®
GeNIe Modeler
USER MANUAL
Version 2.2.1, Built on 8/4/2017
BayesFusion, LLC
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GeNIe Modeler Version 2.2.1, Built on 8/4/2017
Table of Contents
1. Read me first 9
2. Hello GeNIe! 11
3. Introduction 29
3.1 Guide to GeNIe manual ................................................................................................ 30
3.2 GeNIe Modeler ............................................................................................................ 30
3.3 SMILE Engine ............................................................................................................... 31
3.4 Distribution information .............................................................................................. 32
3.5 GeNIe on a Mac ........................................................................................................... 36
3.6 Copyright notice .......................................................................................................... 38
3.7 Disclaimer .................................................................................................................... 39
3.8 Acknowledgments ....................................................................................................... 39
4. Decision-theoretic modeling 41
4.1 Decision analysis .......................................................................................................... 42
4.2 Discrete and continuous variables ............................................................................... 42
4.3 Probability ................................................................................................................... 43
4.4 Utility ........................................................................................................................... 44
4.5 Bayesian networks ....................................................................................................... 45
4.6 Influence diagrams ...................................................................................................... 55
4.7 Bayesian updating ....................................................................................................... 57
4.8 Solving decision models ............................................................................................... 58
4.9 Changes in structure .................................................................................................... 59
4.10 Decision support systems ............................................................................................ 59
5. Building blocks of GeNIe 63
5.1 Introduction ................................................................................................................. 64
5.2 GeNIe workspace ......................................................................................................... 65
Introduction ................................................................................................................ 655.2.1
The menu bar .............................................................................................................. 675.2.2
Graph view .................................................................................................................. 685.2.3
Tree view ..................................................................................................................... 815.2.4
Status bar .................................................................................................................... 845.2.5
Case manager .............................................................................................................. 865.2.6
Output window ........................................................................................................... 915.2.7
Help menu ................................................................................................................... 925.2.8
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GeNIe Modeler Version 2.2.1, Built on 8/4/2017
Table of Contents
5.3 Components of GeNIe models ..................................................................................... 93
Node types .................................................................................................................. 935.3.1
Canonical models ........................................................................................................ 965.3.2
Multi-attribute utility nodes ..................................................................................... 1095.3.3
Submodels ................................................................................................................. 1145.3.4
Arcs ............................................................................................................................ 1245.3.5
Node status icons ...................................................................................................... 1255.3.6
Text boxes ................................................................................................................. 1285.3.7
Annotations ............................................................................................................... 1295.3.8
5.4 Model and component properties ............................................................................. 132
Network properties ................................................................................................... 1325.4.1
Submodel properties ................................................................................................ 1425.4.2
Tools menu and Standard toolbar ............................................................................ 1455.4.3
Node properties ........................................................................................................ 1475.4.4
5.5 Visual appearance, layout, and navigation ................................................................. 182
Introduction .............................................................................................................. 1825.5.1
Viewing nodes in the Graph View ............................................................................. 1825.5.2
Zooming and full screen mode ................................................................................. 1855.5.3
Format toolbar and Layout menu ............................................................................. 1865.5.4
Graph layout functions ............................................................................................. 1915.5.5
Selection of model elements .................................................................................... 1935.5.6
Model navigation tools ............................................................................................. 1955.5.7
5.6 Saving and loading models in GeNIe .......................................................................... 197
Introduction .............................................................................................................. 1975.6.1
File menu ................................................................................................................... 2025.6.2
XDSL file format ......................................................................................................... 2065.6.3
DSL file format ........................................................................................................... 2065.6.4
Ergo file format ......................................................................................................... 2075.6.5
Netica file format ...................................................................................................... 2085.6.6
BN interchange format ............................................................................................. 2095.6.7
Hugin file format ....................................................................................................... 2095.6.8
KI file format .............................................................................................................. 2095.6.9
5.7 Inference algorithms .................................................................................................. 209
Introduction .............................................................................................................. 2095.7.1
Immediate and lazy evaluation ................................................................................. 2125.7.2
Relevance reasoning ................................................................................................. 2135.7.3
Node menu ................................................................................................................ 2165.7.4
Network menu .......................................................................................................... 2185.7.5
Bayesian networks algorithms .................................................................................. 2205.7.6
Exact algorithms ........................................................................................................................... 2205.7.6.1
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GeNIe Modeler Version 2.2.1, Built on 8/4/2017
Table of Contents
Clustering algorithm ............................................................................................................... 220
5.7.6.1.1
Relevance-based decomposition ............................................................................................ 222
5.7.6.1.2
Polytree algorithm .................................................................................................................. 222
5.7.6.1.3
Stochastic sampling algorithms .................................................................................................... 2235.7.6.2
Probabilistic Logic Sampling .................................................................................................... 223
5.7.6.2.1
Likelihood Sampling ................................................................................................................ 223
5.7.6.2.2
Self-Importance Sampling ....................................................................................................... 223
5.7.6.2.3
Backward Sampling ................................................................................................................. 223
5.7.6.2.4
AIS algorithm ........................................................................................................................... 224
5.7.6.2.5
EPIS Sampling .......................................................................................................................... 224
5.7.6.2.6
Special algorithms ........................................................................................................................ 2255.7.6.3
Probability of evidence ........................................................................................................... 225
5.7.6.3.1
Annealed MAP ........................................................................................................................ 229
5.7.6.3.2
Influence diagrams algorithms ................................................................................. 2365.7.7
Policy evaluation .......................................................................................................................... 2365.7.7.1
Find Best Policy ............................................................................................................................ 2375.7.7.2
Algorithms for continuous and hybrid models ......................................................... 2385.7.8
Introduction ................................................................................................................................. 2385.7.8.1
Autodiscretization ........................................................................................................................ 2395.7.8.2
Hybrid Forward Sampling ............................................................................................................. 2425.7.8.3
5.8 Obfuscation ............................................................................................................... 243
5.9 Program options ........................................................................................................ 249
5.10 Keyboard shortcuts .................................................................................................... 255
6. Using GeNIe 259
6.1 Introduction ............................................................................................................... 260
6.2 Bayesian networks ..................................................................................................... 260
Building a Bayesian network ..................................................................................... 2606.2.1
Useful structural transformations ............................................................................. 2606.2.2
Entering and retracting evidence .............................................................................. 2666.2.3
Virtual evidence ........................................................................................................ 2716.2.4
Viewing results .......................................................................................................... 2736.2.5
Strength of influences ............................................................................................... 2806.2.6
Controlling values ...................................................................................................... 2836.2.7
Sensitivity analysis in Bayesian networks ................................................................. 2866.2.8
6.3 Influence diagrams .................................................................................................... 291
Building an influence diagram .................................................................................. 2916.3.1
Viewing results .......................................................................................................... 3006.3.2
Sensitivity analysis in influence diagrams ................................................................. 3016.3.3
Value of information ................................................................................................. 3066.3.4
6.4 Support for diagnosis ................................................................................................. 313
Introduction .............................................................................................................. 3136.4.1
