Solving Double Digest Problem by Genetic Algorithm
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Solving Double Digest Problem by Genetic Algorithm Marek Kukačka & Zdeněk Pátek
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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 - PowerPoint PPT Presentation
Transcript of Solving Double Digest Problem by Genetic Algorithm
Solving Double Digest Problem by Genetic
Algorithm
Marek Kukačka & Zdeněk Pátek
Double Digest Problem (DDP)
• Input:– ΔA – fragment lengths from the complete digest with enzyme A– ΔB – fragment lengths from the complete digest with enzyme B– ΔAB – 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 X1, X2 from population randomly
if fitness(X1) > fitness(X2)
remove X2 from population
else
remove X1 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 DDPNO_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 DDPNO_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 DDPNO_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
