LoFlexMDM-Medium-Shared-BracketSAFE
Variable-length discrete diffusion model for bracket SAFE molecule generation.
Training
| Hyperparameter | Value |
|---|
| Learning rate | 0.0001 |
| Global batch size | 2048 |
| Block size | 256 |
| Training steps | 50000 |
| Weight decay | 0.01 |
| Dataset | Bracket SAFE (datamol-io/safe-gpt, ~1.17B molecules) |
| Checkpoint | EMA weights at step 50000 |
W&B run: learned-noise-icml/safe_lflexmdm_no_lora_fix_b_um_a1
Unconditional generation (de novo)
1024 sampling steps, 1000 molecules per run, mean ± std over 5 seeds (from paper Table 1 / appendix).
| conf. | p | Validity (%) | Diversity | Uniqueness (%) | Quality (%) |
|---|
| yes | 1.0 | 98.300 ± 0.100 | 0.900 ± 0.000 | 99.400 ± 0.200 | 51.500 ± 0.600 |
| yes | 0.9 | 99.200 ± 0.100 | 0.890 ± 0.000 | 99.600 ± 0.100 | 69.200 ± 1.100 |
| yes | 0.5 | 99.800 ± 0.000 | 0.850 ± 0.000 | 96.900 ± 0.200 | 70.800 ± 1.000 |
| no | 1.0 | 98.400 ± 0.100 | 0.900 ± 0.000 | 99.200 ± 0.100 | 52.800 ± 1.100 |
| no | 0.9 | 99.200 ± 0.100 | 0.890 ± 0.000 | 99.300 ± 0.100 | 66.800 ± 0.900 |
| no | 0.5 | 99.500 ± 0.000 | 0.860 ± 0.000 | 99.500 ± 0.100 | 71.200 ± 0.600 |
Conditional generation (fragment-constrained)
Means over 5 runs (from paper Table 2). Tasks: LD (linker design), ME (motif extension), SD (scaffold decoration), SG (superstructure generation).
| Task | Validity (%) | Diversity | Uniqueness (%) | Quality (%) |
|---|
| Linker design | 99.6 | 0.576 | 64.4 | 51.7 |
| Motif extension | 99.9 | 0.608 | 79.2 | 53.6 |
| Scaffold decoration | 99.8 | 0.601 | 82.6 | 40.5 |
| Superstructure generation | 100.0 | 0.593 | 72.6 | 37.0 |
Usage
See the
https://github.com/dhruvdcoder/LoFlexMDM release repository for training and evaluation instructions.
