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Java GUI for Genetic
Programming
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Dr. David
Wedge,
has produced a Java genetic
programming library 'geneticWedge' that
can be easily be called
from a command
line Java program.
To provide wider access to the software within the research group, I
have developed a Graphical User Interface (GUI) front end for the
library.
At the moment, the GUI software is best regarded as in first draft alpha development phase, however it
should be usable.
I'm particularly keen to get feedback, bug reports naturally, but I
would also welcome suggestions for improvement and new features.
As yet, there's no documentation, help or instructions - hopefully
anyone familiar with genetic programming will be able to work out the
basic operation of the GUI. I will be adding documentation / help in
due course.
BTW, I'd certainly
like to thank David for coding the gp library in the first place - I
think he had the harder task!
Update: some minor fixes and improvements; and updated to newer
versions of cdk & jfreechart.
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Prerequisites |
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1) Java standard
edition 1.6
To run Java programs, you will need Java run time environment
installed. If you plan to develop or write Java programs, you'll need
the jdk. I've used a little java 1.6 specific code, so users of java
1.5 will need to upgrade.
2) Chemistry Development Kit 1.2.2 I
used the CDK to allow the rendering of SMILES
strings as 2D molecular graphics. Parsing and displaying the graphics
is quite slow - so this feature is not really usable for very large
tables (the current version renders / parses a lot faster than earlier
versions). Current smiles rendering is only implemented for row
labels. The latest version of the CDK can be found here.
Note: Using the CDK, I believe there's potential for adding GP node /
functions which implement chemical operations - let me know if you have
any ideas along these lines.
3) JFreeChart 1.0.13 & JCommon 1.0.16; these Java
libraries were used to provide simple 2D charting e.g. of the fitness
history. The latest versions are here and here.
I've provided links to the versions of these Java libraries I used
during development of the GUI just in case the latest versions
introduce compatibility problems.
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Downloads |
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1) The
GP library.
This library is a slightly modified version compared to David's, as
extra classes were added, and a few modified to enable the GP code to
run interactively. I'll link to his library once he incorporates the
changes into his code.
2) The GP GUI.
3) CDK 1.2.2
4) JFreeChart 1.0.13
5) JCommon 1.0.16
I will release the GP GUI source code once the software moves out of
the alpha development stage. However, if you should be keen to get your
hands on it sooner, please request via email.
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Running the Software
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This really just a quick and dirty explanation
of setting up and running the JavaGPGUI, I'll certainly expand on this
with the proper documentation in due course. If anyone needs help
installing using the software, just give me an (email) shout.
The data to be modelled should be in the form of comma separated values
(.csv) text file.
Assuming all the jar files have been download to the same directory,
the following command will start the GUI:
On Linux (pre-fix the class path with a colon & use the '/'
character):
java -cp :./*
JavaGP.JavaGPGUI
(You might also need to ensure that the files are set to executable
with chmod +x *.jar).
On Windows (pre-fix the class path with a semi-colon & use the '\'
character):
java -cp ;.\*
JavaGP.JavaGPGUI
Once you're sure this works, you can create a program short-cut / link
specifying the same command.
To open your data file use:
File -> Import
Data -> CSV File
You will need to use the check boxes at the right hand side of the open
file dialogue to specify whether there are column headers and / or row
labels.
For row labels, you can also specify that they are SMILES
strings - though as noted above, this feature is only really usable for
small tables.
Once you've loaded your data, it will appear as a table under the Data tab.
Row labels will appear in the left-hand pane, and the data in the
right-hand pane (with scroll bars). It is assumed that the last column
is the target 'y-data', and the remainder are input 'x-data'. If not,
you can right-click the desired target and select 'promote to target'.
The Functions / Data tab
presents the selection of functions to be included; the data
pre-processing required (e.g. normalisation); and the training
set / validation set selection method.
The GP Setting tab allows one
to set the mutation rates, population sizes and the maximum number of
generations etc.. For a typical run, you can can just run with the
default parameters.
Select Run and the GP will
start running with the Fitness History, the Best Individual (so far)
and a plot of the Best Individual Fit to Target appearing in the Data / Results tab.
At the end of the run, you can select File
-> Save -> Save Results to save the results to a csv file.
As the software is at the moment, it's not possible to save the data
table or the 'project' settings, however, this is on the expected
features list for later implementation.
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