Efficient Algorithms for Finding Maximum and Maximal Cliques and Their Applications

The problem of finding a maximum clique or enumerating all maximal cliques is very important and has been explored in several excellent survey papers. Here, we focus our attention on the step-by-step examination of a series of branch-and-bound depth-first search algorithms: Basics, MCQ, MCR, MCS, and MCT. Subsequently, as with the depth-first search as above, we present our algorithm, CLIQUES, for enumerating all maximal cliques. Finally, we describe some of the applications of the algorithms and their variants in bioinformatics, data mining, and other fields

Exact Algorithms for Maximum Clique: a computational study

We investigate a number of recently reported exact algorithms for the maximum clique problem (MCQ, MCR, MCS, BBMC). The program code used is presented and critiqued showing how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and hardware platforms influence algorithm behaviour. The minimum width order (smallest-last) is investigated, and MCS is broken into its consituent parts and we discover that one of these parts degrades performance. It is shown that the standard procedure used for rescaling published results is unsafe.Comment: 40 pages, 14 figures, 10 tables, 12 short java program listings, code afailable to download at http://www.dcs.gla.ac.uk/~pat/maxClique/distribution

Boosting Local Search for the Maximum Independent Set Problem

An independent set of a graph G = (V, E) with vertices V and edges E is a subset S ⊆ V, such that the subgraph induced by S does not contain any edges. The goal of the maximum independent set problem (MIS problem) is to find an independent set of maximum size. It is equivalent to the well-known vertex cover problem (VC problem) and maximum clique problem. This thesis consists of two main parts. In the first one we compare the currently best algorithms for finding near-optimal independent sets and vertex covers in large, sparse graphs. They are Iterated Local Search (ILS) by Andrade et al. [2], a heuristic that uses local search for the MIS problem and NuMVC by Cai et al. [6], a local search algorithm for the VC problem. As of now, there are no methods to solve these large instances exactly in any reasonable time. Therefore these heuristic algorithms are the best option. In the second part we analyze a series of techniques, some of which lead to a significant speed up of the ILS algorithm. This is done by removing specific ver

Algoritmos para o problema da clique máxima : análise e comparação experimental

Orientador : Prof. Dr. Renato CarmoTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 28/09/2017Inclui referências : f. 107-113Resumo: O problema da Clique Máxima (CM) é um problema fundamental e há uma grande motivação pela busca de algoritmos tão eficientes quanto possível para resolvê-lo de forma exata. Como esperado para um problema NP-difícil, os melhores algoritmos com desempenho de pior caso conhecido tem custo de tempo exponencial. Por outro lado, resultados experimentais encontrados na literatura indicam que instâncias de tamanho considerável podem ser resolvidas usando algoritmos baseados na técnica de branch-and-bound. Com isso, observa-se uma distância entre os melhores resultados analíticos e os melhores resultados experimentais. Uma possível explicação para discrepância aparente entre teoria e prática foi encontrada pela análise de instâncias aleatórias. Diversos algoritmos de branch- and-bound para a solução exata do CM foram estudados, analisados e implementados. Com base nos resultados analíticos é proposta uma metodologia para comparação experimental de algoritmos, que tem como principal ponto positivo o fato de que algoritmos podem ser comparados independente de detalhes de implementação e execução. Vários algoritmos foram testados como prova de conceito. Também foram estudadas instâncias de pior caso para algoritmos de branch-and-bound que só utilizam coloração como limitante superior, resultando em um custo exponencial de tempo para estes algoritmos. Uma nova família de algoritmos foi desenvolvida, capaz de resolver tais instâncias em tempo polinomial. Recentemente, técnicas de resolvedores para problemas de satisfatibilidade têm sido aplicadas em algoritmos para CM. Tais técnicas dependem de uma redução entre os dois problemas, mas o significado em termos do grafo fica obscurecido nas descrições originais. Algumas técnicas foram estudadas e convertidas para uma descrição que não usa termos referentes aos problemas de satisfatibilidade. A implementação de vários algoritmos estudados foi disponibilizada em um repositório de acesso público. Palavras-chave: Solução exata. Branch-and-bound. Análise de algoritmos. Comparação experimental.Abstract: e Maximum Clique problem (CM) is a fundamental problem and there is a great motivation for the development of efficient exact algorithms to solve it. As expected for a NP-hard problem, the best algorithms where worst case analyses have been conducted present exponential running times. On the other hand, experimental results available in the literature show that instances of considerable size can be solved by branch and bound algorithms. Therefore, there is an apparent gap between the best theoretical results and the best experimental results. One possible explanation for this discrepancy between theory and practice was found through the analyses of random instances. Several exact branch and bound algorithm for CM were studied, analyzed and implemented. Based on these analytical results, a new methodology for the comparison of algorithms is proposed, where algorithms can be tested and compared regardless of implementation and execution details. Several algorithms were tested as a proof of concept. Worst case instances for some branch and bound algorithms were studied, namely algorithms that adopt only coloring-based bounding techniques to reduce the search space. These algorithms present exponential time cost for the studied instances. A new family of algorithms was developed, which is able to solve the mentioned instances in polinomial time. Recently, techniques from satisfiability solvers have been used in algorithms for CM. Such techniques depend on a reduction between the problems, and the original descriptions in terms of propositional calculus obscures their graph theoretic meaning. Some of these techniques were studied and converted to a description that uses only graph theory terminology. The implementation of several algorithms was made available in a public access repository. Keywords: Exact solution. Branch-and-bound. Analysis of algorithms. Experimental comparison