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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 I1.001.001.001.001.000.670.700.70
Pyruvate → Lysine II1.001.001.001.001.000.670.700.70
Pyruvate → Lysine III1.001.001.001.001.000.611.001.00
Pyruvate → Lysine IV1.001.001.001.001.000.610.780.78
Pyruvate → Lysine V1.001.001.001.001.000.100.300.30
Glutamate → Proline1.001.001.001.001.001.001.001.00
UDP-Galactose → Stachyose1.001.001.001.001.001.001.001.00
alpha-D-glucose → Phenylpyruvate0.710.710.710.620.740.710.710.71
alpha-D-glucose → Dopamine0.760.590.590.600.650.760.760.76
Pyruvate → 3-HP, I1.001.001.001.001.001.001.001.00
Pyruvate → 3-HP, II0.380.500.500.500.500.600.330.33
Pyruvate → 3-HP, III0.550.601.001.000.601.000.780.78
Pyruvate → 3-HP, IV0.380.420.500.500.431.000.710.71
Pyruvate → 3-HP, V0.400.360.360.360.360.360.400.40
Pyruvate → 3-HP, VI0.360.360.180.180.360.670.360.36
Pyruvate → 3-HP, VII0.360.530.770.770.530.770.500.50
Glucose → Glucaric acid1.001.000.380.440.211.001.001.00
alpha-D-glucose → 1,3-propanediol1.001.000.570.891.001.001.001.00
Tryptophan → Melatonin1.001.001.001.001.001.001.001.00
  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