Table 4 Comparison of the prediction performance for three machine learning algorithms on new data set.
From: NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm
Algorithm | Window length | 3-fold cross-validation | 8-fold cross-validation | Jack-Knife validation | Average MCC | Max MCC difference | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ac (%) | Sn (%) | Sp (%) | MCC | Ac (%) | Sn (%) | Sp (%) | MCC | Ac (%) | Sn (%) | Sp (%) | MCC | ||||
Naïve Bayes 1 | 3 | 84.64% | 43.95% | 94.85% | 0.4629 | 85.08% | 44.08% | 95.36% | 0.4767 | 85.27% | 45.31% | 95.29% | 0.4857 | 0.4751 | 0.0228 |
4 | 85.43% | 49.52% | 94.44% | 0.5017 | 85.62% | 51.29% | 94.23% | 0.512 | 85.76% | 51.43% | 94.37% | 0.5162 | 0.51 | 0.0145 | |
5 | 85.49% | 51.97% | 93.89% | 0.5101 | 86.17% | 53.74% | 94.30% | 0.5339 | 86.58% | 54.69% | 94.58% | 0.5479 | 0.5306 | 0.0378 | |
6 | 85.79% | 54.01% | 93.76% | 0.5241 | 86.72% | 57.28% | 94.10% | 0.5582 | 86.74% | 58.37% | 93.86% | 0.5618 | 0.548 | 0.0377 | |
7 | 85.65% | 54.42% | 93.48% | 0.5216 | 86.52% | 56.87% | 93.96% | 0.5519 | 86.58% | 57.14% | 93.96% | 0.5541 | 0.5425 | 0.0325 | |
8 | 85.79% | 55.37% | 93.42% | 0.528 | 86.20% | 57.55% | 93.38% | 0.545 | 86.25% | 56.73% | 93.65% | 0.5442 | 0.5391 | 0.0170 | |
RBF Network 2 | 3 | 84.12% | 45.17% | 93.89% | 0.4516 | 85.05% | 45.44% | 94.98% | 0.4794 | 84.62% | 46.12% | 94.27% | 0.4684 | 0.4665 | 0.0278 |
4 | 84.83% | 46.39% | 94.47% | 0.4755 | 85.57% | 49.12% | 94.71% | 0.5046 | 85.68% | 49.80% | 94.68% | 0.5095 | 0.4965 | 0.0340 | |
5 | 85.32% | 48.98% | 94.44% | 0.4971 | 85.35% | 48.57% | 94.58% | 0.4967 | 86.91% | 54.29% | 95.09% | 0.5565 | 0.5168 | 0.0598 | |
6 | 85.38% | 51.29% | 93.93% | 0.5051 | 85.76% | 50.61% | 94.58% | 0.514 | 85.92% | 50.20% | 94.88% | 0.5178 | 0.5123 | 0.0127 | |
7 | 85.08% | 51.16% | 93.59% | 0.4965 | 86.33% | 53.47% | 94.58% | 0.5379 | 86.99% | 53.88% | 95.29% | 0.558 | 0.5308 | 0.0615 | |
8 | 85.43% | 50.48% | 94.20% | 0.5043 | 86.42% | 54.01% | 94.54% | 0.5416 | 87.15% | 55.51% | 95.09% | 0.5664 | 0.5374 | 0.0621 | |
SVM 3 | 3 | 84.72% | 48.44% | 93.82% | 0.4785 | 85.73% | 48.57% | 95.05% | 0.5081 | 85.35% | 47.35% | 94.88% | 0.4935 | 0.4934 | 0.0296 |
4 | 82.84% | 49.66% | 91.16% | 0.4349 | 84.89% | 51.16% | 93.35% | 0.4914 | 84.78% | 52.24% | 92.94% | 0.4919 | 0.4727 | 0.0570 | |
5 | 83.17% | 52.65% | 90.82% | 0.4541 | 85.32% | 55.24% | 92.87% | 0.5155 | 86.82% | 60.41% | 93.45% | 0.5694 | 0.513 | 0.1153 | |
6 | 82.87% | 52.79% | 90.41% | 0.4478 | 85.30% | 57.55% | 92.26% | 0.5221 | 84.37% | 57.55% | 91.10% | 0.4999 | 0.4899 | 0.0743 | |
7 | 81.53% | 53.33% | 88.60% | 0.4213 | 84.70% | 58.37% | 91.30% | 0.5104 | 88.46% | 64.49% | 94.47% | 0.6234 | 0.5184 | 0.2021 | |
8 | 81.01% | 53.33% | 87.96% | 0.4108 | 84.48% | 60.54% | 90.48% | 0.5132 | 85.52% | 61.22% | 91.61% | 0.5393 | 0.4878 | 0.1285 | |