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Table 7 The comparison of prediction accuracies by HBSA-KNN, PAM and ClaNC on independent test set

From: Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

Methods Dataset Number of the top-ranked genes
2 3 4 5 6 7 8 20 40 60
HBSA-KNN Leukemia (Acc) 84.62 94.23 92.31 94.23 82.69 82.69 82.69 88.46 90.38 92.31
sensitivity 100 100 100 100 100 100 100 100 100 100
specificity 71.43 89.29 85.71 89.29 67.86 67.86 67.86 78.57 82.14 85.71
PPV 75 88.89 85.71 88.89 72.73 72.73 72.73 80 82.76 85.71
NPV 100 100 100 100 100 100 100 100 100 100
DLBCL (Acc) 95.24 100 80.95 85.71 80.95 85.71 85.71 85.71 85.71 90.48
sensitivity 100 100 85.71 85.71 78.57 85.71 85.71 85.71 85.71 92.86
specificity 85.71 100 71.43 85.71 85.71 85.71 85.71 85.71 85.71 85.71
PPV 93.33 100 85.71 92.31 91.67 92.31 92.31 92.31 92.31 92.86
NPV 93.33 100 85.71 92.31 91.67 92.31 92.31 92.31 92.31 92.86
Prostate (Acc) 88.24 76.47 82.35 85.29 82.35 79.41 76.47 76.47 82.35 85.29
Sensitivity 100 100 100 100 100 88.89 88.89 88.89 88.89 100
Specificity 84 68 76 80 76 76 72 72 80 80
PPV 69.23 52.94 60 64.29 60 57.14 53.33 53.33 61.54 64.29
NPV 100 100 100 100 100 95 94.74 94.74 95.24 100
SRBCT 75 95 95 100 95 95 95 95 95 100
ALL 75 82 87 94 92 93 93 96 97 99
Colon (Acc) 65 70 80 75 80 80 75 75 75 75
sensitivity 75 83.33 91.67 91.67 91.67 83.33 83.33 83.33 75 75
specificity 50 50 62.50 50 62.50 75 62.50 62.50 75 75
PPV 69.23 71.43 78.57 73.33 78.57 83.33 76.92 76.92 81.82 81.82
  NPV 57.14 66.67 83.33 80 83.33 75 71.43 71.43 66.67 66.67
PAM Dataset Number of the selected genes
2 4 6 8 10 12 16 20 40 60
Leukemia 82.69 90.38 90.38 90.38 92.31 94.23 96.15 96.15 98.08 98.08
DLBCL 66.67 66.67 66.67 66.67 66.67 66.67 66.67 66.67 66.67 66.67
Prostate 73.53 73.53 73.53 73.53 73.53 73.53 73.53 73.53 73.53 73.53
SRBCT 45 45 75 75 85 95 95 95 95 95
ALL 43 61 61 68 68 83 85 85 86 86
  Colon 65 75 70 70 70 75 75 75 75 75
ClaNC Dataset Number of the selected genes
1 ×  k * 2 ×  k 3 ×  k 4 ×  k 5 ×  k 6 ×  k 7 ×  k 8 ×  k 9 ×  k 10 ×  k
Leukemia 86.54 90.39 90.39 92.31 90.39 94.23 94.23 94.23 94.23 96.15
DLBCL 80.95 95.24 95.24 95.24 95.24 80.95 76.19 71.43 71.43 71.43
Prostate 73.53 85.29 79.41 76.47 76.47 79.41 79.41 76.47 76.47 79.41
SRBCT 85 95 95 95 95 95 95 95 95 95
ALL 86 95 97 99 98 98 99 99 99 98
  Colon 65 65 65 70 70 75 75 75 75 75
  1. * k denotes the number of subclasses in each dataset, which ranges from two to six. For example, for ALL dataset, the size of the gene subset selected ranges from six (1 × 6) to sixty (10 × 6).