Table 1.
Ten-fold CVs of the Oct4 ChIP-chip data
| Method | Tuning parameters | CV-cor | SD |
|---|---|---|---|
| LR-SO | – | 0.446 (0%) | 0.044 |
| LR-Full | – | 0.491 (10%) | 0.064 |
| Step-SO | – | 0.535 (20%) | 0.045 |
| Step-Full | – | 0.513 (15%) | 0.054 |
| NN-SO | # of nodes, weight decay | 0.468 (5%) | 0.063 |
| Step+NN | # of nodes, weight decay | 0.463 (4%) | 0.067 |
| MARS | Interaction d, penalty λ | 0.580 (30%) | 0.043 |
| SVM | Cost C | 0.547 (23%) | 0.054 |
| Boost | # of trees M | 0.581 (30%) | 0.048 |
| BART | # of trees M | 0.600 (35%) | 0.044 |
Reported here are the average CV-cors. The percentage in the parentheses is calculated by the percent of improvement over the CV-cor of LR-SO. SD is the standard deviation across 10 test samples. The detailed definitions of tuning parameters are reviewed in the MATERIALS AND METHODS section and further discussed in Supplementary Text.