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Table 2 GenDev Technique B: Results for 2400 computational experiments when using the General Development Mode (GenDev) with the biomass reaction constrained to a minimum flux of 10−3 but not as part of the objective function

From: Evaluation of reaction gap-filling accuracy by randomization

(1) # rxns removed

1

2

5

10

20

50

(2) Rxns suggested are identical to rxns removed

58

na

29

na

4

na

0

na

0

na

0

na

 

59

65

26

32

4

8

0

1

0

0

0

0

(3) No rxns suggested

25

na

12

na

0

na

0

na

0

na

0

na

 

25

25

12

12

0

1

0

0

0

0

0

0

(4) Rxns suggested are a strict subset of rxns removed

0

na

35

na

37

na

21

na

8

na

0

na

 

0

0

32

37

38

53

20

49

7

20

0

1

(5) # rxns suggested is equal to # rxns re-moved

10

na

9

na

16

na

8

na

3

na

0

na

 

9

9

13

11

17

9

10

3

1

0

0

0

(6) # rxns suggested is less than # rxns re-moved

0

na

8

na

29

na

58

na

83

na

97

na

 

0

0

8

8

29

28

62

47

90

80

100

99

(7) # rxns suggested is greater than # rxns removed

7

na

7

na

14

na

13

na

6

na

2

na

 

7

1

7

0

12

1

8

0

2

0

0

0

(8) # cases where no solution was found

0

na

0

na

0

na

0

na

0

na

1

na

 

0

0

0

0

0

0

0

0

0

0

0

0

Precision (%)

81

na

80

na

75

na

78

na

80

na

77

na

 

83

87

76

84

77

86

78

90

78

87

77

88

Average precision (%)

     

78

na

     
      

78

87

     

Recall (%)

64

na

55

na

58

na

58

na

60

na

59

na

 

65

66

54

55

60

61

59

62

58

60

59

60

Average recall (%)

     

59

na

     
      

59

61

     

# Solutions that do not show growth

    

0

na

    
     

0

4 (0.6%)

    
  1. The meaning of rows and columns are the same as in Table 1