Table 3 Classification accuracy and standard deviation for several kernels and their variant when plugged into the Gaussian RBF kernel

NCI1

64.6 ±0.1

67.2 ±2.8

66.3 ±0.1

71.8 ±0.3

73.2 ±0.3

79.3 ±0.4

85.9 ±0.1

86.2 ±0.1

86.2 ±0.2

86.6 ±0.2

70.5 ±0.2

76.5 ±0.4

NCI109

63.6 ±0.2

68.9 ±1.4

64.9 ±0.1

71.4 ±0.5

72.7 ±0.3

77.6 ±0.3

85.9 ±0.3

86.0 ±0.3

86.2 ±0.2

86.4 ±0.2

69.3 ±0.2

76.0 ±0.4

PTC-FR

67.9 ±0.4

66.9 ±0.5

66.8 ±0.5

65.2 ±1.2

67.1 ±2.0

63.7 ±2.0

67.1 ±1.2

66.8 ±1.5

67.8 ±1.1

67.0 ±1.3

65.5 ±0.9

65.0 ±1.4

PTC-MR

57.8 ±0.9

59.4 ±1.4

56.7 ±1.6

60.5 ±1.8

58.8 ±2.2

62.0 ±1.8

60.4 ±1.5

62.7 ±2.0

62.6 ±1.5

62.7 ±1.0

57.4 ±1.6

60.4 ±1.6

PTC-FM

63.9 ±0.5

62.6 ±0.9

64.5 ±0.4

60.5 ±1.4

62.7 ±1.0

60.2 ±1.3

62.8 ±1.2

60.9 ±0.8

61.6 ±1.2

61.7 ±1.2

60.2 ±3.0

60.7 ±0.8

PTC-MM

66.6 ±0.8

64.7 ±0.4

64.1 ±1.0

62.7 ±1.6

63.3 ±1.2

63.2 ±0.8

67.8 ±2.1

67.7 ±1.3

66.4 ±1.1

66.3 ±1.7

61.4 ±1.7

61.3 ±1.4

MUTAG

85.4 ±0.7

82.9 ±1.0

83.6 ±1.0

88.4 ±2.2

83.1 ±1.3

85.2 ±1.4

86.6 ±0.6

87.9 ±1.0

87.5 ±2.1

87.3 ±1.7

87.2 ±1.1

87.8 ±1.1

Mutagenicity

67.0 ±0.2

73.9 ±0.3

72.4 ±0.1

80.3 ±0.3

77.4 ±0.2

80.1 ±0.2

83.6 ±0.2

84.5 ±0.3

84.2 ±0.2

84.7 ±0.4

79.8 ±0.2

82.7 ±0.3

AIDS

99.7 ±0.0

99.7 ±0.0

99.5 ±0.0

99.4 ±0.0

99.6 ±0.0

99.7 ±0.0

99.7 ±0.0

99.7 ±0.0

99.7 ±0.0

99.7 ±0.0

99.2 ±0.1

99.3 ±0.1

BZR

78.8 ±0.1

86.0 ±0.2

79.1 ±0.5

86.3 ±0.3

86.5 ±0.9

88.1 ±0.5

88.5 ±0.7

87.9 ±0.8

88.2 ±0.4

88.0 ±0.5

81.6 ±0.7

85.4 ±1.0

COX2

78.2 ±0.0

80.6 ±0.3

82.0 ±0.6

83.9 ±0.7

80.6 ±0.9

81.7 ±0.8

81.2 ±1.0

81.7 ±0.7

80.4 ±0.9

80.8 ±1.3

81.3 ±0.7

81.9 ±0.5

DHFR

60.9 ±0.2

74.8 ±1.2

67.9 ±0.6

73.2 ±0.9

77.5 ±0.6

80.7 ±0.7

82.7 ±0.4

83.5 ±0.6

83.0 ±1.0

83.3 ±0.6

74.7 ±0.6

81.2 ±1.0

DD

78.2 ±0.4

80.1 ±0.4

77.5 ±0.6

78.7 ±0.7

79.5 ±0.6

74.5 ±0.2

78.9 ±0.4

80.9 ±0.3

79.2 ±0.4

79.9 ±0.5

79.7 ±0.7

79.1 ±0.6

PROTEINS

71.9 ±0.4

74.7 ±0.4

73.4 ±0.3

75.2 ±0.5

75.9 ±0.4

74.0 ±0.3

75.5 ±0.3

73.9 ±0.7

76.2 ±0.4

75.9 ±0.6

72.7 ±0.6

73.0 ±0.6

ENZYMES

23.4 ±1.1

41.7 ±1.1

27.7 ±0.7

45.1 ±1.2

41.9 ±1.7

59.5 ±1.3

53.7 ±1.5

62.6 ±1.2

59.9 ±1.0

62.3 ±1.1

30.4 ±1.1

58.6 ±1.0

IMDB-BINARY

46.3 ±0.9

56.5 ±0.6

46.0 ±0.9

62.6 ±1.2

57.3 ±0.6

70.2 ±0.8

72.9 ±0.6

71.3 ±1.0

73.1 ±0.7

73.5 ±0.6

59.4 ±0.4

70.1 ±0.8

IMDB-MULTI

31.9 ±0.5

39.5 ±0.9

30.8 ±0.9

46.9 ±0.6

39.6 ±0.2

46.1 ±0.7

50.3 ±0.4

50.7 ±0.6

50.4 ±0.5

50.7 ±0.5

40.6 ±0.4

47.1 ±0.5

REDDIT-BINARY

75.3 ±0.1

77.6 ±0.2

75.1 ±0.1

79.4 ±0.1

81.7 ±0.2

67.8 ±0.2

80.9 ±0.4

83.9 ±0.5

89.3 ±0.2

88.9 ±0.1

60.1 ±0.2

73.6 ±0.1

MSRC-9

88.4 ±1.3

87.7 ±1.0

92.6 ±0.9

90.2 ±0.7

91.4 ±0.8

89.2 ±1.0

90.1 ±0.8

89.1 ±0.9

90.7 ±0.8

90.1 ±0.7

91.6 ±0.7

91.6 ±0.9

MSRC-21

89.4 ±0.3

90.0 ±0.5

89.5 ±0.3

87.3 ±0.4

89.4 ±0.6

37.4 ±1.2

89.3 ±0.6

89.8 ±0.4

90.0 ±0.6

90.5 ±0.4

90.5 ±0.7

85.1 ±0.6

MSRC-21C

81.2 ±1.2

80.8 ±1.7

84.5 ±0.8

81.8 ±1.3

83.8 ±1.2

78.3 ±1.3

81.9 ±0.9

82.1 ±1.1

84.9 ±0.8

84.5 ±1.0

84.0 ±1.7

82.6 ±1.0

Tox21-AR

95.9 ±0.0

96.4 ±0.0

95.9 ±0.0

97.5 ±0.0

97.1 ±0.0

97.5 ±0.0

97.9 ±0.0

98.0 ±0.0

98.0 ±0.0

98.0 ±0.0

96.4 ±0.0

97.6 ±0.0

Tox21-MMP

84.3 ±0.0

86.5 ±0.1

84.5 ±0.0

89.7 ±0.2

86.4 ±0.1

90.7 ±0.2

92.5 ±0.1

93.0 ±0.2

92.7 ±0.1

92.8 ±0.1

87.3 ±0.1

91.2 ±0.2

Tox21-AHR

88.4 ±0.0

89.1 ±0.2

88.6 ±0.1

91.4 ±0.2

88.4 ±0.0

91.9 ±0.1

93.4 ±0.1

93.7 ±0.1

93.5 ±0.1

93.6 ±0.1

89.7 ±0.1

92.8 ±0.2

Average

71.2

74.5

72.2

76.2

75.6

74.9

79.6

80.2

80.5

80.6

73.8

77.5