Biased random walk with restart for essential proteins prediction
Pengli Lu(卢鹏丽)1,†, Yuntian Chen(陈云天)1, Teng Zhang(张腾)1, and Yonggang Liao(廖永刚)2
1 School of Computer and Communication, Lanzhou University of Technology, Lanzhou 730050, China; 2 China Mobile Communications Group Gansu Co., Ltd., Lanzhou 730070, China
Abstract Predicting essential proteins is crucial for discovering the process of cellular organization and viability. We propose biased random walk with restart algorithm for essential proteins prediction, called BRWR. Firstly, the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal, neglecting the influence of the similarity structure on the transition probability. To address this problem, we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity. The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure. Secondly, we use gene ontology (GO) terms score and subcellular score to calculate the initial probability vector of the random walk with restart. Finally, when the biased random walk with restart process reaches steady state, the protein importance score is obtained. In order to demonstrate superiority of BRWR, we conduct experiments on the YHQ, BioGRID, Krogan and Gavin PPI networks. The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance. Especially, compared with the contrast methods, the improvements of BRWR in terms of the ACC results range in 1.4%-5.7%, 1.3%-11.9%, 2.4%-8.8%, and 0.8%-14.2%, respectively. Therefore, BRWR is effective and reasonable.
Received: 23 April 2022
Revised: 06 June 2022
Accepted manuscript online: 18 June 2022
PACS:
89.75.-k
(Complex systems)
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11861045 and 62162040).
Corresponding Authors:
Pengli Lu
E-mail: lupengli88@163.com
Cite this article:
Pengli Lu(卢鹏丽), Yuntian Chen(陈云天), Teng Zhang(张腾), and Yonggang Liao(廖永刚) Biased random walk with restart for essential proteins prediction 2022 Chin. Phys. B 31 118901
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