Skip to main content

Table 6 Machine learning experiment test results on the data representation models of the full gene BOUN10CANCER dataset

From: Statistical representation models for mutation information within genomic data

Algorithm Data Rep. Accuracy F-Score Precision Recall Roc-Auc FPR
NB binary 33.84 ± 0.83 35.25 ± 0.95 37.04 ± 1.34 33.84 ± 0.83 0.62 ± 0.02 8.38 ± 0.11
  c-score 31.10 ± 0.86 32.72 ± 0.74 34.53 ± 1.43 31.10 ± 0.86 0.59 ± 0.01 8.61 ± 0.08
  tf-idf 33.34 ± 0.48 35.04 ± 0.60 37.03 ± 1.03 33.34 ± 0.48 0.62 ± 0.02 7.99 ± 0.07
  tf-rf 38.14 ± 0.57 38.97 ± 0.87 40.08 ± 1.27 38.14 ± 0.57 0.65 ± 0.01 7.99 ± 0.10
  bm25-tf-idf 32.50 ± 0.96 34.19 ± 0.87 36.08 ± 1.35 32.50 ± 0.96 0.60 ± 0.01 8.48 ± 0.10
  bm25-tf-rf 37.94 ± 0.63 38.99 ± 0.60 40.12 ± 1.24 37.94 ± 0.63 0.62 ± 0.01 7.91 ± 0.10
KNN binary 11.54 ± 0.85 16.87 ± 0.66 31.46 ± 2.54 11.54 ± 0.85 0.50 ± 0.04 7.41 ± 0.04
  c-score 15.87 ± 0.63 22.60 ± 0.44 39.27 ± 4.21 15.87 ± 0.63 0.53 ± 0.01 7.96 ± 0.07
  tf-idf 34.96 ± 0.66 37.35 ± 0.95 38.92 ± 0.69 34.96 ± 0.66 0.62 ± 0.03 8.10 ± 0.04
  tf-rf 19.29 ± 0.44 22.23 ± 0.61 40.29 ± 0.82 19.29 ± 0.44 0.55 ± 0.02 7.57 ± 0.07
  bm25-tf-idf 12.72 ± 1.23 20.05 ± 0.58 47.32 ± 5.85 12.72 ± 1.23 0.51 ± 0.01 8.17 ± 0.37
  bm25-tf-rf 11.91 ± 1.13 19.21 ± 0.50 49.74 ± 1.58 11.91 ± 1.13 0.51 ± 0.01 7.88 ± 0.17
SVM-poly binary 17.50 ± 0.00 5.21 ± 0.00 3.06 ± 0.00 17.50 ± 0.00 0.53 ± 0.00 16.34 ± 0.00
  c-score 56.14 ± 0.44 58.90 ± 0.39 61.96 ± 0.46 56.14 ± 0.44 0.73 ± 0.01 5.33 ± 0.06
  tf-idf 17.50 ± 0.00 5.21 ± 0.00 3.06 ± 0.00 17.50 ± 0.00 0.53 ± 0.00 16.35 ± 0.00
  tf-rf 55.51 ± 0.55 56.52 ± 0.65 61.40 ± 0.53 55.51 ± 0.55 0.71 ± 0.03 5.16 ± 0.05
  bm25-tf-idf 36.36 ± 0.66 42.64 ± 0.75 51.56 ± 0.89 36.36 ± 0.66 0.62 ± 0.01 7.93 ± 0.08
  bm25-tf-rf 53.41 ± 0.27 51.46 ± 0.27 63.95 ± 0.65 53.41 ± 0.27 0.66 ± 0.01 7.38 ± 0.04
SVM-rbf binary 66.71 ± 0.36 67.01 ± 0.00 68.01 ± 0.00 67.01 ± 0.01 0.78 ± 0.01 4.04 ± 0.09
  c-score 57.35 ± 0.30 61.31 ± 0.28 65.86 ± 1.10 57.35 ± 0.30 0.72 ± 0.01 7.09 ± 0.05
  tf-idf 50.92 ± 0.19 44.26 ± 0.20 51.64 ± 0.19 50.92 ± 0.19 0.69 ± 0.02 8.30 ± 0.03
  tf-rf 69.53 ± 0.71 69.82 ± 0.72 70.75 ± 0.71 69.53 ± 0.71 0.78 ± 0.03 3.64 ± 0.09
  bm25-tf-idf 66.17 ± 0.56 66.61 ± 0.60 67.20 ± 0.62 66.17 ± 0.56 0.78 ± 0.01 4.40 ± 0.07
  bm25-tf-rf 73.77 ± 0.46 74.00 ± 0.46 74.96 ± 0.40 73.77 ± 0.46 0.83 ± 0.01 3.20 ± 0.07
SVM-linear binary 68.46 ± 0.67 68.01 ± 0.01 69.01 ± 0.01 68.01 ± 0.01 0.78 ± 0.01 4.07 ± 0.09
  c-score 71.91 ± 0.44 72.46 ± 0.45 73.02 ± 0.44 71.91 ± 0.44 0.82 ± 0.01 3.50 ± 0.09
  tf-idf 69.54 ± 0.66 69.01 ± 0.01 70.01 ± 0.01 69.01 ± 0.01 0.78 ± 0.01 3.94 ± 0.06
  tf-rf 68.80 ± 0.62 68.01 ± 0.01 69.51 ± 0.01 69.01 ± 0.01 0.78 ± 0.01 3.74 ± 0.09
  bm25-tf-idf 66.26 ± 0.58 66.35 ± 0.60 67.94 ± 0.66 66.26 ± 0.58 0.78 ± 0.01 4.31 ± 0.07
  bm25-tf-rf 73.44 ± 0.43 73.66 ± 0.45 74.63 ± 0.41 73.44 ± 0.43 0.83 ± 0.01 3.24 ± 0.07
LR binary 67.19 ± 0.41 68.01 ± 0.01 68.01 ± 0.00 67.01 ± 0.01 0.78 ± 0.01 3.85 ± 0.07
  c-score 73.50 ± 0.64 73.89 ± 0.92 74.29 ± 0.66 73.50 ± 0.64 0.83 ± 0.01 3.40 ± 0.08
  tf-idf 63.17 ± 0.30 60.01 ± 0.00 66.01 ± 0.01 63.01 ± 0.00 0.74 ± 0.01 5.68 ± 0.04
  tf-rf 71.51 ± 0.46 72.01 ± 0.01 73.01 ± 0.01 71.01 ± 0.01 0.81 ± 0.01 3.24 ± 0.07
  bm25-tf-idf 67.80 ± 0.45 68.20 ± 0.47 68.61 ± 0.53 67.80 ± 0.45 0.79 ± 0.01 4.09 ± 0.06
  bm25-tf-rf 74.99 ± 0.41 75.19 ± 0.38 75.96 ± 0.37 74.99 ± 0.41 0.83 ± 0.01 3.03 ± 0.06
Perceptron binary 68.50 ± 0.48 69.01 ± 0.01 70.01 ± 0.01 68.01 ± 0.01 0.78 ± 0.03 4.07 ± 0.09
  c-score 71.64 ± 1.54 71.76 ± 1.87 71.89 ± 1.38 71.64 ± 1.54 0.81 ± 0.01 3.67 ± 0.24
  tf-idf 70.23 ± 0.40 70.01 ± 0.00 70.01 ± 0.01 70.01 ± 0.01 0.79 ± 0.01 3.83 ± 0.05
  tf-rf 72.07 ± 1.86 72.01 ± 0.02 74.01 ± 0.01 72.01 ± 0.02 0.82 ± 0.02 3.29 ± 0.12
  bm25-tf-idf 65.52 ± 0.52 65.97 ± 0.52 66.44 ± 0.56 65.52 ± 0.52 0.78 ± 0.01 4.48 ± 0.08
  bm25-tf-rf 74.15 ± 0.51 74.48 ± 0.56 75.46 ± 0.56 74.15 ± 0.51 0.83 ± 0.01 3.07 ± 0.10
Feed-Forward NN binary 69.00 ± 0.76 69.52 ± 0.70 71.00 ± 0.52 69.00 ± 0.81 0.79 ± 0.02 3.65 ± 0.17
  c-score 73.74 ± 0.88 74.07 ± 0.73 74.41 ± 0.67 73.74 ± 0.88 0.84 ± 0.02 3.27 ± 0.24
  tf-idf 62.91 ± 0.79 63.32 ± 0.70 65.04 ± 0.52 62.91 ± 0.83 0.73 ± 0.02 4.00 ± 0.10
  tf-rf 74.13 ± 1.33 74.17 ± 1.47 75.43 ± 1.07 74.13 ± 1.40 0.85 ± 0.02 3.07 ± 0.24
  bm25-tf-idf 68.18 ± 1.83 68.79 ± 1.28 69.42 ± 0.76 68.18 ± 1.83 0.82 ± 0.02 4.07 ± 0.54
  bm25-tf-rf 76.44 ± 0.66 76.95 ± 0.68 77.48 ± 0.78 76.44 ± 0.66 0.86 ± 0.02 2.75 ± 0.13
  1. The row with the best accuracy and f-score is shown in italic for each algorithm. The overall best performance is made bold