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Table 7 Comparison with Literature Results on the Ames Toxicity Benchmark

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

Encoding

AUC ROCa

ECFP

0.87 ± 0.01

LSTAR

0.86 ± 0.01

SVM-dragonXb

0:86 ± 0.01

RAD2D

0.85 ± 0.02

RAD3D

0.85 ± 0.01

ASP

0.85 ± 0.02

GP-dragonXb

0.84 ± 0.01

AT2D

0.83 ± 0.01

RF-dragonXb

0.83 ± 0.01

AT3D

0.81 ± 0.01

kNN-dragonXb

0.79 ± 0.01

DFS

0.78 ± 0.01

AP2D

0.78 ± 0.03

AP3D

0.76 ± 0.02

  1. Benchmarks for the large Ames toxicity benchmark using LIBLINEAR (nested 5-fold cross-validation on defined splits). The features were hashed to 214 bit sparse binary fingerprints.
  2. a Area under the ROC curve b Reference classifier from the study of Hansen et al. using dragonX 1.2, SVM: support vector machine, GP: Gaussian processes, RF: random decision forest, kNN: k-nearest neighbor
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Journal of Cheminformatics

ISSN: 1758-2946

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