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Table 3 Nested Cross-validation MSE Performance on the Sutherland Data Sets

From: jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

Encoding

ACE

ACHE

BZR

COX2

DHFR

GPB

THERM

THR

DFS

1.73 ± 0:74

0.66 ± 0.28

0.61 ± 0.31

1.13 ± 0.30

0.57 ± 0.21

0.66 ± 0.54

2.10 ± 1.31

0.60 ± 0.38

ASP

1.70 ± 0.72

0.62 ± 0.26

0.53 ± 0.27

1.11 ± 0.30

0.58 ± 0.21

0.63 ± 0.48

2.09 ± 1.32

0.59 ± 0.38

AP2D

1.50 ± 0.70

0.85 ± 0.37

0.70 ± 0.37

1.03 ± 0.30

0.73 ± 0.29

0.61 ± 0.45

2.19 ± 1.20

0.50 ± 0.31

AT2D

1.57 ± 0.69

0.74 ± 0.34

0.69 ± 0.35

0.97 ± 0.27

0.66 ± 0.30

0.60 ± 0.47

1.97 ± 1.20

0.49 ± 0.32

CATS2D

1.76 ± 0.72

0.93 ± 0.33

0.89 ± 0.45

1.35 ± 0.43

0.69 ± 0.19

0.64 ± 0.45

2.28 ± 1.14

0.52 ± 0.32

PHAP2PT2D

1.77 ± 0.71

0.96 ± 0.33

0.91 ± 0.45

1.38 ± 0.44

0.72 ± 0.20

0.65 ± 0.48

2.18 ± 1.10

0.53 ± 0.31

PHAP3PT2D

1.81 ± 0.69

0.96 ± 0.33

0.82 ± 0.39

1.23 ± 0.41

0.67 ± 0.21

0.56 ± 0.49

1.89 ± 1.16

0.57 ± 0.37

SHED

2.08 ± 0.76

1.05 ± 0.50

1.09 ± 0.46

1.64 ± 0.48

1.49 ± 0.35

0.70 ± 0.33

2.71 ± 1.54

0.49 ± 0.28

ECFP

1.80 ± 0.77

0.72 ± 0.29

0.66 ± 0.32

1.01 ± 0.28

0.57 ± 0.20

0.68 ± 0.55

2.19 ± 1.36

0.51 ± 0.33

RAD2D

1.87 ± 0.75

0.77 ± 0.33

0.79 ± 0.37

1.08 ± 0.30

0.71 ± 0.27

0.72 ± 0.59

2.20 ± 1.33

0.50 ± 0.35

LSTAR

1.97 ± 0.79

0.72 ± 0.29

0.69 ± 0.30

1.04 ± 0.27

0.62 ± 0.19

0.76 ± 0.61

2.31 ± 1.39

0.50 ± 0.31

AP3D

1.60 ± 0.69

0.69 ± 0.32

0.59 ± 0.32

0.93 ± 0.27

0.67 ± 0.23

0.67 ± 0.51

2.73 ± 1.35

0.57 ± 0.33

AT3D

1.77 ± 0.68

0.64 ± 0.28

0.67 ± 0.36

0.99 ± 0.28

0.57 ± 0.18

0.74 ± 0.60

2.75 ± 1.37

0.60 ± 0.28

CATS3D

1.75 ± 0.70

0.90 ± 0.38

0.81 ± 0.36

1.31 ± 0.41

0.73 ± 0.20

0.79 ± 0.49

2.47 ± 1.32

0.62 ± 0.32

PHAP2PT3D

1.75 ± 0.70

0.87 ± 0.36

0.81 ± 0.40

1.32 ± 0.41

0.73 ± 0.20

0.83 ± 0.54

2.53 ± 1.30

0.65 ± 0.33

PHAP3PT3D

1.99 ± 0.77

0.82 ± 0.29

0.81 ± 0.36

1.14 ± 0.37

0.59 ± 0.17

0.86 ± 0.69

2.84 ± 1.46

0.69 ± 0.30

RAD3D

2.17 ± 0.78

0.78 ± 0.31

0.73 ± 0.35

1.10 ± 0.30

0.57 ± 0.17

0.82 ± 0.69

2.79 ± 1.37

0.58 ± 0.31

  1. Overview of ϵ support vector MSE regression performance on the Sutherland data set using the MinMax kernel function. The performance was evaluated using a nested 10-fold cross-validation repeated 20 times. Bold values indicate the best encodings according to the number of signicant better comparisons (p ≤ 0.05) against the other encodings. The p-values were determined by the corrected resampled t-test [32].
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Journal of Cheminformatics

ISSN: 1758-2946

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