Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

Beukelaer, Herman De; Smýkal, Petr; Davenport, Guy F; Fack, Veerle

doi:10.1186/1471-2105-13-312

Table 3 Comparison of REMC with simpler methods – minimum versus mean MR (int = 0.2)

From: Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

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.

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ISSN: 1471-2105

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