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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