Table 3.
The prediction results with different percentages of protein annotations removed
|
Percent |
Methods |
MF |
CC |
BP |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PPV | TPR | F-Measure | MCC | PPV | TPR | F-Measure | MCC | PPV | TPR | F-Measure | MCC | ||
| 10% |
DSCP |
0.75 |
0.43 |
0.54 |
0.41 |
0.69 |
0.36 |
0.47 |
0.35 |
0.61 |
0.37 |
0.46 |
0.35 |
| DCS |
0.78 |
0.40 |
0.53 |
0.39 |
0.64 |
0.31 |
0.42 |
0.30 |
0.55 |
0.30 |
0.39 |
0.29 |
|
| Zhang-DC |
0.70 |
0.25 |
0.37 |
0.24 |
0.61 |
0.24 |
0.34 |
0.23 |
0.50 |
0.23 |
0.32 |
0.22 |
|
| MRF |
0.47 |
0.19 |
0.27 |
0.15 |
0.23 |
0.20 |
0.21 |
0.11 |
0.25 |
0.20 |
0.22 |
0.13 |
|
| RLC |
0.29 |
0.38 |
0.33 |
0.23 |
0.29 |
0.40 |
0.33 |
0.24 |
0.24 |
0.33 |
0.28 |
0.22 |
|
| 20% |
DSCP |
0.76 |
0.42 |
0.54 |
0.40 |
0.69 |
0.35 |
0.47 |
0.34 |
0.60 |
0.36 |
0.45 |
0.34 |
| DCS |
0.75 |
0.41 |
0.53 |
0.39 |
0.64 |
0.30 |
0.40 |
0.28 |
0.55 |
0.30 |
0.39 |
0.29 |
|
| Zhang-DC |
0.71 |
0.25 |
0.36 |
0.24 |
0.62 |
0.25 |
0.36 |
0.24 |
0.52 |
0.24 |
0.32 |
0.22 |
|
| MRF |
0.37 |
0.21 |
0.27 |
0.13 |
0.24 |
0.19 |
0.21 |
0.10 |
0.26 |
0.21 |
0.23 |
0.13 |
|
| RLC |
0.31 |
0.36 |
0.33 |
0.22 |
0.32 |
0.38 |
0.34 |
0.24 |
0.25 |
0.32 |
0.28 |
0.22 |
|
| 50% |
DSCP |
0.78 |
0.35 |
0.49 |
0.34 |
0.70 |
0.31 |
0.43 |
0.30 |
0.60 |
0.31 |
0.41 |
0.30 |
| DCS |
0.77 |
0.33 |
0.46 |
0.32 |
0.66 |
0.25 |
0.37 |
0.24 |
0.56 |
0.26 |
0.36 |
0.25 |
|
| Zhang-DC |
0.74 |
0.20 |
0.31 |
0.19 |
0.65 |
0.22 |
0.33 |
0.21 |
0.54 |
0.21 |
0.30 |
0.20 |
|
| MRF |
0.35 |
0.18 |
0.24 |
0.11 |
0.22 |
0.16 |
0.18 |
0.08 |
0.22 |
0.17 |
0.19 |
0.09 |
|
| RLC |
0.40 |
0.29 |
0.33 |
0.19 |
0.40 |
0.31 |
0.35 |
0.21 |
0.33 |
0.26 |
0.29 |
0.18 |
|
| 80% |
DSCP |
0.84 |
0.24 |
0.37 |
0.23 |
0.76 |
0.23 |
0.36 |
0.23 |
0.66 |
0.23 |
0.34 |
0.22 |
| DCS |
0.83 |
0.22 |
0.35 |
0.21 |
0.72 |
0.18 |
0.29 |
0.17 |
0.63 |
0.18 |
0.28 |
0.17 |
|
| Zhang-DC |
0.83 |
0.12 |
0.21 |
0.11 |
0.72 |
0.16 |
0.27 |
0.16 |
0.63 |
0.15 |
0.24 |
0.14 |
|
| MRF |
0.32 |
0.09 |
0.14 |
0.06 |
0.18 |
0.08 |
0.11 |
0.04 |
0.16 |
0.09 |
0.11 |
0.04 |
|
| RLC | 0.59 | 0.17 | 0.26 | 0.12 | 0.58 | 0.20 | 0.29 | 0.14 | 0.52 | 0.16 | 0.25 | 0.12 | |
This table shows prediction results of four algorithms (DCS, DSCP, Zhang-DC and RLC) by using leave-percent-out cross validation. The percentage is set as 10%, 20%, 50% and 80%, respectively.