Parallel Algorithms for Bayesian Networks Structure Learning with ...

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Graduate Theses and Dissertations

Graduate College

2012

Parallel Algorithms for Bayesian Networks Structure Learning with Applications in Systems Biology Olga Nikolova Iowa State University

Follow this and additional works at: http://lib.dr.iastate.edu/etd Part of the Bioinformatics Commons Recommended Citation Nikolova, Olga, "Parallel Algorithms for Bayesian Networks Structure Learning with Applications in Systems Biology" (2012). Graduate Theses and Dissertations. 12564. http://lib.dr.iastate.edu/etd/12564

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Parallel algorithms for Bayesian networks structure learning with applications in systems biology

by

Olga Nikolova

A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY

Major: Bioinformatics and Computational Biology

Program of Study Committee: Srinivas Aluru, Co-major Professor Patrick Schnable, Co-major Professor Dan Nettleton Julie Dickerson Guang Song

Iowa State University Ames, Iowa 2012 c Olga Nikolova, 2012. All rights reserved. Copyright

ii

DEDICATION

I dedicate this work to my parents, Svetlana Nikolova and Hristo Nikolov.

iii

TABLE OF CONTENTS

LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

vi

LIST OF TABLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

ix

LIST OF ALGORITHMS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

xi

ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

xiii

CHAPTER 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1

1.1

1.2

Background and Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1

1.1.1

Gene Regulatory Networks . . . . . . . . . . . . . . . . . . . . . . . . .

1

1.1.2

Bayesian Networks as a Model for Gene Regulatory Networks . . . . . .

3

1.1.3

Exact Bayesian Network Structure Learning . . . . . . . . . . . . . . . .

4

1.1.4

Heuristic Bayesian Network Structure Learning . . . . . . . . . . . . . .

6

Concepts of Bayesian Networks and Structure Learning . . . . . . . . . . . . .

7

1.2.1

Markov Assumption and Bayesian Networks . . . . . . . . . . . . . . . .

7

1.2.2

Optimal Structure Learning . . . . . . . . . . . . . . . . . . . . . . . . .

8

1.2.3

Scoring Functions

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

9

1.2.4

Faithfulness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

12

1.2.5

D-separation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

13

1.2.6

Constraints-based Learning . . . . . . . . . . . . . . . . . . . . . . . . .

13

iv 1.2.7

Markov Boundary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

14

1.2.8

Markov Equivalence . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

14

CHAPTER 2. Parallel Globally Optimal Structure Learning of B