Grand Link Library for Genetic Programming, Genetic Algorithms, Genetic Expression Programming, A-Life Games, and anything else we deem relevant to The Project

All of these links are active (not broken) as of December 30, 2009.
Return to The Project.

July 2009: In our heated learning of the scope of genetic programming, before we knew all the players and their inevitable disappearance, we looked hard into finding all the possible sites we could with anything of value. This led to a flurry of emails with about all the applicable sites. Going through all of them is another problem. This is that log for easy searching later. I’ll note the last update on the sites to show the trend of the owners being disappeared.

December 2009: In an attempt to keep track of all these important links, I am reorganizing this list and posting it to, with updates and possible additions as necessary. Organization is no cinch; links definitely can be crossed between the different categories and some may not fit in any category specifically. I am just trying to classify each link by its most important aspect of their contribution to The Project while alphabetizing them within the appropriate category. Also, I have double checked to make sure none of these links is broken (yet). It may be better to do this in XML eventually and sort everything by the appropriate tags instead of trying to do it this way--but for now this will have to do.

January 2010: Adding some updated material. It is also time to begin integrating the Computational Intelligence Hierarchy with the grand link library.


Conscious Entities
UPDATE December 2009: The Project is focused primarily on technology, specifically programming, but there are biological and philosophical ideas at play also. This site deals extensively with the meaning of consciousness, et cetera--physical and philosophical ideas we need to understand to some extent.

UPDATE December 2009: Articles and blogs updated by today's top thinkers. Not always interesting or relevant, but worth checking now and then.
UPDATE December 2009: This has a lot of good (old) articles, but is most useful for its up-to-date RSS feed including any relevant blogs/articles relevant to cutting edge science.

The Multiverse According to Ben Last update – Active
Mostly AI-centric. Information about the singularity and other such stuff.

The Technium
UPDATE December 2009: Lots of good stuff. An oft-updated blog extension of Kevin Kelly's "Out of Control," focusing on "what technology wants."

UPDATE December 2009: Always interesting stuff here. Stuff relevant to The Project always just around the corner. May be good for broader ideas too.

Books Online:

The Field Guide to Genetic Programming.
I don’t suspect it’ll be there forever.

Gene Expression Programming: Mathematical Modeling by an Artificial Intelligence
This is the book for GEP. It’s the first edition but still good. I can’t find the second edition anywhere. I’ve looked too. Hard.

Numerical Computation Guide
This has not so much to do with either GP or GEP but the math behind computer operations. I’ll be willing to bet that it will become invaluable the deeper we delve into these problems. I’ve read to near the into of floating point environments.

Out of Control
UPDATE December 2009: The book by Kevin Kelly that got us into this whole mess. He talks about the game Tierra and other games. Main focus is the biotechnology revolution and the comparisons / lessons we can draw between biology and technology. Crucial to understanding the elements of computer-coded evolution.

Other books we need:
Programming Collective Intelligence: Building Smart Web 2.0 Applications (O’Reilly) - On Amazon
Sync: How Order Emerges From Chaos In the Universe, Nature, and Daily Life by Steven H. Strogatz - On Amazon
Fundamentals of Computational Swarm Intelligence by Andries P. Engelbrecht - On Amazon
Evolutionary Dynamics: Exploring the Equations of Life by Martin A. Nowak - On Amazon
Foundations of Genetic Programming by William B. Langdon, Riccardo Poli - On Amazon
Genetic Algorithms in Search, Optimization, and Machine Learning by David E. Goldberg - On Amazon
Introduction to Evolutionary Computing (Natural Computing Series) by A.E. Eiben, J.E. Smith, David E. Goldberg - On Amazon
How to Solve It: Modern Heuristics (Hardcover) by Zbigniew Michalewicz, David B. Fogel - On Amazon
Swarm Intelligence: From Natural to Artificial Systems (Santa Fe Institute Studies in the Sciences of Complexity Proceedings) by Eric Bonabeau, Marco Dorigo, Guy Theraulaz - On Amazon
Creation: Life and How to Make It by Steve Grand - On Amazon
An Introduction to Genetic Algorithms (Complex Adaptive Systems) by Melanie Mitchell - On Amazon
Artificial Life: A Report from the Frontier Where Computers Meet Biology by Steven Levy - On Amazon

Games / Examples / Source Code:

AI Life Games - Last update unknown
Made Artificial Life base games. Games include: bSerene and DungeonMaker. bSerene is a FPS with AL based enemy tactics (unverified). DungeonMaker is what it sounds but is based on random map generation. I don’t see a source code for anything. They have a big project called BigProject that is to create a true AI or consciousness. They’re third place to Ben Goertzel and Ray Kurzweil.

Aridolan - Last Update unknown
Mostly AI-centric information. Site seems very helpful but most of the links are broken. Likely it’s an abandoned site after the owner’s demise.

Artificial Life
Link dump to about a hundred little programs that mimic life. Tons of Applets.
UPDATE December 2009: Yes, this is a link dump, but I am adding it to the games / examples category because there are lots of useful-looking games here.

Critticall - Last Update 03November2004
Seems like a small application to add an evolution based element to certain C/C++ chucks of code. This is all I could make out of the poorly translated front page. “Critticall is a digital environment, where an input algorithm is a subject to a digital evolution. The fitness may be the speed or the length of the code. Ever better algorithms are surviving small random changes and are the output result.” Sounds awesome and it’s free. Some source code is available but not to the Critticall program.

ECJ 19 - A Java-based Evolutionary Computation Research System
I was planning on going to GMU but I chose UAT (they chose me, more like it). Now I learn they have an EC research lab. Hell. This is the fruits of their labor. I don’t know what it does. I read the description a few times but still no synapses fired in my brain. Lost on this one.

Evolving Game-Playing Strategies with Genetic Programming
Kind of our exact idea. Too bad there’s been nothing done since January 2006. Could also be categorized as "article."

GA --the bike example - Last update unknown
I like this Java applet. I may be able to get source code from the address at the bottom of the site. I think it would make an excellent little game if it were mixed with LineRider and maybe made more open. Excellent first game potential.

The GP Mancala Project - Last Update May 10, 2000
This was a senior project that led to some of the possible limits to GP. He had a evolution based program play a specific (expert) algorithm until it could win most of the time. And then he played the evolved program against 1000 other programs and in turn, lost terribly to each. It grew to thrive in environment and when it was taken out it was lost. It’s a very accurate description of evolution.

Hello World in Genetic Algorithms - Last update July 17, 2007
This site looks fairly recent. It has a couple tutorials on genetic programming. Looks fairly simple and promising. Provides basic source-code in C but most everything else is in C++.

How to use Genetic Algorithm for Traveling Salesman Problem - Written December 20, 2006
UPDATE January 2010: Title says it. Entire article is source code. Good reference for GA.

Karl Sims - Last updated 01May2009 / Last GP update 1994
He used LISP and Koza’s programs to make GP art and Evolved Virtual Creatures which were again used for art. Little imagination beyond this. Interested in the source code. Some use in his papers as they are another take on what Koza wrote, which is something we’ll have to do as well.

Mastermind - Last Update July 22, 2002
UPDATE January 2010: Good example of Genetic Algorithms making good decisions within a few generations. Program built using C#. Downloadable source code included!

Moonlander - Last update unknown
This is an odd little math crunching programming finds the best sort of equation to solve the problem under certain variables. It’s Interesting but over my head right now. I don’t know how you can “genetically” solve a math problem.

The NeuroEvolution of Augmenting Topologies (NEAT) Users Page
“It is a method for evolving artificial neural networks with a genetic algorithm.” Sounds good and it’s very open source. In fact it sounds awesome. And then I saw this page. I began to panic because this is partially what we are doing. But then the last update was in 2007. So it’s all good.

It’s an artificial ecosystem. Just a good reference and watermark.

Survival of the Fittest: Natural Selection with Windows Forms
This shows how to genetically program in C# and CodeDOM(?). It looks horribly useful but way over my head. Even browsing it hurts. A definite must read. The Code has been downloaded to The Project folder. Anything from MSDN looks awesome. Microsoft is fantastic.
UPDATE December 2009: This is no longer so intimidating with new programming experience. This is probably the key starting point for our first game such as Alphabet Soup. Enter the inclusion of this link to The Project here.

Genetic Art. Meh.

Similar to PolyWorld. Good reference. Here’s the download for the distributed world:

Using Genetic Programming To Evolve Soccer Teams
Last update was 2007. Could also be categorized as “article."

We are not alone: Artificial Life Growing on the Internet
This is a small site with several examples of faux life on the internet. Touches briefly on Tierra, Polyworld, Boids, and Conway’s Game of Life. Okay stuff. Links at the bottom. Pictures!

Potentially useful link dumps:

AI, Cognitive Science and Robotics
This site, sigh, had an ass ton of helpful looking links. Eight out of eight that I tried to quickly check failed. As far as I can tell, the whole site is one giant broken link. But there are five books at the title that look interesting. That’s about all there is here.
UPDATE December 2009: I think, based on some random clickage, that this site has been updated to some extent. I did find some broken links, but I found more active than broken, and the date last modified showed December 16, 2009.

Artificial Life Links - Last Updated January 1, 2009
Like the name says, it’s another link dump site. Looks fairly complete. Its onus is more on A-life and not GP but it seems more and more those are intertwined. Although it looks to be updated the most recently there are still a few broken links. The same names keep appearing which is helping me think we’re grasping the major players.

Computer Programming Algorithms Directory
Looks like a link dump for algorithms. It’s helpful but not exactly relevant except the five links to Genetic algorithms; one of which is already broken.

Genetic Programming and Genetic Algorithms - Last Update 2009
This looks like a big thesis link dump. Tons and tons of things that need to be read here. There is no shortage of things that need to be read it seems. Should be easier once we get a better grasp of these programs and have a better idea what we’re doing.

The Genetic Programming Notebook
This has a bunch of current links and a list of books, some of which I’ve never heard. It’s actually a very useful site by the look of things for the book links alone. A found a couple broken links in my quick perusing of the site.

The Genetic Programming Software Paradigm - Last Update May 4, 2003
This is another link dump site. Contains several large GP organizations and One could get lost in these and we need to. When things like this are left on the internet…links break. Information is lost. I need to set aside some time and go through this site before anymore is lost. Trouble is that the links can lead to more links and so forth.

Get A-Life
Not much going on here. Links to Dawkins and something called CoreWars. Also this book called Armchair Universe alongside Out of Control. That might be the fruit of this site.

Neural and Evolutionary Approaches to Domain Independent Object Recognition
Title sums it all up very well. Mostly medical use for genetic search algorithms. Finding tumors and such. I don’t know why I linked this.

Swarm Intelligence Resources - Last update unknown
UPDATE January 2010: Links, some broken.

Swarm Intelligence Resources - Last update February 3, 2005
UPDATE January 2010: Lots of links and applications, good starting point for SI.

Visual Aesthetic Evolutionary Design Links
I hate all the “Art through GP” concept. But this is about the best link for it all I could find. Very complete and verbose.

Tutorials / Articles / Tools:

AI: Population based Incremental Learning in C# and .NET - Written May 22, 2005
UPDATE January 2010: Another mathematical application of GA: computing square roots. Source code included!

AITopics on Genetic Algorithms
This website is scary how close ideas are coming in line with ours. Koza apparently invented an invention machine in 2006. I’m pretty sure it invented a knife to stab its inventor and Koza now lives through his machine. About the site: It’s a subtopic of artificial life on the point of GP and GAs. Lots of really cool links to good reads.

AI: Using the Compact Genetic Algorithm to Compute Square Roots in C# - Written October 9, 2005
UPDATE January 2010: Another mathematical application of GA: computing square roots. Source code included!

Artificial Intelligence Laboratory
A lot about AI. I couldn’t find anything to pique my interest but there could be something. I didn’t want to exclude it because of my hasty browsing.

Computer Simulation of Evolution: Genetic and “Memetic” Ways - Written 2007
UPDATE January 2010: Mostly about modeling biological evolution, this article reviews the patterns of evolution and its usefulness to computer-generated evolution.

DTREG - Software For Predictive Modeling and Forecasting
It’s like a system for building tree hierarchies. And most GP takes after Koza’s initial design of trees in LISP. But this has examples of GEP rather than GP.

Fuzzy Systems: A tutorial - Copyrighted 1985.
UPDATE January 2010: All you need to know about fuzzy systems.

GAUL (Genetic Algorithm Utility Library) - Last Update 2009.
UPDATE December 2009: This has some useful-looking stuff, including GA tutorial and sample programs in various languages along with source code. Some broken links.

Genetic Algorithms and Evolutionary Computation - Posted April 23, 2004.
UPDATE January 2010: In-depth article and discussion about GAs and EC in general. Lots of cool examples, with citations.

Genetic Programming - Last update July 8, 2007
Home of the “Humies” Award. Lots of good official intimidating links that make me more aware that there are many great minds doing exactly what we’re trying to do. Lots of Phds. And Koza’s site is hosted here as the other is abandoned. Also Koza’s last paper was from 2004 and last reference in Wikipedia is from 2006. He’s likely dead.

Gene Expression Programming - Last updated active
Looks like a wealth of information about the math behind all this genetic stuff. This is badly needed for both of us. The book, Gene Expression Programming:
Mathematical Modeling by an Artificial Intelligence, I can’t find for free. This bothers me as the sticker price is between 140 and 180 USD. Find this book.

Gene Expression Programming (GEP) in C# and .NET - Last updated April 11, 2002
I love this article. It explains everything lacking in GEP. It’s a better example of its capabilites than the home website. Plus, it shows how cool C# is.
UPDATE December 2009: Another tough one to categorize. Lots of code and a free .zip download so although this is an article it could easily be placed under games / examples / source code category.

The Home of Genetic Programming - Last updated July 8, 2007
This is the site that hosts Koza’s site. They have tons of papers and is probably the most official site on the subject of genetic programming.

Implementing a Genetic Algorithms in C# and .NET - Written April 14, 2002
UPDATE January 2010: Part of a great series of 2002 articles by Mike Gold on C# Corner. The title explains it well enough. Source code included!

Introduction to AI - Last update unknown
UPDATE January 2010: Good summary for AI, specifically the differences between symbolic and sub-symbolic AI.

The Law of Accelerating Returns
UPDATE December 2009: Great article about the Law of Accelerating Returns and The Singularity. Lots of neat graphs.

Memristor minds intelligence.html?page=1
It’s a maddening article about a new electronic component called the memristor. It was theorized by its absence in the early 70s. Now it’s been discovered and explains so many things about the human mind. It’s being used to build incredibly complex and wholly new circuits to attempt conciseness. Sadly as deep as we are in GP (not very) and how far off this is from commercial use, our AI will be of a different archetype. Maybe we’ll get them to fight. Ours will be an unyielding, unstopping computational hell-spawn, half birthed and trying to become complete. Theirs will be a new life trying to learn how to love in an artificial field of flowers.
UPDATE December 2009: For first application to The Project, see this blog.

Multi Expression Programming [PDF] - Published June 4, 2006.
UPDATE January 2010: 28 pages of MEP.

My Genes Can Do Reverse Engineering
I think this counts as GEP. Still can’t have too much stuff.

Neural Networks - Last update unknown
UPDATE January 2010: Comprehensive report on Neural Networks.

Neural Networks Research Group - Last update unknown
[PDF Here]
The link directly leads to a synopsis on a paper about rtNEAT (real-time NeuroEvolution of Augmented Topologies). I’ve seen that name before on some other site’s I’ve visited. Basically it’s about the neural networks, when taught
specific skills, they tend to forget the old stuff. It’s mostly centric on videogame AI so it’ll be important to understand.

On the Origins of Circuits
UPDATE December 2009: The Damn Interesting article that started it all. This led to Kevin Kelly and "Out of Control," and the rest is history. Still good to keep in mind that The Project may be useful for more than just software.

Simulated evolution gets complex, snowflake example of self-organization - Last updated January 25, 2009
UPDATE January 2010: Ignore the snowflake bit, the program described after this is pretty interesting. I like the idea of keeping track of the evolutionary genealogy of successful breeders of the genome, while "purging those with no living descendants."

Systems Biology Markup Language - Last updated December 16, 2009
UPDATE January 2010: A potentially useful programming tool. From the SBML website: "... a computer-readable format for representing models of biological processes. It's applicable to simulations of metabolism, cell-signaling, and many other topics."

Using Multiple Expressions to derive the Pythagorean Theorem
UPDATE January 2010: Good introduction to MEP and its usefulness.

Wikipedia / Scholarpedia Entries:

(ADDED January 2010)

Artificial Evolution
Artificial Intelligence
Bottom-up AI
Computational Intelligence
Evolutionary Algorithm
Evolutionary Computation
Evolutionary Programming
Evolution Strategy
Evolution Strategy (Scholarpedia)
Gene Expression Programming
Genetic Algorithm
Genetic Programming
Population-based Incremental Learning
Sub-symbolic AI
Swarm Intelligence
Symbolic AI

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