Announcing GPdotNET v5 and related Book


https://www.igi-global.com/Images/Covers/9781522560050.png

After one year of writing and coding, finally I  can announce my two big achievements which are related to each other:

1. The fifth version of my open source project GPdotNET – genetic programming tool, and

2. The book:Optimized Genetic Programming Applications: Emerging Research and Opportunities, published by IGI-GLobal.

Along the book, I was developing GPdotNET application which is explained in Chapter 5. Actually the Chapter 5 described in depth all aspects of the application, with real world examples.

As can be seen GPdotNET v5 is completely rewritten application, with new logo and GUI. As Introduction of the application I have prepared several videos on youtube with quick explanation how to use some of the main modules in GPdotNET.

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GPdotNET v4.0 Beta 2 released


Download GPdotNET v4 beta2

The last few days I am preparing the new build for publishing of GPdotNET v4.0 which will include lot of new features. In the last post I have announced ANN modul and compleately new modul for preparing tha data for modelling. Here is a quick overview of the new features comming in this build:

  1. Since this build the GP modul is also integrated with the new way of data preparation. Now with the latest version of GPdotNET the user will have the same user  experience in modelling with GP and ANN.
  2. The big news for this build is ability for modelling classification problems (two-class as well ) with Genetic programming. Multy -classs GP solver will be released soon.
  3. Separation of the previous and new version. Both are included in the latest build.
  4. Disable protected operations.

 

As picture shows below you can choose models from prevous version on the left side. On the right side of the new model dialog, you can select modeling and prediction with ANN or GP.

GPdotNET v4.0 Beta 2

After you select the solver GPdotNET is ready to accept the data.

GPdotNET v4.0 Beta 2 02

From the previous blog post you can see more info about loading and handling data.  The same user experimence you can see regadles of the solver type (ANN or GP).

Beside this GP integration there are several bug fix which were reported from the users.

In GP solver the new feature has been added: Ability to disable protected operations. In the previuous version of GPdotNET protected operations (eg. /, log, ln, etc) are enabled in the model. Whenever operation was undefined for the current value. GPdotNET returned default value (0 or 1). So with protected operation the model is always defined. With protected operations we collect much good genetic material dufirng evolution. In case the option is disable any upprotected operation can discar the model. This option is available in new and previous GP solver.

GPdotNET v4.0 Beta 2 03

Features not implemented in this beta

1. Exporting GP/ANN model

2. Open/Save gpa file for new Solvers.

GPdotNET 4.0 first look: Classification with Neural Networks


After some time of implementation and testing, the new version of GPdotNET is out. Go to codeplex page and download it. This is huge step in development of this project, because it contains completely new module based on Artificial Neural Network and other optimization methods e.g. Particle Swarm Optimization. gpdotnetv4_firstlook1

Almost all aspects of the architecture are changed, or will be changed when this version would be released.

The new Experiment class will replace existing classes for handling experimental data in GA based models, which is not implemented yet. Also New start page will contain more pre-calculated examples.

For this beta here are the new features:

  1. New Start Page will be extended with new examples of Neural Nets : – binary classification, – multiclass classification and – regressions examples.
  2. Improved module for loading experimental data, which now supports nonnumeric data like categorical or binary data.
  3. Depending of the output column of loaded experimental data different learning algorithm is selected. For example if the column is of categorical type, GPdotNET selects Neural Net algorithm with Cross-Entropy and Particle Swarm optimization learning algorithm. If the output column is numerical, GPdotNET selects the Neural Nets with Backpropagation learning algorithm. Currently only two learning algorithms are implemented. More will be implemented in the next beta release.

Classification problem with GPdotNET

This topic will give quick tutorial how to model classification problem with GPdotNET by using Neural Nets. For this tutorial you need some experimental data which you can download from this location.

  • Open GPdotNET choose New Command
  • New Dialog pops up, check Artificial Neural Nets, and Press Ok Button.

gpdotnetv4_firstlook2

After Solver Type selection, GPdotNET Creates “Load Experiment” Page in which you can load experimental data, and define the percentage of data for testing the model. gpdotnetv4_firstlook3

  • Press Load Data button.
  • New Popup dialog appears.
  • Press File button select the file you previously downloaded.
  • Check Semicolon and First Row Header check buttons.

Note: When the data is analyzed correctly you should see vertical line “|” between columns. Otherwise data will not be loaded correctly.

  • When the experimental data is formatted correctly, press the “Import Data” button.

The next step is preparing columns for modeling. gpdotnetv4_firstlook4

For each columns we have to set:

  • a) proper type of the column (numeric, categorical or binary),
  • b) type of the parameter (input, output or ignore)
  • c) normalization method (MinMax,Gauss or Custom normalization of the column values ).

To change Column Type, double click on the cell which shows the column type, combo box appears with list of available types.

gpdotnetv4_firstlook5

  • To change Parameter Type, double click on the cell which shows the param type, combobox appears with list of available parameter types.
  • gpdotnetv4_firstlook6
  • To change Normalization Type, double click on the cell which shows MinMax value, combobox appears with list of available normalization types.

gpdotnetv4_firstlook7

Note: you can set only one Output column. Put Parameter Type to Ignore if you want to skip column from modelling.

Now we have experimental data, and we can start modelling process. Before that we need to choose how much data will be treated for testing. Enter 10% for testing the data and press Start Modelling button.

Now we have more Pages:

1. Settings page for setting the parameters of the Neural Nets

2. Run page for simulation of searching solution

3. Prediction page which you can see how solution is good against testing data.

Settings Page

gpdotnetv4_firstlook8

As you can see in Settings Page you can set various parameters for Neural Nets and Particle Swarm Optimization. Try to train the model with different parameters values. For this tutorial you can leave parameters as are.

Modeling Page

Modeling page contains two diagrams. The first diagram shows errors with respect of the iteration number which is very useful for monitoring the searching process. The second diagram which is below the previous shows current best solution (blue line) in comparison with the experimental data (red line). Also on the left side of the page, you can see several iteration number, error, and other information about searching process. gpdotnetv4_firstlook9

Prediction Page

Prediction page shows how current best model predict data. Predict page contains tabular and graphical representation of predicted data, which is compared with data for testing. gpdotnetv4_firstlook10

Features don’t work in this BETA

1. Exporting Neural Network model

2. Saving to gpa file Neural Network Models

Brood Recombination new feature in GPdotNET


As currently implemented GPdotNET has classic crossover implementation without any intelligent way to exchange genetic materials. In most time classic crossover operation is destructive operation wasting lot of good genetic materials. By including brood recombination crossover can be slightly improved.

Brood recombination simple repeats crossover operation several time on the same parents, with different crossover points. After fitness evaluation of offspring, the best two child are kept and others are discarded. On that way there is a better chance to get better child than with classic crossover. The picture below graphically describes brood recombination.

brood_recombination

Brood Size – new GPdotNET parameter

The first feature which will be implemented is manually setting the Brood Size of crossover. By adding Brood Recombination, we will increase possibility that two chromosomes will exchange the best genetic material they have.

brood_recombination_parameter

The next feature will be brood size which will be generating dynamically and will be dependent of the generation number.

Citations of GPdotNET


gpdotnetv3beta2

Recently I have googled about GPdotNET to find out how people use GPdotNET. I was surprised that there are plenty of sites which are published GPdotNET as freeware software. I have also found several scientific papers which citated GPdotNT as well. Some other people used it as elegant example in their  lessons. Some students used GPdotNET in seminars and diploma works, master and phd thesis.

All in all I was very excited about it. So lets list some interested web sites and scientific paper which mentioned GPdotNET.

1.  Softpedia http://www.softpedia.com/get/Science-CAD/GPdotNET.shtml

2. StackOverflow : http://stackoverflow.com/questions/14761910/genetic-evolution-of-source-code/14762077#14762077

3.  Genetic Programming article:  http://www.answers.com/topic/genetic-programming

4.  Teaching lessons from  Faculty of Informatics, Burapha University, Thailand:  Evolutionary Algorithms Applied to Finance

5.  Karlsruhe Institute of Technology Paper Work: Evolutionary Algorithms.

6. Scientific paper, ACS Vol.14:  Use of Learning Methods to Improve Kinematic Models

7. Scientific paper, JPE Vol.15: Modeling of Discharge Energy in Electrical Discharge Machining by the use of Genetic Programming

8. Scientific paper, Thermophysics 2012: Evolution algorithms as toolfor optimization of water vapour transport properties of cellular concrete.

9. Scientific paper,  : Application Of Neuro Fuzzy Systems and Genetic Programming for Modelling Surface Roughness in Electrical Discharge Machining

10. Scientific paper, : Aspects regarding the use of Genetic Programming in modelling the cutting process

11. Scientific paper, IJMECH Vol.3, : Predicting Of Machining Quality In Electric Discharge Machining Using Intelligent Optimization Techniques

12. Scientific paper, SLAAI Jornal: Framework for Discovery of Data Models Using Genetic Programming

13. Book By AKERKAR, RAJENDRA, Introduction of Artifical Intelligence.

GPdotNET v3.0 is out


GPdotNET3.0Beta1

I am very proud to announce GPdotNET v3.0, the new version which brings 3 new solvers based on Genetic Algorithm and several new features. In previous posts I was  writing about those new features:

1. TSP and vector based chromosome implementation in GPdotNET

2. Exporting GP Model in to Wolfram Mathematica

3. Matrix based chromosome implementation

4. Introduction to Assignment and transportation problems based on Genetic Algorithm

The source code and Click Once installation are uploaded in codeplex site, so go and grab the new version. hppt://gpdotnet.codeplex.com

I am asking for feedback and bug reports. If you find something strange post a comment here on anywhere in blog site or codeplex site. I will try to answer as quickly as possible.

Here are screenshots with new Assignment and Transportation solvers in GPdotNET:

GPdotNET3.0Beta1sl3
Loaded  training data of Assignment problem

GPdotNET3.0Beta1sl4

Simulation Tab page with optimal result of Assignment problem

GPdotNET3.0Beta1sl5

Loaded  training data of Transportation problem

GPdotNET3.0Beta1sl6
Simulation Tab page with optimal result of Transportation problem

Function optimization with Genetic Algorithm by using GPdotNET


Content

1. Introduction
2. Analytic function optimization module in GPdotNET
3. Examples of function optimizations
4. C# Implementation behind GPdotNET Optimization module

Introduction

GPdotNET is artificial intelligence tool for applying Genetic Programming and Genetic Algorithm in modeling and optimization of various engineering problems. It is .NET (Mono) application written in C# programming language which can run on both Windows and Linux based OS, or any OS which can run Mono framework. On the other hand GPdotNET is very easy to use. Even if you have no deep knowledge of GP and GA, you can apply those methods in finding solution. The project can be used in modeling any kind of engineering process, which can be described with discrete data. It is also be used in education during teaching students about evolutionary methods, mainly GP and GA. GPdotNET is open source project hosted at http://gpdotnet.codeplex.com

With releasing of  GPdotNET v2 it is also possible to find optimum for any analytic function regardless of independent variables. For example you can find optimum value for an analytically defined function with 2, 5, 10 or 100 independent variables. By using classic methods, function optimization of 3 or more independent variables is very difficult and sometimes impossible. It is also very hard to find optimum value for functions which are relatively complex regardless of number of independent variables.
Because GPdotNET is based on Genetic Algorithm we can find approximated optimum value of any function regardless of the limitation of number of independent variables, or complex definition. This blog post is going to give you a detailed and full description how to use GPdotNET to optimize function. Blog post will also cover C# implementation behind optimization proce by showing representation of Chromosome with real number, as well as Fitness calculation which is based on Genetic Programming tree expression. In this blog post it will also be presented several real world problem of optimization which will be solved with GPdotNET.

Analitic Function Optimization Module in GPdotNET

When GPdotNET is opened you can choose several predefined and calucalted models from various domain problems, as weel as creating New model among other options. By choosing New model new dialog box appears like picture below.

image1

By choosing Optimization of Analytic Function (see pic above) and pressing OK button, GPdotNET prepares model for optimization and opens 3 tab pages:

  1. Analytic function,
  2. Settings and
  3. Optimize Model.

Analytic function

By using “Analytic function” tab you can define expression of a function. More information about how to define mathematics expression of analytic function can be found on this blog post.

image2

By using “Analytic definition tool” at the bottom of the page, it is possible to define analytic expression. Expression tree builder generates function in Genetic Programming Expression tree, because GPdotNET fully implements both methods. Sharing features of Genetic programming  in Optimization based Genetic Algorithm is unique and it is implement only in GPdotNET.

When the process of defining function is finished, press Finish button in order to proceed with further actions. Finish button action apply all changes with Optimization Model Tab. So if you have made some changed in function definition, by pressing Finish button changes will be send to optimization tab.
Defining expression of function is relatively simple, but it is still not natural way for defining function, and will be changed in the future. For example on picture 2, you can see Expression tree which represent:

f(x,y)=y sin{4x}+1.1 x sin{2y} .

Setting GA parameters

The second step in optimization is setting Genetic Algorithm parameter which will be used in optimization process. Open the Setting tab and set the main GA parameters, see pic. 3.

image3

To successfully applied GA in the Optimization, it is necessary to define:

  1.  population size,
  2. probabilities of genetic operators and
  3. selection methods.

These parameters are general for all GA and GP models. More information about parameters you can find at https://bhrnjica.net/gpdotnet.

Optimize model (running optimization)

When GA parameters are defined, we can start with optimization by selecting Optimization model tab. Before run, we have to define constrains for each independent variables. This is only limitation we have to define i  order to start optimization. The picture below shows how to define constrains in 3 steps:

  1.  select row by left mouse click,
  2. enter min and max value in text boxes
  3. Press update button.

Perform these 3 actions for each independent variable defined in the function.

image4

When the process of defining constrains is finished, it is time to run the calculation by pressing Optimize button, from the main toolbar(green button). During optimization process GPdotNET is presenting nice animation of fitness values, as well as showing current best optimal value. The picture above shows the result of optimization process with GPdotNET. It can be seen that the optimal value for this sample is f_{opt}(9.96)=-100.22.

image5

Examples of function optimization

In this topic we are going to calculate optimal value for some functions by using GPdotNET. Zo be prove that the optimal value is correct or very close to correct value we will use Wolfram Alpha or other method.

Function: x sin(4x)+1.1 x sin(2y)

GP Expression tree looks like the following picture (left size):

image6 image7

Optimal value is found (right above picture) for 0.054 min, at 363 generation of total of 500 generation. Optimal value is f(8.66,9.03)=-18.59.

Here is Wolfram Alpha calculation of the same function. http://www.wolframalpha.com/input/?i=min+x*sin%284*x%29%2B+1.1+*y*+sin%282+*y%29%2C+0%3Cx%3C10%2C0%3Cy%3C10

Function:  (x^2+x)cos(x),  -10≤x≤10

GP expression tree looks like the following picture (left size):

image9image10

Optimal value is found for 0.125 min, at 10 generation of total of 500 generation. Optimal value is F(9.62)=-100.22.

Here is Wolfram Alpha calculation of the same function. http://www.wolframalpha.com/input/?i=minimum+%28x%5E2%2Bx%29*cos%28x%29+over+%5B-10%2C10%5D

Easom’s function fEaso(x1,x2)=-cos(x1)•cos(x2)•exp(-((x1-pi)^2+(x2-pi)^2)), -100<=x(i)<=100, i=1:2.

GP expression tree looks like the following picture (left size):

image12image13

Optimal value is found for 0.061 min, at 477 generation of total of 500 generation. Optimal value is F(9.62)=-1, for x=y=3.14.

Function can be seen at this MatLab link.

C# Implementation behind GPdotNET Optimization module

GPdotNET Optimization module is just a part which is incorporated in to GPdotNET Engine. Specific implementation for this module is Chromosome implementation, as well as Fitness function. Chromosome implementation is based on  floating point value instead of classic binary representation. Such a Chromosome contains array of floating point values and each element array represent function independent variable. If the function contains two independent variables (x,y) chromosome implementation will contains array with two floating points. Constrains of chromosome values represent constrains we defined during settings of the optimization process. The following source code listing shows implementation of GANumChrosomome class in GPdotNET:

public class GANumChromosome: IChromosome
 {
 private double[] val = null;
 private float fitness = float.MinValue;
 //... rest of implementation
}

When the chromosome is generated array elements get values randomly generated between min and max value defined by function definition. Here is a source code of Generate method.

///
/// Generate values for each represented variable
///
public void Generate(int param = 0)
{
	if(val==null)
		val = new double[functionSet.GetNumVariables()];
	else if (val.Length != functionSet.GetNumVariables())
		val = new double[functionSet.GetNumVariables()];

	for (int i = 0; i < functionSet.GetNumVariables(); i++)
		val[i] = Globals.radn.NextDouble(functionSet.GetTerminalMinValue(i), functionSet.GetTerminalMaxValue(i));

}

Mutation is accomplish when randomly chosen array element randomly change itc value. Here is a listing:

///
///  Select array element randomly and randomly change itc value
///
public void Mutate()
{
	//randomly select array element
	int crossoverPoint = Globals.radn.Next(functionSet.GetNumVariables());
	//randomly generate value for the selected element
	val[crossoverPoint] = Globals.radn.NextDouble(functionSet.GetTerminalMinValue(crossoverPoint), functionSet.GetTerminalMaxValue(crossoverPoint));
}

Crossover is little bit complicated. It is implemented based on Book Practical Genetic Algoritms see pages 56,57,48,59. Here is an implementation:

///
/// Generate number between 0-1.
/// For each element array of two chromosomes exchange value based on random number.
///
///
public void Crossover(IChromosome ch2)
{
	GANumChromosome p = (GANumChromosome)ch2;
	int crossoverPoint = Globals.radn.Next(functionSet.GetNumVariables());
	double beta;
	for (int i = crossoverPoint; i < functionSet.GetNumVariables(); i++)
	{
		beta = Globals.radn.NextDouble();
		val[i] = val[i] - beta * (val[i] - p.val[i]);
		p.val[i] = p.val[i] + beta * (val[i] - p.val[i]);
	}
}

Fitness function for Optimization is straightforward, it evaluates each chromosome against tree expression. For minimum the better chromosome is lower value. For maximum better chromosome is the chromosome with higher fitness value. Here is a implementation of Optimizatio Fitness function:

///
/// Evaluates function agains terminals
///
///
///
///
public float Evaluate(IChromosome chromosome, IFunctionSet functionSet)
{
	GANumChromosome ch = chromosome as GANumChromosome;
	if (ch == null)
		return 0;
	else
	{
		//prepare terminals
		var term = Globals.gpterminals.SingleTrainingData;
		for (int i = 0; i < ch.val.Length; i++)
			term[i] = ch.val[i];

		var y = functionSet.Evaluate(_funToOptimize, -1);

		if (double.IsNaN(y) || double.IsInfinity(y))
			y = float.NaN;

		//Save output in to output variable
		term[term.Length - 1] = y;

		if (IsMinimize)
			y *= -1;

		return (float)y;
	}
}

Summary

We have seen that Function optimization module within GPdotNET is powerful optimization tool. It can find pretty close solution for very complex functions regardless of number of independent variables. Optimization module use Genetic Algorithm method with floating point value chromosome representation described in several books about GA. It is fast, simple and can be used in education as well as in solving real problems. More info about GPdotNET can be found at https://bhrnjica.net/gpdotnet.