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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