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Table 1 Feature selection: Average testing set error rate and sparsity (in parentheses) for 10 random partitions of the data

From: Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Dataset SCM χ 2+CART χ 2+L1SVM χ 2+L2SVM χ 2+SCM Baseline
C. difficile       
Azithromycin 0.030 (3.3) 0.086 (7.2) 0.064 (20326.0) 0.056 (106) 0.075 (3.0) 0.446
Ceftriaxone 0.073 (2.6) 0.117 (6.8) 0.087 (8114.1) 0.102 (106) 0.111 (3.2) 0.306
Clarithromycin 0.011 (3.0) 0.070 (8.0) 0.062 (36686.1) 0.059 (106) 0.069 (3.5) 0.446
Clindamycin 0.021 (1.4) 0.011 (2.0) 0.009 (598.2) 0.021 (106) 0.008 (2.3) 0.136
Moxifloxacin 0.020 (1.0) 0.020 (1.3) 0.020 (25.6) 0.048 (106) 0.021 (1.1) 0.390
M. tuberculosis       
Ethambutol 0.179 (1.4) 0.185 (1.9) 0.153 (201.3) 0.221 (106) 0.174 (3.2) 0.351
Isoniazid 0.021 (1.0) 0.021 (1.1) 0.017 (104.7) 0.125 (106) 0.021 (1.2) 0.421
Pyrazinamide 0.318 (3.1) 0.371 (4.4) 0.353 (481.2) 0.342 (106) 0.366 (5.8) 0.347
Rifampicin 0.031 (1.4) 0.031 (1.5) 0.031 (130.0) 0.196 (106) 0.029 (1.3) 0.452
Streptomycin 0.050 (1.0) 0.052 (1.6) 0.043 (98.8) 0.137 (106) 0.050 (2.1) 0.435
P. aeruginosa       
Amikacin 0.175 (4.9) 0.206 (14.1) 0.187 (11514.6) 0.164 (106) 0.164 (9.7) 0.216
Doripenem 0.270 (1.4) 0.261 (1.9) 0.261 (950.0) 0.275 (106) 0.307 (8.5) 0.359
Levofloxacin 0.072 (1.2) 0.076 (1.0) 0.085 (148.9) 0.212 (106) 0.083 (3.5) 0.463
Meropenem 0.267 (1.6) 0.261 (1.0) 0.328 (5368.5) 0.327 (106) 0.331 (9.1) 0.404
S. pneumoniae       
Benzylpenicillin 0.013 (1.1) 0.012 (2.3) 0.011 (124.9) 0.013 (106) 0.013 (1.3) 0.073
Erythromycin 0.037 (2.0) 0.047 (3.8) 0.041 (328.8) 0.042 (106) 0.041 (5.1) 0.142
Tetracycline 0.031 (1.1) 0.029 (1.2) 0.032 (1108.5) 0.037 (106) 0.033 (2.2) 0.106
  1. Results are shown for the SCM, which uses the entire feature, and the feature selection-based methods: χ 2+CART, χ 2+L1SVM, χ 2+L2SVM and χ 2+SCM. The baseline method predicts the most abundant class in the training set. The smallest error rates are in bold