Table 3 DRP performance comparison for mask-drugs.

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

4.455 ± 4.964

-13.7%

0.922

0.216 ± 0.196

+47.2%

0.432

WD

3.844 ± 3.139

0.318 ± 0.217

512-bit Morgan FP

ND

2.867 ± 0.569

-9.4%

0.084

0.242 ± 0.151

+71.1%

0.006

WD

2.596 ± 0.559

0.414 ± 0.176*

1024-bit Morgan FP

ND

3.479 ± 1.602

-18.7%

0.065

0.208 ± 0.157

+103.4%

0.002

WD

2.828 ± 1.346

0.423 ± 0.188*

2048-bit Morgan FP

ND

2.893 ± 0.509

+115.4%

0.084

0.241 ± 0.149

+77.1%

0.002

WD

6.232 ± 12.083

0.427 ± 0.209*

PubChem FP

ND

9.948 ± 20.023

+253.7%

0.084

0.126 ± 0.136

+201.6%

0.020

WD

35.187 ± 103.350

0.380 ± 0.275*

HiDRA

256-bit Morgan FP

ND

2.723 ± 0.417

-5.6%

0.275

0.232 ± 0.073

+60.3%

0.375

WD

2.571 ± 0.471

0.372 ± 0.201

512-bit Morgan FP

ND

2.729 ± 0.502

-9.3%

0.027

0.215 ± 0.202

+89.3%

0.014

WD

2.475 ± 0.440*

0.407 ± 0.183*

1024-bit Morgan FP

ND

2.710 ± 0.472

-10.3%

0.065

0.259 ± 0.176

+55.6%

0.106

WD

2.431 ± 0.448

0.403 ± 0.142

2048-bit Morgan FP

ND

2.703 ± 0.540

-10.8%

0.106

0.264 ± 0.229

+59.8%

0.106

WD

2.411 ± 0.495

0.422 ± 0.159

PubChem FP

ND

2.770 ± 0.530

-13.3%

0.049

0.211 ± 0.159

+112.8%

0.027

WD

2.402 ± 0.428*

0.449 ± 0.181*

PaccMann

SMILES

ND

2.746 ± 0.368

-6.8%

0.193

0.303 ± 0.108

+27.1%

0.492

WD

2.559 ± 0.478

0.385 ± 0.249

SRMF

256-bit Morgan FP

ND

3.734 ± 0.346

-7.4%

0.004

-0.016 ± 0.184

+1043.8%

0.020

WD

3.457 ± 0.474*

0.183 ± 0.167*

512-bit Morgan FP

ND

3.734 ± 0.346

-7.4%

0.002

-0.016 ± 0.184

+650.0%

0.084

WD

3.458 ± 0.462*

0.120 ± 0.216

1024-bit Morgan FP

ND

3.734 ± 0.346

-5.6%

0.002

-0.016 ± 0.184

+1225.0%

0.020

WD

3.524 ± 0.391*

0.212 ± 0.188*

2048-bit Morgan FP

ND

3.734 ± 0.346

-8.3%

0.002

-0.016 ± 0.184

+1850.0%

0.002

WD

3.424 ± 0.355*

0.280 ± 0.191*

PubChem FP

ND

3.734 ± 0.346

-18.4%

0.002

-0.016 ± 0.184

+2074.0%

0.004

WD

3.048 ± 0.599*

0.317 ± 0.172*

ADRML

256-bit Morgan FP

ND

3.731 ± 0.346

-6.6%

0.002

0.050 ± 0.058

+520.0%

0.002

WD

3.483 ± 0.364*

0.310 ± 0.062*

512-bit Morgan FP

ND

3.731 ± 0.346

-5.2%

0.002

0.050 ± 0.058

+528.0%

0.002

WD

3.537 ± 0.359*

0.314 ± 0.070*

1024-bit Morgan FP

ND

3.731 ± 0.346

-5.1%

0.002

0.050 ± 0.058

+548.0%

0.002

WD

3.539 ± 0.361*

0.324 ± 0.072*

2048-bit Morgan FP

ND

3.731 ± 0.346

-4.7%

0.002

0.050 ± 0.058

+558.0%

0.002

WD

3.557 ± 0.359*

0.329 ± 0.086*

  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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