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Introduction
1. GeneXproTools Environment
1.1. Getting Started
1.1.1. Starting GeneXproTools
1.1.2. Loading Data
1.1.3. Evolving a Model
1.1.4. Optimizing a Model Evolved by
GeneXproTools
1.1.5. Simplifying a Model Evolved by GeneXproTools
1.1.6. Evaluating the Accuracy of a Model
1.1.7. Testing the Generalizing Capabilities of a Model
1.1.8. Generating Code Automatically
1.1.9. Visualizing Parse Trees
1.1.10. Scoring a Model
1.2. Modeling Tools
1.2.1. Function Finding Tools
1.2.2. Classification Tools
1.2.3. Time Series Analysis Tools
1.2.4. Logic Synthesis Tools
1.3.
GeneXproTools Panels
1.3.1. Report
1.3.2. Data
1.3.2.1. Training Data
1.3.2.2. Testing Data
1.3.3. Settings
1.3.3.1. General Settings
1.3.3.2. Fitness Function
1.3.3.3. Genetic Operators
1.3.3.4. Numerical Constants
1.3.4. Functions
1.3.4.1. Mathematical Functions
1.3.4.2. Logical Functions
1.3.4.3. Static UDFs
1.3.5. Run
1.3.6. History
1.3.7. Results
1.3.7.1. Training Results
1.3.7.2. Testing Results
1.3.8. Predictions
1.3.9. Model
1.3.10. Scoring
1.3.10.1. Databases
1.3.10.2. Text Files
1.4. Creating Models with GeneXproTools
1.4.1. Preparing and Analyzing Data
1.4.2. Choosing the Function Set
1.4.3. Choosing the Chromosome Architecture
1.4.4. Choosing the Population Size
1.4.5. Choosing the Degree of Genetic Modification
1.4.6. Choosing the Fitness Function
1.4.7. Creating the Model
1.4.8. Evaluating the Model
1.4.9. Modeling from Seed
1.4.10. Simplifying the Model
1.5. Making Predictions with a Model
1.5.1. Scoring from Excel
& Databases
1.5.2. Scoring from Text Files
1.5.3. Making Predictions with Time Series Models
2. Working with Function Finding Tools
2.1. Loading Data
2.2. Available Functions
2.2.1. Mathematical Functions and Dynamic UDFs
2.2.2. Static UDFs
2.3. Available Chromosomal Architectures
2.4. Fitness Functions
2.5. Available Algorithms
2.6. Evolutionary Strategies
3. Working with Classification Tools
3.1. Loading Data
3.2. Available Functions
3.2.1. Mathematical Functions and Dynamic UDFs
3.2.2. Static UDFs
3.3. Available Chromosomal Architectures
3.4. Fitness Functions and the Rounding Threshold
3.5. Available Algorithms
3.6. Evolutionary Strategies
4. Working with Time Series Prediction Tools
4.1. Loading Data
4.2. Available Functions
4.2.1. Mathematical Functions and Dynamic UDFs
4.2.2. Static UDFs
4.3. Available Chromosomal Architectures
4.4. Fitness Functions
4.5. Available Algorithms
4.6. Evolutionary Strategies
5. Working with Logic Synthesis Tools
5.1. Loading Truth Tables
5.2. Available Functions
5.2.1. Logical Functions and Dynamic UDFs
5.2.2. Static UDFs
5.3. Available Chromosomal Architectures
5.4. Fitness Functions
5.5. Available Algorithms
5.6. Evolutionary Strategies
6. The Architectures of
GeneXproTools Learning Algorithms
6.1. Gene Expression Programming
6.1.1. An Overview of Gene Expression Programming
6.1.2. The Architecture of GEP Programs
6.1.3. Multigenic Chromosomes and Linking Functions
6.1.4. User Defined Functions
6.2. Gene Expression Programming with Random Numerical Constants
6.2.1. Function Finding and the Creation of Numerical Constants
6.2.2. The Architecture of GEP-RNC Programs
6.3. Karva Notation:
The Endogenous Code of GeneXproTools
6.3.1. Karva Notation and the Manipulation of K-expressions
6.3.2. The Symbols of Karva Notation
6.3.2.1. Built-in Mathematical Functions
6.3.2.2. Built-in Logical Functions
7. Genetic Operators
7.1. Mutation
7.2. Inversion
7.3. Transposition
7.3.1. IS Transposition
7.3.2. RIS Transposition
7.3.3. Gene Transposition
7.4. Recombination
7.4.1. One-point Recombination
7.4.2. Two-point Recombination
7.4.3. Gene Recombination
7.5. Genetic Operators for Random Numerical Constants
7.5.1. Dc Mutation
7.5.2. Dc Inversion
7.5.3. Dc IS Transposition
7.5.4. Direct Mutation of Random Numerical Constants
8. Designing New Models from Old Models
8.1. Optimizing Models Evolved by
GeneXproTools
8.2. Modifying Models Evolved by
GeneXproTools
8.3. Optimizing an External Model
8.4. Simplifying a Model
8.5. Refreshing a Model
8.6. Adding a Neutral Gene
9. Choosing the Fitness Function
9.1. Fitness Functions for Function Finding
9.1.1. Fitness Functions and Parsimony Pressure
9.1.2. Absolute Error Based Fitness Functions
9.1.2.1. Absolute Error with Selection Range
9.1.2.2. Absolute/Hits
9.1.2.3. Mean Squared Error
9.1.2.4. Root Mean Squared Error
9.1.2.5. Mean Absolute Error
9.1.2.6. Relative Squared Error
9.1.2.7. Root Relative Squared Error
9.1.2.8. Relative Absolute Error
9.1.3. Relative Error Based Fitness Functions
9.1.3.1. Relative Error with Selection Range
9.1.3.2. Relative/Hits
9.1.3.3. Mean Squared Error
9.1.3.4. Root Mean Squared Error
9.1.3.5. Mean Absolute Error
9.1.3.6. Relative Squared Error
9.1.3.7. Root Relative Squared Error
9.1.3.8. Relative Absolute Error
9.1.4. R-square
9.1.5. Correlation Coefficient
9.1.6. User Defined Fitness Functions
9.2. Fitness Functions for Classification
9.2.1. Fitness Functions and Parsimony Pressure
9.2.2. Number of Hits
9.2.3. Hits with Penalty
9.2.4. Accuracy
9.2.5. Squared Accuracy
9.2.6. Sensitivity/Specificity
9.2.7. PPV/NPV
9.2.8. Sensitivity/Specificity/PPV/NPV
9.2.9. Mean Squared Error
9.2.10. Root Mean Squared Error
9.2.11. Mean Absolute Error
9.2.12. Relative Squared Error
9.2.13. Root Relative Squared Error
9.2.14. Relative Absolute Error
9.2.15. R-square
9.2.16. Correlation Coefficient
9.2.17. User Defined Fitness Functions
9.3. Fitness Functions for Time Series Prediction
9.3.1. Fitness Functions and Parsimony Pressure
9.3.2. Absolute Error Based Fitness Functions
9.3.2.1. Absolute Error with Selection Range
9.3.2.2. Absolute/Hits
9.3.2.3. Mean Squared Error
9.3.2.4. Root Mean Squared Error
9.3.2.5. Mean Absolute Error
9.3.2.6. Relative Squared Error
9.3.2.7. Root Relative Squared Error
9.3.2.8. Relative Absolute Error
9.3.3. Relative Error Based Fitness Functions
9.3.3.1. Relative Error with Selection Range
9.3.3.2. Relative/Hits
9.3.3.3. Mean Squared Error
9.3.3.4. Root Mean Squared Error
9.3.3.5. Mean Absolute Error
9.3.3.6. Relative Squared Error
9.3.3.7. Root Relative Squared Error
9.3.3.8. Relative Absolute Error
9.3.4. R-square
9.3.5. Correlation Coefficient
9.3.6. User Defined Fitness Functions
9.4. Fitness Functions for Logic Synthesis
9.4.1. Fitness Functions and Parsimony Pressure
9.4.2. Number of Hits
9.4.3. Hits with Penalty
9.4.4. Accuracy
9.4.5. Squared Accuracy
9.4.6. Sensitivity/Specificity
9.4.7. PPV/NPV
9.4.8. Sensitivity/Specificity/PPV/NPV
9.4.9. Mean Squared Error
9.4.10. Root Mean Squared Error
9.4.11. Mean Absolute Error
9.4.12. Relative Squared Error
9.4.13. Root Relative Squared Error
9.4.14. Relative Absolute Error
9.4.15. R-square
9.4.16. Correlation Coefficient
9.4.17. User Defined Fitness Functions
10. Analyzing
GeneXproTools Models Statistically
10.1. Statistical Analysis of Function Finding Models
10.1.1. R-square
10.1.2. Correlation Coefficient
10.1.3. Mean Squared Error
10.1.4. Root Mean Squared Error
10.1.5. Mean Absolute Error
10.1.6. Relative Squared Error
10.1.7. Root Relative Squared Error
10.1.8. Relative Absolute Error
10.2. Statistical Analysis of Classification Models
10.2.1. Classification Error
10.2.2. Classification Accuracy
10.2.3. Confusion Matrix
10.2.4. Sensitivity
10.2.5. Specificity
10.2.6. Positive Predictive Value
10.2.7. Negative Predictive Value
10.2.8. R-square
10.2.9. Correlation Coefficient
10.2.10. Mean Squared Error
10.2.11. Root Mean Squared Error
10.2.12. Mean Absolute Error
10.2.13. Relative Squared Error
10.2.14. Root Relative Squared Error
10.2.15. Relative Absolute Error
10.3. Statistical Analysis of Time Series Prediction Models
10.3.1. R-square
10.3.2. Correlation Coefficient
10.3.3. Mean Squared Error
10.3.4. Root Mean Squared Error
10.3.5. Mean Absolute Error
10.3.6. Relative Squared Error
10.3.7. Root Relative Squared Error
10.3.8. Relative Absolute Error
10.4. Statistical Analysis of Logic Synthesis Models
10.4.1. Classification Error
10.4.2. Classification Accuracy
10.4.3. Confusion Matrix
10.4.4. Sensitivity
10.4.5. Specificity
10.4.6. Positive Predictive Value
10.4.7. Negative Predictive Value
10.4.8. R-square
10.4.9. Correlation Coefficient
10.4.10. Mean Squared Error
10.4.11. Root Mean Squared Error
10.4.12. Mean Absolute Error
10.4.13. Relative Squared Error
10.4.14. Root Relative Squared Error
10.4.15. Relative Absolute Error
11. Generating Code Automatically
11.1. Endogenous Karva Code
11.2. Expression Trees
11.3. Built-in Grammars
11.3.1. Ada
11.3.2. C
11.3.3. C++
11.3.4. C#
11.3.5. Fortran
11.3.6. Java
11.3.7. Java Script
11.3.8. Matlab
11.3.9. Pascal
11.3.10. Perl
11.3.11. PHP
11.3.12. Python
11.3.13. Visual Basic
11.3.14. VB.Net
11.3.15. Verilog
11.3.16. VHDL
11.4. Built-in Logical Systems for Automatic Code Generation
11.4.1. Ada
11.4.2. C
11.4.3. C++
11.4.4. C#
11.4.5. Fortran
11.4.6. Java
11.4.7. Java Script
11.4.8. Matlab
11.4.9. Pascal
11.4.10. Perl
11.4.11. PHP
11.4.12. Python
11.4.13. Visual Basic
11.4.14. VB.Net
11.4.15. Verilog
11.4.16. VHDL
11.5. User Defined Grammars
12. Making Predictions with a Model
12.1. Scoring from
Excel & Databases
12.2. Scoring from Text Files
12.3. Making Predictions with Time Series Models
13. Settings and Features
13.1. Settings and Features for Function Finding Problems
13.1.1. New Run Wizard
13.1.1.1. Run Category Window
13.1.1.2. Training Data Window - Text Files
13.1.1.3. Testing Data Window - Text Files
13.1.1.4. Training Data Window - Excel & Databases
13.1.1.5. Testing Data Window - Excel & Databases
13.1.1.6. Data Source Dialog Box - Excel & Databases
13.1.2. Report Panel
13.1.3. Data Panel
13.1.3.1. Training Set Tab
13.1.3.2. Testing Set Tab
13.1.4. Change/Add Dataset Engine
13.1.4.1. Change Training Data Window - Text Files
13.1.4.2. Change/Add Testing Data Window - Text Files
13.1.4.3. Change Training Data Window - Excel & Databases
13.1.4.4. Change/Add Testing Data Window - Excel & Databases
13.1.4.5. Data Source Dialog Box - Excel & Databases
13.1.5. Settings Panel
13.1.5.1. General Settings Tab
13.1.5.2. Fitness Function Tab
13.1.5.3. Genetic Operators Tab
13.1.5.4. Numerical Constants Tab
13.1.6. Functions Panel
13.1.6.1. Functions Tab
13.1.6.2. Functions Tab – Edit DDF Window
13.1.6.3. Static UDFs Tab
13.1.6.4. Static UDFs Tab – Edit UDF Window
13.1.7. Run Panel
13.1.8. History Panel
13.1.9. Results Panel
13.1.9.1.
Training and Testing Results
13.1.9.2. Grid Option
13.1.9.3. Chart Option
13.1.10. Model Panel
13.1.11. Change Seed Window
13.1.12. Scoring Panel
13.1.12.1. Text Files Tab
13.1.12.2. Databases Tab
13.1.12.3. Data Source Dialog Box - Excel & Databases
13.1.13. Menus
13.1.13.1. File
13.1.13.2. Edit
13.1.13.3. View
13.1.13.4. Reports
13.1.13.5. Data
13.1.13.6. Settings
13.1.13.7. Functions
13.1.13.8. Run
13.1.13.9. Results
13.1.13.10. Model
13.1.13.11. Scoring
13.1.13.12. Help
13.1.14. Run Templates
13.1.15. Sample Runs
13.2. Settings and Features for Classification Problems
13.2.1. New Run Wizard
13.2.1.1. Run Category Window
13.2.1.2. Training Data Window - Text Files
13.2.1.3. Testing Data Window - Text Files
13.2.1.4. Training Data Window - Excel & Databases
13.2.1.5. Testing Data Window - Excel & Databases
13.2.1.6. Data Source Dialog Box - Excel & Databases
13.2.2. Report Panel
13.2.3. Data Panel
13.2.3.1. Training Set Tab
13.2.3.2. Testing Set Tab
13.2.4. Change/Add Dataset Engine
13.2.4.1. Change Training Data Window - Text Files
13.2.4.2. Change/Add Testing Data Window - Text Files
13.2.4.3. Change Training Data Window - Excel & Databases
13.2.4.4. Change/Add Testing Data Window - Excel & Databases
13.2.4.5. Data Source Dialog Box - Excel & Databases
13.2.5. Settings Panel
13.2.5.1. General Settings Tab
13.2.5.2. Fitness Function Tab
13.2.5.3. Genetic Operators Tab
13.2.5.4. Numerical Constants Tab
13.2.6. Functions Panel
13.2.6.1. Functions Tab
13.2.6.2. Functions Tab – Edit DDF Window
13.2.6.3. Static UDFs Tab
13.2.6.4. Static UDFs Tab – Edit UDF Window
13.2.7. Run Panel
13.2.8. History Panel
13.2.9. Results Panel
13.2.9.1. Training & Testing Results
13.2.9.2. Grid Option
13.2.9.3. Chart Option
13.2.10. Model Panel
13.2.11. Change Seed Window
13.2.12. Scoring Panel
13.2.12.1. Text Files Tab
13.2.12.2. Databases Tab
13.2.12.3. Data Source Dialog Box - Excel & Databases
13.2.13. Menus
13.2.13.1. File
13.2.13.2. Edit
13.2.13.3. View
13.2.13.4. Reports
13.2.13.5. Data
13.2.13.6. Settings
13.2.13.7. Functions
13.2.13.8. Run
13.2.13.9. Results
13.2.13.10. Model
13.2.13.11. Scoring
13.2.13.12. Help
13.2.14. Run Templates
13.2.15. Sample Runs
13.3. Settings and Features for Time Series Prediction Problems
13.3.1. New Run Wizard
13.3.1.1. Run Category Window
13.3.1.2. Training Data Window - Text Files
13.3.1.3. Training Data Window - Excel & Databases
13.3.1.4. Data Source Dialog Box - Excel & Databases
13.3.2. Report Panel
13.3.3. Data Panel
13.3.3.1. Transformed Time Series Tab
13.3.3.2. Original Time Series Tab
13.3.4. Change Time Series Engine
13.3.4.1. Change Time Series Window - Text Files
13.3.4.2. Change Time Series Window - Excel & Databases
13.3.4.3. Data Source Dialog Box - Excel & Databases
13.3.5. Settings Panel
13.3.5.1. General Settings Tab
13.3.5.2. Fitness Function Tab
13.3.5.3. Genetic Operators Tab
13.3.5.4. Numerical Constants Tab
13.3.6. Functions Panel
13.3.6.1. Functions Tab
13.3.6.2. Functions Tab – Edit DDF Window
13.3.6.3. Static UDFs Tab
13.3.6.4. Static UDFs Tab – Edit UDF Window
13.3.7. Run Panel
13.3.8. History Panel
13.3.9. Predictions Panel
13.3.10. Model Panel
13.3.11. Change Seed Window
13.3.12. Menus
13.3.12.1. File
13.3.12.2. Edit
13.3.12.3. View
13.3.12.4. Reports
13.3.12.5. Data
13.3.12.6. Settings
13.3.12.7. Functions
13.3.12.8. Run
13.3.12.9. Predictions
13.3.12.10. Model
13.3.12.11. Help
13.3.13. Run Templates
13.3.14. Sample Runs
13.4. Settings and Features for Logic Synthesis Problems
13.4.1. New Run Wizard
13.4.1.1. Run Category Window
13.4.1.2. Training Data Window - Text Files
13.4.1.3. Testing Data Window - Text Files
13.4.1.4. Training Data Window - Excel & Databases
13.4.1.5. Testing Data Window - Excel & Databases
13.4.1.6. Data Source Dialog Box - Excel & Databases
13.4.2. Report Panel
13.4.3. Data Panel
13.4.3.1. Training Set Tab
13.4.3.2. Testing Set Tab
13.4.4. Change/Add Dataset Engine
13.4.4.1. Change Training Data Window - Text Files
13.4.4.2. Change/Add Testing Data Window - Text Files
13.4.4.3. Change Training Data Window - Excel & Databases
13.4.4.4. Change/Add Testing Data Window - Excel & Databases
13.4.4.5. Data Source Dialog Box - Excel & Databases
13.4.5. Settings Panel
13.4.5.1. General Settings Tab
13.4.5.2. Fitness Function Tab
13.4.5.3. Genetic Operators Tab
13.4.5.4. Numerical Constants Tab
13.4.6. Functions Panel
13.4.6.1. Functions Tab
13.4.6.2. Functions Tab – Edit DDF Window
13.4.6.3. Static UDFs Tab
13.4.6.4. Static UDFs Tab – Edit UDF Window
13.4.7. Run Panel
13.4.8. History Panel
13.4.9. Results Panel
13.4.9.1. Training & Testing Results
13.4.9.2. Grid Option
13.4.9.3. Chart Option
13.4.10. Model Panel
13.4.11. Change Seed Window
13.4.12. Scoring Panel
13.4.12.1. Text Files Tab
13.4.12.2. Databases Tab
13.4.12.3. Data Source Dialog Box - Excel & Databases
13.4.13. Menus
13.4.13.1. File
13.4.13.2. Edit
13.4.13.3. View
13.4.13.4. Reports
13.4.13.5. Data
13.4.13.6. Settings
13.4.13.7. Functions
13.4.13.8. Run
13.4.13.9. Results
13.4.13.10. Model
13.4.13.11. Scoring
13.4.13.12. Help
13.4.14. Run Templates
13.4.15. Sample Runs
14. GeneXproTools
Editions
14.1. Editions
14.2. Requirements
14.3. Installation
14.4. Converting APS 3.0 Runs
14.5. License
14.6. Demo
Learning Resources
Support
Contacts
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