A Network Clustering Algorithm for Protein Complex Detection Fused with Power-Law Distribution Characteristic

Abstract

Network clustering for mining protein complexes from protein–protein interaction (PPI) networks has emerged as a prominent research area in data mining and bioinformatics. Accurately identifying complexes plays a crucial role in comprehending cellular organization and functionality. Network characteristics are often useful in enhancing the performance of protein complex detection methods. Many protein complex detection algorithms have been proposed, primarily focusing on local micro-topological structure metrics while overlooking the potential power-law distribution characteristic of community sizes at the macro global level. The effective use of this distribution characteristic information may be beneficial for mining protein complexes. This paper proposes a network clustering algorithm for protein complex detection fused with power-law distribution characteristic. The clustering algorithm constructs a cluster generation model based on scale-free power-law distribution to generate a cluster with a dense center and relatively sparse periphery. Following the cluster generation model, a candidate cluster is obtained. From a global perspective, the number distribution of clusters of varying sizes is taken into account. If the candidate cluster aligns with the constraints defined by the power-law distribution function of community sizes, it is designated as the final cluster; otherwise, it is discarded. To assess the prediction performance of the proposed algorithm, the gold standard complex sets CYC2008 and MIPS are employed as benchmarks. The algorithm is compared to DPClus, IPCA, SEGC, Core, SR-MCL, and ELF-DPC in terms of F-measure and Accuracy on several widely used protein–protein interaction networks. The experimental results show that the algorithm can effectively detect protein complexes and is superior to other comparative algorithms. This study further enriches the connection between analyzing complex network topology features and mining network function modules, thereby significantly contributing to the improvement of protein complex detection performance.