Solving Double Digest Problem by Genetic Algorithm - KSVI

libyantawdryΤεχνίτη Νοημοσύνη και Ρομποτική

23 Οκτ 2013 (πριν από 3 χρόνια και 7 μήνες)

59 εμφανίσεις

Solving Double Digest
Problem by Genetic
Algorithm




Marek Kukačka

&
Zdeněk Pátek

Double Digest Problem (DDP)


Input:


Δ
A



fragment

lengths from the complete digest with enzyme
A


Δ
B



fragment lengths from the complete digest with enzyme
B


Δ
AB



fragment lengths from the complete digest with

both

A

and
B



Output:


A



location of the cuts in the restriction map for the enzyme
A


B



location of the cuts in the restriction map for the enzyme
B



Double Digest Problem is NP
-

complete


Genetic Algorithm (GA)

Mutation



Swap mutation



Insert mutation

Crossover


One
-
point crossover


Selection


Inverse Tournament Selection



while (populationSize > N) do



select individuals X
1
, X
2

from population randomly



if fitness(X
1
) > fitness(X
2
)




remove X
2

from population



else



remove X
1

from population

Results


Random DDPs (1)

Results


Random DDPs (2)

Results


Random DDPs (3)

Results


Random DDPs (4)

Results


Random DDPs (5)

Custom DDPs (1)


1. Custom DDP (moderate)

A: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

B: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

AB: 1, 2, 3, 4, 5, 4, 2, 6, 1, 6, 2, 4, 5, 4, 3, 2, 1



2. Custom DDP (easy)

A: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10

B: 1, 10, 1, 10, 1, 10, 1, 10, 1, 10

AB: 1, 10, 1, 1, 9, 1, 2, 8, 1, 3, 7, 1, 4, 6


Custom DDPs (2)


3. Custom DDP (hard)

A: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

B: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

AB: 1, 2, 3, 4, 2, 3, 6, 2, 5, 5, 3, 6, 3, 5, 5, 2, 6, 3, 2, 4, 3, 2, 1



4. Custom DDP (weird)

A: (1, 3)
100

B: (2, 2)
100

AB: (1, 1, 2)
100


Results


1. Custom DDP

NO_EXP

NO_FAILS

POP_SIZE

MUT_PROB

MUT_RATIO

CRS_PROB

AVG_GEN

BEST_GEN

AVG_MRS

BEST_MRS

20

167

100

0.5

0.1

0.5

466

74

93479

14634

20

44

100

0.5

0.5

0.5

500

176

100111

34963

20

50

100

0.5

0.9

0.5

366

39

73356

7833

20

47

100

0.9

0.1

0.1

310

68

39691

8661

20

12

100

0.9

0.5

0.1

322

63

41253

7988

20

12

100

0.9

0.9

0.1

252

40

32233

5156

20

45

100

1

0.1

0

292

53

29224

5300

20

14

100

1

0.5

0

351

108

35193

10799

20

17

100

1

0.9

0

342

59

34233

5900

20

100

300

0.5

0.1

0.5

494

160

296817

95966

20

38

300

0.5

0.5

0.5

475

96

285085

57797

20

41

300

0.5

0.9

0.5

258

41

155408

24636

20

11

300

0.9

0.1

0.1

346

60

133189

23174

20

4

300

0.9

0.5

0.1

278

65

107046

24861

20

5

300

0.9

0.9

0.1

271

53

104279

20279

20

24

300

1

0.1

0

258

45

77502

13499

20

3

300

1

0.5

0

175

54

52618

16199

20

8

300

1

0.9

0

274

46

82377

13800

20

66

500

0.5

0.1

0.5

536

241

536578

241216

20

11

500

0.5

0.5

0.5

353

106

353710

105502

20

17

500

0.5

0.9

0.5

271

67

271012

67416

20

4

500

0.9

0.1

0.1

365

56

233966

35731

20

0

500

0.9

0.5

0.1

153

38

98060

24225

20

3

500

0.9

0.9

0.1

254

48

162812

30849

20

10

500

1

0.1

0

371

58

185819

28997

20

6

500

1

0.5

0

152

65

75997

32497

20

13

500

1

0.9

0

153

47

76572

23499

Results


2. Custom DDP

NO_EXP

NO_FAILS

POP_SIZE

MUT_PROB

MUT_RATIO

CRS_PROB

AVG_GEN

BEST_GEN

AVG_MRS

BEST_MRS

20

27

100

0.5

0.1

0.5

449

51

89878

10241

20

39

100

0.5

0.5

0.5

428

63

85575

12454

20

28

100

0.5

0.9

0.5

394

18

78904

3533

20

9

100

0.9

0.1

0.1

365

49

46757

6336

20

14

100

0.9

0.5

0.1

317

40

40647

5082

20

11

100

0.9

0.9

0.1

271

30

34842

3788

20

6

100

1

0.1

0

321

56

32164

5600

20

4

100

1

0.5

0

398

33

39883

3300

20

9

100

1

0.9

0

200

36

20044

3600

20

10

300

0.5

0.1

0.5

378

60

227068

35700

20

21

300

0.5

0.5

0.5

356

49

214179

29489

20

12

300

0.5

0.9

0.5

239

43

143611

25985

20

3

300

0.9

0.1

0.1

155

34

59652

13112

20

3

300

0.9

0.5

0.1

200

37

77161

14169

20

2

300

0.9

0.9

0.1

134

27

51464

10347

20

0

300

1

0.1

0

121

20

36568

6000

20

3

300

1

0.5

0

133

48

40153

14399

20

8

300

1

0.9

0

232

22

69717

6600

20

2

500

0.5

0.1

0.5

272

56

272415

55772

20

9

500

0.5

0.5

0.5

300

67

300331

67080

20

9

500

0.5

0.9

0.5

228

50

228515

49822

20

0

500

0.9

0.1

0.1

163

21

104541

13191

20

1

500

0.9

0.5

0.1

91

40

58355

25586

20

5

500

0.9

0.9

0.1

81

33

52147

21092

20

0

500

1

0.1

0

115

11

57923

5499

20

1

500

1

0.5

0

113

19

56698

9499

20

4

500

1

0.9

0

140

18

70272

9000

Results


3. Custom DDP

NO_EXP

NO_FAILS

POP_SIZE

MUT_PROB

MUT_RATIO

CRS_PROB

AVG_GEN

BEST_GEN

AVG_MRS

BEST_MRS

20

200

100

0.5

0.1

0.5



UNSOLVABLE





20

200

100

0.5

0.5

0.5



UNSOLVABLE





20

200

100

0.5

0.9

0.5



UNSOLVABLE





20

200

100

0.9

0.1

0.1



UNSOLVABLE





20

126

100

0.9

0.5

0.1

558

112

71456

14164

20

178

100

0.9

0.9

0.1

365

112

46973

14407

20

200

100

1

0.1

0



UNSOLVABLE





20

200

100

1

0.5

0



UNSOLVABLE





20

200

100

1

0.9

0



UNSOLVABLE





20

200

300

0.5

0.1

0.5



UNSOLVABLE





20

200

300

0.5

0.5

0.5



UNSOLVABLE





20

200

300

0.5

0.9

0.5



UNSOLVABLE





20

161

300

0.9

0.1

0.1

724

439

278213

169016

20

54

300

0.9

0.5

0.1

491

100

188838

38022

20

199

300

0.9

0.9

0.1

466

179

178930

68642

20

200

300

1

0.1

0



UNSOLVABLE





20

123

300

1

0.5

0

481

185

144537

55499

20

152

300

1

0.9

0

372

89

111836

26699

20

200

500

0.5

0.1

0.5



UNSOLVABLE





20

82

500

0.5

0.5

0.5

541

261

541227

261369

20

110

500

0.5

0.9

0.5

533

189

533523

189694

20

86

500

0.9

0.1

0.1

338

109

216641

69882

20

26

500

0.9

0.5

0.1

345

109

221109

69757

20

16

500

0.9

0.9

0.1

343

90

219688

57656

20

139

500

1

0.1

0

564

228

282066

113995

20

50

500

1

0.5

0

365

109

182769

54498

20

76

500

1

0.9

0

371

130

185519

64999