Qualitative Comparison of Community Detection Algorithms

Community detection is a very active field in complex networks analysis, consisting in identifying groups of nodes more densely interconnected relatively to the rest of the network. The existing algorithms are usually tested and compared on real-world and artificial networks, their performance being assessed through some partition similarity measure. However, artificial networks realism can be questioned, and the appropriateness of those measures is not obvious. In this study, we take advantage of recent advances concerning the characterization of community structures to tackle these questions. We first generate networks thanks to the most realistic model available to date. Their analysis reveals they display only some of the properties observed in real-world community structures. We then apply five community detection algorithms on these networks and find out the performance assessed quantitatively does not necessarily agree with a qualitative analysis of the identified communities. It therefore seems both approaches should be applied to perform a relevant comparison of the algorithms.Comment: DICTAP 2011, The International Conference on Digital Information and Communication Technology and its Applications, Dijon : France (2011

Towards realistic artificial benchmark for community detection algorithms evaluation

Assessing the partitioning performance of community detection algorithms is one of the most important issues in complex network analysis. Artificially generated networks are often used as benchmarks for this purpose. However, previous studies showed their level of realism have a significant effect on the algorithms performance. In this study, we adopt a thorough experimental approach to tackle this problem and investigate this effect. To assess the level of realism, we use consensual network topological properties. Based on the LFR method, the most realistic generative method to date, we propose two alternative random models to replace the Configuration Model originally used in this algorithm, in order to increase its realism. Experimental results show both modifications allow generating collections of community-structured artificial networks whose topological properties are closer to those encountered in real-world networks. Moreover, the results obtained with eleven popular community identification algorithms on these benchmarks show their performance decrease on more realistic networks

Comparative Evaluation of Community Detection Algorithms: A Topological Approach

Community detection is one of the most active fields in complex networks analysis, due to its potential value in practical applications. Many works inspired by different paradigms are devoted to the development of algorithmic solutions allowing to reveal the network structure in such cohesive subgroups. Comparative studies reported in the literature usually rely on a performance measure considering the community structure as a partition (Rand Index, Normalized Mutual information, etc.). However, this type of comparison neglects the topological properties of the communities. In this article, we present a comprehensive comparative study of a representative set of community detection methods, in which we adopt both types of evaluation. Community-oriented topological measures are used to qualify the communities and evaluate their deviation from the reference structure. In order to mimic real-world systems, we use artificially generated realistic networks. It turns out there is no equivalence between both approaches: a high performance does not necessarily correspond to correct topological properties, and vice-versa. They can therefore be considered as complementary, and we recommend applying both of them in order to perform a complete and accurate assessment

A Comparison of Network Clustering Algorithms in Keyword Network Analysis: A Case Study with Geography Conference Presentations

The keyword network analysis has been used for summarizing research trends, and network clustering algorithms play important roles in identifying major research themes. In this paper, we performed a comparative analysis of network clustering algorithms to find out their performances, effectiveness, and impact on cluster themes. The AAG (American Association for Geographers) conference datasets were used in this research. We evaluated seven algorithms with modularity, processing time, and cluster members. The Louvain algorithm showed the best performance in terms of modularity and processing time, followed by the Fast Greedy algorithm. Examining cluster members also showed very coherent connections among cluster members. This study may help researchers to choose a suitable network clustering algorithm and understand geography research trends and topical fields

A Comparative Study of Cluster Detection Algorithms in Protein–Protein Interaction for Drug Target Discovery and Drug Repurposing

The interactions between drugs and their target proteins induce altered expression of genes involved in complex intracellular networks. The properties of these functional network modules are critical for the identification of drug targets, for drug repurposing, and for understanding the underlying mode of action of the drug. The topological modules generated by a computational approach are defined as functional clusters. However, the functions inferred for these topological modules extracted from a large-scale molecular interaction network, such as a protein–protein interaction (PPI) network, could differ depending on different cluster detection algorithms. Moreover, the dynamic gene expression profiles among tissues or cell types causes differential functional interaction patterns between the molecular components. Thus, the connections in the PPI network should be modified by the transcriptomic landscape of specific cell lines before producing topological clusters. Here, we systematically investigated the clusters of a cell-based PPI network by using four cluster detection algorithms. We subsequently compared the performance of these algorithms for target gene prediction, which integrates gene perturbation data with the cell-based PPI network using two drug target prioritization methods, shortest path and diffusion correlation. In addition, we validated the proportion of perturbed genes in clusters by finding candidate anti-breast cancer drugs and confirming our predictions using literature evidence and cases in the ClinicalTrials.gov. Our results indicate that the Walktrap (CW) clustering algorithm achieved the best performance overall in our comparative study