CONTENTS
AUTHORSHIP'S DECLARATION ...................................................................... i
ACKNOWLEDGEMENT..................................................................................... ii
CONTENTS ..........................................................................................................iii
ABBREVIATIONS............................................................................................... vi
LIST OF TABLES ............................................................................................... vii
LIST OF FIGURES ............................................................................................ viii
INTRODUCTION ................................................................................................. 1
CHAPTER 1. BACKGROUND .......................................................................... 10
1.1. Basic concepts................................................................................................. 10
1.1.1. Heterogeneous information networks ................................................. 11
1.1.2. Biological systems ............................................................................. 13
1.1.3. Non-coding RNAs (ncRNAs) ............................................................ 14
1.2. Link prediction in heterogeneous information networks .................................. 15
1.2.1. Link prediction problem..................................................................... 15
1.2.2. Link prediction methods .................................................................... 16
1.2.3. Link prediction applications in biological systems ............................. 19
1.3. Computational methods for predicting associations between non-coding RNAs
and diseases ........................................................................................................... 22
1.3.1. Predicting non coding RNA-disease association prediction as a link
prediction problem .......................................................................................... 22
1.3.2. Materials used for ncRNA-disease association prediction .................. 22
1.3.3. Similarity calculation and network construction ................................. 26
1.3.4. Literature review of computational methods to predict ncRNA-disease
associations ..................................................................................................... 27
1.4. Thesis’s research directions ............................................................................. 36
1.5. Some evaluation methods and metrics to evaluate prediction performance ...... 37
1.5.1. Cross-validation ................................................................................. 37
1.5.2. Area under Roc Curve (AUC) ............................................................ 38