Clique Finding Research Articles

Exploratory Data Analysis and Searching Cliques in Graphs

The principal component analysis is a well-known and widely used technique to determine the essential dimension of a data set. Broadly speaking, it aims to find a low-dimensional linear manifold that retains a large part of the information contained in the original data set. It may be the case that one cannot approximate the entirety of the original data set using a single low-dimensional linear manifold even though large subsets of it are amenable to such approximations. For these cases we raise the related but different challenge (problem) of locating subsets of a high dimensional data set that are approximately 1-dimensional. Naturally, we are interested in the largest of such subsets. We propose a method for finding these 1-dimensional manifolds by finding cliques in a purpose-built auxiliary graph.

A universal programmable Gaussian boson sampler for drug discovery

Gaussian boson sampling (GBS) has the potential to solve complex graph problems, such as clique finding, which is relevant to drug discovery tasks. However, realizing the full benefits of quantum enhancements requires large-scale quantum hardware with universal programmability. Here we have developed a time-bin-encoded GBS photonic quantum processor that is universal, programmable and software-scalable. Our processor features freely adjustable squeezing parameters and can implement arbitrary unitary operations with a programmable interferometer. Leveraging our processor, we successfully executed clique finding on a 32-node graph, achieving approximately twice the success probability compared to classical sampling. As proof of concept, we implemented a versatile quantum drug discovery platform using this GBS processor, enabling molecular docking and RNA-folding prediction tasks. Our work achieves GBS circuitry with its universal and programmable architecture, advancing GBS toward use in real-world applications.

CBLA: A Clique Based Louvain Algorithm for Detecting Overlapping Community

Graph mining is one of the significant tasks in the field of computer science. Most of the applications generate a vast amount of data which is represented with the help of a graph. Due to this graph representation, these applications have become complex and increased in size. Finding relevant information from that graph becomes a complicated task. For this community detection algorithms play a vital role in graph partitioning to retrieve relevant information. Finding communities in a graph reduces the complexity of the graph due to related data comes closer to forming a community. Many algorithms have been introduced in the last decade; the Clique percolation method (CPM) is the benchmark algorithm for finding an overlapping community. But in this method, some nodes remain unclassified, nodes that are not part of the clique. Paper proposed the clique-based Louvain algorithm(CBLA), which can classify the non-classified node (NCN) obtained after finding cliques in one of the communities by applying the Louvain algorithm. Louvain algorithm is used to classify the non-overlapped community, but with the help of cliques, it will also detect the overlapped nodes. This paper compared the proposed algorithm with four other benchmark algorithms. The proposed algorithm gives equal or enhanced performance among all compared algorithms.

A new exact algorithm for the maximum-weight clique problem based on a heuristic vertex-coloring and a backtrack search

In this paper we present an exact algorithm for the maximum-weight clique problem on arbitrary undirected graphs. The algorithm based on a fact that vertices from the same independent set couldn’t be included into the same maximum clique. Those independent sets are obtained from a heuristic vertex coloring where each of them is a color class. Color classes and a backtrack search are used for pruning branches of the maximum-weight clique search tree. Those pruning strategies together result in a very effective algorithm for the maximum-weight clique finding. Computational experiments with random graphs show that the new algorithm works faster than earlier published algorithms; especially on dense graphs.

Graph Coloring via Clique Search with Symmetry Breaking

It is known that the problem of proper coloring of the nodes of a given graph can be reduced to finding cliques in a suitably constructed auxiliary graph. In this work, we explore the possibility of reducing the search space by exploiting the symmetries present in the auxiliary graph. The proposed method can also be used for efficient exact coloring of hyper graphs. We also precondition the auxiliary graph in order to further reduce the search space. We carry out numerical experiments to assess the practicality of these proposals. We solve some hard cases and prove a new lower limit of seven for the mycielski7 graph with the aid of the proposed technique.

Circuit design for clique problem and its implementation on quantum computer

Finding cliques in a graph has a wide range of applications due to its pattern matching ability. The k-clique problem, a subset of the clique problem, determines whether or not an arbitrary network has a clique of size k. Modern-day applications include a variation of the k-clique problem that lists all cliques of size k. However, the quantum implementation of such a variation of the k-clique problem has not been addressed yet. In this work, apart from the theoretical solution of such a k-clique problem, practical quantum-gate-based implementation has been addressed using Grover's algorithm. In a classical-quantum hybrid architecture, this approach is extended to build the circuit for the maximum clique problem. Our technique is generalised since the program automatically builds the circuit for any given undirected and unweighted graph and any chosen k. For a small k with regard to a big graph, the proposed solution to addressing the k-clique issue has shown a reduction in qubit cost and circuit depth when compared to the state-of-the-art approach. A framework is also presented for mapping the automated generated circuit for clique problems to quantum devices. Using IBM's Qiskit, an analysis of the experimental results is demonstrated.

Computing cliques and cavities in networks

Complex networks contain complete subgraphs such as nodes, edges, triangles, etc., referred to as simplices and cliques of different orders. Notably, cavities consisting of higher-order cliques play an important role in brain functions. Since searching for maximum cliques is an NP-complete problem, we use k-core decomposition to determine the computability of a given network. For a computable network, we design a search method with an implementable algorithm for finding cliques of different orders, obtaining also the Euler characteristic number. Then, we compute the Betti numbers by using the ranks of boundary matrices of adjacent cliques. Furthermore, we design an optimized algorithm for finding cavities of different orders. Finally, we apply the algorithm to the neuronal network of C. elegans with data from one typical dataset, and find all of its cliques and some cavities of different orders, providing a basis for further mathematical analysis and computation of its structure and function.

Dynamic hypergraphs of renewal processes in mobile networks.

The characteristics of random geometric hypergraphs are studied as mathematical models of scalable wireless computer networks. An efficient algorithm for finding cliques in geometric graphs, constructing hypergraphs from geometric configurations has been developed. The types of hyper-edges in hypergraphs generated by a scalable configuration have been identified. The influence of random failures of nodes of computer networks and their restorations on the dynamics of hypergraphs of networks is considered. The analysis of the dynamics of the number of active nodes depending on the type of probability distributions of uptime and recovery time is carried out. The dependences of the mathematical expectation of the number of hyper-edges of certain types in the geometric hypergraph of a wireless computer network on the network operation time, on the radii of zones of reliable reception / transmission of a signal, on the ratio of the parameters of local recovery processes are obtained. The presentation of the results is accompanied by charts.

A Semi-exact Algorithm for Quickly Computing A Maximum Weight Clique in Large Sparse Graphs

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.

Application of Tolerance Graphs to Combat COVID-19 Pandemic.

Tolerance graphs were introduced in 1982 by Golumbic and Monma as a generalization of interval graphs. In this paper, we propose several applications of tolerance graphs in fighting COVID-19. These applications include finding cliques of a certain size, and calculating the chromatic number of a graph, the problems that are in general NP-complete but for tolerance graphs can be solved in polynomial time.

Mixed Membership Graph Clustering via Systematic Edge Query

This work considers clustering nodes of a largely incomplete graph. Under the problem setting, only a small amount of queries about the edges can be made, but the entire graph is not observable. This problem finds applications in large-scale data clustering using limited annotations, community detection under restricted survey resources, and graph topology inference under hidden/removed node interactions. Prior works tackled this problem from various perspectives, e.g., convex programming-based low-rank matrix completion and active query-based clique finding. Nonetheless, many existing methods are designed for estimating the single-cluster membership of the nodes, but nodes may often have mixed (i.e., multi-cluster) membership in practice. Some query and computational paradigms, e.g., the random query patterns and nuclear norm-based optimization advocated in the convex approaches, may give rise to scalability and implementation challenges. This work aims at learning mixed membership of nodes using queried edges. The proposed method is developed together with a systematic query principle that can be controlled and adjusted by the system designers to accommodate implementation challenges -- e.g., to avoid querying edges that are physically hard to acquire. Our framework also features a lightweight and scalable algorithm with membership learning guarantees. Real-data experiments on crowdclustering and community detection are used to showcase the effectiveness of our method.

Heuristic construction of codeword stabilized codes

The family of codeword stabilized codes encompasses the stabilizer codes as well as many of the best known nonadditive codes. However, constructing optimal $n$-qubit codeword stabilized codes is made difficult by two main factors. The first of these is the exponential growth with $n$ of the number of graphs on which a code can be based. The second is the NP-hardness of the maximum clique search required to construct a code from a given graph. We address the second of these issues through the use of a heuristic clique finding algorithm. This approach has allowed us to find $((9,97\leq K\leq100,2))$ and $((11,387\leq K\leq416,2))$ codes, which are larger than any previously known codes. To address the exponential growth of the search space, we demonstrate that graphs that give large codes typically yield clique graphs with a large number of nodes. The number of such nodes can be determined relatively efficiently, and we demonstrate that $n$-node graphs yielding large clique graphs can be found using a genetic algorithm. This algorithm uses a novel spectral bisection based crossover operation that we demonstrate to be superior to more standard crossover operations. Using this genetic algorithm approach, we have found $((13,18,4))$ and $((13,20,4))$ codes that are larger than any previously known code. We also consider codes for the amplitude damping channel. We demonstrate that for $n\leq9$, optimal codeword stabilized codes correcting a single amplitude damping error can be found by considering standard form codes that detect one of only three of the $3^{n}$ possible equivalent error sets. By combining this error set selection with the genetic algorithm approach, we have found $((11,68))$ and $((11,80))$ codes capable of correcting a single amplitude damping error and $((11,4))$, $((12,4))$, $((13,8))$, and $((14,16))$ codes capable of correcting two amplitude damping

Finding a large submatrix of a Gaussian random matrix

We consider the problem of finding a $k\times k$ submatrix of an $n\times n$ matrix with i.i.d. standard Gaussian entries, which has a large average entry. It was shown in [Bhamidi, Dey and Nobel (2012)] using nonconstructive methods that the largest average value of a $k\times k$ submatrix is $2(1+o(1))\sqrt{\log n/k}$, with high probability (w.h.p.), when $k=O(\log n/\log\log n)$. In the same paper, evidence was provided that a natural greedy algorithm called the Largest Average Submatrix ($\mathcal{LAS}$) for a constant $k$ should produce a matrix with average entry at most $(1+o(1))\sqrt{2\log n/k}$, namely approximately $\sqrt{2}$ smaller than the global optimum, though no formal proof of this fact was provided. In this paper, we show that the average entry of the matrix produced by the $\mathcal{LAS}$ algorithm is indeed $(1+o(1))\sqrt{2\log n/k}$ w.h.p. when $k$ is constant and $n$ grows. Then, by drawing an analogy with the problem of finding cliques in random graphs, we propose a simple greedy algorithm which produces a $k\times k$ matrix with asymptotically the same average value $(1+o(1))\sqrt{2\log n/k}$ w.h.p., for $k=o(\log n)$. Since the greedy algorithm is the best known algorithm for finding cliques in random graphs, it is tempting to believe that beating the factor $\sqrt{2}$ performance gap suffered by both algorithms might be very challenging. Surprisingly, we construct a very simple algorithm which produces a $k\times k$ matrix with average value $(1+o_{k}(1)+o(1))(4/3)\sqrt{2\log n/k}$ for $k=o((\log n)^{1.5})$, that is, with the asymptotic factor $4/3$ when $k$ grows. To get an insight into the algorithmic hardness of this problem, and motivated by methods originating in the theory of spin glasses, we conduct the so-called expected overlap analysis of matrices with average value asymptotically $(1+o(1))\alpha\sqrt{2\log n/k}$ for a fixed value $\alpha\in[1,\sqrt{2}]$. The overlap corresponds to the number of common rows and the number of common columns for pairs of matrices achieving this value (see the paper for details). We discover numerically an intriguing phase transition at $\alpha^{*}\triangleq5\sqrt{2}/(3\sqrt{3})\approx1.3608\ldots\in[4/3,\sqrt{2}]$: when $\alpha \alpha^{*}$, appropriately defined. We conjecture that the OGP observed for $\alpha>\alpha^{*}$ also marks the onset of the algorithmic hardness—no polynomial time algorithm exists for finding matrices with average value at least $(1+o(1))\alpha\sqrt{2\log n/k}$, when $\alpha>\alpha^{*}$ and $k$ is a mildly growing function of $n$.

Finding Maximum Cliques on the D-Wave Quantum Annealer

This paper assesses the performance of the D-Wave 2X (DW) quantum annealer for finding a maximum clique in a graph, one of the most fundamental and important NP-hard problems. Because the size of the largest graphs DW can directly solve is quite small (usually around 45 vertices), we also consider decomposition algorithms intended for larger graphs and analyze their performance. For smaller graphs that fit DW, we provide formulations of the maximum clique problem as a quadratic unconstrained binary optimization (QUBO) problem, which is one of the two input types (together with the Ising model) acceptable by the machine, and compare several quantum implementations to current classical algorithms such as simulated annealing, Gurobi, and third-party clique finding heuristics. We further estimate the contributions of the quantum phase of the quantum annealer and the classical post-processing phase typically used to enhance each solution returned by DW. We demonstrate that on random graphs that fit DW, no quantum speedup can be observed compared with the classical algorithms. On the other hand, for instances specifically designed to fit well the DW qubit interconnection network, we observe substantial speed-ups in computing time over classical approaches.

Slightly Superexponential Parameterized Problems

A central problem in parameterized algorithms is to obtain algorithms with running time $f(k)\cdot n^{O(1)}$ such that $f$ is as slow growing a function of the parameter $k$ as possible. In particular, a large number of basic parameterized problems admit parameterized algorithms where $f(k)$ is single-exponential, that is, $c^k$ for some constant $c$, which makes aiming for such a running time a natural goal for other problems as well. However, there are still plenty of problems where the $f(k)$ appearing in the best-known running time is worse than single-exponential and it remained “slightly superexponential” even after serious attempts to bring it down. A natural question to ask is whether the $f(k)$ appearing in the running time of the best-known algorithms is optimal for any of these problems. In this paper, we examine parameterized problems where $f(k)$ is $k^{O(k)}=2^{O(k\log k)}$ in the best-known running time, and for a number of such problems we show that the dependence on $k$ in the running time cannot be improved to single-exponential. More precisely we prove the following tight lower bounds, for four natural problems, arising from three different domains: (1) In the Closest String problem, given strings $s_1$, $\dots$, $s_t$ over an alphabet $\Sigma$ of length $L$ each, and an integer $d$, the question is whether there exists a string $s$ over $\Sigma$ of length $L$, such that its hamming distance from each of the strings $s_i$, $1\leq i \leq t$, is at most $d$. The pattern matching problem Closest String is known to be solvable in times $2^{O(d\log d)}\cdot n^{O(1)}$ and $2^{O(d\log |\Sigma|)}\cdot n^{O(1)}$. We show that there are no $2^{o(d\log d)}\cdot n^{O(1)}$ or $2^{o(d\log |\Sigma|)}\cdot n^{O(1)}$ time algorithms, unless the Exponential Time Hypothesis (ETH) fails. (2) The graph embedding problem Distortion, that is, deciding whether a graph $G$ has a metric embedding into the integers with distortion at most $d$ can be solved in time $2^{O(d\log d)}\cdot n^{O(1)}$. We show that there is no $2^{o(d\log d)}\cdot n^{O(1)}$ time algorithm, unless the ETH fails. (3) The Disjoint Paths problem can be solved in time $2^{O(w\log w)}\cdot n^{O(1)}$ on graphs of treewidth at most $w$. We show that there is no $2^{o(w\log w)}\cdot n^{O(1)}$ time algorithm, unless the ETH fails. (4) The Chromatic Number problem can be solved in time $2^{O(w\log w)}\cdot n^{O(1)}$ on graphs of treewidth at most $w$. We show that there is no $2^{o(w\log w)}\cdot n^{O(1)}$ time algorithm, unless the ETH fails. To obtain our results, we first prove the lower bound for variants of basic problems: finding cliques, independent sets, and hitting sets. These artificially constrained variants form a good starting point for proving lower bounds on natural problems without any technical restrictions and could be of independent interest. Several follow-up works have already obtained tight lower bounds by using our framework, and we believe it will prove useful in obtaining even more lower bounds in the future.

Parallel Algorithms for Effective Correspondence Problem Solution in Computer Vision

We propose new parallel algorithms for correspondence problem solution in computer vision. We develop an industrial photogrammetric system that uses artificial retroreflective targets that are photometrically identical. Therefore, we cannot use traditional descriptor-based point matching methods, such as SIFT, SURF etc. Instead, we use epipolar geometry constraints for finding potential point correspondences between images. In this paper, we propose new effective graph-based algorithms for finding point correspondences across the whole set of images (in contrast to traditional methods that use 2-4 images for point matching). We give an exact problem solution via superclique and show that this approach cannot be used for real tasks due to computational complexity. We propose a new effective parallel algorithm that builds the graph from epipolar constraints, as well as a new fast parallel heuristic clique finding algorithm. We use an iterative scheme (with backprojection of the points, filtering of outliers and bundle adjustment of point coordinates and cameras’ positions) to obtain an exact correspondence problem solution. This scheme allows using heuristic clique finding algorithm at each iteration. The proposed architecture of the system offers a significant advantage in time. Newly proposed algorithms have been implemented in code; their performance has been estimated. We also investigate their impact on the effectiveness of the photogrammetric system that is currently under development and experimentally prove algorithms’ efficiency.

Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data.

MotivationGrowth phenotype profiling of genome-wide gene-deletion strains over stress conditions can offer a clear picture that the essentiality of genes depends on environmental conditions. Systematically identifying groups of genes from such high-throughput data that share similar patterns of conditional essentiality and dispensability under various environmental conditions can elucidate how genetic interactions of the growth phenotype are regulated in response to the environment.ResultsWe first demonstrate that detecting such ‘co-fit’ gene groups can be cast as a less well-studied problem in biclustering, i.e. constant-column biclustering. Despite significant advances in biclustering techniques, very few were designed for mining in growth phenotype data. Here, we propose Gracob, a novel, efficient graph-based method that casts and solves the constant-column biclustering problem as a maximal clique finding problem in a multipartite graph. We compared Gracob with a large collection of widely used biclustering methods that cover different types of algorithms designed to detect different types of biclusters. Gracob showed superior performance on finding co-fit genes over all the existing methods on both a variety of synthetic data sets with a wide range of settings, and three real growth phenotype datasets for E. coli, proteobacteria and yeast.Availability and ImplementationOur program is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.Supplementary information Supplementary data are available at Bioinformatics online.

Solving the Maximum Clique Problem with Symmetric Rank-One Non-negative Matrix Approximation

Finding complete subgraphs in a graph, that is, cliques, is a key problem and has many real-world applications, e.g., finding communities in social networks, clustering gene expression data, modeling ecological niches in food webs, and describing chemicals in a substance. The problem of finding the largest clique in a graph is a well-known NP-hard problem and is called the maximum clique problem (MCP). In this paper, we formulate a very convenient continuous characterization of the MCP based on the symmetric rank-one nonnegative approximation of a given matrix, and build a one-to-one correspondence between stationary points of our formulation and cliques of a given graph. In particular, we show that the local (resp. global) minima of the continuous problem corresponds to the maximal (resp. maximum) cliques of the given graph. We also propose a new and efficient clique finding algorithm based on our continuous formulation and test it on various synthetic and real data sets to show that the new algorithm outperforms other existing algorithms based on the Motzkin-Straus formulation, and can compete with a sophisticated combinatorial heuristic.

Incremental k-core decomposition: algorithms and evaluation

A k-core of a graph is a maximal connected subgraph in which every vertex is connected to at least k vertices in the subgraph. k-core decomposition is often used in large-scale network analysis, such as community detection, protein function prediction, visualization, and solving NP-hard problems on real networks efficiently, like maximal clique finding. In many real-world applications, networks change over time. As a result, it is essential to develop efficient incremental algorithms for dynamic graph data. In this paper, we propose a suite of incremental k-core decomposition algorithms for dynamic graph data. These algorithms locate a small subgraph that is guaranteed to contain the list of vertices whose maximum k-core values have changed and efficiently process this subgraph to update the k-core decomposition. We present incremental algorithms for both insertion and deletion operations, and propose auxiliary vertex state maintenance techniques that can further accelerate these operations. Our results show a significant reduction in runtime compared to non-incremental alternatives. We illustrate the efficiency of our algorithms on different types of real and synthetic graphs, at varying scales. For a graph of 16 million vertices, we observe relative throughputs reaching a million times, relative to the non-incremental algorithms.

Parameterized clique on inhomogeneous random graphs

Finding cliques in graphs is a classical problem which is in general NP-hard and parameterized intractable. In typical applications like social networks or biological networks, however, the considered graphs are scale-free, i.e., their degree sequence follows a power law. Their specific structure can be algorithmically exploited and makes it possible to solve clique much more efficiently. We prove that on inhomogeneous random graphs with n nodes and power law exponent β, cliques of size k can be found in time O(n) for β≥3 and in time O(nek4) for 2<β<3.