barrettotte/population-genetics-sim

Simulate basic population genetics on fake creatures' DNA. Concepts of mutation, crossover, fitness distribution covered. Prototype algorithm for ProcJam 2018

Population Genetics

Simulate basic population genetics on fake creatures' DNA. Concepts of mutation, crossover, fitness distribution covered

Used for ProcJam 2018, repo located here https://github.com/barrettotte/ProcJam-2018

Process

• Initialize - Population N random DNA
• Selection - Evaluate fitness, generate mating pool
• Reproduction - Repeat N times, pick parents based on "weighted random" of mating rate
• Crossover - Combine DNA through some crossover method
• Mutation - Mutate child based on mutation rate
• Add child to new generation
• Discard old population
• Repeat until ideal organism within ideal error is found

Additional Process

• A percentage of "Top" fitness organisms will asexually reproduce to keep their ideal DNA in the mating pool.
• There is a small chance a random organism will asexually reproduce
• There is a small chance that Parent 1 will not pass any DNA and will be replaced by newly generated DNA.
• An "Ideal Error" was introduced to speed up the algorithm's execution time, since it always got close, but sometimes never made a fitness value of 0.

Summary

• This script will simulate a generation of "creatures" generation after generation until the ideal color allele is found.
• Each creature has one allele in their "DNA" for color and is passed to offspring based on fundamentals of genetics (crossover, mutation).
• Depending on how close the creature's color allele is to the ideal allele, it is given a fitness value which affects its chances of reproducing with another creature.
• This is meant to be a prototype before ProcJam 2018 to work out any janky behavior before implementing in C# and Unity.

Sources:

• Basics of bitwise crossover/mutation http://www.obitko.com/tutorials/genetic-algorithms/crossover-mutation.php
• Noun and Adjective Lists https://github.com/aaronbassett/Pass-phrase

Results

Searching for Ideal DNA: {'color': ['00000000', '11111111', '00000000']}
Parameters: 
   Generation Size: 1000
   Mutation Chance: 0.006
   Mystery DNA Chance: 0.001
   Asexual Reproduction Chance: 0.001
   Top Organisms Asexually Reproduce: 0.001
   Fitness Weights: [1, 2, 4, 6, 8]
   Ideal Organism Allowable Error: 5


Results of Test 01: 
   The Ideal Organism Found: ID: 00061-00194, Name: determined detail, Fitness: 5
   DNA: {'color': ['00000010', '11111110', '00000010']}
   Total Generations Created: 61
   Total Organisms Created:   61000
   Executed for 1.662 seconds


Results of Test 02: 
   The Ideal Organism Found: ID: 00019-00160, Name: subdued friction, Fitness: 5
   DNA: {'color': ['00000001', '11111100', '00000001']}
   Total Generations Created: 19
   Total Organisms Created:   19000
   Executed for 0.522 seconds


Results of Test 03: 
   The Ideal Organism Found: ID: 00123-00461, Name: jagged growth, Fitness: 5
   DNA: {'color': ['00000000', '11111100', '00000010']}
   Total Generations Created: 123
   Total Organisms Created:   123000
   Executed for 3.438 seconds


Results of Test 04: 
   The Ideal Organism Found: ID: 00085-00707, Name: knowledgeable collar, Fitness: 5
   DNA: {'color': ['00000001', '11111011', '00000000']}
   Total Generations Created: 85
   Total Organisms Created:   85000
   Executed for 2.381 seconds


Results of Test 05: 
   The Ideal Organism Found: ID: 00030-00794, Name: festive agreement, Fitness: 4
   DNA: {'color': ['00000001', '11111110', '00000010']}
   Total Generations Created: 30
   Total Organisms Created:   30000
   Executed for 0.835 seconds


Results of Test 06: 
   The Ideal Organism Found: ID: 00147-00003, Name: auspicious burn, Fitness: 5
   DNA: {'color': ['00000001', '11111111', '00000100']}
   Total Generations Created: 147
   Total Organisms Created:   147000
   Executed for 4.258 seconds


Results of Test 07: 
   The Ideal Organism Found: ID: 00247-00272, Name: snotty number, Fitness: 5
   DNA: {'color': ['00000001', '11111100', '00000001']}
   Total Generations Created: 247
   Total Organisms Created:   247000
   Executed for 6.816 seconds


Results of Test 08: 
   The Ideal Organism Found: ID: 00088-00328, Name: cuddly spark, Fitness: 2
   DNA: {'color': ['00000000', '11111110', '00000001']}
   Total Generations Created: 88
   Total Organisms Created:   88000
   Executed for 2.443 seconds


Results of Test 09: 
   The Ideal Organism Found: ID: 00090-00693, Name: frightened brass, Fitness: 2
   DNA: {'color': ['00000000', '11111101', '00000000']}
   Total Generations Created: 90
   Total Organisms Created:   90000
   Executed for 2.547 seconds


Results of Test 10: 
   The Ideal Organism Found: ID: 00001-00021, Name: macabre government, Fitness: 3
   DNA: {'color': ['00000000', '11111111', '00000011']}
   Total Generations Created: 1
   Total Organisms Created:   1000
   Executed for 0.042 seconds


Ran Simulation 10 Time(s).
   Average Error - 4.1
   Average Execution Time - 2.494
   Average Generated Generations - 90.1
   Average Generated Organisms - 89100.0

Console Raw