Table 4 Performance comparison of Transformer and baselines in terms of successful property constraints, successful structure constraints and both metrics simultaneously
From: Transformer-based molecular optimization beyond matched molecular pairs
Dataset | Model | Successful property constraints (%) | Successful structure constraints (%) | Successful property and structure constraints (%) |
|---|---|---|---|---|
MMP | Transformer | 61.90 | 91.55 | 58.09 |
Transformer-U | 33.67 | 93.25 | 31.85 | |
Random | 13.44±0.43 | 100 | 13.44±0.43 | |
Similarity (\(\ge\)0.5) | Transformer | 51.83 | 82.30 | 44.53 |
Transformer-U | 29.04 | 83.63 | 25.32 | |
Random | 15.17±0.27 | 100 | 15.17±0.27 | |
Similarity ([0.5,0.7)) | Transformer | 46.75 | 68.09 | 32.96 |
Transformer-U | 26.23 | 69.13 | 18.72 | |
Random | 14.57±0.37 | 100 | 14.57±0.37 | |
Similarity (\(\ge\)0.7) | Transformer | 65.09 | 82.68 | 56.07 |
Transformer-U | 39.57 | 84.83 | 34.70 | |
Random | 11.48±0.29 | 100 | 11.48±0.29 | |
Scaffold | Transformer | 61.53 | 95.32 | 59.69 |
Transformer-U | 37.16 | 95.69 | 36.26 | |
Random | 17.22±0.74 | 100 | 17.22±0.74 | |
Scaffold generic | Transformer | 55.05 | 96.01 | 53.66 |
Transformer-U | 32.55 | 96.30 | 31.69 | |
Random | 16.48±0.41 | 100 | 16.48±0.41 |