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Table 4 HIV-1 predictor performances on pol fragment classification

From: A machine learning approach for viral genome classification

    COMET REGA CASTOR
   # of instances TPR FPR F-measure TPR FPR F-measure TPR FPR F-measure
CRFs HIV1_01_AE 1000 0.989 0.000 0.993 0.007 0.000 0.014 0.956 0.001 0.975
  HIV1_02_AG 1000 0.952 0.002 0.967 0.000 0.000 0.000 0.853 0.005 0.897
  HIV1_06_cpx 698 0.924 0.000 0.958 0.938 0.000 0.965 0.927 0.003 0.943
  HIV1_07_BC 1000 0.977 0.000 0.988 0.988 0.000 0.993 0.982 0.002 0.980
  HIV1_08_BC 399 0.965 0.000 0.981 0.990 0.000 0.994 0.972 0.001 0.970
  HIV1_11_cpx 58 0.828 0.000 0.906 0.690 0.000 0.816 0.897 0.006 0.588
  HIV1_12_BF 222 0.860 0.000 0.925 0.374 0.000 0.544 0.932 0.008 0.807
  Mean   0.928 0.000 0.960 0.570 0.000 0.618 0.931 0.004 0.880
Pure subtypes HIV1_A 1000 0.966 0.001 0.980 0.968 0.106 0.654 0.891 0.006 0.917
  HIV1_B 1000 0.995 0.001 0.993 0.945 0.000 0.970 0.817 0.007 0.866
  HIV1_C 1000 0.990 0.001 0.991 0.997 0.000 0.997 0.912 0.003 0.942
  HIV1_D 1000 0.938 0.000 0.968 0.911 0.000 0.953 0.892 0.010 0.899
  HIV1_F 1000 0.927 0.000 0.962 0.970 0.000 0.985 0.914 0.003 0.940
  HIV1_G 1000 0.915 0.001 0.952 0.929 0.007 0.931 0.778 0.003 0.860
  Mean   0.955 0.001 0.974 0.953 0.019 0.915 0.867 0.005 0.904
  1. This table contains TPR, FPR and F-measure of COMET, REGA and CASTOR on the prediction of HIV-1 M pure subtypes and CFRs pol fragments. The shown classes belong to the common subtypes sampling. The CASTOR model used in this evaluation is PMSHIV03