Skip to main content

Table 1 Comparison of REMC with simpler methods – original measures (int = 0.2)

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

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 â–¾ (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

   
  1. *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.
  2. **Results shown are those of a pseudo-index containing all seven measures with equal weights.
  3. â–¾These results were computed on the helios server.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us