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Table 2 Results of replenishing missing labels on CollinsPPI wrt

From: Predicting protein functions using incomplete hierarchical labels

Metric m(N m ) PILL ProDM ProWL LkNN TPRw Naive
MicroF1 1(1526) 93.91 ±0.11 83.30 ±0.30 90.31 ±0.08 44.07 ±0.14 50.00 ±0.12 29.00 ±0.01
  3(4330) 81.70 ±0.29 72.16 ±0.77 78.38 ±0.23 41.61 ±0.16 43.60 ±0.18 29.77 ±0.13
  5(6580) 70.53 ±0.31 60.10 ±1.01 66.61 ±0.16 37.54 ±0.21 36.79 ±0.13 30.09 ±0.06
MacroF1 1(1526) 89.29 ±0.25 69.53 ±0.40 85.75 ±0.34 34.23 ±0.21 43.33 ±0.15 4.70 ±0.01
  3(4330) 70.19 ±0.63 60.78 ±1.73 69.03 ±0.46 29.23 ±0.48 35.45 ±0.39 5.06 ±0.04
  5(6580) 55.32 ±0.94 45.37 ±1.90 52.95 ±0.59 24.12 ±0.62 27.06 ±0.75 5.13 ±0.05
AvgROC 1(1526) 99.47 ±0.01 97.44 ±0.06 98.27 ±0.09 66.14 ±0.05 69.67 ±0.18 49.44 ±0.00
  3(4330) 97.77 ±0.16 93.86 ±0.44 93.35 ±0.18 64.86 ±0.11 64.93 ±0.21 49.44 ±0.00
  5(6580) 94.64 ±0.33 87.03 ±1.04 86.24 ±0.49 63.25 ±0.34 60.41 ±0.36 49.44 ±0.00
1-RankLoss 1(1526) 99.43 ±0.03 96.80 ±0.04 98.55 ±0.05 69.38 ±0.04 55.75 ±0.14 79.33 ±0.04
  3(4330) 97.58 ±0.11 92.15 ±0.26 94.62 ±0.17 66.09 ±0.27 46.90 ±0.47 76.72 ±0.22
  5(6580) 94.55 ±0.27 86.63 ±0.67 89.30 ±0.25 59.65 ±0.65 36.88 ±0.41 74.52 ±0.41
Fmax 1(1526) 90.88 ±0.07 76.28 ±0.31 80.49 ±0.34 42.74 ±0.09 58.43 ±0.36 28.32 ±0.00
  3(4330) 76.82 ±0.10 67.39 ±0.84 66.14 ±0.29 42.16 ±0.25 51.12 ±0.50 27.93 ±0.01
  5(6580) 66.11 ±0.50 56.26 ±4.01 57.76 ±0.52 40.39 ±0.37 44.01 ±0.53 27.04 ±0.00
  1. FunCat labels. m is the number of missing labels for a protein and N m in the bracket is the total number of missing labels for all the proteins. The numbers in boldface denote the best performance.
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