Christoph Helma, Micha Rautenberg, Denis Gebele
in silico toxicology gmbh, Basel, Switzerland
lazar
read across frameworklazar
read across frameworkA reproducible version of the read across procedure commonly used in toxicological risk assessment (based on the k-nearest-neighbor algorithm)
lazar
was originally designed for small molecules with a defined chemical structure. The nanoparticle extension was developed and validated within the eNanoMapper project.
Partial least squares and random forest models use the caret
R package with default settings
Prediction intervals: 1.96*RMSE of caret
s bootstrapped model predictions
If PLS/RF modelling or prediction fails, lazar
resorts to using the weighted average method.
Net cell association endpoint of the Protein corona dataset (121 gold and silver particles)
Descriptors | Algorithm | r2 | RMSE | |
---|---|---|---|---|
Physchem | WA | 0.42, 0.46, 0.48 |
2.02, 1.94, 1.92 |
|
Physchem | PLS | 0.53, 0.54, 0.49 |
1.83, 1.8, 1.9 |
|
Physchem | RF | 0.53, 0.52, 0.54 |
1.82, 1.84, 1.79 |
|
Proteomics | WA | 0.66, 0.63, 0.63 * |
1.58, 1.62, 1.66 * |
|
Proteomics | PLS | 0.59, 0.66, 0.63 * |
1.74, 1.56, 1.65 * |
|
Proteomics | RF | 0.66, 0.65, 0.63 * |
1.56, 1.59, 1.64 * |
|
All | WA | 0.73, 0.66, 0.66 * |
1.41, 1.57, 1.58 * |
|
All | PLS | 0.67, 0.64, 0.69 * |
1.53, 1.63, 1.5 * |
|
All | RF | 0.69, 0.69, 0.7 ** |
1.51, 1.5, 1.46 ** |
Gold and silver particles included!
Try the nano-lazar versions at