GNU/Linux AI & Alife HOWTO by John Eikenberry (red scrolls of magic .TXT) 📕

for tree-based genetic

programming, bit string and real-valued genetic algorithms,

evolution strategy, coevolution, and evolutionary multi-objective optimization.

 

PGAPack

Parallel Genetic Algorithm Library

 

� Web site: www—

fp.mcs.anl.gov/CCST/research/reports_pre1998/comp_bio/stalk/pgapack.html

 

� FTP site: ftp.mcs.anl.gov/pub/pgapack/

 

PGAPack is a general-purpose, datastructure-neutral, parallel

genetic algorithm library. It is intended to provide most

capabilities desired in a genetic algorithm library, in an

integrated, seamless, and portable manner. Key features are in

PGAPack V1.0 include:

 

� Callable from Fortran or C.

 

� Runs on uniprocessors, parallel computers, and workstation

networks.

 

� Binary-, integer-, real-, and character-valued native data

types.

 

� Full extensibility to support custom operators and new data

types.

 

� Easy-to-use interface for novice and application users.

 

� Multiple levels of access for expert users.

 

� Parameterized population replacement.

 

� Multiple crossover, mutation, and selection operators.

 

� Easy integration of hill-climbing heuristics.

 

� Extensive debugging facilities.

 

� Large set of example problems.

 

� Detailed users guide.

 

PIPE

 

� Web site: www.idsia.ch/~rafal/research.html

 

� FTP site: ftp.idsia.ch/pub/rafal

 

Probabilistic Incremental Program Evolution (PIPE) is a novel

technique for automatic program synthesis. The software is

written in C. It …

 

� is easy to install (comes with an automatic installation

tool).

 

� is easy to use: setting up PIPE_V1.0 for different problems

requires a minimal amount of programming. User-written,

application-independent program parts can easily be reused.

 

� is efficient: PIPE_V1.0 has been tuned to speed up

performance.

 

� is portable: comes with source code (optimized for SunOS

5.5.1).

� is extensively documented(!) and contains three example

applications.

 

� supports statistical evaluations: it facilitates running

multiple experiments and collecting results in output files.

 

� includes testing tool for testing generalization of evolved

programs.

 

� supports floating point and integer arithmetic.

 

� has extensive output features.

 

� For lil-gp users: Problems set up for lil-gp 1.0 can be

easily ported to PIPE_v1.0. The testing tool can also be used

to process programs evolved by lil-gp 1.0.

 

pygene

 

� Web site: www.freenet.org.nz/python/pygene/

 

pygene is a simple and easily understandable library for genetic

algorithms and genetic programming in python. Includes examples

such as the travelling salesman problem.

 

pygp

 

� Web site: pygp.sourceforge.net/

 

Your basic genetic algorithm package for python.

 

Sugal

 

� Web site: www.trajan-software.demon.co.uk/sugal.htm

 

Sugal [soo-gall] is the SUnderland Genetic ALgorithm system.

The aim of Sugal is to support research and implementation in

Genetic Algorithms on a common software platform. As such, Sugal

supports a large number of variants of Genetic Algorithms, and

has extensive features to support customization and extension.

 

4.2. EC software kits/applications

 

These are various applications, software kits, etc. meant for research

in the field of evolutionary computing. Their ease of use will vary,

as they were designed to meet some particular research interest more

than as an easy to use commercial package.

 

ADATE

 

� Web site: www-ia.hiof.no/~rolando/adate_intro.html

 

ADATE (Automatic Design of Algorithms Through Evolution) is a

system for automatic programming i.e., inductive inference of

algorithms, which may be the best way to develop artificial and

general intelligence.

 

The ADATE system can automatically generate non-trivial and

novel algorithms. Algorithms are generated through large scale

combinatorial search that employs sophisticated program

transformations and heuristics. The ADATE system is particularly

good at synthesizing symbolic, functional programs and has

several unique qualities.

 

esep & xesep

 

� Web site(esep): www.iit.edu/~elrad/esep.html

 

� Web site(xesep): www.iit.edu/~elrad/xesep.html

 

This is a new scheduler, called Evolution Scheduler, based on

Genetic Algorithms and Evolutionary Programming. It lives with

original Linux priority scheduler.This means you don’t have to

reboot to change the scheduling policy. You may simply use the

manager program esep to switch between them at any time, and

esep itself is an all-in-one for scheduling status, commands,

and administration. We didn’t intend to remove the original

priority scheduler; instead, at least, esep provides you with

another choice to use a more intelligent scheduler, which

carries out natural competition in an easy and effective way.

 

Xesep is a graphical user interface to the esep (Evolution

Scheduling and Evolving Processes). It’s intended to show users

how to start, play, and feel the Evolution Scheduling and

Evolving Processes, including sub-programs to display system

status, evolving process status, queue status, and evolution

scheduling status periodically in as small as one mini-second.

 

Corewars

 

� Web site: corewars.sourceforge.net/

 

� SourceForge site: sourceforge.net/projects/corewars/

 

Corewars is a game which simulates a virtual machine with a

number of programs. Each program tries to crash the others. The

program that lasts the longest time wins. A number of sample

programs are provided and new programs can be written by the

player. Screenshots are available at the Corewars homepage.

 

Grany-3

 

� Web site: zarb.org/~gc/html/grany.html

 

Grany-3 is a full-featured cellular automaton simulator, made in

C++ with Gtk—, flex++/bison++, doxygen and gettext, useful to

granular media physicists.

 

JCASim

 

� Web site: www.jweimar.de/jcasim/

 

JCASim is a general-purpose system for simulating cellular

automata in Java. It includes a stand-alone application and an

applet for web presentations. The cellular automata can be

specified in Java, in CDL, or using an interactive dialogue. The

system supports many different lattice geometries (1-D, 2-D

square, hexagonal, triangular, 3-D), neighborhoods, boundary

conditions, and can display the cells using colors, text, or

icons.

 

JGProg

 

� Web site: jgprog.sourceforge.net

 

Genetic Programming (JGProg) is an open-source Java

implementation of a strongly-typed Genetic Programming

experimentation platform. Two example “worlds” are provided, in

which a population evolves and solves the problem.

 

5. Alife & Complex Systems

 

Alife takes yet another approach to exploring the mysteries of

intelligence. It has many aspects similar to EC and Connectionism,

but takes these ideas and gives them a metalevel twist. Alife

emphasizes the development of intelligence through emergent behavior

of complex adaptive systems. Alife stresses the social or group based

aspects of intelligence. It seeks to understand life and survival. By

studying the behaviors of groups of ‘beings’ Alife seeks to discover

the way intelligence or higher order activity emerges from seemingly

simple individuals. Cellular Automata and Conway’s Game of Life are

probably the most commonly known applications of this field. Complex

Systems (abbreviated CS) are very similar to alife in the way the are

approached, just more general in definition (ie. alife is a type of

complex system). Usually complex system software takes the form of a

simulator.

 

5.1. Alife & CS class/code libraries

 

These are libraries of code or classes for use in programming within

the artificial life field. They are not meant as stand alone

applications, but rather as tools for building your own applications.

 

AgentFarms

 

� Web site: www.agentfarms.net

 

Agent Farms is a system for modelling and simulation of complex,

multiagent based systems. The system can be used for:

 

� Creating models of multiagent systems

 

� Interactive and distributed simulation

 

� Observation and visualisation of the simulation

 

� Population modification and migration

 

Biome

 

� Web site: sourceforge.net/projects/biome/

 

Biome is a C++ library aimed at individual-based/agent-based

simulations. It is somewhat similar to Swarm, EcoSim or Simex

but tries to be more efficient and less monolithic without

compromising object-oriented design. Currently there is an

event based scheduling system, a C++ified Mersenne-Twister RNG,

several general analysis classes, some Qt-based GUI classes, a

very basic persistence/database framework (used also for

parameter storage) and many other small useful things.

 

CAGE

 

� Web site: www.alcyone.com/software/cage/

 

CAGE is a fairy generic and complete cellular automaton

simulation engine in Python. It supports both 1D and 2D

automata, a variety of prepackaged rules, and the concept of

“agents” which can move about independently on the map for

implementing agent behavior.

 

Integrating Modelling Toolkit

 

� Web site: sourceforge.net/projects/imt/

 

The Integrating Modelling Toolkit (IMT) is a generic,

comprehensive, and extensible set of abstractions allowing

definition and use of interoperable model components. Modellers

create an IMT “world” made of IMT “agents” that will perform

each a particular phase of a modelling task. The core set of

IMT agents can describe generic, modular, distributed model

components, either native to the IMT or integrating existing

simulation toolkits, specialized for tasks that range from

simple calculation of functions in an interpreted language to

spatially explicit simulation, model optimization, GIS analysis,

visualization and advanced statistical analysis. IMT agents are

designed to easily “glue” together in higher-level simulations

integrating different modelling paradigms and toolkits. The IMT

can be easily extended by users and developers through a

convenient plug-in mechanism

 

MAML

 

� Web site: www.maml.hu

 

The current version of MAML is basically an extension to

Objective-C (using the Swarm libraries). It consists of a couple

of remaining must be filled with pure swarm-code. A MAML-to-Swarm (named xmc) compiler is also being developed which

compiles the source code into a swarm application.

 

MASON

 

� Web site: cs.gmu.edu/~eclab/projects/mason/

 

MASON Stands for MultiAgent Simulator Of Neighborhoods… or

Networks… or something…

 

MASON is a fast discrete-event multiagent simulation library

core in Java, designed to be the foundation for large custom-purpose Java simulations, and also to provide more than enough

functionality for many lightweight simulation needs. MASON

contains both a model library and an optional suite of

visualization tools in 2D and 3D.

 

SimWorld

 

� Web site: www.nd.edu/~airolab/simworld/

 

SimWorld is a free artificial life simulation (based on the free

“” toolkit developed by Aaron Sloman), which provides

functionality for running different interacting agents and

objects in a simulated, continuous environment. The agents are

controlled by rules written in the powerful rule interpreter.

New behaviors of agents can be defined without any programming

knowledge.

 

Swarm

 

� Web site: www.swarm.org/wiki/Swarm_main_page

 

� FTP site: ftp.swarm.org/pub/swarm/

 

The swarm Alife simulation kit. Swarm is a simulation

environment which facilitates development and experimentation

with simulations involving a large number of agents behaving and

interacting within a dynamic environment. It consists of a

collection of classes and libraries written in Objective-C and

allows great flexibility in creating simulations and analyzing

their results. It comes with three demos and good

documentation.

 

5.2. Alife & CS software kits, applications, etc.

 

These are various applications, software kits, etc. meant for research

in the field of artificial life. Their ease of use will vary, as they

were designed to meet some particular research interest more than as

an easy to use commercial package.

 

Achilles

 

� Web site: achilles.sourceforge.net

 

Achilles is an evolution simulation based on Larry Yaeger’s

PolyWorld. It uses Hebbian neural networks, and an extremely

simplified physical model that allows virtual organisms to

interact freely in a simulated environment.

 

AntWars

 

� Web site: ant-wars.com

 

Ant Wars is a competition which pits clever programs against

each other to do battle and compete for food in virtual worlds.

Each contestant is a species of ant, which can visualize only

the world immediately around him and pheromones left by fellow

and enemy ants. Using this information, the ant brain (a simple

state machine) must guide the ant towards collecting food at his

home ant hill, while fending off or attacking enemies.

 

Clever use of pheromones and subtle behaviors can create large

scale tactics such as raiding, defense, harvesting, and scouting

when many ants cooperate.

 

Avida

 

� Web site: dllab.caltech.edu/avida/

 

The computer program avida is an auto-adaptive genetic system

designed primarily for use as a platform in Artificial Life

research. The avida system is based on concepts similar to those

employed by the tierra program, that is to say it is a

population of self-reproducing strings with a Turing-complete

genetic basis subjected to Poisson-random mutations. The

population adapts to the combination of an intrinsic fitness

landscape (self-reproduction) and an externally imposed

(extrinsic) fitness function provided by the researcher. By