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Table 2 Effect of varying k-mer and feature sizes on the Adipose subcutaneous tissue representing the Test-1 dataset and the Brain amygdala tissue representing the Test-2 dataset

From: A novel feature extraction method based on highly expressed SNPs for tissue-specific gene prediction

(a) Adipose subcutaneous tissue
k-mer size Feature size Feature set
  Forward Reverse
  Acc F1 Time Mem Acc F1 Time Mem
2 [6, 7, 8] 0.25 0.19 104 1906 0.26 0.20 105 1905
[7, 8, 9] 0.38 0.31 102 1907 0.39 0.32 102 1907
[8, 9, 10] 0.51 0.44 101 1908 0.51 0.44 104 1907
[9, 10, 11] 0.61 0.54 109 1908 0.61 0.54 102 1906
[10, 11, 12] 0.68 0.62 112 1907 0.68 0.61 106 1906
3 [6, 7, 8] 0.84 0.80 103 1923 0.85 0.82 104 1924
[7, 8, 9] 0.93 0.91 103 1924 0.94 0.93 105 1924
[8, 9, 10] 0.97 0.97 104 1924 0.98 0.97 102 1924
[9, 10, 11] 0.99 0.99 105 1925 0.99 0.99 106 1925
[10, 11, 12] 0.99 0.99 106 1926 1.00 0.99 106 1925
4 [6, 7, 8] 0.97 0.96 103 1986 0.97 0.97 105 1987
[7, 8, 9] 0.99 0.99 104 1987 0.99 0.99 106 1988
[8, 9, 10] 1.00 1.00 105 1988 1.00 1.00 104 1988
[9, 10, 11] 1.00 1.00 106 1990 1.00 1.00 106 1990
[10, 11, 12] 1.00 1.00 108 1990 1.00 1.00 108 1990
5 [6, 7, 8] 0.99 0.99 106 2242 0.99 0.99 104 2242
[7, 8, 9] 1.00 1.00 107 2244 1.00 1.00 106 2243
[8, 9, 10] 1.00 1.00 106 2245 1.00 1.00 107 2245
[9, 10, 11] 1.00 1.00 109 2245 1.00 1.00 109 2245
[10, 11, 12] 1.00 1.00 109 2247 1.00 1.00 110 2246
(b) Brain amygdala tissue
k-mer size Feature size Feature set
  Forward Reverse
  Acc F1 Time Mem Acc F1 Time Mem
2 [6, 7, 8] 0.58 0.51 15 196 0.59 0.52 15 196
[7, 8, 9] 0.70 0.63 13 196 0.69 0.63 13 196
[8, 9, 10] 0.76 0.71 13 196 0.77 0.72 13 196
[9, 10, 11] 0.81 0.76 13 196 0.81 0.76 13 196
[10, 11, 12] 0.84 0.79 13 196 0.84 0.80 14 196
3 [6, 7, 8] 0.97 0.96 13 199 0.97 0.96 13 199
[7, 8, 9] 0.99 0.98 13 199 0.99 0.99 13 199
[8, 9, 10] 1.00 0.99 13 199 1.00 0.99 13 199
[9, 10, 11] 1.00 1.00 13 199 1.00 1.00 13 199
[10, 11, 12] 1.00 1.00 13 199 1.00 1.00 13 199
4 [6, 7, 8] 0.99 0.99 13 210 1.00 0.99 13 210
[7, 8, 9] 1.00 1.00 14 210 1.00 1.00 13 210
[8, 9, 10] 1.00 1.00 13 211 1.00 1.00 14 211
[9, 10, 11] 1.00 1.00 13 211 1.00 1.00 13 211
[10, 11, 12] 1.00 1.00 13 211 1.00 1.00 14 211
5 [6, 7, 8] 1.00 1.00 13 256 1.00 1.00 14 256
[7, 8, 9] 1.00 1.00 14 256 1.00 1.00 14 256
[8, 9, 10] 1.00 1.00 14 256 1.00 1.00 14 256
[9, 10, 11] 1.00 1.00 14 256 1.00 1.00 14 256
[10, 11, 12] 1.00 1.00 14 270 1.00 1.00 14 256
  1. Total run time is reported in seconds and peak memory usage in megabytes. Accuracy indicated by Acc and F1-Score indicated by F1