From welsberr@orca.tamu.edu Thu Jun 26 21:31:45 1997
Newsgroups: talk.origins
Subject: Re: "Weasel" Cumulative Selection Demo
From: welsberr@orca.tamu.edu (Wesley R. Elsberry)
Date: 26 Jun 1997 06:31:45 -0400

I have a Perl script which performs the "weasel" simulation.

Features:
  - Interactive or batch single run
  - Parameters passed on command line for batch
  - Can specify files to pick up "pool" and "target" strings from
  - Produces basic statistics on the run
  - Sends comma-delimited output to a log file
  - For the target, can specify a target string length if collecting
    the target from a file
  - Follows the Dawkins method of generating an initial seed string
    from which generation 2 is derived

Differences from Delphi Weasel
  - A mismatch evaluation operator is provided, but not selectable
    yet
  - No "curses" type support, strictly a tty-style program

The Weasel Perl script is intended to demonstrate the relative
advantages of cumulative selection over random search for finding
targets in large search spaces.  As a simulation of "evolutionary
process", this implementation, like Dawkins' original, is "misleading
in important ways".  Please consult "The Blind Watchmaker" for the
complete discussion of what Weasel is intended -- and not intended --
to demonstrate.

Using Weasel

The files associated with Weasel are

  weasel.pl -- The Weasel Perl script
  mkbat.pl  -- A script to produce a script for running large batches
  pool.wsl  -- A "pool" string file.  Chop is used on the
               first line of this file, so it had better have a
               newline at the end.
  target.wsl -- A "target" string file.  Chop is used on the
                first line of this file, so it had better have a
                newline at the end.
  weasel.log -- The Weasel log file, where comma-delimited information
                about each run is appended.  The comma-delimited
                format is suitable for import into spreadsheets for
                further analysis.

You will need a working Perl interpreter somewhere in your path.
Weasel was developed using bigperl on an MS-DOS machine, which 
naturally led to the use of files rather than simple parameter 
passing for long target strings.

The usage report

Typing "weasel.pl help" at the command line displays this message:

WEASEL. Copyright 1997 by W.R. Elsberry
Usage: WEASEL [popsize mut_rate {pool|file.wsl} {target|[length:]file.wsl}]

By running Weasel with no command-line arguments, Weasel interactively
asks for parameters for the run.

# weasel.pl
Population size? (100):
Mutation rate? (expressed as %) (6):
Target string? : METHINKS
Pool? : _ABCDEFGHIJKLMNOPQRSTUVWXYZ
Generation 1: VJSKLTCJ 44
Generation 2: MJSKLTCJ 35
Generation 3: MJSKLTKJ 27
Generation 4: MJSKLTKQ 20
Generation 5: MJSILKKQ 15
Generation 6: MJSILKKS 13
Generation 7: MFSILKKS 9
Generation 8: MFSILMKS 7
 [...]

At each generation, the closest match to the target in the population
is displayed, along with its distance from the target.

There are two major ways (and several combinations) of using 
command-line arguments with Weasel.

 - Passing all values directly
 - Passing filename information for "pool" and "target"

"Passing all values directly" sample

# weasel.pl 100 5.5 _ABCDEFGHIJKLMNOPQRSTUVWXYZ METHINKS

The above command line sets up a population size of 100, a
mutation rate of 5.5%, a pool containing all alphabetic 
characters plus an underline pressed into duty as a space
to avoid problems with brain-dead OS argument handling, 
and one eight-character target string.

"Passing filename information" examples

# weasel.pl 100 5.5 pool.wsl target.wsl

The above command line sets up a population size of 100, and a
mutation rate of 5.5%.  The pool string is the first line of
text in the file "pool.wsl".  The ".wsl" extension is how 
filenames are distinguished from regular string values.  The
target string is, unsurprisingly, taken as the first line of
text in the file "target.wsl".

$ weasel.pl 100 5.5 pool.wsl 8:target.wsl

The above command line sets up a population size of 100, and a
mutation rate of 5.5%.  The pool string is the first line of text in
the file "pool.wsl".  The target string is the first eight characters
from the first line of text in the file "target.wsl".

Because of the flexibility afforded by this scheme, you can
create batch files to collect data from repeated runs with
the same parameters or explore the solution space by varying
the parameters.  A "mkbat.pl" script is provided as an 
example of batch mode scripting.

The log file format explained

Here is an example line from the weasel.log file:

"LOG",19683,101,9,0.00045724737082761772585,194.88118811881187753,10,2,"THE","_ABCDEFGHIJKLMNOPQRSTUVWXYZ"

Field 1: The initial string was originally intended as a means of
extracting the comma-delimited strings from the stream of program
output.
Field 2: The searchspace size.  searchspace = poolsize ** targetlength
Field 3: The total number of candidate strings considered.
Field 4: The number of unique candidate strings considered.  This
statistic was frighteningly easy to collect using a Perl associative
array, and gives a straightforward quantification of the amount of
the searchspace which was explored.
Field 5: Proportion of searchspace explored by weasel search.
propsearchspace = uniquecandidates / searchspace.
Field 6: Relative advantage over random search.
reladvantage = searchspace / totalcandidates.
Field 7: Population size.
Field 8: Mutation rate, in percent.
Field 9: Target string, quoted.
Field 10: Pool string, quoted.

Have fun.

I would like to amass a database of the log file output.  So if you
run this script and collect statistics, please send your log file to
me with "WEASEL LOG" in the subject line, or upload via anonymous ftp
to inia.tamug.tamu.edu.  (Rename the logfile, please, so that none get
overwritten.)

Wesley

-- 
Wesley R. Elsberry, 6070 Sea Isle, Galveston TX 77554. Information sent to any
of my email addresses is my personal property, to be published as I see fit.
Student in Wildlife & Fisheries Sciences. http://www.rtis.com/nat/user/elsberry
"don t ever tell me insects are any more liberal than humans" - archy