Table 3

Comparison of REMC with simpler methods – minimum versus mean MR (int = 0.2)
Optimized → MR MRmin MixedMR**
Algorithm* MR (t) MRmin MRmin (t) MR MixedMR (t) MRmin MR
Bulk maize data set (275)
Local S. 0.572 0.45s 0.258 0.392 4.9s 0.548 0.471 2.6s 0.380 0.561
MSTRAT 0.572 0.31s 0.258 0.386 1.8s 0.543 0.470 1.2s 0.380 0.560
LR(2,1) 0.572 0.61s 0.258 0.393 1.2s 0.549 0.473 1.5s 0.393 0.553
REMC 0.572 1.0s 0.258 0.397 35.6s 0.549 0.476 23.6s 0.395 0.557
Original 0.440 0.116 0.116 0.440 0.116 0.440
Accession maize data set (521)
Local S. 0.695 2.0s 0.392 0.404 0.40s 0.630 0.582 4.3s 0.471 0.694
MSTRAT 0.695 1.7s 0.392 0.403 0.32s 0.631 0.583 4.1s 0.473 0.694
LR(2,1) 0.695 2.9s 0.392 0.555 4.3s 0.670 0.618 5.9s 0.555 0.681
REMC 0.694 4.0s 0.392 0.497 56.7s 0.646 0.608 51.0s 0.526 0.690
Original 0.630 0.294 0.294 0.630 0.294 0.630
Flax data set (708)
Local S. 0.512 2.1s 0.223 0.226 0.60s 0.468 0.406 6.4s 0.300 0.512
MSTRAT 0.512 5.1s 0.223 0.226 1.2s 0.469 0.404 12.5s 0.296 0.512
LR(2,1) 0.512 7.4s 0.223 0.377 10.6s 0.494 0.443 15.7s 0.386 0.499
REMC 0.511 5.0s 0.213 0.315 30.9s 0.475 0.422 39.5s 0.337 0.508
Original 0.468 0.000 0.000 0.468 0.000 0.468
Pea data set (1283)
Local S. 0.593 3.0s 0.000 0.000 0.10s 0.509 0.302 4.6s 0.011 0.593
MSTRAT 0.593 28.8s 0.000 0.000 0.63s 0.510 0.299 60.7s 0.006 0.592
LR(2,1) 0.593 34.1s 0.000 0.324 50.2s 0.569 0.454 01m15s 0.324 0.583
REMC 0.591 50.0s 0.000 0.006 36.6s 0.510 0.375 60.4s 0.166 0.583
Original 0.509 0.000 0.000 0.509 0.000 0.509
Large pea data set (4429)
LR(2,1) 0.594 42m56s 0.000 0.243 52m46s 0.554 0.411 01h35m 0.243 0.579
REMC 0.577 03m41s 0.000 0.000 0.19s 0.463 0.273 09m08s 0.000 0.546
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