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Table 2 Results of predicting the missing BP functions of partially annotated Yeast proteins (N=5914, \(|\mathcal {T}|=2979\))

From: Predicting protein function via downward random walks on a gene ontology

Metric m dRW-kNN dRW ITSS PILL Naive
MacroF1 1 93.14 ± 0.13 93.61 ± 0.05 91.66 ± 0.09 91.52 ± 0.15 1.99 ± 0.00
  3 82.72 ± 0.25 83.29 ± 0.13 80.14 ± 0.14 79.77 ± 0.16 2.01 ± 0.00
  5 74.67 ± 0.22 75.92 ± 0.17 71.16 ± 0.33 70.96 ± 0.22 2.03 ± 0.00
AvgROC 1 99.88 ± 0.01 99.93 ± 0.00 98.24 ± 0.02 98.77 ± 0.03 45.88 ± 0.00
  3 99.55 ± 0.02 99.59 ± 0.02 94.44 ± 0.08 96.36 ± 0.15 45.88 ± 0.00
  5 99.01 ± 0.02 98.89 ± 0.03 90.48 ± 0.17 93.83 ± 0.06 45.88 ± 0.00
1-RankLoss 1 99.96 ± 0.00 99.97 ± 0.00 98.99 ± 0.02 99.81 ± 0.01 91.13 ± 0.00
  3 99.47 ± 0.03 99.17 ± 0.03 96.89 ± 0.05 99.23 ± 0.03 91.04 ± 0.00
  5 98.20 ± 0.02 97.63 ± 0.03 93.99 ± 0.10 98.42 ± 0.05 90.95 ± 0.01
Fmax 1 97.97 ± 0.00 98.08 ± 0.00 97.90 ± 0.00 97.91 ± 0.00 36.96 ± 0.00
  3 93.99 ± 0.02 93.92 ± 0.01 93.66 ± 0.02 93.61 ± 0.00 36.86 ± 0.00
  5 90.25 ± 0.03 89.88 ± 0.00 89.66 ± 0.02 89.41 ± 0.00 36.84 ± 0.03
RAccuracy 1 38.75 ± 0.66 44.68 ± 0.21 12.41 ± 0.48 21.65 ± 0.37 37.51 ± 0.94
  3 39.75 ± 0.13 36.08 ± 0.24 23.02 ± 0.06 22.27 ± 0.37 37.84 ± 0.75
  5 40.13 ± 0.43 33.58 ± 0.24 27.39 ± 0.29 23.92 ± 0.08 37.69 ± 0.37
Coverage 1 78.24 ± 0.95 66.34 ± 1.10 405.01 ± 9.56 232.52 ± 4.58 1585.06 ± 0.99
  3 191.34 ± 4.88 234.61 ± 4.92 943.54 ± 10.84 524.50 ± 12.33 1605.22 ± 0.95
  5 340.09 ± 4.55 469.13 ± 9.17 1412.81 ± 9.85 806.23 ± 18.18 1625.35 ± 3.17
  1. The numbers in boldface denote the best (or comparable best) statistically significant performance (according to a t-test at 95 % significance level). means the lower the value, the better the performance. m is the number of missing functions for a protein, N m is the total number of missing functions, and \(|\mathcal {T}_{m}^{0}|\) is the number of the second kind of missing functions of N proteins for a given m. m=1, \(|\mathcal {T}_{1}^{0}|=25\), N 1=4705; m=3, \(|\mathcal {T}_{3}^{0}|=106\), N 3=14079; m=5, \(|\mathcal {T}_{5}^{0}|=209\), N 5=23299