Parallel graph partitioning framework for solving the maximum clique problem using Hadoop

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.

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 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.

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.

This paper studies the semidefinite programming SDP problem, i.e., the optimization problem of a linear function of a symmetric matrix subject to linear equality constraints and the additional condition that the matrix be positive semidefinite. First the classical cone duality is reviewed as it is specialized to SDP is reviewed. Next an interior point algorithm is presented that converges to the optimal solution in polynomial time. The approach is a direct extension of Ye’s projective method for linear programming. It is also argued that many known interior point methods for linear programs can be transformed in a mechanical way to algorithms for SDP with proofs of convergence and polynomial time complexity carrying over in a similar fashion. Finally, the significance of these results is studied in a variety of combinatorial optimization problems including the general 0-1 integer programs, the maximum clique and maximum stable set problems in perfect graphs, the maximum k-partite subgraph problem in graph...

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.

<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.

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.

We propose a heuristic for parallel partitioning of graphs into equi-sized components. In particular, we identify a relationship between the graph partitioning problem (GPP) and the traveling saleman problem (TSP), and use that to reduce partitioning to TSP. Given that better performing heuristics are known for TSP than are for GPP, this reduction also leads to improved GPP heuristics. What is more, a good GPP solution can also be used to speed up computation of TSP.We first derive a good bi-partition from a cut of the TSP cycle in time proportional to the number of edges in the graph. We then continue this bi-partitioning recursively until the required number of partitions are left. Further, in order to speed up the computation of TSP, which we use as a subroutine, we perform an initial rough partitioning of the graph into K parts, compute TSP tours in each of these smaller partitions and then merge these local tours to solve the full TSP.We then use this full TSP solution to obtain the final partitioning in parallel. Our empirical analysis shows that for partition count k ≥ 32, our parallel algorithm gives a cut better in size than that of algorithms known for low cut-size (e.g., KaBaPE), and when time is of concern, it finishes in significantly less time with comparable cuts. We also show that our algorithm gives much smaller cuts in comparable time than those known for fast computation (e.g., PT-Scotch).

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.

Maximum clique and independent set problems are classical NP-full optimization problems, the solutions of which are difficult to obtain from conventional methods. Hopfield network in neural network, which simulates the partial functions of a human brain through the ultra-large scale parallel computation, has been proven to have potentials in solving these problems in a reasonable period of time. The main problem of this approach is the difficulty in defining an efficient energy function and the dynamic equation of motion for the Hopfield model. In this paper, we propose solutions to this problem by solving two typical problems in the coloring of graphs, the maximum clique and independent set, through our refined Hopfield network model. Both the mathematical model and the simulation algorithm are given here. It is found that the time complexity to obtain an optimal solution can approach one order of magnitude lower than the current available solutions.KeywordsEnergy FunctionMaximum CliqueHopfield Neural NetworkMaximum Clique ProblemHopfield NetworkThese 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.

A new upper bound for the maximum weight clique problem