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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