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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
  1. The results in bold indicate the best values; higher values are better
  2. Each model is trained on the corresponding dataset for that row