6 | 75.7 | 84.7 | 75.6 | 80.9 | 64.3 | 74.02 | 64 | 73.4 | |
| GTOT-TuningBackbone=GIN (supervised_contextpred)2022.03 | 71.5 | 78.6 | 77.9 | 81.1 | 85.3 | 63.3 | 76.16 | 66.6 | 85 | |
| GraphMVPSplit=scaffold splitting, Seeds=102026.02 | 71.5 | 76.1 | 85.4 | 76 | 81.5 | 64.7 | 74.86 | 64.3 | 74.9 | |
| MolCA-SMILESInput=SMILES2025.06 | 70.8 | 76 | 89 | — | 79.3 | 61.1 | 72.1 | 56.2 | — | |
| MoleculeSTM-SMILESInput=SMILES2025.06 | 70.75 | 75.71 | 86.6 | 77.02 | 81.99 | 63.7 | 73.33 | 65.17 | 65.69 | |
| MOLFORMER2025.06 | 70.74 | 74.74 | 77.64 | 75.64 | 78.64 | 61.75 | 71.53 | 65.51 | 67.58 | |
| MGSSL2023.10 | 70.5 | 76.5 | 80.7 | 79.5 | 79.7 | 61.8 | 74.8 | — | — | |
| MoMu2023.10 | 70.5 | 75.6 | 79.9 | 76.2 | 77.1 | 60.5 | 73.3 | — | — | |
| MGSSL2023.05 | 70.5 | 76.5 | 80.7 | 79.5 | 79.7 | 61.8 | 74.8 | — | — | |
| MoMu2023.05 | 70.5 | 75.6 | 79.9 | 76.2 | 77.1 | 60.5 | 73.3 | — | — | |
| KV-PLM2025.06 | 70.5 | 72.12 | 89.17 | 65.4 | 75.8 | 59.83 | 67.81 | 55.03 | 54.63 | |
| MoMu2025.06 | 70.5 | 75.6 | 79.9 | 75.9 | 76.7 | 60.5 | 71.63 | 63.4 | 70.5 | |
| 3D InfoMaxSplit=scaffold splitting, Seeds=102026.02 | 70.4 | 75.5 | 89.8 | 74.9 | 80.7 | 64.1 | 73.91 | 63.1 | 72.8 | |
| G-Contextual2023.10 | 70.3 | 75.2 | 59.9 | 75.9 | 79.2 | 58.4 | 69.8 | — | — | |
| G-Contextual2023.05 | 70.3 | 75.2 | 59.9 | 75.9 | 79.2 | 58.4 | 69.8 | — | — | |
| SubGDiffBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 70.2 | 77.2 | 88.2 | 77.6 | 82.1 | 62.2 | 74.85 | 65 | 77.3 | |
| ChemBERTa-2 MLM-5MPre-training Objective=MLM, Parameters=5M2024.02 | 70.1 | — | — | — | 79.3 | — | — | — | — | |
| MoleculeSDE(VP)Backbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 70.1 | 77 | 82.6 | 77.3 | 81.4 | 60.8 | 73.73 | 64 | 76.6 | |
| GROVERModel size=base2023.10 | 70 | 74.3 | 81.2 | 62.5 | 82.6 | 64.8 | 72.6 | — | — | |
| GTOT-TuningBackbone=GIN (contextpred)2022.03 | 70 | 75.6 | 72 | 78.2 | 83.4 | 63.5 | 73.34 | 64 | 80 | |
| BSSBackbone=GIN (supervised_contextpred)2022.03 | 70 | 78.3 | 73.7 | 79.9 | 84.2 | 62.8 | 74.16 | 65.8 | 78.6 | |
| GROVERvariant=base2023.05 | 70 | 74.3 | 81.2 | 62.5 | 82.6 | 64.8 | 72.6 | — | — | |
| GROVERSplit=scaffold splitting, Seeds=102026.02 | 70 | 74.3 | 81.2 | 62.5 | 82.6 | 64.8 | 71.01 | 65.4 | 67.3 | |
| StochNormBackbone=GIN (supervised_contextpred)2022.03 | 69.8 | 78.4 | 73.2 | 80.2 | 84.2 | 62.2 | 74.58 | 66.1 | 82.5 | |
| ChemBERTa-2 MLM-77MPre-training Objective=MLM, Parameters=77M2024.02 | 69.8 | — | — | — | 73.5 | — | — | — | — | |
| GraphCLSplit=scaffold splitting, Seeds=102026.02 | 69.7 | 73.9 | 76 | 78.5 | 75.4 | 60.5 | 70.78 | 62.4 | 69.8 | |
| ChemBERTa-2 MLM-10MPre-training Objective=MLM, Parameters=10M2024.02 | 69.6 | — | — | — | 72.9 | — | — | — | — | |
| GROVERModel size=large2023.10 | 69.5 | 73.5 | 76.2 | 68.2 | 81 | 65.4 | 72.3 | — | — | |
| GROVERvariant=large2023.05 | 69.5 | 73.5 | 76.2 | 68.2 | 81 | 65.4 | 72.3 | — | — | |
| No Pretrain2024.02 | 69.4 | — | — | 73 | 76.3 | — | — | — | — | |
| GraphMVPBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 69.4 | 76.2 | 86.5 | 76.2 | 79.8 | 60.5 | 73.66 | 64.5 | 76.2 | |
| StochNormBackbone=GIN (contextpred)2022.03 | 69.3 | 74.9 | 65.5 | 77.6 | 80.5 | 61 | 71.03 | 63.4 | 76 | |
| MegaMolBART2025.06 | 68.89 | 73.89 | 78.12 | 71.04 | 82.46 | 59.52 | 69.84 | 63.32 | 61.51 | |
| Fine-TuningBackbone=GIN (supervised_contextpred)2022.03 | 68.7 | 78.1 | 72.6 | 79.9 | 84.5 | 62.7 | 74.19 | 65.7 | 81.3 | |
| Feature (DELTA w/o ATT)Backbone=GIN (supervised_contextpred)2022.03 | 68.6 | 77.9 | 72.7 | 75.7 | 78.4 | 63 | 73.45 | 65.7 | 85.6 | |
| L2_SPBackbone=GIN (supervised_contextpred)2022.03 | 68.5 | 78.7 | 71.8 | 77.5 | 84.5 | 63.8 | 74.44 | 65.7 | 85 | |
| DELTABackbone=GIN (supervised_contextpred)2022.03 | 68.4 | 77.9 | 72.7 | 75.6 | 79 | 62.9 | 73.5 | 65.6 | 85.9 | |
| 3D InfoMaxBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 68.3 | 76.1 | 79.9 | 75.9 | 79.7 | 60.6 | 72.47 | 64.8 | 74.4 | |
| MoleculeSDE(VE)Backbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 68.3 | 76.9 | 80.8 | 77 | 79.9 | 60.2 | 73.15 | 64.7 | 76.8 | |
| L2_SPBackbone=GIN (contextpred)2022.03 | 68.2 | 73.6 | 68.1 | 75.7 | 82.2 | 61.1 | 70.25 | 62.4 | 76.7 | |
| BSSBackbone=GIN (contextpred)2022.03 | 68.1 | 75.9 | 70.9 | 77.6 | 82.4 | 60.9 | 72.21 | 63.9 | 78 | |
| random initBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 68.1 | 75.3 | 83.7 | 75.2 | 76.7 | 57 | 71.6 | 62.1 | 74.6 | |
| Fine-TuningBackbone=GIN (contextpred)2022.03 | 68 | 75.7 | 65.9 | 77.3 | 79.6 | 60.9 | 70.85 | 63.9 | 75.8 | |
| DELTABackbone=GIN (contextpred)2022.03 | 67.8 | 75.2 | 73.4 | 77.5 | 81.8 | 62.2 | 72.68 | 63.3 | 80.2 | |
| InfoGraphBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 67.5 | 73.2 | 76.5 | 75.1 | 77.8 | 59.9 | 70.96 | 63.7 | 74.1 | |
| InfoGraphSplit=scaffold splitting, Seeds=102026.02 | 67.5 | 73.2 | 76.5 | 75.1 | 77.8 | 59.9 | 70.98 | 63.7 | 74.1 | |
| MolCLRBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 66.6 | 73 | 86.1 | 76.2 | 71.5 | 57.5 | 70.79 | 62.9 | 72.5 | |
| MolCLRSplit=scaffold splitting, Seeds=102026.02 | 66.6 | 73 | 86.1 | 76.2 | 71.5 | 57.5 | 70.79 | 62.9 | 72.5 | |
| G-Motif2023.10 | 66.4 | 73.2 | 77.8 | 73.8 | 73.4 | 60.6 | 70.9 | — | — | |
| G-Motif2023.05 | 66.4 | 73.2 | 77.8 | 73.8 | 73.4 | 60.6 | 70.9 | — | — | |
| Galactica2023.10 | 66.1 | 68.9 | 82.6 | 74.5 | 61.7 | 63.2 | 69.5 | — | — | |
| Galactica2023.05 | 66.1 | 68.9 | 82.6 | 74.5 | 61.7 | 63.2 | 69.5 | — | — | |
| ContextPredBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 65.7 | 74.2 | 77.2 | 77.1 | 76 | 62.2 | 71.28 | 62.5 | 75.3 | |
| ContextPredSplit=scaffold splitting, Seeds=102026.02 | 65.7 | 74.2 | 77.2 | 77.1 | 76 | 62.2 | 71.28 | 62.5 | 75.3 | |
| AttrMaskBackbone=GIN, Splitting=scaffold, Number of random seeds=32024.05 | 65 | 74.8 | 87.7 | 76.8 | 79.7 | 61.2 | 72.68 | 62.9 | 73.4 | |
| AttrMaskSplit=scaffold splitting, Seeds=102026.02 | 65 | 74.8 | 87.7 | 76.8 | 79.7 | 61.2 | 72.68 | 62.9 | 73.4 | |
| Feature (DELTA w/o ATT)Backbone=GIN (contextpred)2022.03 | 61.4 | 71.1 | 64 | 74 | 76.3 | 62.4 | 68.64 | 61.5 | 78.4 |