Table 3 Comparison of the prediction performance for three machine learning algorithms on old 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 | 85.25% | 54.39% | 94.21% | 0.5438 | 86.01% | 55.98% | 94.72% | 0.5679 | 86.33% | 57.42% | 94.72% | 0.5795 | 0.5637 | 0.0357 |
4 | 85.97% | 56.46% | 94.54% | 0.5677 | 86.29% | 56.94% | 94.81% | 0.5776 | 86.44% | 58.85% | 94.44% | 0.5851 | 0.5768 | 0.0174 | |
5 | 85.86% | 58.53% | 93.80% | 0.569 | 86.11% | 58.53% | 94.12% | 0.5757 | 86.22% | 58.37% | 94.31% | 0.5783 | 0.5743 | 0.0093 | |
6 | 85.93% | 60.13% | 93.43% | 0.5744 | 86.58% | 62.68% | 93.52% | 0.5967 | 86.98% | 64.11% | 93.61% | 0.6099 | 0.5937 | 0.0355 | |
7 | 86.15% | 60.61% | 93.56% | 0.5811 | 86.19% | 60.61% | 93.61% | 0.5820 | 86.44% | 61.72% | 93.61% | 0.5909 | 0.5847 | 0.0098 | |
8 | 86.01% | 60.29% | 93.47% | 0.5766 | 86.08% | 60.13% | 93.61% | 0.5781 | 86.01% | 62.20% | 92.92% | 0.5811 | 0.5786 | 0.0045 | |
RBF Network 2 | 3 | 84.39% | 49.92% | 94.40% | 0.5104 | 85.15% | 53.91% | 94.21% | 0.5399 | 83.85% | 50.72% | 93.47% | 0.4975 | 0.5159 | 0.0424 |
4 | 85.11% | 53.59% | 94.26% | 0.5382 | 85.58% | 55.18% | 94.40% | 0.5543 | 86.11% | 57.89% | 94.31% | 0.5745 | 0.5557 | 0.0363 | |
5 | 85.97% | 57.10% | 94.35% | 0.569 | 85.61% | 57.26% | 93.84% | 0.5596 | 85.36% | 57.42% | 93.47% | 0.5534 | 0.5607 | 0.0156 | |
6 | 86.04% | 57.42% | 94.35% | 0.5716 | 86.11% | 59.01% | 93.98% | 0.5767 | 85.79% | 59.33% | 93.47% | 0.5689 | 0.5724 | 0.0078 | |
7 | 85.36% | 58.53% | 93.15% | 0.556 | 85.65% | 57.89% | 93.70% | 0.5620 | 86.65% | 58.85% | 94.72% | 0.591 | 0.5697 | 0.0350 | |
8 | 85.07% | 57.26% | 93.15% | 0.5456 | 85.43% | 57.10% | 93.66% | 0.5545 | 86.76% | 58.85% | 94.86% | 0.594 | 0.5647 | 0.0484 | |
SVM 3 | 3 | 84.46% | 56.62% | 92.55% | 0.5285 | 85.15% | 56.14% | 93.56% | 0.5448 | 86.44% | 59.81% | 94.17% | 0.5869 | 0.5534 | 0.0584 |
4 | 83.82% | 59.97% | 90.74% | 0.5229 | 84.03% | 58.37% | 91.48% | 0.5231 | 82.24% | 52.15% | 90.97% | 0.4616 | 0.5025 | 0.0615 | |
5 | 82.99% | 59.81% | 89.72% | 0.5041 | 83.24% | 59.97% | 90.00% | 0.5100 | 80.52% | 53.11% | 88.47% | 0.4272 | 0.4804 | 0.0828 | |
6 | 83.10% | 62.52% | 89.07% | 0.5156 | 83.75% | 63.48% | 89.63% | 0.5326 | 82.13% | 60.77% | 88.33% | 0.4893 | 0.5125 | 0.0433 | |
7 | 81.45% | 61.72% | 87.18% | 0.4793 | 83.21% | 63.48% | 88.94% | 0.5212 | 83.53% | 63.16% | 89.44% | 0.5269 | 0.5091 | 0.0476 | |
8 | 80.95% | 61.88% | 86.48% | 0.4702 | 82.10% | 63.16% | 87.59% | 0.4974 | 82.45% | 63.16% | 88.06% | 0.5046 | 0.4907 | 0.0344 | |