1. Introduction

2. Review of existing methods for complex detection
2.1. Taxonomy of existing methods
2.2. Methods based solely on graph clustering
2.3. Methods incorporating core-attachment structure
2.4. Methods incorporating functional information
2.5. Methods incorporating evolutionary information
2.6. Methods based on cooperative and exclusive interactions
2.7. Incorporating other possible kinds of information

3. Comparative assessment of existing methods
3.1. Our assessment of some complex detection methods

4. Open challenges in complex detection from PPI networks
4.1. Challenges from interaction datasets
4.2. Challenges from existing complex detection methods

5. Conclusions