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 |