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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
  1. The closer the F1 score is to one, the more similar the found pathway’s reactions are to that of the canonical pathway. The different suffixes in column names indicate how hubs were selected: IO, sum of in- and out-degree; A, from Araki et al. 2015; O, out-degree; I, in-degree; Rn, randomly