Prof Michael O Neill Introduction to Evolutionary Computation
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1 Prof Michael O Neill Introduction to Evolutionary Computation
2 Origin of the Species Million Years Ago Event? Origin of Life 3500 Bacteria 1500 Eukaryotic Cells 600 Multicellular Organisms 1 Human Language
3 Origin of the Species Milestones 200y.a. Jean-Baptiste Lamarck: Lamarckism or soft-inheritance: - Passing of lifetime acquired characteristics. 150y.a. Charles Darwin: Theory of Natural Selection: - Natural vs. Artificial Selection (a.k.a. breeding). 150y.a. Gregor Johann Mendel: Mendelian Inheritance: - Basis of Modern Genetics. 100y.a. Fisher, Haldane & Wright: Population Genetics: - Combined evolution, genetics, and statistical probabilities.
4 Origin of the Species Milestones 70y.a. James D. Watson: Helix structure of DNA: - Watson-Crick base paring of nucleotides. 70y.a. Francis Crick: Helix structure of DNA: - Watson-Crick base paring of nucleotides. 50y.a. Motoo Kimura: Neutral Theory of Molecular Evolution: - Variation at molecular level likely result of genetic drift. 50y.a. Richard Lewontin: Molecular Diversity: - Evolution at molecular level.
5 Origin of the Species The Selfish Gene (Dawkins vs Gould) 1 1 This is my vision of Life: A conversation with Dawkins (30 April 2015) dawkins-this-is-my-vision-of-life
6 Origin of the Species But... Epigenetics: back to Lamarckism!
7 Origin of the Species Genetics Chromosomes: - composed of Deoxyribonucleic acid: Genetic fingerprint of individuals; - Located in nucleus (eukaryotes) or cytoplasm (prokaryotes); - Double helix of base pairs: Adenine, Thymine, Guanine and Cytosine; - Sequence of genes; - Exons and Introns; - Genome.
8 Sequence Space Individual Chromosome Gene Exon Intron.. A G G C A C C G T A G T T T A A T A A G G G C T A... A G G C A C C G T A G T T T A A T A A G G G C T A... A G G C A C C G T A G T T T A A T A A G G G C T A... A G G C A C C G T A G T T T A A T A A G G G C T A. Genome Genome lives in Sequence Space Organism Length Small Virus Bacterium Humans 4 Million 3.5 Billion
9 Evolutionary Computation Brief History Evolution with computers can be traced back to 1948 (Turing); First PhD in Computer Science (John Holland, 1959) popularised Genetic Algorithms; 1960s: Genetic Algorithms (Evolutionary Programming) 1985: First Conference; vs. Evolution Strategies 1992: Genetic Programming (1 st instance 1958!); 1990s: Unified under EC. 2015: GP 2nd largest bibliography in AI
10 Evolutionary Computation
11 Evolutionary Computation x[t + 1] = r(v(s(x[t]))) Evolutionary Algorithm Initialise Population; While (termination condition FALSE): select Parents; create Offspring; Update Population; EndWhile
12 Let s Evolve a Smart Polar Bear! - Colour White Category Legs 4 Integer World s largest carnivore; Descendent of Brown Bear; Separate evolution for last 4-5 million years;2 Clear/White Fur; 4 Legs; Furred Soles; Broad Forepaws; Large and Stocky: m length (tip of nose to tail); kg. Soles Furred Boolean Forepaws 30.4cm Float Length 2.2m Float Weight 785.4kg Float 2 Eh, news flash, try 500,000 y.a.!
13 Polar Bear Example Colour Legs Soles Forepaws Length Weight Fitness White 4 Furred 30.4cm 2.2m 785.4kg 20 years Colour Legs Soles Forepaws Length Weight Fitness Brown 4 Furred 29.9cm 1.1m 203.7kg 3 years Colour Legs Soles Forepaws Length Weight Fitness White 4 No Fur 15.4cm 1.8m 771.6kg 10 years Average Fitness of Population= 11 years Best Individual Fitness = 20 years
14 Polar Bear Example (Selection) Fitness=10 30% Fitness=20 61% Fitness=20 Fitness=3 Fitness=10 Fitness=3 9%
15 Polar Bear Example (Variation) Parents: Colour Legs Soles Forepaws Length Weight Fitness White 4 Furred 30.4cm 2.2m 785.4kg 20 years Brown 4 Furred 29.9cm 1.1m 203.7kg 3 years White 4 No Fur 15.4cm 1.8m 771.6kg 10 years Offspring: Colour Legs Soles Forepaws Length Weight Fitness White 4 Furred 31.2cm 2.2m 798.1kg 23 years White 4 Furred 29.5cm 1.9m 778.1kg 15 years White 4 No Fur 15.4cm 1.7m 741.6kg 7 years
16 Polar Bear Example (Replacement) Several approaches possible; Generational population (offspring replace parents). New Population: Colour Legs Soles Forepaws Length Weight Fitness White 4 Furred 31.2cm 2.2m 798.1kg 23 years White 4 Furred 29.5cm 1.9m 778.1kg 15 years White 4 No Fur 15.4cm 1.7m 741.6kg 7 years Average Fitness of Population= 15 years Best Individual Fitness = 23 years
17 Evolutionary Computation Black Art of EC Population-based search; Stochastic; Design representation; Design fitness measure; Design algorithm (e.g., balanced variety generation operators and selection pressure).
18 Evolutionary Computation Applications - Too many to list!; - Engineering; - Design; - Sound Synthesis; - Circuit Design; - Games; - Financial Modelling; - Bioinformatics; - Human-competitive results.
19 Evolutionary Computation Funes & Pollack (1997)
20 Evolutionary Computation Karl Sims (1991)
21 Evolutionary Computation Al Biles (1993) GenJam
22 Evolutionary Computation Natural Computing Research and Applications (NCRA) Group
23 Evolutionary Computation [video]
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Name Mendelian Genetics SI Date 1. In sheep, eye color is controlled by a single gene with two alleles. When a homozygous brown-eyed sheep is crossed with a homozygous green-eyed sheep, blue-eyed offspring
2013 Holiday Lectures on Science Medicine in the Genomic Era
INTRODUCTION Figure 1. Tasha. Scientists sequenced the first canine genome using DNA from a boxer named Tasha. Meet Tasha, a boxer dog (Figure 1). In 2005, scientists obtained the first complete dog genome