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Table 1 Performance evaluation of DMI and other competing algorithms on a network size 10, 100, or 1,000 at a 10% noise level, based on the arithmetic average over 10 simulation runs

From: A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data

Methods

Size

SN

SP

ACC

MCC

AUC

DMI

10

0.7600 ±0.2119

0.9143 ±0.1380

0.8235 ±0.1301

0.6837 ±0.2180

0.8371 ±0.1187

 

100

0.7321 ±0.1818

0.8807 ±0.0401

0.8069 ±0.0825

0.6264 ±0.1460

0.8064 ±0.0831

 

1000

0.8119 ±0.0472

0.9023 ±0.0147

0.8564 ±0.0245

0.7171 ±0.0460

0.8571 ±0.0242

CLR

10

0.5900 ±0.1776

0.4143 ±0.3125

0.5176 ±0.1331

0.0043 ±0.3125

0.5457 ±0.1331

 

100

0.4854 ±0.0200

0.4916 ±0.0400

0.4885 ±0.0202

-0.0231 ±0.04

0.4768 ±0.0202

 

1000

0.5063 ±0.0134

0.4908 ±0.0269

0.4987 ±0.0135

-0.0029 ±0.0269

0.4292 ±0.0135

PCC

10

0.5600 ±0.0938

0.3714 ±0.1698

0.4824 ±0.0719

-0.0686 ±0.1698

0.5386 ±0.0719

 

100

0.5244 ±0.0268

0.5301 ±0.0536

0.5273 ±0.0268

0.0545 ±0.0536

0.5148 ±0.0268

 

1000

0.5061 ±0.0172

0.4907 ±0.0344

0.4985 ±0.0173

-0.0032 ±0.0344

0.4290 ±0.0173

MINET

10

0.5500 ±0.0834

0.5571 ±0.1745

0.5529 ±0.0915

0.1076 ±0.1745

0.5871 ±0.0915

 

100

0.3378 ±0.0319

0.6988 ±0.0351

0.5194 ±0.0183

0.0391 ±0.0351

0.5073 ±0.0183

 

1000

0.2464 ±0.0164

0.7801 ±0.0196

0.5092 ±0.0096

0.0313 ±0.0196

0.4224 ±0.0096

TIGRESS

10

0.5700 ±0.0949

0.3857 ±0.1355

0.4941 ±0.1116

-0.0443 ±0.2304

0.5171 ±0.0865

 

100

0.3154 ±0.0239

0.6904 ±0.0405

0.5040 ±0.0276

0.0067 ±0.0595

0.4898 ±0.0281

 

1000

0.0062 ±0.0007

0.9941 ±0.0014

0.4926 ±0.0006

0.0024 ±0.0077

0.3630 ±0.0008

ARACNE

10

0.2800 ±0.1200

0.7286 ±0.1966

0.4647 ±0.0962

0.0074 ±0.1966

0.6043 ±0.0962

 

100

0.0598 ±0.0325

0.9514 ±0.0357

0.5083 ±0.0103

0.0225 ±0.0357

0.4860 ±0.0103

 

1000

0.0188 ±0.0094

0.9820 ±0.0246

0.4930 ±0.0040

0.0023 ±0.0246

0.3670 ±0.0040

TimeDelay-ARACNE

10

0.0500 ±0.1214

0.9571 ±0.2029

0.4235 ±0.0744

0.0222 ±0.2029

0.6386 ±0.0744

 

100

0.0118 ±0.0250

0.9912 ±0.0596

0.5044 ±0.0073

0.0000 ±0.0596

0.4793 ±0.0073

 

1000

0.0034 ±0.0028

0.9968 ±0.0179

0.4924 ±0.0015

0.0011 ±0.0179

0.3622 ±0.0015

GENIE3

10

0.5600 ±0.0138

0.3714 ±0.0419

0.4824 ±0.0098

-0.0686 ±0.0419

0.5400 ±0.0098

 

100

0.5093 ±0.0009

0.5153 ±0.0035

0.5123 ±0.0010

0.0246 ±0.0035

0.5007 ±0.0010

 

1000

0.5075 ±0.0001

0.4922 ±0.0003

0.5000 ±0.0001

-0.0003 ±0.0003

0.4304 ±0.0001

Jump3

10

0.6400 ±0.1095

0.4857 ±0.2048

0.5765 ±0.1094

0.1257 ±0.2048

0.6000 ±0.1094

 

100

0.2606 ±0.0431

0.8390 ±0.0474

0.5515 ±0.0245

0.1217 ±0.0474

0.5471 ±0.0245

 

1000

0.0384 ±0.0074

0.9843 ±0.0192

0.5040 ±0.0035

0.0694 ±0.0192

0.3823 ±0.0035

SITPR

10

0.4900 ±0.1197

0.7143 ±0.2020

0.5824 ±0.0757

0.2172 ±0.1819

0.6021 ±0.0862

 

100

0.1610 ±0.0794

0.8253 ±0.0656

0.4952 ±0.0255

-0.0212 ±0.0733

0.4931 ±0.0257

 

1000

0.2382 ±0.0509

0.7599 ±0.0381

0.4950 ±0.0118

-0.0032 ±0.0279

0.4990 ±0.0114