Add evaluated crossdocked-scaffold checkpoint and metrics; simplify GEOM scaffold name
320d7f0 verified | { | |
| "model": "crossdocked-scaffold", | |
| "task": "scaffold_decoration_in_pocket", | |
| "dataset": "CrossDocked", | |
| "variant": "implicit_h", | |
| "hydrogens": "implicit", | |
| "completed_epochs": 100, | |
| "global_step": 40000, | |
| "checkpoint": "epoch_100.ckpt", | |
| "checkpoint_sha256": "4d17db9a77e75e12c452f0512301e5894b2d1a0bd9725186e35bf183a238b2b6", | |
| "checkpoint_bytes": 625018500, | |
| "lora_rank": 8, | |
| "lora_alpha": 8.0, | |
| "base_model": "chembl3d-implicit-h", | |
| "base_completed_epochs": 365, | |
| "finetune_fraction": 0.9, | |
| "in_vacuum_replay_fraction": 0.1, | |
| "training_scaffold_kind": "libinvent", | |
| "freeze_keep_positions": false, | |
| "freeze_keep_charges": true, | |
| "default_eval_weights": "ema", | |
| "integration_steps": 100, | |
| "original_checkpoint_including_optimizer": true, | |
| "evaluation": { | |
| "split": "test", | |
| "protocol": "diffdec", | |
| "panels": { | |
| "single": 43, | |
| "multi": 102 | |
| }, | |
| "seeds": [ | |
| 42, | |
| 43, | |
| 44 | |
| ], | |
| "samples_per_condition": 100, | |
| "total_generation_attempts": 43500, | |
| "precision": "float32 without autocast", | |
| "standard_deviation": "sample (ddof=1)", | |
| "summary": "summary.csv", | |
| "compatibility_notes": [ | |
| "Published DiffDec conditions and metric formulas; original reference CSVs unavailable, so reference scaffold/protein strings are reconstructed.", | |
| "Morph predicted bond topology is retained, rather than inferred from XYZ with Open Babel.", | |
| "RDKit 2025.9.6 and deterministic per-attempt embedding seeds; upstream used older RDKit and unspecified embedding seeds.", | |
| "Docking reconstructs and UFF-minimizes SMILES; the stored generated coordinates are unchanged." | |
| ] | |
| }, | |
| "atom_tokens": [ | |
| "B", | |
| "Br", | |
| "C", | |
| "Cl", | |
| "F", | |
| "I", | |
| "N", | |
| "O", | |
| "P", | |
| "S", | |
| "Se", | |
| "Si" | |
| ], | |
| "edge_tokens": [ | |
| "<NO_BOND>", | |
| "1", | |
| "2", | |
| "3" | |
| ], | |
| "charge_tokens": [ | |
| "-1", | |
| "0", | |
| "1" | |
| ], | |
| "pocket_vocab": { | |
| "atom_tokens": [ | |
| "C", | |
| "N", | |
| "O", | |
| "S" | |
| ], | |
| "edge_tokens": [ | |
| "<NO_BOND>" | |
| ], | |
| "charge_tokens": [ | |
| "0" | |
| ] | |
| }, | |
| "checkpoint_stored_epoch": 100, | |
| "not_unconditional_catalog_entry": true | |
| } | |