Table 3 F1 scores of hub tables of different sizes and hub selections for the known pathway test set, where an F1 score of one indicates that the HPAT search found the exact known pathway
From: Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Number of Hubs | ||||||||
|---|---|---|---|---|---|---|---|---|
20 (O) | 50 (O) | 80 (O) | 139 (A) | 50 (IO) | 50 (I) | 50 (R1) | 50 (R2) | |
Pyruvate → Lysine I | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.67 | 0.70 | 0.70 |
Pyruvate → Lysine II | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.67 | 0.70 | 0.70 |
Pyruvate → Lysine III | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.61 | 1.00 | 1.00 |
Pyruvate → Lysine IV | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.61 | 0.78 | 0.78 |
Pyruvate → Lysine V | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 0.10 | 0.30 | 0.30 |
Glutamate → Proline | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
UDP-Galactose → Stachyose | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
alpha-D-glucose → Phenylpyruvate | 0.71 | 0.71 | 0.71 | 0.62 | 0.74 | 0.71 | 0.71 | 0.71 |
alpha-D-glucose → Dopamine | 0.76 | 0.59 | 0.59 | 0.60 | 0.65 | 0.76 | 0.76 | 0.76 |
Pyruvate → 3-HP, I | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
Pyruvate → 3-HP, II | 0.38 | 0.50 | 0.50 | 0.50 | 0.50 | 0.60 | 0.33 | 0.33 |
Pyruvate → 3-HP, III | 0.55 | 0.60 | 1.00 | 1.00 | 0.60 | 1.00 | 0.78 | 0.78 |
Pyruvate → 3-HP, IV | 0.38 | 0.42 | 0.50 | 0.50 | 0.43 | 1.00 | 0.71 | 0.71 |
Pyruvate → 3-HP, V | 0.40 | 0.36 | 0.36 | 0.36 | 0.36 | 0.36 | 0.40 | 0.40 |
Pyruvate → 3-HP, VI | 0.36 | 0.36 | 0.18 | 0.18 | 0.36 | 0.67 | 0.36 | 0.36 |
Pyruvate → 3-HP, VII | 0.36 | 0.53 | 0.77 | 0.77 | 0.53 | 0.77 | 0.50 | 0.50 |
Glucose → Glucaric acid | 1.00 | 1.00 | 0.38 | 0.44 | 0.21 | 1.00 | 1.00 | 1.00 |
alpha-D-glucose → 1,3-propanediol | 1.00 | 1.00 | 0.57 | 0.89 | 1.00 | 1.00 | 1.00 | 1.00 |
Tryptophan → Melatonin | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |