Table 4 Performance of the AMNet using various choices of features on USPTO-15k test set
From: Learning symmetry-aware atom mapping in chemical reactions through deep graph matching
Selected | Avg. Acc. | %Top@1 | %Top@3 | %Top@5 | %Top@10 |
|---|---|---|---|---|---|
Atom feature | \((\%)\pm \hbox {std}\) | \((\%)\pm \hbox {std}\) | \((\%)\pm \hbox {std}\) | \((\%)\pm \hbox {std}\) | \((\%)\pm \hbox {std}\) |
Whole | \({{\textbf {97.3}}}\pm 0.1\) | \({{\textbf {66.2}}}\pm 0.1\) | \({{\textbf {96.6}}}\pm 0.0\) | \({{\textbf {99.3}}}\pm 0.0\) | \({{\textbf {99.7}}}\pm 0.0\) |
Whole - Atom type | \(47.3\pm 0.5\) | \(0.6\pm 0.4\) | \(4.5\pm 0.7\) | \(12.9\pm 0.7\) | \(27.4\pm 0.6\) |
Whole - # heavy neighbors | \(97.2\pm 0.1\) | \(60.4\pm 0.1\) | \(92.2\pm 0.0\) | \(98.1\pm 0.0\) | \(99.6\pm 0.0\) |
Whole - Formal charge | \(97.1\pm 0.1\) | \(58.1\pm 0.1\) | \(93.0\pm 0.0\) | \(98.2\pm 0.0\) | \(99.5\pm 0.0\) |
Whole - hybridization | \(97.1\pm 0.1\) | \(59.5\pm 0.1\) | \(93.1\pm 0.0\) | \(97.8\pm 0.0\) | \(99.6\pm 0.0\) |
Whole - explicit valence | \(69.8\pm 0.3\) | \(1.5\pm 0.3\) | \(20.8\pm 0.2\) | \(46.0\pm 0.1\) | \(77.8\pm 0.0\) |
Whole - is in ring | \(97.2\pm 0.1\) | \(58.9\pm 0.1\) | \(93.1\pm 0.0\) | \(98.2\pm 0.0\) | \(99.6\pm 0.0\) |
Whole - aromaticity | \(93.0\pm 0.2\) | \(35.8\pm 0.2\) | \(72.1\pm 0.1\) | \(83.2\pm 0.1\) | \(90.8\pm 0.1\) |
Whole - atomic mass scaled | \(97.2\pm 0.1\) | \(60.8\pm 0.1\) | \(93.5\pm 0.0\) | \(98.1\pm 0.0\) | \(99.6\pm 0.0\) |
Whole - VDW radius scaled | \(97.2\pm 0.1\) | \(60.3\pm 0.1\) | \(93.5\pm 0.0\) | \(97.8\pm 0.0\) | \(99.7\pm 0.0\) |
Whole - covalent radius scaled | \(97.1\pm 0.1\) | \(58.1\pm 0.1\) | \(93.0\pm 0.0\) | \(98.2\pm 0.0\) | \(99.5\pm 0.0\) |
Whole - chirality type | \(40.3\pm 0.4\) | \(0.4 \pm 0.1\) | \(2.4\pm 0.4\) | \(8.1 \pm 0.4\) | \(25.7\pm 0.3\) |
Atom type | \(95.3 \pm 0.1\) | \(35.5 \pm 0.1\) | \(87.7\pm 0.0\) | \(94.8 \pm 0.0\) | \(98.9\pm 0.0\) |
Atom type + aromaticity + explicit valence+ chirality type | \(96.4 \pm 0.1\) | \(61.3 \pm 0.1\) | 94.1 ± 0.0 | 98.5 ± 0.0 | 99.5 ±0.0 |