Table 2 DRP performance comparison for mask-cells.

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

1.303 ± 0.074

+0.1%

0.846

0.884 ± 0.013

-0.1%

0.625

WD

1.304 ± 0.056

0.883 ± 0.011

512-bit Morgan FP

ND

1.304 ± 0.065

+1.2%

0.193

0.882 ± 0.013

-0.1%

0.557

WD

1.320 ± 0.071

0.881 ± 0.013

1024-bit Morgan FP

ND

1.300 ± 0.063

+0.7%

0.275

0.884 ± 0.013

-0.2%

0.131

WD

1.309 ± 0.065

0.882 ± 0.012

2048-bit Morgan FP

ND

1.304 ± 0.063

+2.1%

0.065

0.883 ± 0.012

-0.3%

0.065

WD

1.331 ± 0.073

0.880 ± 0.013

PubChem FP

ND

1.298 ± 0.054

-0.2%

1

0.883 ± 0.011

+0.1%

0.846

WD

1.296 ± 0.065

0.884 ± 0.011

HiDRA

256-bit Morgan FP

ND

1.365 ± 0.089

+2.7%

0.432

0.872 ± 0.017

-0.8%

0.193

WD

1.402 ± 0.098

0.865 ± 0.020

512-bit Morgan FP

ND

1.365 ± 0.093

+1.8%

0.557

0.870 ± 0.018

-0.3%

0.432

WD

1.389 ± 0.098

0.867 ± 0.019

1024-bit Morgan FP

ND

1.380 ± 0.098

-0.9%

0.432

0.868 ± 0.019

+0.2%

0.375

WD

1.368 ± 0.111

0.870 ± 0.024

2048-bit Morgan FP

ND

1.394 ± 0.070

-2.3%

0.131

0.867 ± 0.013

+0.6%

0.193

WD

1.362 ± 0.083

0.872 ± 0.017

PubChem FP

ND

1.393 ± 0.065

-2.4%

0.275

0.868 ± 0.013

+0.5%

0.275

WD

1.360 ± 0.082

0.872 ± 0.017

PaccMann

SMILES

ND

1.496 ± 0.060

-12.0%

0.002

0.840 ± 0.014

+4.5%

0.002

WD

1.316 ± 0.064*

0.878 ± 0.013*

SRMF

256-bit Morgan FP

ND

2.686 ± 0.533

-5.2%

0.557

0.828 ± 0.017

-2.0%

0.695

WD

2.546 ± 0.315

0.812 ± 0.041

512-bit Morgan FP

ND

2.686 ± 0.533

-5.1%

0.492

0.828 ± 0.017

-1.0%

0.695

WD

2.550 ± 0.540

0.820 ± 0.035

1024-bit Morgan FP

ND

2.686 ± 0.533

-5.7%

0.557

0.828 ± 0.017

+0.2%

0.922

WD

2.533 ± 0.519

0.830 ± 0.019

2048-bit Morgan FP

ND

2.686 ± 0.533

-4.9%

0.492

0.828 ± 0.017

-2.3%

0.770

WD

2.554 ± 0.521

0.809 ± 0.054

PubChem FP

ND

2.686 ± 0.533

+17.3%

0.049

0.828 ± 0.017

-8.3%

0.232

WD

3.152 ± 0.591*

0.759 ± 0.113

ADRML

256-bit Morgan FP

ND

2.560 ± 0.096

-8.4%

0.002

0.834 ± 0.017

-0.1%

0.106

WD

2.346 ± 0.103*

0.833 ± 0.017

512-bit Morgan FP

ND

2.560 ± 0.096

-14.3%

0.002

0.834 ± 0.017

0.0%

1.000

WD

2.194 ± 0.094*

0.834 ± 0.017

1024-bit Morgan FP

ND

2.560 ± 0.096

-12.3%

0.002

0.834 ± 0.017

0.0%

0.695

WD

2.244 ± 0.097*

0.834 ± 0.017

2048-bit Morgan FP

ND

2.560 ± 0.096

-14.3%

0.002

0.834 ± 0.017

0.0%

1.000

WD

2.194 ± 0.094*

0.834 ± 0.017

  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: \(\sim\) 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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