Table 4 Classification accuracy and standard deviation for several kernels and their variant when plugged into the Gaussian RBF kernel
Dataset | MK-IL | MK-L | PM | DeepGK | DBR a | Prop | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Klin | KRBF | Klin | KRBF | Klin | KRBF | Klin | KRBF | Klin | KRBF | Klin | KRBF |
NCI1 | 76.8 ±0.3 | 78.1 ±0.3 | 72.8 ±0.3 | 75.5 ±0.3 | 73.3 ±0.3 | 80.0 ±0.3 | 74.9 ±0.2 | 78.4 ±0.3 | 67.4 ±0.3 | 76.0 ±0.2 | 84.6 ±0.2 | 85.6 ±0.2 |
NCI109 | 75.4 ±0.3 | 75.9 ±0.3 | 71.9 ±0.3 | 74.1 ±0.4 | 71.1 ±0.3 | 78.8 ±0.2 | 73.3 ±0.2 | 77.7 ±0.3 | 66.6 ±0.2 | 75.3 ±0.2 | 84.1 ±0.2 | 84.7 ±0.2 |
PTC-FR | 69.1 ±0.6 | 68.6 ±0.7 | 68.4 ±0.7 | 68.1 ±0.9 | 65.9 ±0.8 | 65.0 ±1.1 | 66.4 ±1.2 | 63.8 ±1.5 | 65.3 ±0.5 | 64.0 ±0.7 | 66.0 ±1.5 | 65.6 ±1.0 |
PTC-MR | 60.6 ±1.0 | 60.5 ±1.1 | 59.1 ±1.7 | 59.7 ±1.4 | 61.5 ±1.3 | 59.5 ±2.0 | 59.9 ±1.5 | 60.9 ±1.7 | 53.7 ±1.3 | 55.1 ±1.9 | 59.9 ±1.6 | 61.3 ±2.1 |
PTC-FM | 58.6 ±1.8 | 64.7 ±0.6 | 60.4 ±0.9 | 61.4 ±1.6 | 59.7 ±1.4 | 62.2 ±0.8 | 62.6 ±0.9 | 60.9 ±1.1 | 56.2 ±1.5 | 59.8 ±1.5 | 60.9 ±1.6 | 61.7 ±1.6 |
PTC-MM | 62.1 ±1.6 | 65.0 ±1.4 | 63.8 ±1.2 | 63.1 ±0.7 | 62.9 ±1.3 | 62.2 ±1.0 | 63.3 ±0.9 | 61.8 ±1.4 | 59.4 ±1.1 | 63.5 ±1.0 | 63.9 ±1.0 | 64.6 ±1.9 |
MUTAG | 82.8 ±1.4 | 83.7 ±0.8 | 83.1 ±1.3 | 83.5 ±1.0 | 84.9 ±1.2 | 86.7 ±0.8 | 85.1 ±1.5 | 84.4 ±0.7 | 86.2 ±1.6 | 84.6 ±0.7 | 90.3 ±0.9 | 86.1 ±1.1 |
Mutagenicity | 70.7 ±0.3 | 75.2 ±0.2 | 70.9 ±0.3 | 75.3 ±0.2 | 72.1 ±0.2 | 75.5 ±0.3 | 79.4 ±0.3 | 80.2 ±0.2 | 66.2 ±0.1 | 66.8 ±0.5 | 67.5 ±0.2 | 76.7 ±0.4 |
AIDS | 99.6 ±0.0 | 99.6 ±0.1 | 99.6 ±0.0 | 99.6 ±0.0 | 99.7 ±0.0 | 99.7 ±0.0 | 99.6 ±0.0 | 99.6 ±0.0 | 99.3 ±0.1 | 99.7 ±0.0 | 99.7 ±0.0 | 99.7 ±0.0 |
BZR | 88.1 ±0.8 | 88.2 ±0.8 | 88.1 ±0.6 | 87.8 ±0.7 | 84.5 ±1.0 | 85.5 ±0.7 | 86.5 ±0.6 | 87.8 ±0.6 | 82.8 ±0.9 | 84.1 ±0.8 | 87.1 ±0.5 | 87.7 ±1.0 |
COX2 | 81.2 ±1.0 | 81.1 ±0.5 | 80.5 ±0.8 | 80.5 ±0.7 | 80.7 ±0.5 | 80.3 ±0.7 | 80.4 ±1.1 | 81.4 ±0.6 | 78.1 ±0.1 | 77.3 ±0.7 | 81.7 ±0.8 | 81.5 ±0.9 |
DHFR | 81.5 ±0.8 | 82.1 ±0.3 | 79.2 ±0.8 | 80.0 ±0.7 | 75.3 ±0.7 | 78.1 ±0.8 | 80.7 ±1.0 | 81.0 ±0.8 | 75.1 ±0.5 | 78.3 ±0.7 | 82.8 ±0.6 | 83.2 ±0.7 |
DD | 78.3 ±0.3 | 78.2 ±0.3 | 77.3 ±0.4 | 77.3 ±0.4 | 78.7 ±0.3 | 79.2 ±0.9 | 79.4 ±0.4 | 71.0 ±0.2 | 78.8 ±0.6 | 78.2 ±0.6 | 78.9 ±0.3 | 81.6 ±0.5 |
PROTEINS | 76.6 ±0.6 | 76.8 ±0.4 | 75.1 ±0.2 | 74.8 ±0.5 | 74.5 ±0.4 | 74.6 ±0.5 | 75.7 ±0.3 | 74.2 ±0.4 | — | — | 74.3 ±0.5 | 74.6 ±0.5 |
ENZYMES | 64.1 ±1.3 | 63.5 ±1.1 | 61.6 ±1.2 | 62.0 ±1.2 | 40.2 ±1.0 | 49.3 ±1.1 | 42.3 ±1.0 | 58.9 ±1.1 | 37.6 ±0.7 | 39.5 ±1.3 | 49.0 ±1.6 | 62.6 ±0.9 |
IMDB-BINARY | 69.4 ±0.6 | 69.9 ±0.5 | 70.6 ±0.5 | 70.1 ±0.4 | 70.7 ±0.6 | 71.1 ±0.9 | 60.5 ±0.3 | 70.2 ±0.7 | — | — | 73.5 ±0.3 | 71.2 ±0.7 |
IMDB-MULTI | 46.1 ±0.7 | 47.0 ±0.5 | 47.1 ±0.6 | 47.6 ±0.4 | 47.8 ±0.6 | 47.8 ±0.6 | 40.8 ±1.1 | 46.1 ±0.7 | — | — | 49.8 ±0.6 | 51.0 ±0.7 |
REDDIT-BINARY | — | — | — | — | 82.3 ±0.2 | 82.7 ±0.4 | 82.4 ±0.1 | 67.8 ±0.2 | — | — | 78.2 ±0.3 | 85.5 ±0.3 |
MSRC-9 | 90.9 ±1.0 | 90.4 ±0.5 | 90.4 ±1.2 | 90.4 ±0.8 | 90.4 ±1.4 | 90.1 ±1.0 | 91.8 ±0.8 | 88.2 ±1.2 | — | — | 89.4 ±1.3 | 89.7 ±0.9 |
MSRC-21 | 89.0 ±0.6 | 89.0 ±0.8 | 89.3 ±0.5 | 89.3 ±0.5 | 91.3 ±0.5 | 91.2 ±0.5 | 89.9 ±0.5 | 27.5 ±1.2 | — | — | 88.6 ±0.5 | 89.8 ±0.6 |
MSRC-21C | 85.7 ±0.6 | 85.6 ±0.9 | 85.6 ±0.9 | 84.8 ±1.1 | 84.4 ±0.9 | 84.6 ±0.9 | 85.1 ±1.4 | 76.8 ±1.3 | — | — | 81.4 ±1.1 | 81.8 ±1.1 |
Tox21-AR | 97.7 ±0.0 | 97.7 ±0.0 | 97.4 ±0.0 | 97.4 ±0.0 | 97.6 ±0.0 | 97.7 ±0.0 | 97.0 ±0.0 | 97.6 ±0.0 | — | — | 97.8 ±0.0 | 97.8 ±0.0 |
Tox21-MMP | 86.9 ±0.1 | 87.2 ±0.1 | 86.8 ±0.1 | 87.2 ±0.1 | 86.6 ±0.2 | 89.7 ±0.1 | 86.3 ±0.1 | 90.4 ±0.1 | — | — | 84.7 ±0.1 | 89.6 ±0.2 |
Tox21-AHR | 89.6 ±0.0 | 89.6 ±0.0 | 89.4 ±0.1 | 89.5 ±0.0 | 89.4 ±0.1 | 91.7 ±0.1 | 88.7 ±0.1 | 91.8 ±0.1 | — | — | 89.2 ±0.0 | 91.1 ±0.1 |
Average | 77.4 | 78.2 | 76.9 | 77.3 | 76.1 | 77.6 | 76.3 | 74.1 | 69.5 | 71.6 | 77.6 | 78.1 |