Table 1 The table reports the root mean squared error (RMSE) on QM9, the mean absolute error (MAE) for ZINC, and R2 for DOCKSTRING (DOCK) and MoleculeNet, presented as mean ± standard deviation over 5 runs
From: An end-to-end attention-based approach for learning on graphs
Target | DropGIN | GAT | GATv2 | PNA | Graphormer | TokenGT | GPS | ESA | |
|---|---|---|---|---|---|---|---|---|---|
QM9 (↓) | μ | 0.55 ± 0.01 | 0.55 ± 0.01 | 0.55 ± 0.01 | 0.53 ± 0.01 | 0.63 ± 0.01 | 0.76 ± 0.02 | 0.94 ± 0.17 | 0.56 ± 0.00 |
α | 0.44 ± 0.03 | 0.48 ± 0.02 | 0.46 ± 0.02 | 0.48 ± 0.07 | 0.40 ± 0.02 | 0.45 ± 0.01 | 0.60 ± 0.13 | 0.40 ± 0.00 | |
ϵHOMO | 0.11 ± 0.00 | 0.11 ± 0.00 | 0.10 ± 0.00 | 0.10 ± 0.00 | 0.11 ± 0.00 | 0.12 ± 0.00 | 0.11 ± 0.00 | 0.10 ± 0.00 | |
ϵLUMO | 0.12 ± 0.00 | 0.12 ± 0.00 | 0.13 ± 0.00 | 0.11 ± 0.00 | 0.11 ± 0.00 | 0.13 ± 0.00 | 0.11 ± 0.00 | 0.11 ± 0.00 | |
Δϵ | 0.17 ± 0.00 | 0.16 ± 0.01 | 0.16 ± 0.00 | 0.14 ± 0.00 | 0.16 ± 0.00 | 0.18 ± 0.01 | 0.15 ± 0.01 | 0.15 ± 0.00 | |
〈R2〉 | 29.87 ± 0.34 | 30.91 ± 0.15 | 30.15 ± 0.36 | 28.50 ± 0.44 | 29.63 ± 0.35 | 31.54 ± 0.42 | 30.42 ± 1.19 | 28.33 ± 0.32 | |
ZPVE | 0.03 ± 0.00 | 0.03 ± 0.00 | 0.03 ± 0.00 | 0.03 ± 0.00 | 0.06 ± 0.03 | 0.03 ± 0.00 | 0.03 ± 0.01 | 0.03 ± 0.00 | |
U0 | 29.82 ± 6.32 | 27.82 ± 3.98 | 25.40 ± 3.62 | 31.64 ± 6.49 | 24.60 ± 4.70 | 15.48 ± 4.67 | 14.50 ± 4.34 | 4.78 ± 0.67 | |
U | 24.74 ± 6.31 | 30.91 ± 2.62 | 24.92 ± 4.18 | 25.04 ± 5.48 | 15.55 ± 8.23 | 12.45 ± 1.86 | 15.82 ± 4.26 | 6.80 ± 2.81 | |
H | 34.02 ± 5.66 | 28.92 ± 4.11 | 23.42 ± 2.77 | 27.34 ± 8.17 | 19.01 ± 4.65 | 11.42 ± 3.72 | 12.92 ± 4.29 | 6.02 ± 1.32 | |
G | 25.41 ± 4.86 | 31.49 ± 1.86 | 23.24 ± 2.54 | 22.31 ± 3.45 | 31.20 ± 4.61 | 29.72 ± 8.79 | 13.08 ± 4.81 | 6.10 ± 1.33 | |
cV | 0.19 ± 0.01 | 0.19 ± 0.01 | 0.19 ± 0.00 | 0.18 ± 0.01 | 0.18 ± 0.02 | 0.18 ± 0.00 | 0.19 ± 0.03 | 0.16 ± 0.00 | |
\({U}_{0}^{{{\rm{ATOM}}}}\) | 0.38 ± 0.02 | 0.39 ± 0.03 | 0.38 ± 0.02 | 0.35 ± 0.02 | 0.29 ± 0.00 | 0.30 ± 0.02 | 0.33 ± 0.05 | 0.24 ± 0.01 | |
UATOM | 0.40 ± 0.04 | 0.48 ± 0.07 | 0.40 ± 0.04 | 0.36 ± 0.02 | 0.30 ± 0.01 | 0.30 ± 0.00 | 0.33 ± 0.06 | 0.24 ± 0.01 | |
HATOM | 0.38 ± 0.04 | 0.38 ± 0.02 | 0.41 ± 0.06 | 0.37 ± 0.03 | 0.30 ± 0.01 | 0.31 ± 0.01 | 0.36 ± 0.09 | 0.25 ± 0.00 | |
GATOM | 0.37 ± 0.04 | 0.34 ± 0.02 | 0.33 ± 0.01 | 0.31 ± 0.02 | 0.26 ± 0.01 | 0.27 ± 0.01 | 0.36 ± 0.08 | 0.22 ± 0.02 | |
A | 0.90 ± 0.06 | 0.97 ± 0.12 | 1.08 ± 0.16 | 1.01 ± 0.10 | 64.88 ± 29.77 | 3.82 ± 2.05 | 1.42 ± 0.44 | 0.75 ± 0.11 | |
B | 0.19 ± 0.05 | 0.21 ± 0.04 | 0.26 ± 0.01 | 0.26 ± 0.02 | 0.10 ± 0.03 | 0.11 ± 0.01 | 0.16 ± 0.05 | 0.08 ± 0.01 | |
C | 0.27 ± 0.02 | 0.27 ± 0.01 | 0.28 ± 0.00 | 0.28 ± 0.01 | 0.12 ± 0.04 | 0.10 ± 0.02 | 0.12 ± 0.05 | 0.05 ± 0.01 | |
DOCK (↑) | ESR2 | 0.68 ± 0.00 | 0.67 ± 0.00 | 0.65 ± 0.00 | 0.70 ± 0.00 | OOM | 0.64 ± 0.01 | 0.68 ± 0.00 | 0.70 ± 0.00 |
F2 | 0.89 ± 0.00 | 0.89 ± 0.00 | 0.89 ± 0.00 | 0.89 ± 0.00 | OOM | 0.87 ± 0.01 | 0.88 ± 0.00 | 0.89 ± 0.00 | |
KIT | 0.83 ± 0.00 | 0.83 ± 0.00 | 0.83 ± 0.00 | 0.84 ± 0.00 | OOM | 0.80 ± 0.01 | 0.83 ± 0.00 | 0.84 ± 0.00 | |
PARP1 | 0.92 ± 0.00 | 0.92 ± 0.00 | 0.92 ± 0.00 | 0.92 ± 0.00 | OOM | 0.91 ± 0.00 | 0.92 ± 0.01 | 0.93 ± 0.00 | |
PGR | 0.70 ± 0.00 | 0.68 ± 0.01 | 0.67 ± 0.01 | 0.72 ± 0.00 | OOM | 0.68 ± 0.01 | 0.70 ± 0.01 | 0.73 ± 0.00 | |
MoleculeNet (↑) | FREESOLV | 0.97 ± 0.00 | 0.96 ± 0.01 | 0.97 ± 0.01 | 0.95 ± 0.01 | 0.93 ± 0.00 | 0.93 ± 0.02 | 0.86 ± 0.03 | 0.98 ± 0.00 |
LIPO | 0.81 ± 0.01 | 0.82 ± 0.01 | 0.82 ± 0.01 | 0.83 ± 0.01 | 0.61 ± 0.04 | 0.55 ± 0.02 | 0.79 ± 0.00 | 0.81 ± 0.01 | |
ESOL | 0.94 ± 0.01 | 0.93 ± 0.01 | 0.93 ± 0.00 | 0.94 ± 0.01 | 0.91 ± 0.02 | 0.89 ± 0.03 | 0.91 ± 0.00 | 0.94 ± 0.00 | |
PCQM4MV2 (↓) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 0.0235 | |
Dataset (↓) | GAT | GATv2 | PNA | Graphormer | TokenGT | GPS | ESA | ESA (PE) |
|---|---|---|---|---|---|---|---|---|
ZINC | 0.078 ± 0.01 | 0.079 ± 0.00 | 0.057 ± 0.01 | 0.036 ± 0.00 | 0.047 ± 0.01 | 0.024 ± 0.01 | 0.027 ± 0.00 | 0.015 ± 0.00 |
