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Table 4 Classification accuracy and standard deviation for several kernels and their variant when plugged into the Gaussian RBF kernel

From: A survey on graph kernels

Dataset

MK-IL

MK-L

PM

DeepGK

DBR a

Prop

 

Klin

KRBF

Klin

KRBF

Klin

KRBF

Klin

KRBF

Klin

KRBF

Klin

KRBF

NCI1

76.8 ±0.3

78.1 ±0.3

72.8 ±0.3

75.5 ±0.3

73.3 ±0.3

80.0 ±0.3

74.9 ±0.2

78.4 ±0.3

67.4 ±0.3

76.0 ±0.2

84.6 ±0.2

85.6 ±0.2

NCI109

75.4 ±0.3

75.9 ±0.3

71.9 ±0.3

74.1 ±0.4

71.1 ±0.3

78.8 ±0.2

73.3 ±0.2

77.7 ±0.3

66.6 ±0.2

75.3 ±0.2

84.1 ±0.2

84.7 ±0.2

PTC-FR

69.1 ±0.6

68.6 ±0.7

68.4 ±0.7

68.1 ±0.9

65.9 ±0.8

65.0 ±1.1

66.4 ±1.2

63.8 ±1.5

65.3 ±0.5

64.0 ±0.7

66.0 ±1.5

65.6 ±1.0

PTC-MR

60.6 ±1.0

60.5 ±1.1

59.1 ±1.7

59.7 ±1.4

61.5 ±1.3

59.5 ±2.0

59.9 ±1.5

60.9 ±1.7

53.7 ±1.3

55.1 ±1.9

59.9 ±1.6

61.3 ±2.1

PTC-FM

58.6 ±1.8

64.7 ±0.6

60.4 ±0.9

61.4 ±1.6

59.7 ±1.4

62.2 ±0.8

62.6 ±0.9

60.9 ±1.1

56.2 ±1.5

59.8 ±1.5

60.9 ±1.6

61.7 ±1.6

PTC-MM

62.1 ±1.6

65.0 ±1.4

63.8 ±1.2

63.1 ±0.7

62.9 ±1.3

62.2 ±1.0

63.3 ±0.9

61.8 ±1.4

59.4 ±1.1

63.5 ±1.0

63.9 ±1.0

64.6 ±1.9

MUTAG

82.8 ±1.4

83.7 ±0.8

83.1 ±1.3

83.5 ±1.0

84.9 ±1.2

86.7 ±0.8

85.1 ±1.5

84.4 ±0.7

86.2 ±1.6

84.6 ±0.7

90.3 ±0.9

86.1 ±1.1

Mutagenicity

70.7 ±0.3

75.2 ±0.2

70.9 ±0.3

75.3 ±0.2

72.1 ±0.2

75.5 ±0.3

79.4 ±0.3

80.2 ±0.2

66.2 ±0.1

66.8 ±0.5

67.5 ±0.2

76.7 ±0.4

AIDS

99.6 ±0.0

99.6 ±0.1

99.6 ±0.0

99.6 ±0.0

99.7 ±0.0

99.7 ±0.0

99.6 ±0.0

99.6 ±0.0

99.3 ±0.1

99.7 ±0.0

99.7 ±0.0

99.7 ±0.0

BZR

88.1 ±0.8

88.2 ±0.8

88.1 ±0.6

87.8 ±0.7

84.5 ±1.0

85.5 ±0.7

86.5 ±0.6

87.8 ±0.6

82.8 ±0.9

84.1 ±0.8

87.1 ±0.5

87.7 ±1.0

COX2

81.2 ±1.0

81.1 ±0.5

80.5 ±0.8

80.5 ±0.7

80.7 ±0.5

80.3 ±0.7

80.4 ±1.1

81.4 ±0.6

78.1 ±0.1

77.3 ±0.7

81.7 ±0.8

81.5 ±0.9

DHFR

81.5 ±0.8

82.1 ±0.3

79.2 ±0.8

80.0 ±0.7

75.3 ±0.7

78.1 ±0.8

80.7 ±1.0

81.0 ±0.8

75.1 ±0.5

78.3 ±0.7

82.8 ±0.6

83.2 ±0.7

DD

78.3 ±0.3

78.2 ±0.3

77.3 ±0.4

77.3 ±0.4

78.7 ±0.3

79.2 ±0.9

79.4 ±0.4

71.0 ±0.2

78.8 ±0.6

78.2 ±0.6

78.9 ±0.3

81.6 ±0.5

PROTEINS

76.6 ±0.6

76.8 ±0.4

75.1 ±0.2

74.8 ±0.5

74.5 ±0.4

74.6 ±0.5

75.7 ±0.3

74.2 ±0.4

74.3 ±0.5

74.6 ±0.5

ENZYMES

64.1 ±1.3

63.5 ±1.1

61.6 ±1.2

62.0 ±1.2

40.2 ±1.0

49.3 ±1.1

42.3 ±1.0

58.9 ±1.1

37.6 ±0.7

39.5 ±1.3

49.0 ±1.6

62.6 ±0.9

IMDB-BINARY

69.4 ±0.6

69.9 ±0.5

70.6 ±0.5

70.1 ±0.4

70.7 ±0.6

71.1 ±0.9

60.5 ±0.3

70.2 ±0.7

73.5 ±0.3

71.2 ±0.7

IMDB-MULTI

46.1 ±0.7

47.0 ±0.5

47.1 ±0.6

47.6 ±0.4

47.8 ±0.6

47.8 ±0.6

40.8 ±1.1

46.1 ±0.7

49.8 ±0.6

51.0 ±0.7

REDDIT-BINARY

82.3 ±0.2

82.7 ±0.4

82.4 ±0.1

67.8 ±0.2

78.2 ±0.3

85.5 ±0.3

MSRC-9

90.9 ±1.0

90.4 ±0.5

90.4 ±1.2

90.4 ±0.8

90.4 ±1.4

90.1 ±1.0

91.8 ±0.8

88.2 ±1.2

89.4 ±1.3

89.7 ±0.9

MSRC-21

89.0 ±0.6

89.0 ±0.8

89.3 ±0.5

89.3 ±0.5

91.3 ±0.5

91.2 ±0.5

89.9 ±0.5

27.5 ±1.2

88.6 ±0.5

89.8 ±0.6

MSRC-21C

85.7 ±0.6

85.6 ±0.9

85.6 ±0.9

84.8 ±1.1

84.4 ±0.9

84.6 ±0.9

85.1 ±1.4

76.8 ±1.3

81.4 ±1.1

81.8 ±1.1

Tox21-AR

97.7 ±0.0

97.7 ±0.0

97.4 ±0.0

97.4 ±0.0

97.6 ±0.0

97.7 ±0.0

97.0 ±0.0

97.6 ±0.0

97.8 ±0.0

97.8 ±0.0

Tox21-MMP

86.9 ±0.1

87.2 ±0.1

86.8 ±0.1

87.2 ±0.1

86.6 ±0.2

89.7 ±0.1

86.3 ±0.1

90.4 ±0.1

84.7 ±0.1

89.6 ±0.2

Tox21-AHR

89.6 ±0.0

89.6 ±0.0

89.4 ±0.1

89.5 ±0.0

89.4 ±0.1

91.7 ±0.1

88.7 ±0.1

91.8 ±0.1

89.2 ±0.0

91.1 ±0.1

Average

77.4

78.2

76.9

77.3

76.1

77.6

76.3

74.1

69.5

71.6

77.6

78.1

  1. aComputation of the DBR kernel did not finish within 48h on some datasets, as indicated by a line (—). The DBR kernel does not make use of label information
  2. The highest accuracy value is highlighted in bold for each dataset.