Thoth is a C++ genetic programming system. It was created to find patterns and make predictions from large quantities of real numbers. Thoth is highly configurable and has several available methods for creating and combining members, population size, optimisation and bloat.
It can save and load its results and has an inbuilt graphing system for displaying the program structure and its performance. Once saved, population members can be used to solve new cases. See the 'Tutorial' and 'Graphs and visualisation' sections for more information
- Threaded with OMP
- Optimisation loops
- Constant generation, load and save
- Population and Bloat control systems
- Function selection system
- Reverse Polish Notation solving loop ( Instead of tree recursion )
- Graphing of results with matplotlib
- Unit testing and a basic profiler
- Highly configurable
Thoth is licensed under GPL 2.0. Please contact me if this is not suitable for your purpose.
I'm happy to receive any and all feedback, please contact me via: Joe_butler99@hotmail.com
Thoth requires at least the following to run on an Ubuntu system, there may be more i've missed. Please let me know to include them if you find any.
# Main Binary
sudo apt-get install make g++ libboost-random-dev libcppunit-dev
# Graphing Tools (Not required for main functionality)
sudo apt-get install python-pydot python-matplotlib python-pip python-dev imagemagick python-imaging
sudo pip install PIL
# Main Binary
yum install boost-devel cppunit-devel make gcc-c++
# Graphing Tools
yum install pydot python-matplotlib python-pip python-devel ImageMagick python-imaging
pip install PIL
For other Linux distributions check your package manager, these should be pretty common packages. I'll add instructions for other distributions as I find time to test. (Feel free to help out here) The same requirements
Checkout the project from github and cd into the directory. Once you have satisfied the dependencies, you should be able to build all the binaries with:
make clean Thoth
make test
make profiler
You can change the flags by un-commenting CCFLAGS settings of your choice in the Makefile
Currently all binaries should be accessed from the root directory, that is - once compiled run with
bin/Thoth
bin/test_cases
bin/profiler <num_reps>
bin/Thoth -h # Displays help
The main configuration has recently moved into a JSON structure. These where previously held in globals which were be compiled into the program. You are now able to edit the values, but there is little checking in place to make sure the values are suitable. ( More checking is planned in the future.) The default file loaded is "conf/config.json". This can be overridden with the CLI argument --config-file "your-config-filename".
Example:
bin/Thoth --config-file conf/myconfig.json --fitness-cases fitness_cases/gp_test
Make sure you've compiled successfully first. Thoths going to run very fast with these settings - You can slow it down a bit by compiling with the debug settings.
-
Using a text editor, look at the conf/config.json file.
-
check that the FITNESS_CASE_FILE is "fitness_cases/testSinx_20c"
-
check that the POPULATION is set to 1000
-
check that the NODE_WEIGHT equals 0.5 - Its probably smaller, but we'll to examine changing this.
-
check that the GENERATIONS number is small, something in the range 40-100 is fine
-
Now run Thoth through a couple of times
bin/Thoth
After a couple of loops you will notice this 'gets stuck'. It also kept a small Tree size, so lets look at what it produced
cat nodetree.0 # View the raw nodetree structure
cat program_guesses # View the targets and results
bin/graphtool.py -a nodetreeGraphviz # Draw the nodetree with Graphviz
bin/graphtool.py -a plotAllLines # Plot the targets and results lines
bin/graphtool.py -a depthBarChart # View the programs nodes per depth
- Now using the editor again, lets 'loosen' the node weight in conf/config.json so it may grow more freely
- check that the NODE_WEIGHT equals 0.0005
- Now run Thoth through a couple of times "bin/Thoth"
- If you now repeat the graphing and output steps above, you should see that the program has grown considerably and is much better at solving
- Now is a good time to play with the settings and run it through some more
Making a prediction outside of the test cases
- Thoth can now use the generated structure to make guesses outside of the test case range. Try the following to see how it scores
bin/Thoth --action solve --num-vars 1 --nodetree nodetree.0 --case-variables 10
bin/Thoth --action solve --num-vars 1 --nodetree nodetree.0 --case-variables -10
bin/Thoth --action solve --num-vars 1 --nodetree nodetree.0 --case-variables 50
bin/Thoth --action solve --num-vars 1 --nodetree nodetree.0 --case-variables 999
You can find the real answers with sin x on a calculator. Google also has the answers!
Your program may or may not be good at solving these, but we can evolve a better program by using the extended sin test cases.
Run Thoth again, specifying these cases.
bin/Thoth --fitness-cases fitness_cases/testTwoSinx_20c
If the program scored very poorly with the extended cases, its likely to find a brand new member to fill its place, otherwise it will continue with the nodetree you have already grown.
Thoth comes with unit testing tools. You can run these from the root directory with
make clean test && bin/test_cases
Thoth has a crude profiler which you can run with
make clean profiler && bin/profiler 50
Depending on how many repetitions you specify, this may take a long time. Due to the very random nature of genetic programming. Profiling should be run through a few times before making decisions based on its outcome.
- GraphViz drawings of a nodetree
- Target and result line charts
- Function & Terminal use bar charts
- Node depth bar charts
Before you can graph anything, you'll need to run Thoth to generate some nodetrees and guesses. See the tutorial for examples.
bin/graphtool.py -h # Usage
bin/graphtool.py -a plotResultsLine # Plot the programs results
bin/graphtool.py -a plotTargetsLine # Plot the targets from the fitness cases
bin/graphtool.py -a plotAllLines # Plot the results against the targets
bin/graphtool.py -a plotResultsPoints # Plot the results using points
bin/graphtool.py -a plotTargetsPoints # Plot the targets using points
bin/graphtool.py -a plotAllPoints # Plot the points for targets and results
bin/graphtool.py -a functionsBarChart # Plot a bar chart of function usage
bin/graphtool.py -a terminalsBarChart # Plot a bar chart of terminal usage
bin/graphtool.py -a depthBarChart # Plot a bar chart of the number of nodes at each depth
bin/graphtool.py -a nodetreeGraphviz # Draw the nodetrees structure with GraphViz
- Constant optimisation -> Its something I'd like to have in place very soon
- Making the fitness case settings more verbose. ( Instead of the numbers at the top. )
- Genetic Islands -> Separating parts of the population into distinct islands so they may evolve with more diversity.
- Re-using threads to save on initialisation cost.
- Better profiling with saved structures
- A configure script
- Standardisation of string methods. There's a big mix of c & c++ styles in there.
- The test cases need a good clean up, and the recent changes to the configuration system are not covered.
- Check that you don't have any nodetrees not suitable for the chosen fitness cases. I'll be adding protection against this soon
_____ _ _ _
|_ _| |__ ___ | |_| |__
| | | '_ \ / _ \| __| '_ \
| | | | | | (_) | |_| | | |
|_| |_| |_|\___/ \__|_| |_|
____
/ ___| _ _
| | _| |_ _| |_
| |___ |_ _|_ _|
\____| |_| |_|
____ _ _
/ ___| ___ _ __ ___| |_(_) ___
| | _ / _ \ '_ \ / _ \ __| |/ __|
| |_| | __/ | | | __/ |_| | (__
\____|\___|_| |_|\___|\__|_|\___|
____ _
| _ \ _ __ ___ __ _ _ __ __ _ _ __ ___ _ __ ___ (_)_ __ __ _
| |_) | '__/ _ \ / _` | '__/ _` | '_ ` _ \| '_ ` _ \| | '_ \ / _` |
| __/| | | ( ) | ( | | | | ( | | | | | | | | | | | | | | | | ( | |
|_| |_| \___/ \__, |_| \__,_|_| |_| |_|_| |_| |_|_|_| |_|\__, |
|___/ |___/
_.-/|o_0|\-._ Copyright (C) 2013-2014 Joe Butler _.-/|0_o|\-._
Contact: joe_butler99@hotmail.com
Thoth CLI Settings:
Action: improve
Nodetree:
Case Vars:
Fitness Cases:
Config File: conf/config.json
Num Vars: 0
Thoth Settings - (JSON & Defaults):
FUNCTION_SET: Basic+
POPULATION: 8000
KEEP_TOP_PERCENT: 25
NODE_WEIGHT: 0.05
GENERATIONS: 20
INITIAL_MAX_DEPTH: 3
USE_CUT_SCORING: true
EXIT_SCORE: 0
SAVE_EVERY: 2
SAVE_TOTAL: 5
SAVE_AFTER_EACH_OPTIMISE: true
LOAD_SAVED: true
LOAD_TOTAL: 5
SHOW_GUESSES: true
GUESSES_FILE: program_guesses
GUESSES_EVERY: 5
OPTIMISE_CUTTER_EVERY: 20
OPTIMISE_TERMINALS_EVERY: 40
OPTIMISE_FUNCTIONS_EVERY: 30
ITERATE_CUTTER: false
ITERATE_TERMINALS: false
ITERATE_FUNCTIONS: false
MUTATE_NODE_PERCENT: 5
MUTATE_TREE_PERCENT: 30
CUT_TREE_PERCENT: 25
CROSSOVER_PERCENT: 30
MUTATE_TREE_MAX_DEPTH: 2
CROSSOVER_NEW_ROOT_PERCENT: 10
SHOW_HEADINGS_EVERY: 30
FITNESS_CASE_FILE: fitness_cases/large_test_case
Fitness Case settings: - (fitness_cases/large_test_case)
TOTAL_CASES: 3000
TERMINALS: 274
NUM_VARS: 274
NUM_CONSTS: 0
CONST_LOWER: 0
CONST_UPPER: 0
TARGET_SCORE: 0
SCALING_ENABLED: true
SCALING_LOWER: 0.5
SCALING_UPPER: 1.5
Time Gen Pop BestScore CreatedBy Tree Size Cut Score Total Cut
16:48:07 1 8000 140494.964747 grow 15 258090.630104 0
16:48:07 2 8000 140336.240219 Cut Tree 14 194084.507276 2067
16:48:07 3 8000 140080.773347 Mut Tree 21 170583.448970 2633
16:48:08 4 8000 140080.773347 Mut Tree 21 149147.789604 3306
16:48:08 5 8000 139782.846192 Crossover 21 143219.319883 3304
16:48:09 6 8000 139782.846192 Crossover 21 142345.211675 3376
16:48:09 7 8000 139523.680732 Mut Tree 32 140919.889513 3180
16:48:10 8 8000 139523.680732 Mut Tree 32 140414.814174 3134
16:48:10 9 8000 139483.000249 Mut Node 24 140337.109547 3453
16:48:11 10 8000 139433.158099 Crossover 38 140293.078029 3720
16:48:11 11 8000 139245.459985 Crossover 46 140113.204735 3505
16:48:12 12 8000 138834.090247 Crossover 24 139911.288064 3378
16:48:12 13 8000 138710.633354 Cut Tree 20 139611.539001 3095
16:48:13 14 8000 138707.350113 Crossover 20 139528.621386 2870
16:48:14 15 8000 138640.546008 Cut Tree 71 139459.273042 2981
16:48:15 16 8000 138535.787187 Mut Tree 35 139286.785688 3264
16:48:16 17 8000 138106.602372 Mut Tree 78 139099.881641 3286
16:48:16 18 8000 137888.567332 Crossover 73 138792.597824 3039
16:48:17 19 8000 137888.567332 Crossover 73 138720.866829 2988
16:48:18 20 8000 137888.567332 Crossover 73 138679.616891 3041
Starting Branch Cutter - Tree size 73 - Started at: 16:48:18
Position Was Func Now Term Old Score New Score
7 7 206 137888.567332 137888.467332
11 2 138 137888.467332 137888.267332
20 6 139 137888.267332 137452.845857
21 7 212 137452.845857 137289.615763
24 5 138 137289.615763 137270.102261
25 1 222 137270.102261 137256.593467
27 6 222 137256.593467 137214.110390
Finished Branch Cutter - Tree size 29