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

Table 5 Results of Mixed Replica search vs. REMC – original measures (int = 0.2)

Algorithm^∗	MR	(t)	CE	(t)	SH	(t)	HE	(t)	NE	(t)	Mixed^∗∗	(t)
	Bulk maize data set (275)
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
MixRep	0.572	0.45s	0.641	0.46s	4.531	0.49s	0.667	0.50s	3.446	0.59s	10.680	2.2s
Original	0.440		0.521		4.399		0.620		2.937
	Accession maize data set (521)
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
MixRep	0.695	1.1s	0.752	0.68s	4.670	1.1s	0.676	0.67s	3.502	3.8s	11.087	17.1s
Original	0.630		0.696		4.467		0.591		2.742
	Flax data set (708)
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
MixRep	0.512	1.6s	0.512	1.7s	5.340	0.80s	0.263	0.83s	1.469	1.6s	8.878	13.0s
Original	0.468		0.468		5.285		0.222		1.377
	Pea data set (1283)
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
MixRep	0.593	3.2s	0.597	3.1s	3.556	1.5s	0.440	1.4s	1.867	7.7s	7.945	37.6s
Original	0.509		0.515		3.482		0.381		1.713
	Large pea data set ^▾ (4429)
REMC	0.577	03m41s	0.580	08m49s	3.470	08m37s	0.448	04m29s	1.875	05m22s	7.621	10m03s
MixRep	0.594	01m18s	0.596	53.5s	3.486	39.6s	0.465	36.3s	1.886	47.3s	7.811	10m21s
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.
^**Results shown are those of a pseudo-index containing all seven measures with equal weights.
^▾These results were computed on the helios server.

ISSN: 1471-2105