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Learning Bayesian Networks(Neapolitan, Richard) pdf

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Learning Bayesian Networks

Richard E. Neapolitan - Prentice Hall (2003) - PDF 4,57 MB

Cover book





Contents

Preface ix

I Basics 1

1 Introduction to Bayesian Networks 3

1.1 Basics of Probability Theory . . . . . . . . . . . . . . . . . . . . 5

1.1.1 Probability Functions and Spaces . . . . . . . . . . . . . . 6

1.1.2 Conditional Probability and Independence . . . . . . . . . 9

1.1.3 Bayes’ Theorem . . . . . . . . . . . . . . . . . . . . . . . 12

1.1.4 Random Variables and Joint Probability Distributions . . 13

1.2 Bayesian Inference . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1.2.1 Random Variables and Probabilities in Bayesian Applications . . . . . . . 20

1.2.2 A Definition of Random Variables and Joint Probability

Distributions for Bayesian Inference . . . . . . . . . . . . 24

1.2.3 A Classical Example of Bayesian Inference . . . . . . . . . 27

1.3 Large Instances / Bayesian Networks . . . . . . . . . . . . . . . . 29

1.3.1 The Difficulties Inherent in Large Instances . . . . . . . . 29

1.3.2 TheMarkov Condition . . . . . . . . . . . . . . . . . . . . 31

1.3.3 Bayesian Networks . . . . . . . . . . . . . . . . . . . . . . 40

1.3.4 A Large BayesianNetwork . . . . . . . . . . . . . . . . . 43

1.4 Creating BayesianNetworks Using Causal Edges . . . . . . . . . 43

1.4.1 Ascertaining Causal Influences Using Manipulation . . . . 44

1.4.2 Causation and theMarkov Condition . . . . . . . . . . . 51

2 More DAG/Probability Relationships 65

2.1 Entailed Conditional Independencies . . . . . . . . . . . . . . . . 66

2.1.1 Examples of Entailed Conditional Independencies . . . . . 66

2.1.2 d-Separation . . . . . . . . . . . . . . . . . . . . . . . . . 70

2.1.3 Finding d-Separations . . . . . . . . . . . . . . . . . . . . 76

2.2 Markov Equivalence . . . . . . . . . . . . . . . . . . . . . . . . . 84

2.3 EntailingDependencies with aDAG . . . . . . . . . . . . . . . . 92

2.3.1 Faithfulness . . . . . . . . . . . . . . . . . . . . . . . . . . 95

2.3.2 Embedded Faithfulness . . . . . . . . . . . . . . . . . . . 99

2.4 Minimality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

2.5 Markov Blankets and Boundaries . . . . . . . . . . . . . . . . . . 108

2.6 More on Causal DAGs . . . . . . . . . . . . . . . . . . . . . . . . 110

2.6.1 The CausalMinimality Assumption . . . . . . . . . . . . 110

2.6.2 The Causal Faithfulness Assumption . . . . . . . . . . . . 111

2.6.3 The Causal Embedded Faithfulness Assumption . . . . . 112

II Inference 121

3 Inference: Discrete Variables 123

3.1 Examples of Inference . . . . . . . . . . . . . . . . . . . . . . . . 124

3.2 Pearl’sMessage-Passing Algorithm . . . . . . . . . . . . . . . . . 126

3.2.1 Inference in Trees . . . . . . . . . . . . . . . . . . . . . . . 127

3.2.2 Inference in Singly-Connected Networks . . . . . . . . . . 142

3.2.3 Inference inMultiply-Connected Networks . . . . . . . . . 153

3.2.4 Complexity of the Algorithm . . . . . . . . . . . . . . . . 155

3.3 The Noisy OR-GateModel . . . . . . . . . . . . . . . . . . . . . 156

3.3.1 TheModel . . . . . . . . . . . . . . . . . . . . . . . . . . 156

3.3.2 Doing InferenceWith theModel . . . . . . . . . . . . . . 160

3.3.3 FurtherModels . . . . . . . . . . . . . . . . . . . . . . . . 161

3.4 Other Algorithms that Employ the DAG. . . . . . . . . . . . . . 161

3.5 The SPI Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . 162

3.5.1 The Optimal Factoring Problem . . . . . . . . . . . . . . 163

3.5.2 Application to Probabilistic Inference . . . . . . . . . . . 168

3.6 Complexity of Inference . . . . . . . . . . . . . . . . . . . . . . . 170

3.7 Relationship to Human Reasoning . . . . . . . . . . . . . . . . . 171

3.7.1 The Causal NetworkModel . . . . . . . . . . . . . . . . . 171

3.7.2 Studies Testing the Causal NetworkModel . . . . . . . . 173

4 More Inference Algorithms 181

4.1 Continuous Variable Inference . . . . . . . . . . . . . . . . . . . . 181

4.1.1 The Normal Distribution . . . . . . . . . . . . . . . . . . 182

4.1.2 An Example Concerning Continuous Variables . . . . . . 183

4.1.3 An Algorithm for Continuous Variables . . . . . . . . . . 185

4.2 Approximate Inference . . . . . . . . . . . . . . . . . . . . . . . . 205

4.2.1 A Brief Review of Sampling . . . . . . . . . . . . . . . . . 205

4.2.2 Logic Sampling . . . . . . . . . . . . . . . . . . . . . . . . 211

4.2.3 LikelihoodWeighting . . . . . . . . . . . . . . . . . . . . . 217

4.3 Abductive Inference . . . . . . . . . . . . . . . . . . . . . . . . . 221

4.3.1 Abductive Inference in Bayesian Networks . . . . . . . . . 221

4.3.2 A Best-First Search Algorithm for Abductive Inference . . 224

5 Influence Diagrams 239

5.1 Decision Trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239

5.1.1 Simple Examples . . . . . . . . . . . . . . . . . . . . . . . 239

5.1.2 Probabilities, Time, and Risk Attitudes . . . . . . . . . . 242

5.1.3 SolvingDecision Trees . . . . . . . . . . . . . . . . . . . . 245

5.1.4 More Examples . . . . . . . . . . . . . . . . . . . . . . . . 245

5.2 Influence Diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . 259

5.2.1 Representing with Influence Diagrams . . . . . . . . . . . 259

5.2.2 Solving Influence Diagrams . . . . . . . . . . . . . . . . . 266

5.3 Dynamic Networks . . . . . . . . . . . . . . . . . . . . . . . . . . 272

5.3.1 Dynamic Bayesian Networks . . . . . . . . . . . . . . . . 272

5.3.2 Dynamic Influence Diagrams . . . . . . . . . . . . . . . . 279

III Learning 291

6 Parameter Learning: Binary Variables 293

6.1 Learning a Single Parameter . . . . . . . . . . . . . . . . . . . . . 294

6.1.1 Probability Distributions of Relative Frequencies . . . . . 294

6.1.2 Learning a Relative Frequency . . . . . . . . . . . . . . . 303

6.2 More on the Beta Density Function . . . . . . . . . . . . . . . . . 310

6.2.1 Non-integral Values of a and b . . . . . . . . . . . . . . . 311

6.2.2 Assessing the Values of a and b . . . . . . . . . . . . . . . 313

6.2.3 Why the BetaDensity Function? . . . . . . . . . . . . . . 315

6.3 Computing a Probability Interval . . . . . . . . . . . . . . . . . . 319

6.4 Learning Parameters in a Bayesian Network . . . . . . . . . . . . 323

6.4.1 Urn Examples . . . . . . . . . . . . . . . . . . . . . . . . 323

6.4.2 Augmented Bayesian Networks . . . . . . . . . . . . . . . 331

6.4.3 Learning Using an Augmented Bayesian Network . . . . . 336

6.4.4 A Problem with Updating; Using an Equivalent Sample

Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348

6.5 Learning withMissing Data Items . . . . . . . . . . . . . . . . . 357

6.5.1 Data ItemsMissing at Random . . . . . . . . . . . . . . . 358

6.5.2 Data ItemsMissing Not at Random . . . . . . . . . . . . 363

6.6 Variances in ComputedRelative Frequencies . . . . . . . . . . . . 364

6.6.1 A Simple Variance Determination . . . . . . . . . . . . . 364

6.6.2 The Variance and Equivalent Sample Size . . . . . . . . . 366

6.6.3 Computing Variances in Larger Networks . . . . . . . . . 372

6.6.4 When Do Variances Become Large? . . . . . . . . . . . . 373

7 More Parameter Learning 381

7.1 Multinomial Variables . . . . . . . . . . . . . . . . . . . . . . . . 381

7.1.1 Learning a Single Parameter . . . . . . . . . . . . . . . . 381

7.1.2 More on the Dirichlet Density Function . . . . . . . . . . 388

7.1.3 Computing Probability Intervals andRegions . . . . . . . 389

7.1.4 Learning Parameters in a Bayesian Network . . . . . . . . 392

7.1.5 Learning withMissing Data Items . . . . . . . . . . . . . 398

7.1.6 Variances in Computed Relative Frequencies . . . . . . . 398

7.2 Continuous Variables . . . . . . . . . . . . . . . . . . . . . . . . . 398

7.2.1 Normally Distributed Variable . . . . . . . . . . . . . . . 399

7.2.2 Multivariate Normally Distributed Variables . . . . . . . 413

7.2.3 Gaussian Bayesian Networks . . . . . . . . . . . . . . . . 425

8 Bayesian Structure Learning 441

8.1 Learning Structure: Discrete Variables . . . . . . . . . . . . . . . 441

8.1.1 Schema for Learning Structure . . . . . . . . . . . . . . . 442

8.1.2 Procedure for Learning Structure . . . . . . . . . . . . . . 445

8.1.3 Learning From a Mixture of Observational and Experimental

Data. . . . . . . . . . . . . . . . . . . . . . . . . . 449

8.1.4 Complexity of Structure Learning . . . . . . . . . . . . . 450

8.2 Model Averaging . . . . . . . . . . . . . . . . . . . . . . . . . . . 451

8.3 Learning Structure withMissingData . . . . . . . . . . . . . . . 452

8.3.1 Monte CarloMethods . . . . . . . . . . . . . . . . . . . . 453

8.3.2 Large-Sample Approximations . . . . . . . . . . . . . . . 462

8.4 ProbabilisticModel Selection . . . . . . . . . . . . . . . . . . . . 468

8.4.1 ProbabilisticModels . . . . . . . . . . . . . . . . . . . . . 468

8.4.2 TheModel Selection Problem . . . . . . . . . . . . . . . . 472

8.4.3 Using the Bayesian Scoring Criterion for Model Selection 473

8.5 Hidden Variable DAGModels . . . . . . . . . . . . . . . . . . . . 476

8.5.1 Models ContainingMore Conditional Independencies than

DAGModels . . . . . . . . . . . . . . . . . . . . . . . . . 477

8.5.2 Models Containing the Same Conditional Independencies

as DAGModels . . . . . . . . . . . . . . . . . . . . . . . . 479

8.5.3 Dimension of Hidden Variable DAGModels . . . . . . . . 484

8.5.4 Number ofModels andHidden Variables . . . . . . . . . . 486

8.5.5 EfficientModel Scoring . . . . . . . . . . . . . . . . . . . 487

8.6 Learning Structure: Continuous Variables . . . . . . . . . . . . . 491

8.6.1 The Density Function of D . . . . . . . . . . . . . . . . . 491

8.6.2 The Density function of D Given aDAGpattern . . . . . 495

8.7 Learning Dynamic Bayesian Networks . . . . . . . . . . . . . . . 505

9 Approximate Bayesian Structure Learning 511

9.1 ApproximateModel Selection . . . . . . . . . . . . . . . . . . . . 511

9.1.1 Algorithms that Search over DAGs . . . . . . . . . . . . . 513

9.1.2 Algorithms that Search over DAGPatterns . . . . . . . . 518

9.1.3 An Algorithm Assuming Missing Data or Hidden Variables529

9.2 ApproximateModel Averaging . . . . . . . . . . . . . . . . . . . 531

9.2.1 AModel Averaging Example . . . . . . . . . . . . . . . . 532

9.2.2 ApproximateModel Averaging UsingMCMC . . . . . . . 533

10 Constraint-Based Learning 541

10.1 Algorithms Assuming Faithfulness . . . . . . . . . . . . . . . . . 542

10.1.1 Simple Examples . . . . . . . . . . . . . . . . . . . . . . . 542

10.1.2 Algorithms for Determining DAGpatterns . . . . . . . . 545

10.1.3 Determining if a Set Admits a Faithful DAG Representation552

10.1.4 Application to Probability . . . . . . . . . . . . . . . . . . 560

10.2 Assuming Only Embedded Faithfulness . . . . . . . . . . . . . . 561

10.2.1 Inducing Chains . . . . . . . . . . . . . . . . . . . . . . . 562

10.2.2 A Basic Algorithm . . . . . . . . . . . . . . . . . . . . . . 568

10.2.3 Application to Probability . . . . . . . . . . . . . . . . . . 590

10.2.4 Application to Learning Causal Influences1 . . . . . . . . 591

10.3 Obtaining the d-separations . . . . . . . . . . . . . . . . . . . . . 599

10.3.1 Discrete Bayesian Networks . . . . . . . . . . . . . . . . . 600

10.3.2 Gaussian Bayesian Networks . . . . . . . . . . . . . . . . 603

10.4 Relationship to Human Reasoning . . . . . . . . . . . . . . . . . 604

10.4.1 Background Theory . . . . . . . . . . . . . . . . . . . . . 604

10.4.2 A Statistical Notion of Causality . . . . . . . . . . . . . . 606

11 More Structure Learning 617

11.1 Comparing theMethods . . . . . . . . . . . . . . . . . . . . . . . 617

11.1.1 A Simple Example . . . . . . . . . . . . . . . . . . . . . . 618

11.1.2 Learning College Attendance Influences . . . . . . . . . . 620

11.1.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . 623

11.2 Data Compression Scoring Criteria . . . . . . . . . . . . . . . . . 624

11.3 Parallel Learning of Bayesian Networks . . . . . . . . . . . . . . 624

11.4 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624

11.4.1 Structure Learning . . . . . . . . . . . . . . . . . . . . . . 625

11.4.2 Inferring Causal Relationships . . . . . . . . . . . . . . . 633

IV Applications 647

12 Applications 649

12.1 Applications Based on Bayesian Networks . . . . . . . . . . . . . 649

12.2 Beyond Bayesian networks . . . . . . . . . . . . . . . . . . . . . . 655

Bibliography 657

Index 686