Skip to main content

Table 2 Performance rates for three different ML approaches: mean (sd)

From: A machine learning approach for predicting methionine oxidation sites

Feature set AUC Accuracy Sensitivity Specificity F-measure MCC
TRAINING SET
RF
Primary 1.0000 (0) 0.8957 (0.0480) 1 (0) 0.8807 (0.0546) 0.7176 (0.0938) 0.7054 (0.0920)
Tertiary 0.9996 (0.0003) 0.8316 (0.0591) 1 (0) 0.8074 (0.0674) 0.6096 (0.0898) 0.5977 (0.0882)
Whole 1.0000 (0) 0.8948 (0.0533) 1 (0) 0.8797 (0.0609) 0.7192 (0.1053) 0.7071 (0.1046)
mRMR 1.0000 (0) 0.8932 (0.0480) 1 (0) 0.8777 (0.0550) 0.7138 (0.0966) 0.7015 (0.0960)
SVM
Primary 0.9997 (0.0011) 0.9069 (0.1990) 0.9990 (0.0034) 0.8939 (0.2270) 0.8751 (0.2584) 0.8670 (0.2747)
Tertiary 0.9924 (0.0090) 0.7425 (0.1501) 0.9865 (0.0217) 0.7077 (0.1729) 0.5562 (0.2335) 0.5390 (0.2407)
Whole 0.9992 (0.0025) 0.9310 (0.1542) 0.9980 (0.0058) 0.9210 (0.1772) 0.8936 (0.2254) 0.8874 (0.2370)
mRMR 0.9995 (0.0018) 0.9044 (0.1766) 0.9982 (0.0043) 0.8907 (0.2026) 0.8545 (0.2561) 0.8463 (0.2690)
NN
Primary 0.9482 (0.0339) 0.7248 (0.1607) 0.9377 (0.0416) 0.6938 (0.1841) 0.5195 (0.1975) 0.4835 (0.2133)
Tertiary 0.9336 (0.0227) 0.7552 (0.1040) 0.9079 (0.0322) 0.7334 (0.1195) 0.5082 (0.1322) 0.4706 (0.1378)
Whole 0.9616 (0.0247) 0.8273 (0.1170) 0.9491 (0.0327) 0.8098 (0.1333) 0.6292 (0.1883) 0.6063 (0.1958)
mRMR 0.9533 (0.0232) 0.7897 (0.1160) 0.9373 (0.0314) 0.7684 (0.1325) 0.5696 (0.1738) 0.5413 (0.1822)
TESTING SET
RF
Primary 0.6947 (0.0416) 0.6207 (0.0666) 0.6737 (0.1296) 0.6139 (0.0883) 0.3026 (0.0439) 0.1936 (0.0573)
Tertiary 0.7614 (0.0375) 0.6975 (0.0485) 0.7064 (0.1029) 0.6959 (0.0633) 0.3638 (0.0463) 0.2781 (0.0547)
Whole 0.7957 (0.0355) 0.7458 (0.0622) 0.6849 (0.1195) 0.7540 (0.0813) 0.4003 (0.0563) 0.3205 (0.0625)
mRMR 0.7998 (0.0334) 0.7468 (0.0567) 0.6817 (0.0982) 0.7557 (0.0721) 0.4003 (0.0562) 0.3190 (0.0622)
SVM
Primary 0.5660 (0.0431) 0.5604 (0.0847) 0.5383 (0.1381) 0.5641 (0.1112) 0.2286 (0.0414) 0.0688 (0.0573)
Tertiary 0.6480 (0.0534) 0.6434 (0.0825) 0.5500 (0.1329) 0.6561 (0.1070) 0.2741 (0.0459) 0.1437 (0.0605)
Whole 0.6753 (0.0424) 0.6441 (0.0704) 0.6037 (0.1301) 0.6501 (0.0954) 0.2924 (0.0417) 0.1744 (0.0498)
mRMR 0.6700 (0.0450) 0.6348 (0.0802) 0.5986 (0.1309) 0.6398 (0.1047) 0.2865 (0.0461) 0.1641 (0.0585)
NN
Primary 0.5601 (0.0479) 0.5477 (0.0907) 0.5465 (0.1349) 0.5474 (0.1178) 0.2274 (0.0411) 0.0637 (0.0567)
Tertiary 0.6887 (0.0470) 0.6662 (0.0687) 0.5998 (0.1412) 0.6745 (0.0907) 0.3047 (0.0523) 0.1907 (0.0658)
Whole 0.6846 (0.0469) 0.6650 (0.0680) 0.5793 (0.1194) 0.6765 (0.0886) 0.2981 (0.0453) 0.1791 (0.0581)
mRMR 0.6903 (0.0486) 0.6573 (0.0696) 0.6101 (0.1224) 0.6640 (0.0903) 0.3044 (0.0474) 0.1900 (0.0627)