Table 5 Performance comparison of the Transformer models trained on different types of molecular pairs on the restricted intersection test set (numbers in bracket represent the absolute increase or decrease compared to the corresponding Transformer model performance on the original test set in Table 4)
From: Transformer-based molecular optimization beyond matched molecular pairs
Test set | Type of molecular pairs where Transformer is trained | Successful property constraints (%) | Successful structure constraints (%) | Successful property and structure constraints (%) |
|---|---|---|---|---|
| Â | MMP | 65.71 (\(\uparrow\) 3.81) | 91.68 (\(\uparrow\) 0.13) | 61.82 (\(\uparrow\) 3.73) |
| Â | Similarity (\(\ge\)0.5) | 55.55 (\(\uparrow\) 3.72) | 84.47 (\(\uparrow\) 2.17) | 48.97 (\(\uparrow\) 4.44) |
Restricted | Similarity ([0.5,0.7)) | 50.17 (\(\uparrow\) 3.42) | 68.66 (\(\uparrow\) 0.57) | 35.28 (\(\uparrow\) 2.32) |
intersection | Similarity (\(\ge\)0.7) | 65.39 (\(\uparrow\) 0.30) | 81.49 (\(\downarrow\) 1.19) | 55.55 (\(\downarrow\) 0.52) |
| Â | Scaffold | 62.91 (\(\uparrow\) 1.38) | 94.42 (\(\downarrow\) 0.90) | 60.70 (\(\downarrow\) 1.01) |
| Â | Scaffold generic | 59.07 (\(\uparrow\) 4.02) | 96.14 (\(\uparrow\) 0.13) | 57.68 (\(\uparrow\) 4.02) |