title: Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms.
abstract: The inference of gene regulatory networks is a core problem in systems biology. Many inference algorithms have been proposed and all suffer from false positives. In this paper, we use the minimum description length (MDL) principle to reduce the rate of false positives for best-fit algorithms. The performance of these algorithms is evaluatedviatwo metrics: the normalized-edge Hamming distance and the steady-state distribution distance. Results for synthetic networks and a well-studied budding-yeast cell cycle network show that MDL-based filtering is more effective than filtering based on conditional mutual information (CMI). In addition, MDL-based filtering provides better inference than the MDL algorithm itself.
authors.affiliation: Department of Physics and Electronic information engineering, Wenzhou University, Wenzhou, 325035 Zhejiang China.
authors.forename: Jie
authors.initials: J
authors.lastname: Fang
authors.affiliation: Department of Physics and Electronic information engineering, Wenzhou University, Wenzhou, 325035 Zhejiang China.
authors.forename: Hongjia
authors.initials: H
authors.lastname: Ouyang
authors.affiliation: Department of Physics and Electronic information engineering, Wenzhou University, Wenzhou, 325035 Zhejiang China.
authors.forename: Liangzhong
authors.initials: L
authors.lastname: Shen
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University, College Station, 33101 TX USA.|Center for Bioinformatics and Genomics Systems, College Station, 33101 TX USA.
authors.forename: Edward R
authors.initials: ER
authors.lastname: Dougherty
authors.affiliation: Department of Physics and Electronic information engineering, Wenzhou University, Wenzhou, 325035 Zhejiang China.|Department of Electrical and Computer Engineering, Texas A&M University, College Station, 33101 TX USA.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Liu
keywords: Best-fit; Boolean network; Conditional mutual information; Minimum description length principle