Table 3.
The performance of four vector representing schemes for protein sequences
Organism | Methods | Benchmark negatives | Random negatives | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
AUC | Acc | Sn | Sp | Pre | AUC | Acc | Sn | Sp | Pre | ||
E. coli | AG-QP360 | 0.994 | 0.982 | 0.996 | 0.982 | 0.894 | 0.899 | 0.811 | 0.821 | 0.802 | 0.804 |
AG-CTF | 0.996 | 0.968 | 0.987 | 0.940 | 0.889 | 0.886 | 0.797 | 0.794 | 0.799 | 0.798 | |
AG-P100 | 0.994 | 0.965 | 0.989 | 0.979 | 0.889 | 0.889 | 0.799 | 0.798 | 0.799 | 0.799 | |
AG-Q340 | 0.989 | 0.964 | 0.987 | 0.959 | 0.807 | 0.854 | 0.771 | 0.743 | 0.789 | 0.787 | |
S. cerevisiae | AG-QP360 | 0.993 | 0.968 | 0.998 | 0.969 | 0.786 | 0.960 | 0.902 | 0.887 | 0.929 | 0.917 |
AG-CTF | 0.991 | 0.964 | 0.986 | 0.960 | 0.767 | 0.948 | 0.880 | 0.879 | 0.927 | 0.909 | |
AG-P100 | 0.991 | 0.963 | 0.985 | 0.959 | 0.765 | 0.947 | 0.849 | 0.798 | 0.899 | 0.889 | |
AG-Q340 | 0.989 | 0.945 | 0.982 | 0.939 | 0.684 | 0.902 | 0.844 | 0.788 | 0.898 | 0.877 |
Cutoff for each method was set according to the maximal F-measure statistic. Acc: accuracy; Sn: sensitivity; Sp: Specificity; Pre: precision.