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Gene Expression Programming


The first step in using GeneXproTools is launching it and opening existing files or creating new ones.

To Start GeneXproTools 5.0

  1. In Windows, click Start, point to Programs, and point to the Gepsoft GeneXproTools 5.0 folder.
    The icons in the Gepsoft GeneXproTools 5.0 folder appear in a list.
  2. Click the GeneXproTools 5.0 program icon.
    The Home Panel appears. This panel presents you with several choices, including start a new run or open an existing run.
  3. To start a new run, click the File menu and then choose New.
    The New Run Wizard appears. This wizard helps you gather the necessary information to start evolving a model.
  4. To open an existing run, in the Home Panel either choose a recent or sample run or click the File menu and then choose Open.
    In the Report Panel you will find relevant information concerning this run, including all the settings used in the run, the statistical evaluation of the best-of-run or active model, and a detailed account of all the models in the run History.
The new Home Panel of GeneXproTools 5.0

The GeneXproTools 5.0 modeling environment contains 10 basic panels:

Report Panel

In the Report Panel you can find relevant information concerning the run, including all the settings used in the run, the statistical evaluation of the best-of-run or active model (highlighted in yellow in the History heading), and a detailed account of the evolutionary history of the run.

Report Panel – Full & Short Report

Data Panel

The multifunctional Data Panel goes beyond a simple platform for analyzing and visualizing input data. Besides allowing the analysis and visualization of input variables, it also allows the visualization and analysis of all your models and derived variables, giving you access to a rich web of analyses between all these types of variables and across different datasets.

New Multifunctional Data Panel

The analyses you can do in the Data Panel include scatter plots and regression analysis between all possible pairs of variables (input variables, models and derived variables); histograms and summary statistics for all variables and across different datasets; different line charts for outlier detection and model analysis; and evaluation of the variable importance and display of the variable importance chart for all the models.

Variable importance of model variables

The multifunctional Data Panel also supports extensive record analyses, allowing you to study different types of records using different charts and browsing tools. For example, you can compare each record with different record prototypes in order to gain insight into both your data and your models. By selecting just the outliers or the misclassified records to browse, you can also perform error analysis in the Data Panel.

Error Analysis – Browsing Misclassifications

Settings Panel

The Settings Panel gives you access to the most important settings of GeneXproTools, which are organized into four different tabs: General Settings, Fitness Function, Genetic Operators, and Numerical Constants.

General Settings Tab

In the General Settings Tab you can change the number of training and validation/test records, choose different sub-sampling schemes for the training and validation/test datasets, change the chromosome architecture, the linking function, the number of chromosomes. Moreover, you can also choose the parameters for the Complexity Increase Engine of GeneXproTools and choose different modes of Model Management.

General Settings

Fitness Function Tab

In the Fitness Function Tab you can choose one of the 100+ GeneXproTools built-in fitness functions or design and test a fitness function of your own.

Logistic Regression – Fitness Function Tab

Genetic Operators Tab

In the Genetic Operators Tab you can change the degree of genetic modification you want to use during evolution by choosing the kind of genetic operators and their corresponding rates. Moreover, GeneXproTools provides 4 built-in modeling strategies that cover some of the most common modeling needs, namely a strategy for fine-tuning the numerical constants of your models (Constant Fine-Tuning); a strategy for model fine-tuning where the overall structure of the model remains basically unchanged making only small changes in the model’s structure (Model Fine-Tuning); a strategy for Sub-set Selection which is ideal for creating good random forests, especially for datasets with many variables, as it works only with the elements that were randomly drawn for the initial population; and of course a strategy designed for Optimal Evolution which tries to give a good blend of diversity versus stability in order to optimize and accelerate evolution.

New Genetic Operators & Modeling Strategies

Numerical Constants Tab

In the Numerical Constants Tab you can activate the algorithm that enables the use of random numerical constants and customize both the type and range of your constants, and the number of constants per gene.

Numerical Constants Tab

Functions Panel

In the Functions Panel you choose the functions GeneXproTools will use to model your data. For mathematical problems, there are a total of 279 built-in functions and comparison rules, whereas for Boolean problems there are a total of 258 built-in logical functions.

Functions Panel – Function Set Defaults

Run Panel

From the Run Panel you command and visualize the creation, optimization, and simplification of your models through the use of different model fitting charts, including different kinds of curve fitting charts, scatter plots, and residual charts. For Classification and Logistic Regression the model visualization tools include different binomial fitting charts, the classification scatter plot and the classification tapestry.

Run Panel – Classification & Logistic Regression

History Panel

The History Panel allows you to manage your models by selecting and re-ordering them using different Favorite Statistics. Moreover, you can also delete and import models from different runs and deploy models or model ensembles to Excel.

Model Selection in the History Panel

Results Panel

In the Results Panel a thorough statistical analysis of the evolved model is done on the fly both for the training and validation/test datasets. Furthermore, the model output and the target are compared using both a table and several charts. The number and type of available charts varies with the modeling category of the run.

Logistic Regression – Measures of Fit in the Results Panel

Predictions Panel

In the Predictions Panel is where you use your models to make predictions about future events in the Time Series Prediction Platform. Here is also where a thorough statistical analysis of your models takes place and, if in Testing Mode, it's also where you can test the predictive accuracy on past historical observations.

Curve Fitting – Time Series Prediction

Model Panel

In the Model Panel you can see the mathematical/logical intricacies of the evolved models in the universal representation of Expression Trees or automatically translate the native Karva Code into several programming languages (Ada, C, C++, C#, Excel VBA, Fortran, Java, JavaScript, Matlab, Octave, Pascal, Perl, PHP, Python, R, Visual Basic, VB.Net, Verilog, and VHDL).

Logistic Regression Model in Python - Probability Output

Scoring Panel

In the Scoring Panel you can apply your models immediately without leaving the GeneXproTools environment. The scoring engine of GeneXproTools uses the JavaScript code of your models to score your data. Both Excel/Databases and Text Files can be scored and the output saved to Excel (csv) or text files. In addition, for small datasets, the output can also be observed in its entirety in the Scoring Panel.

Logistic Regression - Model Scoring


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3 8 4

"Finally, a world class user interface in the field of genetic programming and evolutionary computation !! GeneXproTools is simply unrivaled in its marvelous user interface, the breadth of its Fitness Functions, the choice and flexibility in Math and Logic functions, the clarity of its final Model Presentation, and a built in panel for Scoring new data, right inside the interface. This kind of functionality and ease of use has never been seen before in the field of Genetic Programming. Additionally, Dr Ferreira's specific methodology of Gene Expression Programming makes important contributions to the field of evolutionary computation, and the various algorithms she has developed and deployed inside of GeneXproTools are brilliantly conceived, and her methodologies evolve highly predictive models that solve real business problems. GeneXproTools is an extraordinary structural tour de force."

Brian C. Watt, CRM
Chief Risk Officer / Chief Financial Officer


"I have been using GeneXproTools against a variety of drug research related problems and have found the GUI to be readily-usable and well-attuned to the stages of predictive modeling..."

Steven J Barrett, Ph.D
Principal Scientist
New Applications Team
Data Exploration Sciences GlaxoSmithKline


"Gene Expression Programming, combined with GeneXproTools, allow us here at Mercator GeoSystems to explore new and exciting methods for spatially modelling the relationship between a company's outlets and their customers. The GeneXproTools software is simple to use, well-designed and very flexible. In particular the ability to load training data from a database, and the option to create models in the programming language of our choice, really make this product stand out. Product support is excellent and very responsive - heartily recommended!"

Steve Hall
Mercator GeoSystems Ltd
United Kingdom

"As a professional software developer, I could have attempted to read up on all the latest developments in the field of evolutionary programming and start writing my own modeling tools. One look at the GeneXproTools demo, however, was enough to convince me of the absurdity of that thought. Not only does GeneXproTools have all the power that I would ever need, but it also allows me to customize all parts of the modeling process. I don't have to know the first thing about evolutionary algorithms and yet I can write my own grammars or fitness functions if I wanted to. It is obvious that a huge amount of work went into the making of GeneXproTools, and I am now a very happy customer. Keep up the great work, Gepsoft!"

Glenn Lewis
Software developer, USA

"I've been working as a coastal engineer and mathematical modeler for more than 10 years and now I'm using GeneXproTools to discover complex nonlinear relations that exist in hydraulic and wave processes. For example, GeneXproTools recently helped me establish several explicit approximations to the Wave Dispersion Equation and now with the new version, which allows more independent variables, fitness functions and unlimited records, I plan to develop my own formulae to evaluate the wave overtopping of breakwaters and seawalls. Thanks Gepsoft for providing such an exciting, creative and useful software tool to the scientific community."

Ricardo Carvalho
PROMAN - Centro de Estudos & Projectos, SA
Lisbon, Portugal

"GeneXproTools is being used to look at problems involving parasite populations, where the data is highly skewed. The results using GeneXproTools are considerably better than those obtained using conventional statistics."

Prof John Barrett
Head of the Parasitology Group
University of Wales, UK

"We are using GeneXproTools for modeling the rainfall-runoff process and time series forecasting. GeneXproTools has a nice graphical user interface system and a lot of flexibility in choosing the type of input file. Configuring the problem setup, running and visualizing the graphical outputs with GeneXproTools is indeed user friendly. Being able to get the final model in the languages of our choice makes GeneXproTools stand out from other packages."

Professor S. Mohan
Professor & Head of the Department
Department of Civil Engineering
Indian Institute of Technology, Madras


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