Table 2 Comparison of the performances by different machine learning algorithms
Number of peaks | Number of peaks with ERE motif | Ratio of peaks with ERE motif match | |
|---|---|---|---|
MACS p = 1E-10 | 1,286 | 941 | 0.73 |
MACS p = 1E-8 | 1,966 | 1,416 | 0.72 |
MACS p = 1E-5 | 4,678 | 3,077 | 0.66 |
k-means (city block) | |||
Cluster 1 | 26,211 | 11,943 | 0.46 |
Cluster 2 | 12,113 | 3,245 | 0.27 |
supervised-NB(th = 0.8,1:2) | |||
Positively labeled | 11,835 | 8,196 | 0.69 |
Negatively labeled | 26,489 | 6,992 | 0.26 |
supervised-SVM(kernel = polynomal,1:2) | |||
Positively labeled | 14,915 | 8,425 | 0.56 |
Negatively labeled | 23,409 | 6,763 | 0.29 |
supervised-RF(th = 0.7,1:2) | |||
Positively labeled | 10,428 | 6,514 | 0.62 |
Negatively labeled | 27,896 | 8,674 | 0.31 |
semi-supervised-NB(th = 0.8,1:2, I = 75) | |||
Positively labeled | 12,597 | 8,458 | 0.67 |
Negatively labeled | 25,727 | 6,730 | 0.26 |