A continuous characterization of the maximum vertex-weighted clique in hypergraphs

Optimal parallel time bounds for the maximum clique problem on intervals

In this paper, we give a comprehensive overview of the development of clique algorithms and their use for drug design based on the search for cliques in protein product graphs. The maximum clique problem is a computational problem of finding largest subsets of vertices in a graph that are all pairwise adjacent. A related problem is the maximum weight clique problem and the highest weight k-clique problem, which both extend the algorithm to weighted graphs. The review covers our developed algorithms, starting with our improved branch-and-bound algorithm for finding maximum cliques in undirected graphs from 2007 up to the recent developments of algorithms for weighted graphs in 2024. We show the application of these algorithms to early stages of drug discovery, in particular to protein binding site detection based on protein similarity search in large protein databases and to protein-ligand molecular docking.

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

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.

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 Steiner multi-ring network design problem with revenues consists of designing node-disjoint multiple rings connected by a specific node (hub) and passing through all the nodes with high priority of service and some of the nodes with low priority of service. The number of nodes in each ring has an upper bound to assure a certain level of service. Besides the usual arc link costs, we also consider revenues between each pair of nodes in the same ring, even when they are not connected by a direct link. The objective is to minimize the difference between the total connection cost and total revenue. The problem is a generalization of the problem studied in Gouveia and Pires (Eur J Oper Res 133:21–31, 2001a) and it can also be seen as a combination of variants of two NP-Hard problems, the vehicle routing problem and the maximum edge-weighted clique problem. We introduce and discuss two types of integer linear programming formulations and propose some valid inequalities to strengthen the linear programming relaxation. Computational results are presented to evaluate the quality of the linear programming relaxation bounds associated with these formulations as well as efficiency of the models to obtain the optimal integer solutions.

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.

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.

Let R be a commutative ring with non-zero identity and Z^∗(R) be the set of non-zero zero-divisors of R. The zero-divisor graph of R, denoted by Γ(R), is a simple undirected graph with all non-zero zero-divisors as vertices and two distinct vertices x, y ∈ Z^∗(R) are adjacent if and only if xy = 0. In this paper, the eigenvalues of Γ(Zn) for n = p^2q^2, where p and q are distinct primes, are investigated. Also, the girth, diameter, clique number and stability number of this graph are found.

Graph pattern mining is an important part of the emerging social network science, and the research of the maximum clique problem is one of the most important research branches. In the big data environment, the mass of nodes and complexity of edges in the graph set a higher requirement on the speed and accuracy of the maximum clique (MCP) study. In this paper, we present a parallel graph partitioning framework for solving the maximum clique problem(PPMC) based on Hadoop. Firstly, This paper presents a new graph partition method based on degree sorting(GPD), the subgraph scale is greatly reduced. In order to balance the workload of solving the maximum clique problems. Secondly, the improved ant algorithm proposed by our team is used to solve the maximum clique of each subgraph. Finally, the framework is deployed on Hadoop distributed cloud computing platform and tested by Stanford large-scale datasets. The experimental results show that GPD algorithm can greatly reduce the subgraph scale, the subgraph number, and the complexity of time and space of solving the maximum clique problem of large-scale instances. And the efficiency and scalability of the Hadoop based parallel graph partitioning framework for solving the maximum clique problems has been further proved.

How to decrease the volume in DNA computers is of a great significance in the research of DNA computing.For the objective to decrease the DNA volume of the maximum clique problem which is a famous NP-complete problem,the pruning strategy is introduced into the DNA supercomputing and a new DNA algorithm is proposed.The new algorithm consists of a Degree Searcher,a Clique Generator,a Dense Parallel Searcher,a Sparse Parallel Searcher and a Maximum Clique Searcher.In a computer simulation,the DNA strands of maximum number required is O(3~(1/2)~n)on the condition of not varying the time complexity where n is the number of the vertex in a graph,while O(2n)DNA strands are needed in present molecular algorithms for the maximum clique problems.Furthermore,this algorithm is highly space-efficient and error-tolerant compared to conventional brute-force searching.

The maximum clique problem ( <i>MCP</i> ) has various applications to reveal the structure and function of graphs. Graphs are constantly updated in the real life. However, no algorithm is specifically designed for dynamic graph. Although <i>MCP</i> in dynamic graphs can be solved by simply invoking a state-of-the-art static approach, such as <i>PMC</i> , when the graph is updated, such an approach of simply re-calculating from scratch is inefficient. The key issue with <i>MCP</i> algorithm is to find a large clique, namely a <i>seed</i> , as fast as possible. Thus, search space can be pruned based on the seed. Size of the seed greedily found by <i>PMC</i> cannot be guaranteed, as it fluctuates considerably. Moreover, the time required to find a seed under <i>PMC</i> is up to <inline-formula><tex-math notation="LaTeX">$O(| E| \cdot \Delta (G))$</tex-math></inline-formula> , where <inline-formula><tex-math notation="LaTeX">$\Delta (G)$</tex-math></inline-formula> is the highest degree in <i>G</i> . In this article, we intend to find a sizable seed by updating the previous maximum clique with the incident vertices of the inserted/deleted edge. Size of the seed now is guaranteed to be no less than <inline-formula><tex-math notation="LaTeX">$\omega (G^{\prime})\; - \;1$</tex-math></inline-formula> , where <inline-formula><tex-math notation="LaTeX">$\omega (G^{\prime})$</tex-math></inline-formula> is the size of the maximum clique on the updated graph. Moreover, the seed can be found in a time complexity of <inline-formula><tex-math notation="LaTeX">$O(\Delta (G)^{2})$</tex-math></inline-formula> . Two other crucial issues related to the <i>MCP</i> in dynamic graphs are refreshing rate and refreshing overhead. After a tight upper bound is imposed on <inline-formula><tex-math notation="LaTeX">$\omega (G^{\prime})$</tex-math></inline-formula> , the necessity of refreshing is evaluated by comparing the seed with its largest challenger, then unnecessary refreshing is wiped out effectively. The size of the largest challenger is judiciously estimated using a lazy growth strategy. Subsequently, the search space in refreshing is confined on a much smaller subgraph using a local refreshing strategy. Extensive experiments indicate that the proposed approach outperforms the baseline algorithm by approximately one order of magnitude.

<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 paraclique algorithm provides an effective means for biological data clustering. It satisfies the mathematical quest for density, while fulfilling the pragmatic need for noise abatement on real data. Given a finite, simple, edge-weighted and thresholded graph, the paraclique method first finds a maximum clique, then incorporates additional vertices in a controlled manner, and finally extracts the subgraph thereby defined. When more than one maximum clique is present, however, deciding which to employ is usually left unspecified. In practice, this frequently and quite naturally reduces to using the first maximum clique found. In this paper, maximum clique selection is studied in the context of well-annotated transcriptomic data, with ontological classification used as a proxy for cluster quality. Enrichment p-values are compared using maximum cliques chosen in a variety of ways. The most appealing and intuitive option is almost surely to start with the maximum clique having the highest average edge weight. Although there is of course no guarantee that such a strategy is any better than random choice, results derived from a large collection of experiments indicate that, in general, this approach produces a small but statistically significant improvement in overall cluster quality. Such an improvement, though modest, may be well worth pursuing in light of the time, expense and expertise often required to generate timely, high quality, high throughput biological data.

Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree. This article introduces a new method of clustering which partitions S into subsets such that the overlap of each pair of sequences within a subset is at least a given percentage c of the lengths of the two sequences. We show that this problem can be reduced to finding all maximal cliques in a special kind of max-tolerance graph which we call a c-max-tolerance graph. Previously we have shown that finding all maximal cliques in general max-tolerance graphs can be done efficiently in O(n3 + out). Here, using a new kind of sweep-line algorithm, we show that the restriction to c-max-tolerance graphs yields a better runtime of O(n2 log n + out). Furthermore, we present another algorithm which is much easier to implement, and though theoretically slower than the first one, is still running in polynomial time. We then experimentally analyze the number and structure of all maximal cliques in a c-max-tolerance graph, depending on the chosen c-value. We apply our simple algorithm to artificial and biological data and we show that this implementation is much faster than the well-known application Cliquer. By introducing a new heuristic that uses the set of all maximal cliques to partition S, we finally show that the computed partition gives a reasonable clustering for biological data sets.