Table 3.
Evaluating inductive performance with supervised GRN inferring methods on balanced datasets. Feature E is the explicit expression features and G is graph embedding.
| Methods | Features |
E. coli |
S. cerevisiae |
Note |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Accuracy | Precision | Recall | MCC | Accuracy | Precision | Recall | MCC | – | ||
| SVM | E | 0.621 ± 0.000 | 0.628 ± 0.000 | 0.594 ± 0.000 | 0.242 ± 0.000 | 0.505 ± 0.000 | 0.557 ± 0.000 | 0.056 ± 0.000 | 0.026 ± 0.000 | Baseline |
| G + E | 0.704 ± 0.027 | 0.761 ± 0.009 | 0.596 ± 0.092 | 0.420 ± 0.045 | 0.643 ± 0.000 | 0.941 ± 0.001 | 0.304 ± 0.000 | 0.387 ± 0.001 | Enclosed Graph + SVM | |
| RF | E | 0.568 ± 0.000 | 0.595 ± 0.000 | 0.423 ± 0.000 | 0.141 ± 0.000 | 0.507 ± 0.000 | 0.520 ± 0.000 | 0.186 ± 0.000 | 0.019 ± 0.000 | Baseline |
| G + E | 0.635 ± 0.031 | 0.807 ± 0.057 | 0.359 ± 0.070 | 0.326 ± 0.061 | 0.658 ± 0.004 | 0.848 ± 0.012 | 0.384 ± 0.007 | 0.377 ± 0.009 | Enclosed Graph + RF | |
| GRGNN_PC (hop0) | E | 0.653 ± 0.001 | 0.652 ± 0.001 | 0.726 ± 0.153 | 0.306 ± 0.001 | 0.537 ± 0.000 | 0.674 ± 0.001 | 0.145 ± 0.000 | 0.121 ± 0.001 | – |
| G + E | 0.670 ± 0.150 | 0.677 ± 0.160 | 0.776 ± 0.134 | 0.352 ± 0.286 | 0.630 ± 0.072 | 0.777 ± 0.155 | 0.492 ± 0.290 | 0.306 ± 0.171 | – | |
| GRGNN_PC (hop1) | E | 0.586 ± 0.007 | 0.580 ± 0.007 | 0.625 ± 0.009 | 0.173 ± 0.014 | 0.566 ± 0.000 | 0.662 ± 0.002 | 0.395 ± 0.280 | 0.164 ± 0.000 | – |
| G + E | 0.696 ± 0.078 | 0.677 ± 0.062 | 0.773 ± 0.100 | 0.395 ± 0.160 | 0.655 ± 0.059 | 0.746 ± 0.121 | 0.518 ± 0.078 | 0.343 ± 0.115 | – | |
| GRGNN_MI (hop0) | E | 0.614 ± 0.002 | 0.581 ± 0.001 | 0.810 ± 0.025 | 0.251 ± 0.003 | 0.536 ± 0.000 | 0.678 ± 0.000 | 0.136 ± 0.001 | 0.119 ± 0.000 | – |
| G + E | 0.820 ± 0.008 | 0.874 ± 0.015 | 0.741 ± 0.034 | 0.647 ± 0.011 | 0.632 ± 0.175 | 0.866 ± 0.269 | 0.396 ± 0.070 | 0.321 ± 0.424 | – | |
| GRGNN_MI (hop1) | E | 0.652 ± 0.003 | 0.635 ± 0.002 | 0.718 ± 0.019 | 0.306 ± 0.006 | 0.534 ± 0.001 | 0.571 ± 0.001 | 0.326 ± 0.117 | 0.079 ± 0.002 | – |
| G + E | 0.767 ± 0.068 | 0.744 ± 0.077 | 0.847 ± 0.025 | 0.540 ± 0.134 | 0.566 ± 0.202 | 0.695 ± 0.283 | 0.579 ± 0.149 | 0.150 ± 0.453 | – | |
| GRGNN_EN (hop0) | E | 0.643 ± 0.000 | 0.619 ± 0.001 | 0.743 ± 0.002 | 0.293 ± 0.002 | 0.537 ± 0.000 | 0.676 ± 0.001 | 0.141 ± 0.000 | 0.120 ± 0.000 | – |
| G + E | 0.771 ± 0.100 | 0.766 ± 0.141 | 0.862 ± 0.076 | 0.568 ± 0.187 | 0.662 ± 0.090 | 0.818 ± 0.221 | 0.568 ± 0.229 | 0.388 ± 0.195 | Baseline Compared | |
| GRGNN_EN (hop1) | E | 0.656 ± 0.000 | 0.637 ± 0.000 | 0.730 ± 0.000 | 0.318 ± 0.003 | 0.570 ± 0.000 | 0.630 ± 0.002 | 0.340 ± 0.002 | 0.158 ± 0.001 | – |
| G + E | 0.809 ± 0.033 | 0.743 ± 0.069 | 0.853 ± 0.112 | 0.564 ± 0.153 | 0.684 ± 0.056 | 0.770 ± 0.147 | 0.574 ± 0.083 | 0.393 ± 0.135 | Proposed Method | |