Brock COSC 4P82 Genetic Programming

COSC 4P82 Genetic Programming

Instructor: Brian Ross
Lecture hours, Winter 2024: Mon, Thurs 8-9:30am
Location: AS 216
Office hours: TBA
TA: Sumaia Aktar ( sa21xt@brocku.ca )

Brightspace page.

GP-based non-photorealistic image by Maryam Baniasadi. Web site.

Course info

Textbook:
A Field Guide to Genetic Programming
by Riccardo Poli, William B. Langdon, and Nicholas F. McPhee.
Lulu Press. ISBN 978-1-4092-0073-4. 2008.
- Free PDF (and paperback ordering info): here.
- Book web site: www.gp-field-guide.org.uk
- Local copy (Brock only): poli08_fieldguide.pdf
Course outline
Project description (updated Feb 22 2024)
- Project deadline: 9:00am April 30.
- Project marking scheme. (updated Feb 22 2024)
Introduction to DEAP and ECJ Tutorials (repeated)
1. 2-3pm Tuesday January 16
2. 12-1pm Wednesday January 17
3. Location: MC D205
Last day to withdraw without academic penalty: March 8, 2024
Term test date: (in class) Monday March 18, 2024
Seminar schedule and topics. --> NOW OPEN!
- Approximate mark breakdown: (total 10)
  - Content (4): enough technical content (GP related); not too short of talk.
  - Presentation (4): organization, clear discussion, slides, answers questions.
  - Discretionary (2).
Misc files (local access)
Assignment 1
- Marking scheme.
- Please hand in your electronic submission at the 4P82 course page on Brightspace. One submission per group.
Assignment 2 (updated Feb 22 2024)
- Marking scheme. (updated Feb 22 2024)
- Please hand in your electronic submission at the 4P82 course page on Brightspace. One submission per group.
- Procedural Texture noise code examples:
  - Perlin noise (C)
  - Perlin noise and others (C, lilgp1.1)
  - Perlin noise and others (Java, old ECJ)
  - Plus look at Github, StackOverflow, etc. for example code (just cite your sources!)
General assignment information
- Some example assignment reports...
  - An example report by Nick Aksamit. (local access)
  - An example report by Alanna McNulty. (local access)
  - An example report by Ethan Gibbons. (local access)
  - An example report by Robert Flack. (local access)
  - An example report by Alex Bailey. (local access)
- ACM GECCO Latex files (zip). Unzip and replace tex and bib files with your own. Remember to remove conference information!
- IEEE formatting information. If you use word, then use this file here as a template: TRANS-JOUR.doc. Latex templates are there as well.
- Latex (Windows): Miktex and Texmaker editor
- Access the COSC assignment cover pages (individual and group).

Supplementary lecture material:

Field Guide to GP:
- Ch. 1, 2, 3, 4
- Selected topics: Ch. 6-10 (whatever discussed in class)
Research paper:
- On the futility of blind search: An algorithmic view of "no free lunch"
  J.C. Culberson, Evolutionary Computation, 6(2), 1998.
  PDF location (via Brock network)
Genetic algorithm
Example of bloat
Fitness table
lilGP notes
Course notes on multi-objective optimization.
MOP table
Many-objectives and sum-of-ranks
Wikipedia articles...

GP Systems

ECJ (Java)

ECJ: A Java-based GP system.
Be sure to look at the The ECJ Owner's Manual.
Must read! Illya Bakurov's Symbolic Regression Tutorial.
- Documentation: ECJ_tutorial.pdf.
- Tutorial including source code: RegressionProblemOnGPWithECJ.zip
Must read! Justin Maltese's ECJ FAQ.
ECJ Statistics Guide by Tyler Cowan.
Also look at Tutorial 4: Symbolic Regression.
parameters.params: example parameter file for typed GP.
SumOfRanks.zip by Michael Gircys. Java implementation of many-objective sum-of-ranks strategy for ECJ.
(based on earlier Rank.java by S. Bergen and A. Harrington)
Hornby's ALPS strategy implemented in ECJ by Anthony Awuley.
island_model_in_ecj.pdf by Abdul Wazed Chowdhury . (Some advice for fixing a technical problem using Island model parallelism in ECJ.)
Here is a Linux script file that does multiple runs of ECJ with different parameters, including seeds: A1_Script.sh

DEAP (Python)

DEAP documentation @ U Laval
DEAP @Github (Python).
"DEAP: Evolutionary Algorithms Made Easy" (PDF, Journal of Machine Learning Research)
Wikipedia
You may want to run DEAP/Python using Google Colab. Here is DEAP on Colab.
If you want maximum performance, you will probably want to run it locally on your own computer.

lilGP 1.1 (C)

lilGP 1.1 Home Page
Complete lilGP1.1 and user manual (PDF) (local)
Patched lilGP1.1 with strong typing, etc. (local)
Source files are available here (local)
BST lilGP : an enhanced version programmed by Brock students
- unix: bstlilgp-0.5.0.zip and installation instructions.
- Windows Visual Studio .NET: bstlilgp-0.5.4-win32.zip and installation instructions.
- Windows Code Warrior: bstlilgp-0.5.4-win32.zip and installation instructions.
Example application: Symbolic regression (for strongly typed lilGP 1.1 or BSTlilGP)

Other GP systems:

Open BEAGLE: A C++ based GP system.
- Here are some notes on getting it running.
RobGP (C++): Robust Genetic Programming System by Brock student Robert Flack.
GPLAB - a GP system for Matlab
CNGGGPS - Grammar-based system developed by Brock student Stephen Baker (Linux)
Discipulus - commercial linear GP system (dead; was at www. rmltech.com)
List of GP Implementations (originally from Wikipedia GP article)

Other useful things:

OpenAI Gymnasium: Project ideas? Use GP as the machine learning system!
Linux command cheat sheet
Linux All-in-One for Dummies (8 books in 1).
(Any book on Linux and command lines/scripting is useful).

COSC 4P82 Genetic Programming

Course info

GP Systems

In the News...

Machine learning problem sets

Useful Links

Interactive Online GA's

Videos

Go to Brock Computer Science home page.