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可视化贝叶斯网络建模软件GeNIe2.2用户手册.pdf

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    Table of Contents
    Read me first
    Hello GeNIe!
    Introduction
    Guide to GeNIe manual
    GeNIe Modeler
    SMILE Engine
    Distribution information
    GeNIe on a Mac
    Copyright notice
    Disclaimer
    Acknowledgments
    Decision-theoretic modeling
    Decision analysis
    Discrete and continuous variables
    Probability
    Utility
    Bayesian networks
    Influence diagrams
    Bayesian updating
    Solving decision models
    Changes in structure
    Decision support systems
    Building blocks of GeNIe
    Introduction
    GeNIe workspace
    Introduction
    The menu bar
    Graph view
    Tree view
    Status bar
    Case manager
    Output window
    Help menu
    Components of GeNIe models
    Node types
    Canonical models
    Multi-attribute utility nodes
    Submodels
    Arcs
    Node status icons
    Text boxes
    Annotations
    Model and component properties
    Network properties
    Submodel properties
    Tools menu and Standard toolbar
    Node properties
    Visual appearance, layout, and navigation
    Introduction
    Viewing nodes in the Graph View
    Zooming and full screen mode
    Format toolbar and Layout menu
    Graph layout functions
    Selection of model elements
    Model navigation tools
    Saving and loading models in GeNIe
    Introduction
    File menu
    XDSL file format
    DSL file format
    Ergo file format
    Netica file format
    BN interchange format
    Hugin file format
    KI file format
    Inference algorithms
    Introduction
    Immediate and lazy evaluation
    Relevance reasoning
    Node menu
    Network menu
    Bayesian networks algorithms
    Exact algorithms
    Clustering algorithm
    Relevance-based decomposition
    Polytree algorithm
    Stochastic sampling algorithms
    Probabilistic Logic Sampling
    Likelihood Sampling
    Self-Importance Sampling
    Backward Sampling
    AIS algorithm
    EPIS Sampling
    Special algorithms
    Probability of evidence
    Annealed MAP
    Influence diagrams algorithms
    Policy evaluation
    Find Best Policy
    Algorithms for continuous and hybrid models
    Introduction
    Autodiscretization
    Hybrid Forward Sampling
    Obfuscation
    Program options
    Keyboard shortcuts
    Using GeNIe
    Introduction
    Bayesian networks
    Building a Bayesian network
    Useful structural transformations
    Entering and retracting evidence
    Virtual evidence
    Viewing results
    Strength of influences
    Controlling values
    Sensitivity analysis in Bayesian networks
    Influence diagrams
    Building an influence diagram
    Viewing results
    Sensitivity analysis in influence diagrams
    Value of information
    Support for diagnosis
    Introduction
    Diagnosis menu
    Diagnosis toolbar
    Enabling diagnostic extensions
    Spreadsheet view
    Testing window
    Diagnostic case management
    Cost of observation
    Learning
    Accessing data
    Data menu
    Cleaning data
    Knowledge editor
    Pattern editor
    Structural learning
    Introduction
    Bayesian Search
    PC
    Essential Graph Search
    Greedy Thick Thinning
    Tree Augmented Naive Bayes
    Augmented Naive Bayes
    Naive Bayes
    Learning parameters
    Generating a data file
    Validation
    Dynamic Bayesian networks
    Introduction
    Creating DBN
    Inference in DBNs
    Learning DBN parameters
    Equation-based and hybrid models
    Introduction
    Constructing equation-based models
    Writing equations in GeNIe
    Introduction
    Functions
    Probability distributions
    Arithmetic functions
    Combinatoric functions
    Trigonometric functions
    Hyperbolic functions
    Logical/Conditional functions
    Operators
    Hybrid models
    Inference in equation-based and hybrid models
    Viewing results in equation-based models
    Resources
    Books
    Research papers
    Conferences
    Model repositories
    Social Media
    References
    Index
    GeNIe Modeler USER MANUAL ® Version 2.2.1, Built on 8/4/2017 BayesFusion, LLC
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    Table of Contents 3 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 1. Read me first 9 2. Hello GeNIe! 11 Introduction 29 3. Guide to GeNIe manual ................................................................................................ 30 GeNIe Modeler ............................................................................................................ 30 SMILE Engine ............................................................................................................... 31 Distribution information .............................................................................................. 32 GeNIe on a Mac ........................................................................................................... 36 Copyright notice .......................................................................................................... 38 Disclaimer .................................................................................................................... 39 Acknowledgments ....................................................................................................... 39 4. Decision-theoretic modeling 41 Decision analysis .......................................................................................................... 42 Discrete and continuous variables ............................................................................... 42 Probability ................................................................................................................... 43 Utility ........................................................................................................................... 44 Bayesian networks ....................................................................................................... 45 Influence diagrams ...................................................................................................... 55 Bayesian updating ....................................................................................................... 57 Solving decision models ............................................................................................... 58 Changes in structure .................................................................................................... 59 Decision support systems ............................................................................................ 59 5. Building blocks of GeNIe 63 Introduction ................................................................................................................. 64 GeNIe workspace ......................................................................................................... 65 Introduction ................................................................................................................ 65 The menu bar .............................................................................................................. 67 Graph view .................................................................................................................. 68 Tree view ..................................................................................................................... 81 Status bar .................................................................................................................... 84 Case manager .............................................................................................................. 86 Output window ........................................................................................................... 91 Help menu ................................................................................................................... 92 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 4.10 5.1 5.2 5.2.1 5.2.2 5.2.3 5.2.4 5.2.5 5.2.6 5.2.7 5.2.8 GeNIe Modeler Version 2.2.1, Built on 8/4/2017
    Table of Contents 4 5.3 5.3.1 5.3.2 5.3.3 5.3.4 5.3.5 5.3.6 5.3.7 5.3.8 5.4 5.4.1 5.4.2 5.4.3 5.4.4 5.5 5.5.1 5.5.2 5.5.3 5.5.4 5.5.5 5.5.6 5.5.7 5.6 5.6.1 5.6.2 5.6.3 5.6.4 5.6.5 5.6.6 5.6.7 5.6.8 5.6.9 5.7 5.7.1 5.7.2 5.7.3 5.7.4 5.7.5 5.7.6 Components of GeNIe models ..................................................................................... 93 Node types .................................................................................................................. 93 Canonical models ........................................................................................................ 96 Multi-attribute utility nodes ..................................................................................... 109 Submodels ................................................................................................................. 114 Arcs ............................................................................................................................ 124 Node status icons ...................................................................................................... 125 Text boxes ................................................................................................................. 128 Annotations ............................................................................................................... 129 Model and component properties ............................................................................. 132 Network properties ................................................................................................... 132 Submodel properties ................................................................................................ 142 Tools menu and Standard toolbar ............................................................................ 145 Node properties ........................................................................................................ 147 Visual appearance, layout, and navigation ................................................................. 182 Introduction .............................................................................................................. 182 Viewing nodes in the Graph View ............................................................................. 182 Zooming and full screen mode ................................................................................. 185 Format toolbar and Layout menu ............................................................................. 186 Graph layout functions ............................................................................................. 191 Selection of model elements .................................................................................... 193 Model navigation tools ............................................................................................. 195 Saving and loading models in GeNIe .......................................................................... 197 Introduction .............................................................................................................. 197 File menu ................................................................................................................... 202 XDSL file format ......................................................................................................... 206 DSL file format ........................................................................................................... 206 Ergo file format ......................................................................................................... 207 Netica file format ...................................................................................................... 208 BN interchange format ............................................................................................. 209 Hugin file format ....................................................................................................... 209 KI file format .............................................................................................................. 209 Inference algorithms .................................................................................................. 209 Introduction .............................................................................................................. 209 Immediate and lazy evaluation ................................................................................. 212 Relevance reasoning ................................................................................................. 213 Node menu ................................................................................................................ 216 Network menu .......................................................................................................... 218 Bayesian networks algorithms .................................................................................. 220 Exact algorithms ........................................................................................................................... 220 5.7.6.1 GeNIe Modeler Version 2.2.1, Built on 8/4/2017
    Table of Contents 5 5.7.6.1.1 5.7.6.1.2 5.7.6.1.3 5.7.6.2 5.7.6.3 5.7.7 5.7.8 5.7.6.3.1 5.7.6.3.2 5.8 5.9 5.10 5.7.7.1 5.7.7.2 5.7.8.1 5.7.8.2 5.7.8.3 5.7.6.2.1 5.7.6.2.2 5.7.6.2.3 5.7.6.2.4 5.7.6.2.5 5.7.6.2.6 Clustering algorithm ............................................................................................................... 220 Relevance-based decomposition ............................................................................................ 222 Polytree algorithm .................................................................................................................. 222 Stochastic sampling algorithms .................................................................................................... 223 Probabilistic Logic Sampling .................................................................................................... 223 Likelihood Sampling ................................................................................................................ 223 Self-Importance Sampling ....................................................................................................... 223 Backward Sampling ................................................................................................................. 223 AIS algorithm ........................................................................................................................... 224 EPIS Sampling .......................................................................................................................... 224 Special algorithms ........................................................................................................................ 225 Probability of evidence ........................................................................................................... 225 Annealed MAP ........................................................................................................................ 229 Influence diagrams algorithms ................................................................................. 236 Policy evaluation .......................................................................................................................... 236 Find Best Policy ............................................................................................................................ 237 Algorithms for continuous and hybrid models ......................................................... 238 Introduction ................................................................................................................................. 238 Autodiscretization ........................................................................................................................ 239 Hybrid Forward Sampling ............................................................................................................. 242 Obfuscation ............................................................................................................... 243 Program options ........................................................................................................ 249 Keyboard shortcuts .................................................................................................... 255 6. Using GeNIe 259 Introduction ............................................................................................................... 260 Bayesian networks ..................................................................................................... 260 Building a Bayesian network ..................................................................................... 260 Useful structural transformations ............................................................................. 260 Entering and retracting evidence .............................................................................. 266 Virtual evidence ........................................................................................................ 271 Viewing results .......................................................................................................... 273 Strength of influences ............................................................................................... 280 Controlling values ...................................................................................................... 283 Sensitivity analysis in Bayesian networks ................................................................. 286 Influence diagrams .................................................................................................... 291 Building an influence diagram .................................................................................. 291 Viewing results .......................................................................................................... 300 Sensitivity analysis in influence diagrams ................................................................. 301 Value of information ................................................................................................. 306 Support for diagnosis ................................................................................................. 313 Introduction .............................................................................................................. 313 6.2.1 6.2.2 6.2.3 6.2.4 6.2.5 6.2.6 6.2.7 6.2.8 6.3 6.3.1 6.3.2 6.3.3 6.3.4 6.4.1 6.4 6.1 6.2 GeNIe Modeler Version 2.2.1, Built on 8/4/2017
    Table of Contents 6 6.4.2 6.4.3 6.4.4 6.4.5 6.4.6 6.4.7 6.4.8 6.5 6.5.1 6.5.2 6.5.3 6.5.4 6.5.5 6.5.6 6.5.7 6.5.8 6.5.9 6.6 6.6.1 6.6.2 6.6.3 6.6.4 6.7 6.7.1 6.7.2 6.7.3 6.5.6.1 6.5.6.2 6.5.6.3 6.5.6.4 6.5.6.5 6.5.6.6 6.5.6.7 6.5.6.8 Diagnosis menu ......................................................................................................... 314 Diagnosis toolbar ...................................................................................................... 317 Enabling diagnostic extensions ................................................................................. 318 Spreadsheet view ...................................................................................................... 327 Testing window ......................................................................................................... 334 Diagnostic case management ................................................................................... 341 Cost of observation ................................................................................................... 344 Learning ..................................................................................................................... 349 Accessing data ........................................................................................................... 349 Data menu ................................................................................................................. 361 Cleaning data ............................................................................................................ 363 Knowledge editor ...................................................................................................... 383 Pattern editor ............................................................................................................ 386 Structural learning .................................................................................................... 389 Introduction ................................................................................................................................. 389 Bayesian Search ............................................................................................................................ 391 PC ................................................................................................................................................. 393 Essential Graph Search ................................................................................................................. 399 Greedy Thick Thinning .................................................................................................................. 402 Tree Augmented Naive Bayes ...................................................................................................... 403 Augmented Naive Bayes .............................................................................................................. 405 Naive Bayes .................................................................................................................................. 408 Learning parameters ................................................................................................. 410 Generating a data file ................................................................................................ 417 Validation .................................................................................................................. 421 Dynamic Bayesian networks ...................................................................................... 443 Introduction .............................................................................................................. 443 Creating DBN ............................................................................................................. 443 Inference in DBNs ...................................................................................................... 450 Learning DBN parameters ......................................................................................... 460 Equation-based and hybrid models ............................................................................ 466 Introduction .............................................................................................................. 466 Constructing equation-based models ....................................................................... 466 Writing equations in GeNIe ....................................................................................... 472 Introduction ................................................................................................................................. 472 Functions ...................................................................................................................................... 476 Probability distributions .......................................................................................................... 476 Arithmetic functions ............................................................................................................... 482 Combinatoric functions ........................................................................................................... 485 Trigonometric functions ......................................................................................................... 485 Hyperbolic functions ............................................................................................................... 486 Logical/Conditional functions ................................................................................................. 486 Operators ..................................................................................................................................... 488 6.7.3.1 6.7.3.2 6.7.3.2.1 6.7.3.2.2 6.7.3.2.3 6.7.3.2.4 6.7.3.2.5 6.7.3.2.6 6.7.3.3 GeNIe Modeler Version 2.2.1, Built on 8/4/2017
    Table of Contents 7 6.7.4 6.7.5 6.7.6 Hybrid models ........................................................................................................... 489 Inference in equation-based and hybrid models ...................................................... 492 Viewing results in equation-based models ............................................................... 500 7. Resources 509 Books ......................................................................................................................... 510 Research papers ......................................................................................................... 510 Conferences ............................................................................................................... 511 Model repositories ..................................................................................................... 512 Social Media .............................................................................................................. 512 References ................................................................................................................. 513 521 7.1 7.2 7.3 7.4 7.5 7.6 Index GeNIe Modeler Version 2.2.1, Built on 8/4/2017
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