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Table 6 Performance of the two-tier extraction system: our rule-based system in the second tier

From: On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach

Min #Inst. per Relation

#Uniq. Relation

#Instances

Methods

Per-Relation

Per-Instance

 

Pos

Neg

 

Neg

 

TP

FP

Precision

Recall

F-Score

TP

FP

Precision

Recall

F-Score

1

618

2,312

1,000

4,834

ours

132

7

0.950

0.214

0.349

153

10

0.939

0.153

0.263

     

hybrid+

479

344

0.582

0.775

0.665

705

584

0.547

0.705

0.616

     

SST-PT+

257

108

0.704

0.416

0.523

322

178

0.644

0.322

0.429

     

SVM+

131

57

0.697

0.212

0.325

140

84

0.625

0.140

0.229

     

NB+

235

247

0.488

0.380

0.427

261

410

0.389

0.261

0.312

     

DT+

157

73

0.683

0.254

0.370

169

120

0.585

0.169

0.262

     

kNN+

219

260

0.457

0.354

0.399

237

366

0.393

0.237

0.296

2

197

695

579

2,827

ours

80

3

0.964

0.406

0.571

101

5

0.953

0.174

0.294

     

hybrid+

183

164

0.527

0.929

0.673

399

327

0.550

0.689

0.612

     

SST-PT+

132

73

0.644

0.670

0.657

203

118

0.632

0.351

0.451

     

SVM+

88

48

0.647

0.447

0.529

106

78

0.576

0.183

0.278

     

NB+

107

113

0.486

0.543

0.513

140

230

0.378

0.242

0.295

     

DT+

88

41

0.682

0.447

0.540

104

85

0.550

0.180

0.271

     

kNN+

125

151

0.453

0.635

0.529

152

250

0.378

0.263

0.310

3

89

314

363

1,835

ours

51

2

0.962

0.573

0.718

67

3

0.957

0.185

0.310

     

hybrid+

88

98

0.473

0.989

0.640

262

236

0.526

0.722

0.609

     

SST-PT+

71

48

0.597

0.798

0.683

136

82

0.624

0.375

0.468

     

SVM+

43

28

0.606

0.483

0.538

59

40

0.596

0.163

0.256

     

NB+

59

69

0.461

0.663

0.544

82

113

0.421

0.226

0.294

     

DT+

49

17

0.742

0.551

0.632

61

26

0.701

0.168

0.271

     

kNN+

59

86

0.407

0.663

0.504

84

151

0.357

0.231

0.281

4

51

181

249

1,349

ours

35

2

0.946

0.686

0.795

50

3

0.943

0.201

0.331

     

hybrid+

50

67

0.427

0.980

0.595

171

171

0.500

0.687

0.579

     

SST-PT+

45

32

0.584

0.882

0.703

98

57

0.632

0.394

0.485

     

SVM+

33

19

0.635

0.647

0.641

47

35

0.573

0.189

0.284

     

NB+

41

53

0.436

0.804

0.565

64

116

0.356

0.257

0.299

     

DT+

32

7

0.821

0.627

0.711

43

11

0.796

0.173

0.284

     

kNN+

39

61

0.390

0.765

0.517

59

118

0.333

0.237

0.277

5

28

107

157

984

ours

23

1

0.958

0.821

0.884

37

1

0.974

0.236

0.380

     

hybrid+

28

44

0.389

1

0.560

114

105

0.521

0.726

0.607

     

SST-PT+

25

16

0.610

0.893

0.725

66

31

0.680

0.420

0.519

     

SVM+

21

14

0.600

0.750

0.667

29

22

0.569

0.185

0.279

     

NB+

23

41

0.359

0.821

0.500

35

73

0.324

0.223

0.264

     

DT+

18

3

0.857

0.643

0.735

26

4

0.867

0.166

0.279

     

kNN+

24

38

0.387

0.857

0.533

35

68

0.340

0.223

0.269