Table 1

Comparison of REMC with simpler methods – original measures (int = 0.2)
Algorithm* MR (t) CE (t) SH (t) HE (t) NE (t) Mixed** (t)
Bulk maize data set (275)
Local S. 0.572 0.45s 0.641 0.55s 4.531 0.35s 0.667 0.25s 3.446 0.65s 10.680 15.0s
MSTRAT 0.572 0.31s 0.641 0.32s 4.531 0.38s 0.667 0.43s 3.446 0.43s 10.678 1.5s
LR(2,1) 0.572 0.61s 0.641 0.64s 4.531 1.1s 0.667 1.0s 3.446 1.0s 10.680 4.2s
REMC 0.572 1.0s 0.641 2.0s 4.531 2.0s 0.667 1.0s 3.446 3.0s 10.680 15.0s
Original 0.440 0.521 4.399 0.620 2.937
Accession maize data set (521)
Local S. 0.695 2.0s 0.752 1.0s 4.670 1.0s 0.676 0.45s 3.501 2.0s 11.086 15.0s
MSTRAT 0.695 1.7s 0.752 1.7s 4.670 1.6s 0.676 1.5s 3.501 1.5s 11.083 8.2s
LR(2,1) 0.695 2.9s 0.752 2.9s 4.670 4.2s 0.676 3.9s 3.502 3.9s 11.087 17.5s
REMC 0.694 4.0s 0.752 4.0s 4.670 5.0s 0.676 3.0s 3.502 20.0s 11.086 50.1s
Original 0.630 0.696 4.467 0.591 2.742
Flax data set (708)
Local S. 0.512 2.1s 0.512 2.1s 5.340 0.58s 0.263 0.58s 1.469 1.1s 8.878 12.7s
MSTRAT 0.512 5.1s 0.512 5.1s 5.340 3.7s 0.263 3.8s 1.469 3.8s 8.877 25.1s
LR(2,1) 0.512 7.4s 0.512 7.4s 5.340 13.3s 0.263 12.9s 1.469 12.8s 8.878 50.4s
REMC 0.511 5.0s 0.511 4.0s 5.340 30.0s 0.262 4.0s 1.469 30.0s 8.874 60.4s
Original 0.468 0.468 5.285 0.222 1.377
Pea data set (1283)
Local S. 0.593 3.0s 0.597 2.7s 3.556 1.1s 0.440 1.0s 1.867 6.3s 7.946 53.6s
MSTRAT 0.593 28.8s 0.597 28.5s 3.556 17.5s 0.440 18.3s 1.867 18.2s 7.851 60.6s
LR(2,1) 0.593 34.1s 0.597 34.3s 3.556 24.5s 0.440 28.3s 1.867 27.9s 7.946 03m03s
REMC 0.591 50.0s 0.595 30.0s 3.553 7.0s 0.437 15.0s 1.865 15.0s 7.876 61.2s
Original 0.509 0.515 3.482 0.381 1.713
Large pea data set (4429)
Local S. 0.594 49.4s 0.596 38.1s 3.486 18.3s 0.465 16.9s 1.886 23.8s 7.947 07m43s
MSTRAT 0.555 10m03s 0.558 10m03s 3.478 10m03s 0.458 10m03s 1.866 10m02s 7.396 10m07s
LR(2,1) 0.594 42m56s 0.596 42m35s 3.486 21m18s 0.465 21m24s 1.886 21m23s 7.947 04h08m
REMC 0.577 03m41s 0.580 08m49s 3.470 08m37s 0.448 04m29s 1.875 05m22s 7.621 10m03s
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