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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 Kukaka & Zdenk Ptek

• Double Digest Problem (DDP)Input:A fragment lengths from the complete digest with enzyme AB fragment lengths from the complete digest with enzyme BAB fragment lengths from the complete digest with both A and B

Output:A location of the cuts in the restriction map for the enzyme AB 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

• CrossoverOne-point crossover

• SelectionInverse Tournament Selection

while (populationSize > N) doselect individuals X1, X2 from population randomlyif fitness(X1) > fitness(X2)remove X2 from populationelseremove 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, 10B: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10AB: 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, 10B: 1, 10, 1, 10, 1, 10, 1, 10, 1, 10AB: 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, 12B: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12AB: 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) 100B: (2, 2) 100AB: (1, 1, 2) 100

• Results 1. Custom DDP

NO_EXPNO_FAILSPOP_SIZEMUT_PROBMUT_RATIOCRS_PROBAVG_GENBEST_GENAVG_MRSBEST_MRS201671000.50.10.546674934791463420441000.50.50.55001761001113496320501000.50.90.53663973356783320471000.90.10.13106839691866120121000.90.50.13226341253798820121000.90.90.125240322335156204510010.1029253292245300201410010.503511083519310799201710010.9034259342335900201003000.50.10.54941602968179596620383000.50.50.5475962850855779720413000.50.90.5258411554082463620113000.90.10.134660133189231742043000.90.50.127865107046248612053000.90.90.12715310427920279202430010.1025845775021349920330010.5017554526181619920830010.9027446823771380020665000.50.10.553624153657824121620115000.50.50.535310635371010550220175000.50.90.527167271012674162045000.90.10.136556233966357312005000.90.50.11533898060242252035000.90.90.12544816281230849201050010.10371581858192899720650010.50152657599732497201350010.90153477657223499

• Results 2. Custom DDP

NO_EXPNO_FAILSPOP_SIZEMUT_PROB MUT_RATIOCRS_PROBAVG_GENBEST_GENAVG_MRSBEST_MRS20271000.50.10.544951898781024120391000.50.50.542863855751245420281000.50.90.5394187890435332091000.90.10.13654946757633620141000.90.50.13174040647508220111000.90.90.12713034842378820610010.103215632164560020410010.503983339883330020910010.902003620044360020103000.50.10.5378602270683570020213000.50.50.5356492141792948920123000.50.90.523943143611259852033000.90.10.11553459652131122033000.90.50.12003777161141692023000.90.90.113427514641034720030010.101212036568600020330010.5013348401531439920830010.90232226971766002025000.50.10.527256272415557722095000.50.50.530067300331670802095000.50.90.522850228515498222005000.90.10.116321104541131912015000.90.50.1914058355255862055000.90.90.18133521472109220050010.101151157923549920150010.501131956698949920450010.9014018702729000

• Results 3. Custom DDP

NO_EXPNO_FAILSPOP_SIZEMUT_PROBMUT_RATIOCRS_PROBAVG_GENBEST_GENAVG_MRSBEST_MRS202001000.50.10.5UNSOLVABLE202001000.50.50.5UNSOLVABLE202001000.50.90.5UNSOLVABLE202001000.90.10.1UNSOLVABLE201261000.90.50.15581127145614164201781000.90.90.136511246973144072020010010.10UNSOLVABLE2020010010.50UNSOLVABLE2020010010.90UNSOLVABLE202003000.50.10.5UNSOLVABLE202003000.50.50.5UNSOLVABLE202003000.50.90.5UNSOLVABLE201613000.90.10.172443927821316901620543000.90.50.149110018883838022201993000.90.90.1466179178930686422020030010.10UNSOLVABLE2012330010.50481185144537554992015230010.903728911183626699202005000.50.10.5UNSOLVABLE20825000.50.50.5541261541227261369201105000.50.90.553318953352318969420865000.90.10.13381092166416988220265000.90.50.13451092211096975720165000.90.90.134390219688576562013950010.10564228282066113995205050010.5036510918276954498207650010.9037113018551964999