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Table 5 Comparing the performance of CPLEX on our new ILP models against that on Chen et al.’s models [27] for HuRef

From: Better ILP models for haplotype assembly

All-heterozygous Case

General Case

Opt

Old

New

Old

New

MEC

Time

Time

MEC

Time

MEC

Time

19665

7301

818

16853

80665

16853

7280

14647

1418

218

12618

1532

12618

374

10688

1221

156

9296

1236

9296

276

11537

1421

202

9958

1481

9958

351

10558

1550

211

9195

1770

9195

358

9884

1344

150

8637

1389

8637

270

11246

1362

182

9782

1504

9782

345

9800

2104

280

8480

3042

8480

848

9264

882

107

8051

956

8051

229

9815

1568

237

8550

1772

8550

431

8179

1156

169

7027

1193

7027

269

8213

921

135

7136

891

7136

235

5811

741

114

5090

788

5090

163

5844

545

70

5086

571

5086

145

9310

87425

11006

8130

89135

8093

87551

8235

1487

209

7176

1883

7176

445

6535

681

96

5739

756

5739

159

5019

789

94

4403

946

4403

168

5311

606

96

4628

629

4628

155

3741

371

55

3243

453

3243

93

3896

658

105

3360

1081

3360

370

4507

24327

592

3915

86746

3908

39866

  1. Note: The i-th row shows the result for the i-th chromosome in HuRef, Old (respectively, New) means that the result is obtained with the old (respectively, new) model, MEC means the MEC score, MEC scores in bold mean non-optimal MEC scores, Time means the running time (in seconds) taken by CPLEX, and running time in bold means that CPLEX failed to optimally solve at least one reduced block of the chromosome within the time limit