A review on algorithms for maximum clique problems

The maximum clique problem (MCP) is to determine in a graph a clique (i.e., a complete subgraph) of maximum cardinality. The MCP is notable for its capability of modeling other combinatorial problems and real-world applications. As one of the most studied NP-hard problems, many algorithms are available in the literature and new methods are continually being proposed. Given that the two existing surveys on the MCP date back to 1994 and 1999 respectively, one primary goal of this paper is to provide an updated and comprehensive review on both exact and heuristic MCP algorithms, with a special focus on recent developments. To be informative, we identify the general framework followed by these algorithms and pinpoint the key ingredients that make them successful. By classifying the main search strategies and putting forward the critical elements of the most relevant clique methods, this review intends to encourage future development of more powerful methods and motivate new applications of the clique approaches

On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks

Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed

Fine-grained Search Space Classification for Hard Enumeration Variants of Subset Problems

We propose a simple, powerful, and flexible machine learning framework for (i) reducing the search space of computationally difficult enumeration variants of subset problems and (ii) augmenting existing state-of-the-art solvers with informative cues arising from the input distribution. We instantiate our framework for the problem of listing all maximum cliques in a graph, a central problem in network analysis, data mining, and computational biology. We demonstrate the practicality of our approach on real-world networks with millions of vertices and edges by not only retaining all optimal solutions, but also aggressively pruning the input instance size resulting in several fold speedups of state-of-the-art algorithms. Finally, we explore the limits of scalability and robustness of our proposed framework, suggesting that supervised learning is viable for tackling NP-hard problems in practice.Comment: AAAI 201

Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

Construction of near-optimal vertex clique covering for real-world networks

We propose a method based on combining a constructive and a bounding heuristic to solve the vertex clique covering problem (CCP), where the aim is to partition the vertices of a graph into the smallest number of classes, which induce cliques. Searching for the solution to CCP is highly motivated by analysis of social and other real-world networks, applications in graph mining, as well as by the fact that CCP is one of the classical NP-hard problems. Combining the construction and the bounding heuristic helped us not only to find high-quality clique coverings but also to determine that in the domain of real-world networks, many of the obtained solutions are optimal, while the rest of them are near-optimal. In addition, the method has a polynomial time complexity and shows much promise for its practical use. Experimental results are presented for a fairly representative benchmark of real-world data. Our test graphs include extracts of web-based social networks, including some very large ones, several well-known graphs from network science, as well as coappearance networks of literary works' characters from the DIMACS graph coloring benchmark. We also present results for synthetic pseudorandom graphs structured according to the Erdös-Renyi model and Leighton's model

Parallel Maximum Clique Algorithms with Applications to Network Analysis and Storage

We propose a fast, parallel maximum clique algorithm for large sparse graphs that is designed to exploit characteristics of social and information networks. The method exhibits a roughly linear runtime scaling over real-world networks ranging from 1000 to 100 million nodes. In a test on a social network with 1.8 billion edges, the algorithm finds the largest clique in about 20 minutes. Our method employs a branch and bound strategy with novel and aggressive pruning techniques. For instance, we use the core number of a vertex in combination with a good heuristic clique finder to efficiently remove the vast majority of the search space. In addition, we parallelize the exploration of the search tree. During the search, processes immediately communicate changes to upper and lower bounds on the size of maximum clique, which occasionally results in a super-linear speedup because vertices with large search spaces can be pruned by other processes. We apply the algorithm to two problems: to compute temporal strong components and to compress graphs.Comment: 11 page

Partitioning networks into cliques: a randomized heuristic approach

In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes

A Tutorial on Clique Problems in Communications and Signal Processing

Since its first use by Euler on the problem of the seven bridges of K\"onigsberg, graph theory has shown excellent abilities in solving and unveiling the properties of multiple discrete optimization problems. The study of the structure of some integer programs reveals equivalence with graph theory problems making a large body of the literature readily available for solving and characterizing the complexity of these problems. This tutorial presents a framework for utilizing a particular graph theory problem, known as the clique problem, for solving communications and signal processing problems. In particular, the paper aims to illustrate the structural properties of integer programs that can be formulated as clique problems through multiple examples in communications and signal processing. To that end, the first part of the tutorial provides various optimal and heuristic solutions for the maximum clique, maximum weight clique, and $k$-clique problems. The tutorial, further, illustrates the use of the clique formulation through numerous contemporary examples in communications and signal processing, mainly in maximum access for non-orthogonal multiple access networks, throughput maximization using index and instantly decodable network coding, collision-free radio frequency identification networks, and resource allocation in cloud-radio access networks. Finally, the tutorial sheds light on the recent advances of such applications, and provides technical insights on ways of dealing with mixed discrete-continuous optimization problems

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool