Table 1 DRP performance comparison for mask-pairs.

From: Drug molecular representations for drug response predictions: a comprehensive investigation via machine learning methods

Model

Drug representations

Setting

RMSE ± SE

Change

p-value

PCC ± SE

Change

p-value

PathDSP

256-bit Morgan FP

ND

0.965 ± 0.024

− 0.9%

0.322

0.937 ± 0.003

+0.1%

0.232

WD

0.956 ± 0.019

0.938 ± 0.003

512-bit Morgan FP

ND

0.956 ± 0.027

+0.9%

0.131

0.938 ± 0.003

−0.1%

0.049

WD

0.962 ± 0.024

0.937 ± 0.003*

1024-bit Morgan FP

ND

0.959 ± 0.019

− 0.4%

0.557

0.938 ± 0.002

0.0%

0.557

WD

0.955 ± 0.023

0.938 ± 0.003

2048-bit Morgan FP

ND

0.959 ± 0.021

− 0.3%

0.432

0.938 ± 0.002

0.0%

0.695

WD

0.956 ± 0.021

0.938 ± 0.002

PubChem FP

ND

0.986 ± 0.036

− 1.0%

0.557

0.934 ± 0.004

+0.1%

0.557

WD

0.976 ± 0.017

0.935 ± 0.002

HiDRA

256-bit Morgan FP

ND

1.000 ± 0.024

− 1.5%

0.020

0.932 ± 0.004

+0.3%

0.020

WD

0.985 ± 0.022*

0.935 ± 0.003*

512-bit Morgan FP

ND

0.998 ± 0.022

− 1.0%

0.193

0.932 ± 0.002

+0.4%

0.193

WD

0.988 ± 0.025

0.936 ± 0.003

1024-bit Morgan FP

ND

0.998 ± 0.021

− 1.6%

0.006

0.932 ± 0.003

+0.2%

0.014

WD

0.982 ± 0.015*

0.934 ± 0.002*

2048-bit Morgan FP

ND

0.992 ± 0.017

− 1.6%

0.020

0.933 ± 0.003

+0.2%

0.014

WD

0.976 ± 0.022*

0.935 ± 0.003*

PubChem FP

ND

1.007 ± 0.014

− 3.3%

0.002

0.931 ± 0.002

+0.5%

0.002

WD

0.974 ± 0.020*

0.935 ± 0.003*

PaccMann

SMILES

ND

1.345 ± 0.052

− 15.5%

0.002

0.875 ± 0.009

+4.3%

0.002

WD

1.137 ± 0.029*

0.913 ± 0.003*

SRMF

256-bit Morgan FP

ND

1.493 ± 0.026

+46.8%

0.002

0.895 ± 0.004

−5.6%

0.002

WD

2.192 ± 0.082*

0.845 ± 0.014*

512-bit Morgan FP

ND

1.493 ± 0.026

− 15.6%

0.002

0.895 ± 0.004

+1.0%

0.131

WD

1.260 ± 0.090*

0.904 ± 0.016

1024-bit Morgan FP

ND

1.493 ± 0.026

− 12.2%

0.002

0.895 ± 0.004

+0.2%

0.375

WD

1.310 ± 0.083*

0.888 ± 0.017

2048-bit Morgan FP

ND

1.493 ± 0.026

− 16.4%

0.002

0.895 ± 0.004

+0.2%

0.695

WD

1.248 ± 0.114*

0.897 ± 0.018

PubChem FP

ND

1.493 ± 0.026

+36.4%

0.002

0.895 ± 0.004

−10.3%

0.002

WD

2.036 ± 0.051*

0.803 ± 0.020*

ADRML

256-bit Morgan FP

ND

1.555 ± 0.027

+4.4%

0.002

0.864 ± 0.006

+1.6%

0.002

WD

1.624 ± 0.023*

0.878 ± 0.005*

512-bit Morgan FP

ND

1.555 ± 0.027

+6.6%

0.002

0.864 ± 0.006

−0.1%

0.002

WD

1.657 ± 0.026*

0.863 ± 0.006*

1024-bit Morgan FP

ND

1.555 ± 0.027

+4.8%

0.002

0.864 ± 0.006

+0.3%

0.002

WD

1.630 ± 0.025*

0.867 ± 0.006*

2048-bit Morgan FP

ND

1.555 ± 0.027

+5.7%

0.002

0.864 ± 0.006

−0.3%

0.002

WD

1.645 ± 0.026*

0.861 ± 0.006*

  1. SE standard errors, ND null-drug, WD with-drug. Change \(=\frac{\text {Mean (WD)}-\text {Mean (ND)}}{|\text {Mean (ND)}|}\); Italics: WD is worse than ND, Bold italics: WD is better than ND. p-value: the p-value of Wilcoxon rank-sum test. *Statistically significant change. Significant values are in bold.
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