De Novo 3D Molecule Generation on GEOM-Drugs
100Atom Stability (2D)Train
Evaluation results
| Method | Links | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Train2025.12 | 100 | 0.251 | 100 | 100 | 100 | 0 | 58.5 | 99.9 | 58.4 | 13.73 | 86.1 | 2.8 | 0.0002 | 0.0002 | 0.0002 | — | |
| JODO2025.12 | 100 | 2.523 | 98.1 | 87.4 | 90.5 | 90.2 | 41.7 | 99.3 | 48.3 | 19.99 | 84.5 | 1 | 0.0849 | 0.0115 | 0.0007 | — | |
| EQGAT-diff2025.12 | 100 | 5.898 | 98.9 | 84.5 | 86.3 | 85.9 | 37.7 | 98.3 | 16.1 | 26.33 | 82.5 | 0.7 | 0.155 | 0.0521 | 0.0021 | — | |
| NExT-Mol2025.12 | 100 | 0.334 | 99.9 | 100 | 99.9 | 94.5 | 52.9 | 99.9 | 55.2 | 14.69 | 84.8 | — | 0.0205 | 0.0082 | 0.0002 | — | |
| UDM-3D2025.12 | 100 | 0.692 | 92.5 | 87.9 | 91.3 | 90.7 | 52.5 | 99 | 54 | 17.36 | 85.2 | 1.4 | 0.0099 | 0.0051 | 0.0002 | — | |
| MolSculpt2025.12 | 100 | 0.33 | 99.9 | 100 | 99.9 | 94.7 | 53.1 | 99.9 | 60.5 | 13.67 | 85.4 | 2.6 | 0.0787 | 0.0097 | 0.0003 | — | |
| JODOn=10,0002026.06 | 100 | — | 98.1 | 87.4 | 90.2 | — | — | — | — | 19.99 | 84.5 | 1 | — | — | — | 2.523 | |
| EQGAT-diffn=10,0002026.06 | 100 | — | 98.9 | 84.5 | 86.3 | — | — | — | — | 26.33 | 82.5 | 0.7 | — | — | — | 5.898 | |
| UDM-3Dn=10,0002026.06 | 100 | — | 92.5 | 87.9 | 90.7 | — | — | — | — | 17.36 | 85.2 | 1.4 | — | — | — | 0.692 | |
| TopVAE+DiTn=10,0002026.06 | 100 | — | 98.1 | 95.1 | 100 | — | — | — | — | 8.25 | 83.2 | 2 | — | — | — | 2.68 | |
| GeoLDMn=10,0002026.06 | 99.6 | — | 90.9 | 48.2 | 99.8 | — | — | — | — | 30.68 | 84.3 | 0.8 | — | — | — | 39.81 | |
| CDGS2025.12 | 99.1 | 22.051 | 70.6 | 28.5 | 28.5 | 28.5 | 26.2 | 78.9 | 2.2 | — | — | — | — | — | — | — | |
| EDMn=10,0002026.06 | 99.1 | — | 91.4 | 35.9 | 99.1 | — | — | — | — | 31.29 | 83.1 | 0.2 | — | — | — | 40.14 | |
| CDGSn=10,0002026.06 | 99.1 | — | 70.6 | 28.5 | 28.5 | — | — | — | — | — | — | — | — | — | — | 22.05 | |
| MiDi2025.12 | 96.8 | 7.054 | 82.2 | 63.3 | 65.4 | 65.2 | 39.2 | 95.1 | 19.6 | 23.14 | 75 | 0.3 | 0.117 | 0.0957 | 0.0045 | — | |
| MiDin=10,0002026.06 | 96.8 | — | 82.2 | 63.3 | 65.4 | — | — | — | — | 23.14 | 75 | 0.3 | — | — | — | 7.054 | |
| EDM2025.12 | — | — | — | — | — | — | — | — | — | 31.29 | 83.1 | 0.2 | 0.429 | 0.496 | 0.0146 | — | |
| EDM2026.06 | — | — | — | — | — | — | — | — | — | — | — | — | 0.429 | 0.496 | 0.0146 | — | |
| GeoLDM2025.12 | — | — | — | — | — | — | — | — | — | 30.68 | 84.3 | 0.8 | 0.391 | 0.422 | 0.0169 | — | |
| GeoLDM2026.06 | — | — | — | — | — | — | — | — | — | — | — | — | 0.391 | 0.422 | 0.0169 | — | |
| JODO2026.06 | — | — | — | — | — | — | — | — | — | — | — | — | 0.0849 | 0.0115 | 0.0007 | — | |
| TopVAE+DiT2026.06 | — | — | — | — | — | — | — | — | — | — | — | — | 0.0178 | 0.0158 | 0.0049 | — | |
| UDM-3D2026.06 | — | — | — | — | — | — | — | — | — | — | — | — | 0.0099 | 0.0051 | 0.0002 | — |