Research Article
A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data
Table 4
Summary of three classification methods using real data.
| Datasets | FS | Logistic regression | RF | SVM | PPV | NPV | AUC | PPV | NPV | AUC | PPV | NPV | AUC |
| BRCA | baySeq | 0.53 | 0.53 | 0.53 | 1.00 | 0.99 | 0.99 | 0.95 | 0.96 | 0.96 | DESeq | 0.70 | 0.72 | 0.70 | 1.00 | 0.99 | 1.00 | 1.00 | 0.94 | 0.97 | edgeR | 0.54 | 0.55 | 0.55 | 1.00 | 0.99 | 0.99 | 0.54 | 0.55 | 0.55 | Lasso | 0.97 | 0.98 | 0.98 | 1.00 | 0.99 | 0.99 | 0.97 | 0.98 | 0.98 | Rank sum | 0.55 | 0.55 | 0.55 | 1.00 | 0.99 | 0.99 | 0.55 | 0.55 | 0.55 | PSODT | 0.85 | 0.86 | 0.86 | 0.99 | 0.98 | 0.98 | 0.85 | 0.86 | 0.86 |
| HNSC | baySeq | 0.35 | 0.38 | 0.37 | 0.54 | 0.56 | 0.55 | 0.63 | 0.52 | 0.58 | DESeq | 0.52 | 0.57 | 0.55 | 0.53 | 0.52 | 0.52 | 0.91 | 0.47 | 0.69 | edgeR | 0.32 | 0.35 | 0.33 | 0.54 | 0.54 | 0.54 | 0.32 | 0.35 | 0.33 | Lasso | 0.52 | 0.76 | 0.64 | 0.55 | 0.55 | 0.55 | 0.52 | 0.76 | 0.64 | Rank sum | 0.35 | 0.31 | 0.33 | 0.54 | 0.54 | 0.54 | 0.35 | 0.31 | 0.33 | PSODT | 0.43 | 0.44 | 0.43 | 0.55 | 0.54 | 0.54 | 0.43 | 0.44 | 0.43 |
| KICH | baySeq | 0.36 | 0.38 | 0.37 | 0.65 | 0.66 | 0.66 | 0.68 | 0.70 | 0.69 | DESeq | 0.37 | 0.39 | 0.38 | 0.66 | 0.65 | 0.66 | 0.68 | 0.84 | 0.76 | edgeR | 0.40 | 0.38 | 0.39 | 0.66 | 0.65 | 0.66 | 0.40 | 0.38 | 0.39 | Lasso | 0.64 | 0.82 | 0.73 | 0.65 | 0.66 | 0.65 | 0.64 | 0.82 | 0.73 | Rank sum | 0.39 | 0.38 | 0.39 | 0.66 | 0.66 | 0.66 | 0.39 | 0.38 | 0.39 | PSODT | 0.37 | 0.38 | 0.37 | 0.66 | 0.65 | 0.66 | 0.37 | 0.38 | 0.37 |
| LUAD | baySeq | 0.40 | 0.47 | 0.43 | 0.46 | 0.45 | 0.46 | 0.45 | 0.69 | 0.57 | DESeq | 0.30 | 0.78 | 0.54 | 0.46 | 0.41 | 0.44 | 0.95 | 0.36 | 0.65 | edgeR | 0.44 | 0.47 | 0.46 | 0.47 | 0.45 | 0.46 | 0.44 | 0.47 | 0.46 | Lasso | 0.47 | 0.74 | 0.61 | 0.47 | 0.45 | 0.46 | 0.47 | 0.74 | 0.61 | Rank sum | 0.30 | 0.36 | 0.33 | 0.47 | 0.45 | 0.46 | 0.30 | 0.36 | 0.33 | PSODT | 0.36 | 0.50 | 0.43 | 0.47 | 0.45 | 0.46 | 0.36 | 0.50 | 0.43 |
| STAD | baySeq | 0.42 | 0.56 | 0.49 | 0.44 | 0.45 | 0.44 | 0.44 | 0.63 | 0.54 | DESeq | 0.14 | 0.85 | 0.49 | 0.41 | 0.38 | 0.40 | 0.91 | 0.25 | 0.58 | edgeR | 0.37 | 0.42 | 0.40 | 0.49 | 0.46 | 0.47 | 0.37 | 0.42 | 0.40 | Lasso | 0.43 | 0.77 | 0.60 | 0.46 | 0.46 | 0.46 | 0.43 | 0.77 | 0.60 | Rank sum | 0.40 | 0.48 | 0.44 | 0.44 | 0.46 | 0.45 | 0.40 | 0.48 | 0.44 | PSODT | 0.36 | 0.44 | 0.44 | 0.44 | 0.46 | 0.45 | 0.36 | 0.44 | 0.40 |
| THCA | baySeq | 0.49 | 0.63 | 0.56 | 0.56 | 0.57 | 0.57 | 0.77 | 0.50 | 0.63 | DESeq | 0.49 | 0.85 | 0.67 | 0.54 | 0.58 | 0.56 | 0.54 | 0.82 | 0.68 | edgeR | 0.53 | 0.59 | 0.56 | 0.56 | 0.60 | 0.58 | 0.53 | 0.59 | 0.56 | Lasso | 0.54 | 0.88 | 0.71 | 0.56 | 0.59 | 0.57 | 0.54 | 0.88 | 0.71 | Rank sum | 0.44 | 0.44 | 0.44 | 0.57 | 0.58 | 0.58 | 0.44 | 0.44 | 0.44 | PSODT | 0.48 | 0.56 | 0.52 | 0.56 | 0.56 | 0.56 | 0.48 | 0.56 | 0.52 |
|
|