Advanced clique algorithms for protein product graphs

Optimal parallel time bounds for the maximum clique problem on intervals

Improving the performance of stochastic local search for maximum vertex weight clique problem using programming by optimization

A new upper bound for the maximum weight clique problem

In communication networks such as social networks, wireless networks and biology networks, it is of importance to find all cliques which can help understand the network topology. The clique structures can also be utilized in facilitating message forwarding in wireless networks. For instance, using a set of cliques of maximal and disjoint, one of the nodes in each clique can be elected to forward messages, by which the duplicate message transmissions can be efficiently reduced. Further, it is well known that the maximum clique problem (MCP) is closely related to the maximum independent set and the vertex cover problems. In recent years, the fundamental problem of finding maximal cliques or maximum cliques has attracted lots of attentions. However, few of these works focus on distributed solutions in wireless networks. In this paper, we pay our attention to this missing corner of research. Specifically, we first give a distributed algorithm which can compute all maximal cliques in a wireless network represented by a graph. The algorithm takes O(n) time and uses O(mn) messages, where n is the number of nodes and m the number of edges. Then, with the proposed algorithms MCP (maximum clique problem) and UMCP (unique MCP), we show that a unique maximum clique can be selected from all maximal cliques in O(n) rounds and using O(mn) messages. To the best of our knowledge, our algorithms are the first deterministic distributed solutions for MCP in wireless networks.

The intent of maximum clique problem is to discover a clique of largest size or a complete subgraph in a graph; for a graph clique is a subgraph which is complete i.e., every vertex of that subgraph are adjacent to each other. It belongs to the category of the NP-hard problems, for which many solutions exist and many more are continuously being proposed. We are recapitulating the core idea and search strategies of few of the branch and bound based recently proposed algorithms. Intent of this work is to give a comparative study of newly proposed solutions to maximum clique problem which will be helpful to decide which algorithm is efficient for a given graph. It also instigates to design more efficient solutions for maximum clique problem.

This paper explores techniques to quickly solve the maximum weight clique problem (MWCP) in very large scale sparse graphs. Due to their size, and the hardness of MWCP, it is infeasible to solve many of these graphs with exact algorithms. Although recent heuristic algorithms make progress in solving MWCP in large graphs, they still need considerable time to get a high-quality solution. In this work, we focus on solving MWCP for large sparse graphs within a short time limit. We propose a new method for MWCP which interleaves clique finding with data reduction rules. We propose novel ideas to make this process efficient, and develop an algorithm called FastWClq. Experiments on a broad range of large sparse graphs show that FastWClq finds better solutions than state-of-the-art algorithms while the running time of FastWClq is much shorter than the competitors for most instances. Further, FastWClq proves the optimality of its solutions for roughly half of the graphs, all with at least 105 vertices, with an average time of 21 seconds.

<title>Abstract</title> The maximum clique problem(MCP) is to find the largest complete subgraph in an undirected graph, that is, the subgraph in which there are edges between every two different vertices. It is an NP-Hard problem with wide applications, including bioinformatics, social networks, data mining, and other fields. This paper proposes an improved algorithm that dynamically tracks the maximum clique size by encoding prior constraints on the vertex count—derived from Turán's theorem and complete graph properties—into global variables through quantum circuit pre-detection. The algorithm further synergizes with Grover's search to optimize the solution space. Our auxiliary-qubit encoding scheme dynamically tracks clique sizes during quantum search, eliminating iterative measurements, achieving MCP solution with $O\left ( \sqrt{2^{n } } \right ) $ Grover iterations and $O\left ( 1 \right ) $ measurements. This represents an $\boldsymbol{n}$-fold improvement over state-of-the-art Grover-based methods, which require $O(n\sqrt{2^n})$ iterations and $O(n)$ measurements for $n$-vertex graphs. We validate algorithmic correctness through simulations on IBM's Qiskit platform and benchmark qubit/gate efficiency against existing Grover-based MCP solvers.

The faces in a 2D fine drawing of an object provide important information for the reconstruction of its 3D geometry. In this paper, a graph-based optimization method is proposed for identifying the faces is a line drawing. The face identification is formulated as a maximum weight clique problem. This formulation is proven to be equivalent to the formulation proposed by Shpitalni and Upson (1996). The advantage of our formulation is that it enables one to develop a much faster algorithm to find the faces in a drawing. The significant improvement in speed is derived from two algorithms provided: the depth-first graph search for quickly generating possible faces from a drawing; and the maximum weight clique finding for obtaining the optimal face configurations of the drawing. The experimental results shown that our algorithm generates the same results of face identification as Shpitalni and Lipson's method, but is much faster when dealing with objects of more than 20 faces.

Computing maximum k-defective cliques in massive graphs

In this paper, we study the problem of designing in-place algorithms for finding the maximum clique in the intersection graphs of axis-parallel rectangles and disks in 2D. We first propose O(n 2logn) time in-place algorithms for finding the maximum clique of the intersection graphs of a set of axis-parallel rectangles of arbitrary sizes. For the rectangle intersection graph of fixed height rectangles, the time complexity can be slightly improved to O(nlogn + nK), where K is the size of the maximum clique. For disk graphs, we consider two variations of the maximum clique problem, namely geometric clique and graphical clique. The time complexity of our algorithm for finding the largest geometric clique is O(n 2logn), and it works for disks of arbitrary radii. For graphical clique, our proposed algorithm works for unit disks (i.e., of same radii) and the worst case time complexity is O(n 2 + mK 4); m is the number of edges in the unit disk intersection graph, and K is the size of the largest clique in that graph. It uses O(n 4) time in-place computation of maximum matching in a bipartite graph, which is of independent interest. All these algorithms need O(1) work space in addition to the input array \(\cal R\).KeywordsBipartite GraphUnit DiskBottom BoundaryMaximum CliqueIntersection GraphThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This paper considers a family of cutting planes, recently developed for mixed 0–1 polynomial programs and shows that they define facets for the maximum edge-weighted clique problem. There exists a polynomial time exact separation algorithm for these inequalities. The result of this paper may contribute to the development of more efficient algorithms for the maximum edge-weighted clique problem that use cutting planes.

In this paper, we single out the following particular case of the clique search problem. The vertices of the given graph are legally colored with k colors and we are looking for a clique with k nodes in the graph. In other words, we want to decide if a given k-partite graph contains a clique with k nodes. The maximum clique problem asks for finding a maximum clique in a given finite simple graph. The problem of deciding if the given graph contains a clique with k vertices is called the k-clique problem. The first problem is NP-hard and the second one is NP-complete. The special clique search problem, we propose, is still an NP-complete problem. We will show that the k-clique problem in the special case of k-partite graphs is more tractable than in the general case. In order to illustrate the possible practical utility of this restricted type clique search problem we will show that the job shop scheduling problem can be reduced to such a clique search problem in a suitable constructed graph. We carry out numerical experiments to assess the efficiency of the approach. It is a common practice that before one embarks on a large scale clique search typically one attempts to simplify and tidy up the given graph. This procedure is commonly referred as preconditioning or kernelization of the given graph. Of course, the preconditioning or kernelization is meant with respect to the given type of clique search problem. The other main topic of the paper is to describe a number of kernelization methods tailored particularly to the proposed special k-clique problem. Some of these techniques works in connection with the generic k-clique problem. In these situations, we will see that they are more efficient in the case of k-partite graphs. Some other preconditioning methods applicable only to k-partite graphs. We illustrate how expedient these preconditioning methods can be by solving non-trivial scheduling problems to optimality employing only kernelization techniques dispensing with exhaustive clique search algorithms altogether.

The radio-frequency (RF) technology is a scalable solution for the backhaul planning. However, its performance is limited in terms of data rate and latency. Free Space Optical (FSO) backhaul, on the other hand, offers a higher data rate but is sensitive to weather conditions. To combine the advantages of RF and FSO backhauls, this paper proposes a cost-efficient backhaul network using the hybrid RF/FSO technology. To ensure a resilient backhaul, the paper imposes a given degree of redundancy by connecting each node through K link-disjoint paths so as to cope with potential link failures. Hence, the network planning problem considered in this paper is the one of minimizing the total deployment cost by choosing the appropriate link type, i.e., either hybrid RF/FSO or optical fiber (OF), between each couple of base-stations while guaranteeing K link-disjoint connections, a data rate target, and a reliability threshold. The paper solves the problem using graph theory techniques. It reformulates the problem as a maximum weight clique problem in the planning graph, under a specified realistic assumption about the cost of OF and hybrid RF/FSO links. Simulation results show the cost of the different planning and suggest that the proposed heuristic solution has a close-to-optimal performance for a significant gain in computation complexity.

The maximum weighted clique (MWC) problem, as a typical NP-complete problem, is difficult to be solved by the electronic computer algorithm. The aim of the problem is to seek a vertex clique with maximal weight sum in a given undirected graph. It is an extremely important problem in the field of optimal engineering scheme and control with numerous practical applications. From the point of view of practice, we give a parallel biological algorithm to solve the MWC problem. For the maximum weighted clique problem withmedges andnvertices, we use fixed length DNA strands to represent different vertices and edges, fully conduct biochemical reaction, and find the solution to the MVC problem in certain length range withO(n2)time complexity, comparing to the exponential time level by previous computer algorithms. We expand the applied scope of parallel biological computation and reduce computational complexity of practical engineering problems. Meanwhile, we provide a meaningful reference for solving other complex problems.

Graphs and Algorithms A graph class has few cliques if there is a polynomial bound on the number of maximal cliques contained in any member of the class. This restriction is equivalent to the requirement that any graph in the class has a polynomial sized intersection representation that satisfies the Helly property. On any such class of graphs, some problems that are NP-complete on general graphs, such as the maximum clique problem and the maximum weighted clique problem, admit polynomial time algorithms. Other problems, such as the vertex clique cover and edge clique cover problems remain NP-complete on these classes. Several classes of graphs which have few cliques are discussed, and the complexity of some partitioning and covering problems are determined for the class of all graphs which have fewer cliques than a given polynomial bound.