Table 4 Prediction performance on biological process classes, over the cross-validation dataset.
Function | # Training Protein | # Test Protein | Text-KNN | Base-Prior | Base-Seq | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | P | R | F | P | R | F | P | R | F |
GO:0065007 | 3626 | 906 | 0.23 | 0.52 | 0.31 | 0.20 | 0.24 | 0.22 | 0.32 | 0.48 | 0.38 |
GO:0032502 | 3338 | 835 | 0.22 | 0.19 | 0.20 | 0.12 | 0.17 | 0.14 | 0.22 | 0.24 | 0.23 |
GO:0009987 | 1790 | 447 | 0.24 | 0.29 | 0.26 | 0.17 | 0.14 | 0.15 | 0.26 | 0.27 | 0.27 |
GO:0050896 | 1780 | 445 | 0.25 | 0.16 | 0.19 | 0.10 | 0.10 | 0.10 | 0.16 | 0.09 | 0.11 |
GO:0008152 | 1658 | 415 | 0.23 | 0.14 | 0.17 | 0.08 | 0.06 | 0.07 | 0.28 | 0.34 | 0.31 |
GO:0051234 | 1204 | 301 | 0.32 | 0.20 | 0.25 | 0.05 | 0.05 | 0.05 | 0.44 | 0.45 | 0.45 |
GO:0016043 | 1145 | 286 | 0.13 | 0.05 | 0.07 | 0.06 | 0.05 | 0.06 | 0.15 | 0.12 | 0.13 |
GO:0023052 | 965 | 241 | 0.18 | 0.11 | 0.14 | 0.05 | 0.04 | 0.04 | 0.30 | 0.28 | 0.29 |
GO:0032501 | 606 | 151 | 0.12 | 0.02 | 0.04 | 0.04 | 0.03 | 0.04 | 0.24 | 0.11 | 0.16 |
GO:0022414 | 346 | 86 | 0.51 | 0.15 | 0.24 | 0.02 | 0.02 | 0.02 | 0.14 | 0.03 | 0.05 |
GO:0051704 | 272 | 68 | 0.29 | 0.09 | 0.14 | 0.01 | 0.01 | 0.01 | 0.09 | 0.04 | 0.05 |
GO:0040011 | 170 | 42 | 0.13 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 1.00 | 0.05 | 0.09 |
GO:0040007 | 165 | 41 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0051179 | 151 | 38 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0022610 | 128 | 32 | 0.07 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0008283 | 118 | 29 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0000003 | 96 | 24 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0002376 | 74 | 19 | 0.06 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
GO:0016265 | 64 | 16 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 |
GO:0071554 | 46 | 11 | 0.38 | 0.08 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
GO:0048511 | 43 | 11 | 0.31 | 0.06 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
GO:0023046 | 35 | 9 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
GO:0044085 | 16 | 4 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
GO:0043473 | 13 | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |