Table 3 Final correlation rates of the selected marker sets on the test sets.
From: GMStool: GWAS-based marker selection tool for genomic prediction from genomic data
Data | Phenotype | Method | Selected markers | RRB (train/val./test) | RF (train/val./test) | DNN (train/val./test) | CNN (train/val./test) |
|---|---|---|---|---|---|---|---|
Rice | DTF | RRB | 746 | 0.997/0.870/0.380 | 0.976/0.845/0.529 | 0.932/0.912/0.334 | 0.948/0.895/0.469 |
BTS | 120 | 0.849/0.710/0.398 | 0.969/0.869/0.454 | 0.920/0.759/0.407 | 0.902/0.748/0.501 | ||
RRB and BTS | 817 | 0.996/0.854/0.394 | 0.977/0.847/0.508 | 0.977/0.895/0.388 | 0.942/0.840/0.424 | ||
PC | RRB | 805 | 0.998/0.831/0.509 | 0.974/0.742/0.520 | 0.873/0.811/0.450 | 0.917/0.833/0.480 | |
BTS | 114 | 0.879/0.746/0.457 | 0.971/0.767/0.528 | 0.826/0.769/0.408 | 0.868/0.801/0.506 | ||
RRB and BTS | 873 | 0.998/0.845/0.504 | 0.975/0.745/0.535 | 0.907/0.802/0.423 | 0.937/0.854/0.547 | ||
PH | RRB | 620 | 0.992/0.924/0.579 | 0.981/0.915/0.654 | 0.977/0.932/0.630 | 0.956/0.909/0.615 | |
BTS | 115 | 0.937/0.862/0.607 | 0.979/0.918/0.668 | 0.973/0.930/0.588 | 0.958/0.925/0.524 | ||
RRB and BTS | 675 | 0.992/0.923/0.599 | 0.981/0.918/0.653 | 0.922/0.905/0.679 | 0.943/0.903/0.672 | ||
SOY | DTF | RRB | 2126 | 0.989/0.936/0.742 | 0.914/0.897/0.772 | 0.965/0.928/0.735 | 0.980/0.838/0.792 |
BTS | 224 | 0.853/0.821/0.774 | 0.816/0.820/0.775 | 0.855/0.839/0.774 | 0.973/0.823/0.772 | ||
RRB and BTS | 2256 | 0.989/0.935/0.743 | 0.922/0.907/0.750 | 0.967/0.923/0.741 | 0.980/0.837/0.794 |
