Table 4

Comparison of REMC with simpler methods – minimum versus mean MR (int = 0.05)
Optimized → MR MRmin MixedMR**
Algorithm* MR (t) MRmin MRmin (t) MR MixedMR (t) MRmin MR
Bulk maize data set (275)
Local S. 0.643 0.25s 0.438 0.529 0.60s 0.613 0.578 0.50s 0.516 0.641
MSTRAT 0.643 0.14s 0.353 0.522 0.42s 0.608 0.578 0.31s 0.513 0.643
LR(2,1) 0.643 0.34s 0.513 0.534 0.52s 0.622 0.576 0.72s 0.523 0.628
REMC 0.643 0.35s 0.513 0.539 1.8s 0.615 0.582 4.7s 0.534 0.629
Original 0.440 0.116 0.116 0.440 0.116 0.440
Accession maize data set (521)
Local S. 0.723 0.45s 0.511 0.495 0.10s 0.634 0.663 1.5s 0.607 0.719
MSTRAT 0.722 0.26s 0.476 0.490 0.17s 0.635 0.651 0.59s 0.581 0.721
LR(2,1) 0.723 1.2s 0.510 0.620 1.8s 0.699 0.674 2.3s 0.635 0.712
REMC 0.723 0.75s 0.519 0.630 58.7s 0.700 0.678 56.0s 0.638 0.717
Original 0.630 0.294 0.294 0.630 0.294 0.630
Flax data set (708)
Local S. 0.533 1.0s 0.337 0.309 0.20s 0.470 0.475 2.6s 0.418 0.532
MSTRAT 0.533 0.66s 0.341 0.320 0.36s 0.470 0.468 1.6s 0.405 0.532
LR(2,1) 0.533 3.3s 0.357 0.446 4.1s 0.515 0.481 6.2s 0.446 0.517
REMC 0.533 3.0s 0.337 0.429 44.3s 0.505 0.487 20.3s 0.446 0.529
Original 0.468 0.000 0.000 0.468 0.000 0.468
Pea data set (1283)
Local S. 0.626 1.4s 0.200 0.122 0.10s 0.510 0.481 2.7s 0.338 0.624
MSTRAT 0.626 1.5s 0.209 0.104 0.25s 0.510 0.454 4.3s 0.282 0.625
LR(2,1) 0.626 3.5s 0.229 0.429 5.3s 0.595 0.520 7.7s 0.429 0.611
REMC 0.626 10.0s 0.246 0.328 60.5s 0.552 0.510 26.1s 0.397 0.622
Original 0.509 0.000 0.000 0.509 0.000 0.509
Large pea data set (4429)
LR(2,1) 0.635 01m18s 0.000 0.343 01m55s 0.597 0.488 03m04s 0.364 0.611
REMC 0.633 06m05s 0.000 0.000 0.13s 0.462 0.313 02m03s 0.000 0.626
Original 0.464 0.000 0.000 0.464 0.000 0.464

*For each combination of algorithm, dataset and evaluation measure, 20 independent runs were performed from which averaged results are reported. By default runs were limited by a runtime of 60 seconds, except for the large pea dataset where a runtime limit of 10 minutes was applied. Furthermore the LR method does not accept a runtime limit but continues search until the desired core size has been reached.

**Results shown are those of a pseudo-index containing both minimum and mean MR distance, with equal weight = 0.5.

Not used during optimization, but computed afterwards on the constructed core sets.

Components of mixed MR measure.

These results were computed on the helios server.

Beukelaer et al.

Beukelaer et al. BMC Bioinformatics 2012 13:312   doi:10.1186/1471-2105-13-312

Open Data