PT  - JOURNAL ARTICLE
AU  - Dong Li
AU  - Zexuan Zhu
AU  - Zhisong Pan
AU  - Guyu Hu
AU  - Shan He
TI  - Extracting active modules from multilayer PPI network: a continuous optimization approach
AID  - 10.1101/211433
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 211433
4099  - http://biorxiv.org/content/early/2017/10/30/211433.short
4100  - http://biorxiv.org/content/early/2017/10/30/211433.full
AB  - Active modules identification has received much attention due to its ability to reveal regulatory and signaling mechanisms of a given cellular response. Most existing algorithms identify active modules by extracting connected nodes with high activity scores from a graph. These algorithms do not consider other topological properties such as community structure, which may correspond to functional units. In this paper, we propose an active module identification algorithm based on a novel objective function, which considers both and network topology and nodes activity. This objective is formulated as a constrained quadratic programming problem, which is convex and can be solved by iterative methods. Furthermore, the framework is extended to the multilayer dynamic PPI networks. Empirical results on the single layer and multilayer PPI networks show the effectiveness of proposed algorithms.Availability: The package and code for reproducing all results and figures are available at https://github.com/fairmiracle/ModuleExtraction.