Table 2

Comparison of REMC with simpler methods – original measures (int = 0.05)
Algorithm* MR (t) CE (t) SH (t) HE (t) NE (t) Mixed** (t)
Bulk maize data set (275)
Local S. 0.643 0.25s 0.700 0.25s 4.567 0.25s 0.685 0.25s 3.625 0.35s 10.781 0.9s
MSTRAT 0.643 0.14s 0.699 0.14s 4.567 0.15s 0.685 0.15s 3.616 0.15s 10.772 0.46s
LR(2,1) 0.643 0.34s 0.700 0.37s 4.565 0.68s 0.685 0.62s 3.605 0.59s 10.790 2.2s
REMC 0.643 0.35s 0.700 0.35s 4.568 0.65s 0.685 0.55s 3.631 3.0s 10.790 7.0s
0.440 0.521 4.399 0.620 2.937
Accession maize data set (521)
Local S. 0.723 0.45s 0.781 0.35s 4.724 0.95s 0.701 0.35s 3.880 2.0s 11.210 4.0s
MSTRAT 0.722 0.26s 0.781 0.27s 4.723 0.34s 0.701 0.32s 3.874 0.32s 11.200 1.1s
LR(2,1) 0.723 1.2s 0.781 1.2s 4.724 2.1s 0.701 2.1s 3.861 2.1s 11.206 6.8s
REMC 0.723 0.75s 0.782 2.0s 4.724 2.0s 0.702 5.0s 3.886 6.0s 11.216 50.0s
Original 0.630 0.696 4.467 0.591 2.742
Flax data set (708)
Local S. 0.533 1.0s 0.533 1.0s 5.358 0.60s 0.278 0.69s 1.504 1.2s 8.965 12.8s
MSTRAT 0.533 0.66s 0.533 0.67s 5.358 0.73s 0.278 1.1s 1.504 1.1s 8.960 3.5s
LR(2,1) 0.533 3.3s 0.533 3.3s 5.358 7.3s 0.278 7.0s 1.504 7.0s 8.962 22.0s
REMC 0.533 3.0s 0.533 3.0s 5.358 2.0s 0.278 3.0s 1.504 4.0s 8.965 30.0s
Original 0.468 0.468 5.285 0.222 1.377
Pea data set (1283)
Local S. 0.626 1.4s 0.629 1.2s 3.578 0.50s 0.451 0.40s 1.898 0.70s 8.084 33.1s
MSTRAT 0.626 1.5s 0.629 1.6s 3.578 1.1s 0.451 1.0s 1.898 1.0s 8.083 6.9s
LR(2,1) 0.626 3.5s 0.629 3.5s 3.578 4.8s 0.451 4.8s 1.898 4.8s 8.083 18.3s
REMC 0.626 10.0s 0.629 7.0s 3.578 2.0s 0.451 3.0s 1.898 2.0s 8.083 40.0s
Original 0.509 0.515 3.482 0.381 1.713
Large pea data set (4429)
Local S. 0.635 09.4s 0.637 23.9s 3.518 02.4s 0.496 15.1s 1.983 27.5s 8.158 04m17s
MSTRAT 0.635 49.6s 0.637 49.6s 3.518 24.5s 0.496 25.4s 1.983 25.5s 8.158 03m44s
LR(2,1) 0.635 01m18s 0.637 01m19s 3.518 01m05s 0.495 01m18s 1.981 01m09s 8.158 07m42s
REMC 0.633 06m05s 0.634 36.8s 3.515 27.6s 0.492 13.9s 1.982 06m53s 8.147 09m36s
Original 0.464 0.466 3.348 0.352 1.609

*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 all seven measures with equal weights.

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