LAGEP: An open-sourced genetic programming tool

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     LAGEP, Layered Architecture GEnetic Programming, is an open-sourced genetic programming tool which implements genetic programming for function generating. The LAGEP project is aimed to provide a friendly tool for developers/users who want to use GP. Source codes of LAGEP are available under GPL license.

     LAGEP is not only capable of running layered architecture GP [Lin 2007] but also standard single population GP. Users who may not need GP-related background can easily apply LAGEP or revise codes for their problems. Currently, LAGEP is designed as a classifier.

     Many techniques including code optimization and algorithm optimization are used in LAGEP, for example, the random numbers are generated by Agnor's RNG [Agnor 2007].

     Any suggestion about the LAGEP is welcomed. Moreover, any suggestion about program coding is also appreciated.

Please sent me feedback after you use LAGEP, thank you!

References

1. [Lin 2007] J. Y. Lin, H. R. Ke, B. C. Chien, W. P. Yang, Designing a Classifier by a Layered Multi-Population Genetic Programming Approach, Pattern Recognition, Vol. 40, Issue 8, Aug. 2007, pp. 2211-2225
2. [Lin 2008] J. Y. Lin, H. R. Ke, B. C. Chien, W. P. Yang, Classifier Design with Feature Selection and Feature Extraction Using Layered Genetic Programming, Expert Systems with Applications, supposed to be appear at 35(2), 2008.
3. [Agnor 2007] Agnor Fog, Pseudo random number generator - uniform and non-uniform distributions, http://www.agner.org/random/

If you use LAGEP in your work, please cite [Lin 2007].

General features

1. Platform: 32bit Windows
2. Program language: C/C++
3. Windows API used: No
4. User interface: console mode
5. Linear function: supported
6. Non-linear operators: supported (division, multiply, sine, cosine, natural log, exponential)
7. Validation process: supported (A function evaluaing "score" is used to determine which individual is the best [Lin 2007])
8. Configuration: XML and INI formats (using TinyXML)
9. XML file output: supported
10. Instances can be stored in either row order or column order.
11. Preparing data format of instances in the same way to SVM^light.
12. OpenMP is used.
13. Documented by Doxygen (not fully completed...)

GP-related features

1. Individuals are represented by binary trees.
2. Four basic binary arithmatic operators +, -, *, / (protected division)
3. Use weight to disable unwanted operators, for example, user can turn off operators sin and cos by giving them a zero weight.
4. The percentage of using grow method in population initialization is adjustable
5. Determinant tournament selection method is used.
6. A method to tune mutation rate named AMRT is used [Lin 2007]
7. Constants can be real numbers.
8. Support user-defined constants, e.g. PI and e. (define them at constants.ini)

• Function simplification process
• Graph representation

v0.81 -> v0.811

• To avoid NaN error, any x in ln(x) is transformed by the abs function to be positive.
• Added one more function: Exp function.

v0.811 -> v0.812

• Re-organize files.
• Fix problems of the growing method.
• Fix the problem of dataAlignment. (2008/04/14)
• Fitness functions is selectable. Use "-fn X" to choose between accuracy, precison, recall, F-Measure and specificity.
• Fix a problem of calculating true-positive, true-negative, false-positive, and false-negative. (2008/04/18)

v0.812 -> v0.82

• documentation (by doxygen)
• configuration file can be orgazined in XML format
• A new tree evaluation function is used to improve efficiency
• Configuration will be shown on screen at first stage, this could be easier for user to identify whether the configuration has mistakes or not.
• fix other bugs.

v0.82 -> v0.83

• Add allowSelfCrossover option.
• LGP Config Maker now can generate configuration file in both ini and xml formats.
• Code quality is improved a little bit...

1. Modify io.h and io.cpp to fit the data format.
2. Modify fitnessFunc.cpp to add new fitness functions.

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Current version: 0.83 Date: 2008/07/21

Download 0.83 with installer(ZIP format, including source codes)

Download 0.83 with installer(RAR format, including source codes)

0.82 release 0615 Date: 2008/06/15

Download 0.82 with installer(ZIP format, including source codes)

0.812 release 0418
Date: 2008/04/18

Download 0.812 with installer(ZIP format, including source codes)

The execution file is lgp.exe. lgp is called by

lgp.exe -t training_file -p test_file -v validation_file -c target_class -i configuration.ini -j job_name [optional]

Necessary arguments:
-t : following the training set file name
-c : following the target class symbol

optional arguments:
-p : following the test set file name
-v : following the validation set file name
-i : following the configuration INI file name
-j : following the job name, use job name to distinct different runs
-silence : do not display any information on console
-linear : generate only linear discriminant functions
-xml : output in XML format. (Not available if -silence used)
-showTest : show test accuracy of the best individual every generation
-fn : select a fitness function. fn 1 -> accuracy(default), fn 2 -> precision, fn 3 -> recall, fn 4 -> F-measure, fn 5 -> Specificity.

Example:
lgp -t TRAIN.txt -p TEST.txt -c 1 -j 20070101
lgp -t TRAIN.txt -p TEST.txt -c 1 -i multilayer.ini -j 20070101 -fn 2

1. If the configuration file is not specified, default values are used.
2. We strongly recommand users to have a proper job name. However, this argument is optional

Instances should be represented as following format:

<target> <feature>:<feature value>.... #<comment>

target field could be a string, but an integer if prefered.
feature field begins at 1.
Any line begins with a "#" is a comment and will be ignored.
Users can find an executable file "FileChecker" from the download file.
FileChecker checks correctness of the input files.

Example:

1 1:12.3 2:32.5 3:44.3 #this is an example instance having three features belonging to class 1 2 1:12.5 2:33.3 3:64.3 1 1:22.3 2:12.3 3:82.6

     There are many settings available in LAGEP. User can read the exampleINI.ini to know what setting is needed.

This software is free only for non-commercial use. It must not be distributed without prior permission of the author. The author is not responsible for implications from the use of this software.

Copyright (c) 2005 Jung-Yi Lin All rights reserved. Redistribution and use in 
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