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 |