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FAQ: comp.ai.genetic part 1/6 (A Guide to Frequently Asked Questions)

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Archive-name: ai-faq/genetic/part1
Last-Modified: 4/12/01
Issue: 9.1

See reader questions & answers on this topic! - Help others by sharing your knowledge
Important note: Do NOT send email to the cs.cf.ac.uk address above: it will 
    be ignored. Corrections and other correspondence should be sent to 
    david.beasley@iee.org

				      The

				 Hitch-Hiker's

				    Guide to

			   Evolutionary Computation

			   (FAQ for comp.ai.genetic)

				   edited by

			       Joerg Heitkoetter
			     UUnet Deutschland GmbH
				 Sebrathweg 20
			   D-44149 Dortmund, Germany
			       <joke@de.uu.net>
			     or <joke@santafe.edu>

				      and

				 David Beasley
				  ingenta ltd
				BUCS Building,
			      University of Bath,
			 Bath, United Kingdom BA2 7AY
			    <david.beasley@iee.org>

				    PLEASE:
	       Search this document first if you have a question
				      and
     If someone posts a question to the newsgroup which is answered in here
		    DON'T POST THE ANSWER TO THE NEWSGROUP:
			  POINT THE ASKER TO THIS FAQ
				  and finally

				  DON'T PANIC!

     Copyright  (c)  1993-2001 by Joerg Heitkoetter and David Beasley, all
			       rights reserved.

     This FAQ may be posted to any USENET newsgroup, on-line  service,  or
     BBS  as  long  as  it  is  posted  in  its entirety and includes this
     copyright statement.  This FAQ may not be distributed  for  financial
     gain.   This  FAQ  may  not  be included in commercial collections or
     compilations without express permission from the author.

     FAQ  /F-A-Q/ or /fak/ [USENET] n.  1. A  Frequently  Asked  Question.
	  2.  A  compendium  of  accumulated  lore, posted periodically to
	  high-volume  newsgroups  in  an  attempt   to   forestall   such
	  questions.   Some  people  prefer  the term `FAQ list' or `FAQL'
	  /fa'kl/, reserving `FAQ' for sense 1.

     RTFAQ
	  /R-T-F-A-Q/ [USENET: primarily written, by  analogy  with  RTFM]
	  imp. Abbrev. for `Read the FAQ!', an exhortation that the person
	  addressed ought to read the newsgroup's FAQ list before  posting
	  questions.

     RTFM /R-T-F-M/ [UNIX] imp. Acronym for `Read The Fucking Manual'.  1.
	  Used by gurus to brush off questions they  consider  trivial  or
	  annoying.   Compare Don't do that, then!  2. Used when reporting
	  a problem to  indicate  that  you  aren't  just  asking  out  of
	  randomness.  "No, I can't figure out how to interface UNIX to my
	  toaster, and yes, I have RTFM."  Unlike sense  1,  this  use  is
	  considered polite. ...

		 --- "The on-line hacker Jargon File, version 3.0, 29 July
								     1993"

PREFACE
     This guide is intended to help, provide basic information, and  serve
     as a first straw for individuals, i.e.  uninitiated hitch-hikers, who
     are stranded in the mindboggling universe of Evolutionary Computation
     (EC);  that  in  turn  is  only  a  small  footpath  to  an even more
     mindboggling scientific universe, that, incorporating Fuzzy  Systems,
     and   Artificial   Neural  Networks,  is  sometimes  referred  to  as
     Computational Intelligence (CI); that in turn is only part of an even
     more  advanced scientific universe of mindparalysing complexity, that
     incorporating Artificial Life, Fractal Geometry,  and  other  Complex
     Systems  Sciences might someday be referred to as Natural Computation
     (NC).

     Over the course of the past  years,  GLOBAL  OPTIMIZATION  algorithms
     imitating  certain  principles of nature have proved their usefulness
     in various domains of  applications.  Especially  worth  copying  are
     those  principles  where  nature  has  found  "stable  islands"  in a
     "turbulent ocean" of solution possibilities. Such  phenomena  can  be
     found  in annealing processes, central nervous systems and biological
     EVOLUTION, which in turn have  lead  to  the  following  OPTIMIZATION
     methods:  Simulated Annealing (SA), Artificial Neural Networks (ANNs)
     and the field of Evolutionary Computation (EC).

     EC may currently be characterized by the following pathways:  Genetic
     Algorithms  (GA), Evolutionary Programming (EP), Evolution Strategies
     (ES), Classifier Systems (CFS), Genetic Programming (GP), and several
     other  problem  solving  strategies,  that  are based upon biological
     observations, that date back to Charles Darwin's discoveries  in  the
     19th  century: the means of natural selection and the survival of the
     fittest, and theories of evolution.  The inspired algorithms are thus
     termed Evolutionary Algorithms (EA).

     Moreover, this guide is intended to help those who are just beginning
     to read the comp.ai.genetic newsgroup, and those  who  are  new  "on"
     USENET.  It shall help to avoid lengthy discussions of questions that
     usually arise for beginners of one or the other kind, and  which  are
     boring to read again and again by comp.ai.genetic "old-timers."

     You  will  see  this  guide  popping  up  periodically  in the Usenet
     newsgroup comp.ai.genetic (and also comp.answers , and news.answers ,
     where it should be locatable at any time).

ORIGIN
     This guide was produced by Joerg Heitkoetter (known as Joke) in early
     1993, using material from many sources (see Acknowledgements ), mixed
     with  his  own brand of humour. Towards the end of 1993, Joerg handed
     over editorial responsibility to David Beasley . He  reorganised  the
     guide  in  various  ways,  and  generally attempted to inject his own
     brand of orderliness. Thus, any jokes  are  the  work  of  Joke.  The
     mundane bits are David's responsibility.

     The  guide  is  kept up to date, as far as possible, and new versions
     are issued several times a  year.  However,  we  do  rely  on  useful
     information  being  sent  to  us  for inclusion in the guide (we dont
     always  have  time  to   read   comp.ai.genetic   ,   for   example).
     Contributions,  additions,  corrections,  cash,  etc.  are  therefore
     always welcome.  Send e-mail to the address at the beginning  of  the
     guide.

DISCLAIMER
     This periodic posting is not meant to discuss any topic exhaustively,
     but should be thought of as a list of  reference  pointers,  instead.
     This  posting is provided on an "as is" basis, NO WARRANTY whatsoever
     is expressed or implied, especially, NO WARRANTY that the information
     contained  herein  is  up-to-date,  correct  or  useful  in  any way,
     although all this is intended.

     Moreover, please note that  the  opinions  expressed  herein  do  not
     necessarily  reflect those of the editors' institutions or employers,
     neither as a whole, nor in part. They are just  the  amalgamation  of
     the  editors'  collections  of  ideas, and contributions gleaned from
     other sources.

     NOTE: some portions of this otherwise rather dry guide  are  intended
     to  be  satirical.   If you do not recognize it as such, consult your
     local doctor or a professional comedian.

HOW TO USE THIS GUIDE
 HITCH-HIKING THE FAQNIVERSE
     This guide is big. Really big. You just  won't  believe  how  hugely,
     vastly, mindbogglingly big it is. That's why it has been split into a
     "trilogy" -- which, like all successful trilogies, eventually ends up
     consisting of more than three parts.

 Searching for answers
     To  find  the answer of question number x, just search for the string
     "Qx:". (So the answer to question 42 is at "Q42:"!)

 What does [xxxx99] mean?
     Some books are referenced again and again, that's why they have  this
     kind of "tag", that an experienced hitch-hiker will search for in the
     list of books (see Q10 and Q12 and  other  places)  to  dissolve  the
     riddle.  Here,  they have a ":" appended, thus you can search for the
     string "[ICGA85]:" for example.

 Why all this UPPERCASING in running text?
     Words written  in  all  uppercase  letters  are  cross-references  to
     entries  in  the Glossary (see Q99). Again, they have a ":" appended,
     thus if you find, say  EVOLUTION,  you  can  search  for  the  string
     "EVOLUTION:" in the Glossary.

 FTP and HTTP naming conventions
     A  file  available  on an FTP server will be specified as: <ftp-site-
     name>/<the-complete-filename> So for example, the file bar.tar.gz  in
     the  directory  /pub/foo  on the ftp server ftp.certain.site would be
     specified as: ftp.certain.site/pub/foo/bar.tar.gz

     A specification  ending  with  a  "/"  is  a  reference  to  a  whole
     directory, e.g.  ftp.certain.site/pub/foo/
     HTTP  files  are  specified  in  a  similar way, but with the prefix:
     http://

WHERE TO FIND THIS GUIDE
     Between postings to comp.ai.genetic  , this FAQ is available  on  the
     World  Wide  Web.   Get  it  from  any  ENCORE  site (See Q15.3). The
     following Encore sites can be accessed by HTTP. If you  use  the  one
     closest  to  you,  you  should get the best speed of service.  (Note,
     however, that some sites are not always up to  date.   The  guide  is
     normally issued every 3 months.)

     o  UUnet    Deutschland   GmbH   (Germany)   (definitive   location):
	http://surf.de.uu.net/encore/www/

	o   The    Chinese    University    of    Hong    Kong    (China):
	http://www.cs.cuhk.hk/pub/EC/FAQ/www/top.htm

	o             Ecole             Polytechnique            (France):
	http://www.eark.polytechnique.fr/EC/FAQ/www/top.htm

	o       The       University       of       Oviedo        (Spain):
	http://www.etsimo.uniovi.es/ftp/pub/EC/FAQ/www/

	o        The       University       of       Birmingham       (UK)
	http://www.cs.bham.ac.uk/Mirrors/ftp.de.uu.net/EC/clife/www/

	o        The        Santa        Fe        Institute        (USA):
	http://alife.santafe.edu/~joke/encore/www/

     Other  Encore  sites can be accessed by FTP, and the FAQ can be found
     in the file FAQ/www/top.htm or something similar.  The  FAQ  is  also
     available    in    plain    text   format   on   Encore,   and   from
     rtfm.mit.edu/pub/usenet/news.answers/ai-faq/genetic/  as  the  files:
     part1  to  part6. The FAQ may also be retrieved by e-mail from <mail-
     server@rtfm.mit.edu>. Send a message to the mail-server  with  "help"
     and "index" in the body on separate lines for more information.

     A  PostScript  version  is  also  available.  This looks really crisp
     (using boldface, italics, etc.),  and  is  available  for  those  who
     prefer  offline reading.  Get it from Encore in file FAQ/hhgtec.ps.gz
     (the plain text versions are in the same directory too).

	  "As a net is made up of a series of ties, so everything in  this
       world is connected by a series of ties.  If anyone thinks  that the
     mesh of a net is an independent, isolated thing, he is  mistaken.  It
      is called a net because it is made up of a series  of interconnected
				   meshes, and each mesh has its place and
			      responsibility in relation to other meshes."

								--- Buddha

 Referencing this Guide
     If you want to reference this guide it should look like:

     Heitkoetter, Joerg and  Beasley,  David,  eds.   (2001)  "The  Hitch-
     Hiker's Guide to Evolutionary Computation: A list of Frequently Asked
     Questions (FAQ)", USENET: comp.ai.genetic.  Available  via  anonymous
     FTP  from  rtfm.mit.edu/pub/usenet/news.answers/ai-faq/genetic/ About
     110 pages.

     Or simply call it "the Guide", or "HHGTEC" for acronymaniacs.

The ZEN Puzzle
     For some weird reason this guide contains some puzzles which can only
     be  solved  by  cautious  readers  who have (1) a certain amount of a
     certain kind of humor, (2) a certain amount of patience and time, (3)
     a  certain  amount of experience in ZEN NAVIGATION, and (4) a certain
     amount of books of a certain author.

     Usually, puzzles search either for certain answers (more  often,  ONE
     answer)  to  a  question;  or,  for the real smartasses, sometimes an
     answer is presented, and a certain question  is  searched  for.   ZEN
     puzzles are even more challenging: you have to come up with an answer
     to a question, both of which are not  explicitly,  rather  implicitly
     stated  somewhere  in  this  FAQ.   Thus, you are expected to give an
     answer AND a question!

     To give an impression what this is all about, consider the following,
     submitted  by  Craig  W.  Reynolds.  The correct question is: "Why is
     Fisher's `improbability quote' (cf EPILOGUE ) included in this FAQ?",
     Craig's correct answer is: `This is a GREAT quotation, it sounds like
     something directly out of  a  turn  of  the  century  Douglas  Adams:
     Natural Selection:
      the  original "Infinite Improbability Drive"' Got the message? Well,
     this  was  easy  and  very  obvious.  The  other  puzzles  are   more
     challenging...

     However,  all  this is just for fun (mine and hopefully yours), there
     is nothing like the $100 price, some big shots in  computer  science,
     e.g.   Don  Knuth  usually  offer;  all  there  is  but  a  honorable
     mentioning of the ZEN navigator, including the  puzzle  s/he  solved.
     It's  thus  like  in  real life: don't expect to make money from your
     time being a scientist, it's all just for the fun of it...

     Enjoy the trip!

TABLE OF CONTENTS
 Part1

     Q0: How about an introduction to comp.ai.genetic?

 Part2

     Q1: What are Evolutionary Algorithms (EAs)?
     Q1.1: What's a Genetic Algorithm (GA)?
     Q1.2: What's Evolutionary Programming (EP)?
     Q1.3: What's an Evolution Strategy (ES)?
     Q1.4: What's a Classifier System (CFS)?
     Q1.5: What's Genetic Programming (GP)?

 Part3

     Q2: What applications of EAs are there?

     Q3: Who is concerned with EAs?

     Q4: How many EAs exist? Which?
     Q4.1: What about Alife systems, like Tierra and VENUS?

     Q5: What about all this Optimization stuff?

 Part4

     Q10: What introductory material on EAs is there?
     Q10.1: Suitable background reading for beginners?
     Q10.2: Textbooks on EC?
     Q10.3: The Classics?
     Q10.4: Introductory Journal Articles?
     Q10.5: Introductory Technical Reports?
     Q10.6: Not-quite-so-introductory Literature?
     Q10.7: Biological Background Readings?
     Q10.8: On-line bibliography collections?
     Q10.9: Videos?
     Q10.10: CD-ROMs?
     Q10.11: How do I get a copy of a dissertation?

     Q11: What EC related journals and magazines are there?

     Q12: What are the important conferences/proceedings on EC?

     Q13: What Evolutionary Computation Associations exist?

     Q14: What Technical Reports are available?

     Q15: What information is available over the net?
     Q15.1: What digests are there?
     Q15.2: What mailing lists are there?
     Q15.3: What online information repositories are there?
     Q15.4: What relevant newsgroups and FAQs are there?
     Q15.5: What about all these Internet Services?

 Part5

     Q20: What EA software packages are available?
     Q20.1: Free software packages?
     Q20.2: Commercial software packages?
     Q20.3: Current research projects?

 Part6

     Q21: What are Gray codes, and why are they used?

     Q22: What test data is available?

     Q42: What is Life all about?
     Q42b: Is there a FAQ to this group?

     Q98: Are there any patents on EAs?

     Q99: A Glossary on EAs?


Subject: Q0: How about an introduction to comp.ai.genetic? Certainly. See below. What is comp.ai.genetic all about? The newsgroup comp.ai.genetic is intended as a forum for people who want to use or explore the capabilities of Genetic Algorithms (GA), Evolutionary Programming (EP), Evolution Strategies (ES), Classifier Systems (CFS), Genetic Programming (GP), and some other, less well- known problem solving algorithms that are more or less loosely coupled to the field of Evolutionary Computation (EC). How do I get started? What about USENET documentation? The following guidelines present the essentials of the USENET online documentation, that is posted each month to news.announce.newusers If you are already familiar with "netiquette" you can skip to the end of this answer; if you don't know what the hell this is all about, proceed as follows: (1) carefully read the following paragraphs, (2) read all the documents in news.announce.newusers before posting any article to USENET. At least you should give the introductory stuff a try, i.e. files "news-answers/introduction" and "news-answers/news- newusers-intro". Both are survey articles, that provide a short and easy way to get an overview of the interesting parts of the online docs, and thus can help to prevent you from drowning in the megabytes to read. Both can be received either by subscribing to news.answers , or sending the following message to <mail-server@rtfm.mit.edu>: send usenet/news.answers/introduction send usenet/news.answers/news-newusers-intro quit Netiquette "Usenet is a convention, in every sense of the word." Although USENET is usually characterized as "an anarchy, with no laws and no one in charge" there have "emerged" several rules over the past years that shall facilitate life within newsgroups. Thus, you will probably find the following types of articles: 1. Requests Requests are articles of the form "I am looking for X" where X is something public like a book, an article, a piece of software. If multiple different answers can be expected, the person making the request should prepare to make a summary of the answers he/she got and announce to do so with a phrase like "Please e-mail, I'll summarize" at the end of the posting. The Subject line of the posting should then be something like "Request: X" 2. Questions As opposed to requests, questions are concerned with something so specific that general interest cannot readily be assumed. If the poster thinks that the topic is of some general interest, he/she should announce a summary (see above). The Subject line of the posting should be something like "Question: this-and-that" (Q: this-and-that) or have the form of a question (i.e., end with a question mark) 3. Answers These are reactions to questions or requests. As a rule of thumb articles of type "answer" should be rare. Ideally, in most cases either the answer is too specific to be of general interest (and should thus be e-mailed to the poster) or a summary was announced with the question or request (and answers should thus be e-mailed to the poster). The subject lines of answers are automatically adjusted by the news software. 4. Summaries In all cases of requests or questions the answers for which can be assumed to be of some general interest, the poster of the request or question shall summarize the answers he/she received. Such a summary should be announced in the original posting of the question or request with a phrase like "Please answer by e-mail, I'll summarize" In such a case answers should NOT be posted to the newsgroup but instead be mailed to the poster who collects and reviews them. After about 10 to 20 days from the original posting, its poster should make the summary of answers and post it to the net. Some care should be invested into a summary: a) simple concatenation of all the answers might not be enough; instead redundancies, irrelevances, verbosities and errors should be filtered out (as good as possible), b) the answers shall be separated clearly c) the contributors of the individual answers shall be identifiable unless they requested to remain anonymous [eds note: yes, that happens]) d) the summary shall start with the "quintessence" of the answers, as seen by the original poster e) A summary should, when posted, clearly be indicated to be one by giving it a Subject line starting with "Summary:" Note that a good summary is pure gold for the rest of the newsgroup community, so summary work will be most appreciated by all of us. (Good summaries are more valuable than any moderator!) 5. Announcements Some articles never need any public reaction. These are called announcements (for instance for a workshop, conference or the availability of some technical report or software system). Announcements should be clearly indicated to be such by giving them a subject line of the form "Announcement: this-and-that", or "ust "A: this-and-that". Due to common practice, conference announcements usually carry a "CFP:" in their subject line, i.e. "call for papers" (or: "call for participation"). 6. Reports Sometimes people spontaneously want to report something to the newsgroup. This might be special experiences with some software, results of own experiments or conceptual work, or especially interesting information from somewhere else. Reports should be clearly indicated to be such by giving them a subject line of the form "Report: this-and-that" 7. Discussions An especially valuable possibility of USENET is of course that of discussing a certain topic with hundreds of potential participants. All traffic in the newsgroup that can not be subsumed under one of the above categories should belong to a discussion. If somebody explicitly wants to start a discussion, he/she can do so by giving the posting a subject line of the form "Start discussion: this-and-that" (People who react on this, please remove the "Start discussion: " label from the subject line of your replies) It is quite difficult to keep a discussion from drifting into chaos, but, unfortunately, as many other newsgroups show there seems to be no secure way to avoid this. On the other hand, comp.ai.genetic has not had many problems with this effect, yet, so let's just go and hope... Thanks in advance for your patience! The Internet For information on internet services, see Q15.5. ------------------------------ Copyright (c) 1993-2000 by J. Heitkoetter and D. Beasley, all rights reserved. This FAQ may be posted to any USENET newsgroup, on-line service, or BBS as long as it is posted in its entirety and includes this copyright statement. This FAQ may not be distributed for financial gain. This FAQ may not be included in commercial collections or compilations without express permission from the author. End of ai-faq/genetic/part1 *************************** --

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