3D Molecule Generation on QM9 (test)
100ValidityGeoLDM
Evaluation results
| Method | Links | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GeoLDMSamples=10,0002026.03 | 100 | 99.9 | 97.5 | — | 98 | — | — | — | — | — | 0.005 | 0.017 | 0.003 | 0.007 | 0.435 | |
| FuncMolSamples=10,0002026.03 | 100 | 99 | 89.2 | — | 92.8 | — | — | — | — | — | 0.021 | 0.012 | 0.006 | 0.005 | 1.56 | |
| QM9 (Ground Truth)Bond assignment algorithm=xyz2mol2023.11 | 99.99 | — | — | — | 99.84 | — | — | — | — | — | — | — | — | — | — | |
| EDMSamples=10,0002026.03 | 99 | 99.8 | 97.9 | — | 98.5 | — | — | — | — | — | 0.011 | 0.021 | 0.002 | 0.001 | 0.44 | |
| Permutation-Symmetrized DiffusionBackbone=SemlaFlow, Feature Representation=continuous, Sampling=MCMC2026.03 | 98.74 | 99.89 | 98.48 | — | 100 | 67.72 | — | — | — | — | — | — | — | — | — | |
| EDM + Soft Metropolis–HastingsBackbone=EDM, Guidance=Soft Metropolis–Hastings2026.01 | 98.7 | 99.56 | 91.7 | 83.2 | — | — | — | — | — | — | — | — | — | — | — | |
| VoxMolSamples=10,0002026.03 | 98.7 | 99.2 | 89.3 | — | 92.1 | — | — | — | — | — | 0.023 | 0.029 | 0.009 | 0.003 | 1.96 | |
| VECMOL_NFSamples=10,0002026.03 | 98.6 | 99.8 | 97.6 | — | 99.9 | — | — | — | — | — | 0.023 | 0.009 | 0.004 | 0.019 | 0.9 | |
| EQGAT-DiffSetup=default QM9 setup2026.03 | 98.58 | 99.87 | 98.24 | — | 100 | 61.62 | — | — | — | — | — | — | — | — | — | |
| VECMOLSamples=10,0002026.03 | 98.4 | 99.8 | 97.4 | — | 98 | — | — | — | — | — | 0.038 | 0.011 | 0.006 | 0.024 | 1.01 | |
| VECMOL_DiffSamples=10,0002026.03 | 98.4 | 99.8 | 97.4 | — | 99.7 | — | — | — | — | — | 0.037 | 0.011 | 0.006 | 0.022 | 0.99 | |
| Elign (EDM + UMA-1p1-M)Backbone=EDM, Reward Model=UMA-1p1-M2026.01 | 98.32 | 99.33 | 93.7 | 95.31 | — | — | — | — | — | — | — | — | — | — | — | |
| RLPF (EDM + DFT PPO)Backbone=EDM, Optimization=DFT PPO2026.01 | 98.22 | 99.08 | 93.37 | 92.87 | — | — | — | — | — | — | — | — | — | — | — | |
| MiDiBond Generation Strategy=generate bonds directly, NFE=5002024.06 | 97.9 | 99.8 | 97.5 | — | 97.6 | — | — | — | — | — | — | — | — | — | — | |
| Data2023.05 | 97.7 | 99 | 95.2 | 97.7 | — | — | — | — | — | — | — | — | — | — | — | |
| QM9 (Ground Truth)Bond assignment algorithm=Lookup Table2023.11 | 97.6 | — | — | — | 99.89 | — | — | — | — | — | — | — | — | — | — | |
| FlowMolBond Generation Strategy=generate bonds directly, NFE=1002024.06 | 97.3 | 99.7 | 96.2 | — | — | — | — | — | — | — | — | — | — | — | — | |
| Geo2Seq2025.12 | 97.1 | 98.9 | 93.2 | — | 81.7 | — | — | — | — | — | — | — | — | — | — | |
| GeoBFNBond Generation Strategy=infer bonds from coordinates, NFE=20002024.06 | 96.9 | 99.3 | 93.3 | — | 95.4 | — | — | — | — | — | — | — | — | — | — | |
| GFMDiffBond Generation Strategy=infer bonds from coordinates, NFE=5002024.06 | 96.3 | 98.9 | 87.7 | — | 98.8 | — | — | — | — | — | — | — | — | — | — | |
| GeoBFN2026.01 | 95.31 | 99.08 | 90.87 | 92.96 | — | — | — | — | — | — | — | — | — | — | — | |
| MUDiffBond Generation Strategy=infer bonds from coordinates, NFE=10002024.06 | 95.3 | 98.8 | 89.9 | — | 99.1 | — | — | — | — | — | — | — | — | — | — | |
| GeoLDM + Soft Metropolis–HastingsBackbone=GeoLDM, Guidance=Soft Metropolis–Hastings2026.01 | 95.1 | 99.09 | 91.3 | 94.9 | — | — | — | — | — | — | — | — | — | — | — | |
| UniGEM2026.01 | 95 | 99 | 89.8 | 93.2 | — | — | — | — | — | — | — | — | — | — | — | |
| GCDMBond Generation Strategy=infer bonds from coordinates, NFE=10002024.06 | 94.8 | 98.7 | 85.7 | — | 98.4 | — | — | — | — | — | — | — | — | — | — | |
| EDN2026.01 | 94.8 | 98.9 | 89.1 | 92.6 | — | — | — | — | — | — | — | — | — | — | — | |
| EquiFMBond Generation Strategy=infer bonds from coordinates, NFE=2102024.06 | 94.7 | 98.9 | 88.3 | — | 98.7 | — | — | — | — | — | — | — | — | — | — | |
| QM9 (Ground Truth)Bond assignment algorithm=OpenBabel2023.11 | 94.6 | — | — | — | 99.97 | — | — | — | — | — | — | — | — | — | — | |
| QUETZALsource_code_and_model_weights_available=true, evaluation_runs=mean of 3 independent runs2025.12 | 94.6 | 98.3 | 87.5 | — | 90.1 | 24.7 | — | — | — | — | — | — | — | — | — | |
| NEATevaluation_runs=mean of 3 independent runs2025.12 | 93.9 | 98.1 | 84.2 | — | 88.8 | 63.9 | — | — | — | — | — | — | — | — | — | |
| GEOLDM2023.05 | 93.8 | 98.9 | 89.4 | 92.7 | — | — | — | — | — | — | — | — | — | — | — | |
| GeoLDMBond Generation Strategy=infer bonds from coordinates, NFE=10002024.06 | 93.8 | 98.9 | 89.4 | — | 98.8 | — | — | — | — | — | — | — | — | — | — | |
| GeoLDM2026.01 | 93.8 | 98.9 | 89.4 | 92.7 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM + Rejection SamplingBackbone=EDM, Method=Rejection Sampling2026.01 | 93.2 | 98.99 | 89.47 | 92.6 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM + UMA-1p1-M GuidanceBackbone=EDM, Guidance=UMA-1p1-M2026.01 | 92.98 | 98.94 | 87.25 | 92.98 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM + UMA-1p1-S GuidanceBackbone=EDM, Guidance=UMA-1p1-S2026.01 | 92.54 | 98.9 | 87 | 92.34 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM-Bridge2023.05 | 92 | 98.8 | 84.6 | 90.7 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM-BRIDGE2026.01 | 92 | 98.8 | 84.6 | 90.7 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM2023.05 | 91.9 | 98.7 | 82 | 90.7 | — | — | — | — | — | — | — | — | — | — | — | |
| EDMBond Generation Strategy=infer bonds from coordinates, NFE=10002024.06 | 91.9 | 98.7 | 82 | — | 98.9 | — | — | — | — | — | — | — | — | — | — | |
| EDMBackbone=EDM2026.01 | 91.9 | 98.7 | 82 | 90.7 | — | — | — | — | — | — | — | — | — | — | — | |
| GeoLDM + xTB GuidanceBackbone=GeoLDM, Guidance=xTB2026.01 | 91.4 | 99.02 | 90.6 | 91.4 | — | — | — | — | — | — | — | — | — | — | — | |
| EDMBond assignment algorithm=Lookup Table2023.11 | 90.77 | — | — | — | 98.64 | — | — | — | — | — | — | — | — | — | — | |
| GRAPHLDMData Augmentation=true2023.05 | 90.5 | 97.9 | 78.7 | 89.5 | — | — | — | — | — | — | — | — | — | — | — | |
| GDMData Augmentation=true2023.05 | 90.4 | 97.6 | 71.6 | 89.5 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM + DPM Solver++ + UMA-1p1-S GuidanceBackbone=EDM, Sampler=DPM Solver++, Guidance=UMA-1p1-S2026.01 | 89.84 | 97.72 | 76.23 | 89.84 | — | — | — | — | — | — | — | — | — | — | — | |
| EDM + DPM Solver++Backbone=EDM, Sampler=DPM Solver++2026.01 | 87.82 | 95.72 | 72.23 | 87.82 | — | — | — | — | — | — | — | — | — | — | — | |
| EDMBond assignment algorithm=xyz2mol2023.11 | 86.74 | — | — | — | 99.16 | — | — | — | — | — | — | — | — | — | — | |
| G-Schnet2023.05 | 85.5 | 95.7 | 68.1 | 80.3 | — | — | — | — | — | — | — | — | — | — | — | |
| GRAPHLDMData Augmentation=false2023.05 | 83.6 | 97.2 | 70.5 | 82.7 | — | — | — | — | — | — | — | — | — | — | — | |
| SymphonyBond assignment algorithm=xyz2mol2023.11 | 83.5 | — | — | — | 97.98 | — | — | — | — | — | — | — | — | — | — | |
| G-SchNetBond assignment algorithm=Lookup Table2023.11 | 80.13 | — | — | — | 93.2 | — | — | — | — | — | — | — | — | — | — | |
| G-SchNetre-evaluated with paper pipeline=true2025.12 | 80.1 | 93.7 | 63.6 | — | 74.7 | 55.1 | — | — | — | — | — | — | — | — | — | |
| EDMBond assignment algorithm=OpenBabel2023.11 | 77.75 | — | — | — | 99.95 | — | — | — | — | — | — | — | — | — | — | |
| G-SchNetBond assignment algorithm=xyz2mol2023.11 | 74.97 | — | — | — | 96.73 | — | — | — | — | — | — | — | — | — | — | |
| SymphonyBond assignment algorithm=OpenBabel2023.11 | 74.69 | — | — | — | 99.61 | — | — | — | — | — | — | — | — | — | — | |
| SymphonyBond assignment algorithm=Lookup Table2023.11 | 68.11 | — | — | — | 97.68 | — | — | — | — | — | — | — | — | — | — | |
| Symphonyre-evaluated with paper pipeline=true2025.12 | 68.1 | 90.8 | 43.9 | — | 66.5 | 41.3 | — | — | — | — | — | — | — | — | — | |
| G-SchNetBond assignment algorithm=OpenBabel2023.11 | 61.83 | — | — | — | 98.71 | — | — | — | — | — | — | — | — | — | — | |
| ENF2023.05 | 40.2 | 85 | 4.9 | 39.4 | — | — | — | — | — | — | — | — | — | — | — | |
| G-SphereNetBond assignment algorithm=xyz2mol2023.11 | 26.92 | — | — | — | 21.69 | — | — | — | — | — | — | — | — | — | — | |
| G-SphereNetre-evaluated with paper pipeline=true2025.12 | 16.4 | 67.8 | 14 | — | 3.8 | 6.7 | — | — | — | — | — | — | — | — | — | |
| G-SphereNetBond assignment algorithm=Lookup Table2023.11 | 16.36 | — | — | — | 23.29 | — | — | — | — | — | — | — | — | — | — | |
| G-SphereNetBond assignment algorithm=OpenBabel2023.11 | 9.86 | — | — | — | 7.51 | — | — | — | — | — | — | — | — | — | — | |
| EDMModel Category=Diffusion, RDKit Version (xyz2mol)=v2023.3.3 or unspecified2025.12 | — | 98.7 | 82 | — | — | — | 91.9 | 90.7 | 86.7 | 86 | — | — | — | — | — | |
| G-SchNetModel Category=Autoregressive, Evaluation Source=Re-evaluated with our pipeline2025.12 | — | 93.7 | 63.6 | — | — | — | 80.1 | 74.7 | 73 | 70.6 | — | — | — | — | — | |
| G-SphereNetModel Category=Autoregressive, Evaluation Source=Re-evaluated with our pipeline2025.12 | — | 67.8 | 14 | — | — | — | 16.4 | 3.8 | 37.7 | 7.2 | — | — | — | — | — | |
| GCDMModel Category=Diffusion2025.12 | — | 98.7 | 86 | — | — | — | 94.9 | 93.4 | — | — | — | — | — | — | — | |
| GDMData Augmentation=false2023.05 | — | 97 | 63.2 | — | — | — | — | — | — | — | — | — | — | — | — | |
| Geo2SeqModel Category=Autoregressive2025.12 | — | 98.9 | 93.2 | — | — | — | 97.1 | 81.7 | — | — | — | — | — | — | — | |
| GeoBFNModel Category=Diffusion2025.12 | — | 99.3 | 93.3 | — | — | — | 96.9 | 92.4 | — | — | — | — | — | — | — | |
| GeoLDMModel Category=Diffusion, RDKit Version (xyz2mol)=v2023.3.3 or unspecified2025.12 | — | 98.9 | 89.4 | — | — | — | 93.8 | 92.7 | 91.3 | 90.3 | — | — | — | — | — | |
| NEATModel Category=Autoregressive2025.12 | — | 98.1 | 84.2 | — | — | — | 93.9 | 88.8 | 94.4 | 90.5 | — | — | — | — | — | |
| QUETZALModel Category=Autoregressive, Evaluation Source=Source code and weights re-evaluated2025.12 | — | 98.3 | 87.5 | — | — | — | 94.6 | 90.1 | 93.7 | 89.1 | — | — | — | — | — | |
| SymDiffModel Category=Diffusion, RDKit Version (xyz2mol)=v2023.3.3 or unspecified2025.12 | — | 98.9 | 89.7 | — | — | — | 96.4 | 94.1 | 92.8 | 91.4 | — | — | — | — | — | |
| SymphonyModel Category=Autoregressive, Evaluation Source=Re-evaluated with our pipeline2025.12 | — | 90.8 | 43.9 | — | — | — | 68.1 | 66.5 | 77 | 75.2 | — | — | — | — | — | |
| Test dataDescription=Ground truth reference from test set2025.12 | — | 99.3 | 94.8 | — | — | — | 97.5 | 97.5 | 100 | 100 | — | — | — | — | — | |
| UniGEMModel Category=Diffusion2025.12 | — | 99 | 89.8 | — | — | — | 95 | 93.2 | — | — | — | — | — | — | — |