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Table 3 Rare disease classification performance on ChinaRe corpus

From: Improving rare disease classification using imperfect knowledge graph

Percentage Bins

(0, 0.02%]

(0.02%, 0.05%]

(0.05%, 0.1%]

(0.1%, 0.5%]

(0.5%, 1%]

 

5 diseases

3 diseases

2 diseases

7 diseases

9 diseases

 

F1

MRR

F1

MRR

F1

MRR

F1

MRR

F1

MRR

BOW

91.58

93.36

29.76

53.97

90.49

93.49

88.69

92.64

92.6

95.09

LSTM

0.00

4.03

0.00

4.75

0.00

9.64

22.38

44.68

85.86

93.55

UpSample

88.36

94.81

52.22

66.54

90.11

93.06

89.36

94.27

92.62

95.76

χ2

91.38

95.83

47.97

65.12

90.40

93.68

91.92

95.41

93.84

96.45

BOW+ χ2

93.37

97.55

42.14

62.80

90.73

93.95

92.01

95.55

94.05

96.43

KG1

91.06

97.47

22.63

43.64

48.52

48.11

80.54

86.67

74.32

77.33

KG12

92.26

97.70

31.20

43.91

85.61

91.42

83.71

87.96

80.05

83.18

BOW+KG\(^{\text {pseudo-doc}}_{1}\)

75.68

82.49

34.86

52.08

83.20

87.84

78.79

85.57

88.34

91.86

BOW+KG\(^{\text {pseudo-count}}_{1}\)

88.14

91.02

30.04

52.62

89.02

93.61

85.54

88.64

90.8

93.34

BOW+KG\(^{\text {late-fusion}}_{1}\)

89.01

95.41

29.76

48.8

68.63

70.80

86.18

89.65

86.89

86.21

BOW+KG\(^{\text {early-fusion}}_{1}\)

92.30

97.66

54.73

69.88

90.27

92.54

91.00

95.05

93.59

95.92

BOW+KG\(^{\text {early-fusion}}_{12}\)

93.43

97.13

47.78

62.04

91.68

95.41

90.70

94.49

93.46

95.70

  1. See the footnote below Table 2 for details