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Excuses first
• ‘Work in progress’ – loose ends, e.g. easy to crash the interface
• Some features are untested (none of them necessary for coursework)
• Documentation is a first draft• (Almost) never been used by
students (other than me)
Technologies, concepts & paradigms
• C++• Object-Oriented Programming (OOP)
– Encapsulation– Multiple inheritance– Polymorphism
• Event-driven architectures• Templates (generic programming)• Standard Template Library (STL)• Ironically, the aim of all this is to make it easy…• You don’t need to know about the above (except
C++) but if you do it’ll help
How beast is organisedWorld
2D arena where assessments go on
Simulation
PopulationAs Group, but uses a
GA on its contents
GroupPuts WorldObjects and Animats into Simulation
GeneticAlgorithm
MiceSimulation,ShrewSimulation
WorldObject
Animat
Cheeses, Dots,Targets…
Shrews, Mice…
(Evo)FFNAnimat,(Evo)DNNAnimat
Braitenbergs
Evolver
FeedForwardNet, DynamicalNet
Built-in classes
Custom classes
Built-in classes you may never see
AB
A is used by B
A
BA inherits from B
The Simulation class
• Simulations are set up by inheriting from Simulation, adding Groups of WorldObjects (i.e. Cheeses), Populations of Animats (i.e. Mice), and one or more GAs.
• Initialisation – persistent objects are set up, parameters for the GA, the number of Animats, the objects in the World etc.
• Simulation is responsible for– Putting objects (Mice, Cheeses) into World– Letting them buzz around (e.g. collecting cheese) for a number of
timesteps– Taking them out again and putting them through the GA– Repeating for a number of generations
• The Simulation object is like a lab technician, who sets up the simulation, then sits up all night repositioning robots and rerunning assessments until the simulation is complete.
Developing with beast
• Documentation at http://www.comp.leeds.ac.uk/ar23/BEAST/doc/
• Tutorials, example code• Ask in newsgroups• C++ problems – use http://groups.google.com• Problems: executables large, compile times slow
– AR23 students now have extra space– Remove –O3 from Makefile until you’re ready to run– Compile on cslin-gps (don’t run on it though!)
• CPU limit– limit cputime unlimited – add to .cshrc
The bacteria model
• The bacteria are based on a complex mathematical model
• The BEAST implementation is a faithful reproduction of the mathematical model (sort of…)
• To use it, you don’t need to know the details of either
Getting started
• New stuff is now available – download BEAST_project.tar.gz as before
• ‘baccyexamples’ – demonstrate how bacteria move, swarm, use repellents, reproduce and use attractants
• ‘bacteria’ – source code for Q3 of coursework
Two new classes
• Distribution– 2D grid which covers the World– Models nutrients, chemoattractants and
chemorepellents in a solution– Implements diffusion, so distribution ‘dissolves’
over time• Bacterium
– Models groups of bacteria– Direction of movement depends on gradients
detected in nutrient, attractant and repellent distributions
– Can reproduce, swarm, sporulate and die– Properties are controlled by a big list of
variables– Full description in bacteria.h or look in
documentation
Distribution
EvoBacterium
Animat
WorldObject
Bacterium
What Bacterium does 1
• Eact timestep, each Bacterium absorbs some nutrient (if available) from its surroundings, and converts it into energy
• Then takes a look around:– Looks at the nutrient
distribution and the repellent/attractant distributions (if available)
– Looks at the other bacteria around it (depending on its swarmRadius)
What Bacterium does 2• Moves a little in a direction
determined by the above information and a bunch of variables set within Bacterium
• When bacteria move or die, they leave a dot on another distribution object, called trail
• If the Bacterium is in a place with plenty of nutrient, it might release attractant
• If there is not enough nutrient, it might release repellent
What Bacterium does 3
• Reproduces
• Dies
What Distribution does• Every frame, everything becomes a little more
blurred/diffuse• Diffusion speed can be changed in two ways –
see code for details
Working with EvoBacterium
• Same as Bacterium, but with additional GetGenotype, SetGenotype and GetFitness functions for the GA
• Most stuff is commented out, so it basically doesn’t work
How to do the coursework
• Disable/enable features (detailed in comments)
• Muck about with variables (speed, amount of nutrient, reproduction rate)
• Use a Genetic Algorithm…
How to create a fitness function• GetFitness()• Examples are in the code• Possible metrics:
– Number of offspring– Area covered– Distance from start– Amount of food eaten– Fractal dimension?
• Fitness function does not have to match real bacteria– Could an ‘artificial’ fitness function
produce better results than a realistic one?
Note: two sorts of reproduction
• Bacteria reproduce during the assessment– Offspring are identical, no mutation goes on
• A Genetic Algorithm will work on a population of bacteria between assessments– Reproduction and evolution quite different to
actual bacterial evolution – e.g. crossover not present in asexual species
– Fitness function can be anything you like
Pretty pictures
• Nutrient, attractant, repellent and trail distributions can be any colour (in comments)
• World can be any colour (also in comments)
• Save using import <filename.jpg>
Later this week…
• Demonstration session Wednesday 1pm
• Instructions for batch (coming up in newsgroup)
• Arrangements for computer availability over Easter (also coming up in newsgroup)
