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Table 4 Cross validation experiments for predicting the enzymatic-reaction likeness.

From: KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics

Chemical descriptors

Vector dimension

Diff-common L1SVM

Diff-only L1SVM

Baseline

Random

  

AUC

AUPR

AUC

AUPR

AUC

AUPR

AUC

AUPR

KCF-S k3

53679

0.9841

0.2483

0.9827

0.1872

0.8254

0.0584

0.4981

0.0052

 

10000

0.9839

0.2481

0.9824

0.1840

0.8299

0.0594

0.4985

0.0052

 

1000

0.9814

0.2269

0.9773

0.1508

0.8397

0.0592

0.5006

0.0053

KCF-S k2

28152

0.9761

0.2144

0.9691

0.1330

0.8122

0.0503

0.4995

0.0053

 

10000

0.9763

0.2148

0.9698

0.1366

0.8143

0.0501

0.4997

0.0053

 

1000

0.9720

0.2012

0.9596

0.1029

0.8178

0.0481

0.4988

0.0053

KCF-S k1

11133

0.9702

0.1835

0.9620

0.1300

0.8184

0.0776

0.4962

0.0052

 

10000

0.9699

0.1835

0.9600

0.1197

0.8187

0.0769

0.4960

0.0052

 

1000

0.9676

0.1757

0.9475

0.0868

0.8208

0.0744

0.4963

0.0052

PubChem FP

879

0.9531

0.1341

0.9067

0.0571

0.8883

0.0667

0.5006

0.0052

MACCS FP

164

0.9275

0.0932

0.9097

0.0510

0.8200

0.0336

0.5001

0.0052

ATOM k3

99

0.9532

0.1362

0.9378

0.0703

0.8195

0.0492

0.4983

0.0052

BOND k3

973

0.9773

0.2023

0.9713

0.1319

0.8260

0.0546

0.5001

0.0053