How Good are Genetic Algorithms at Finding Large Cliques: An Experimental Study

This paper investigates the power of genetic algorithms at solving the MAX-CLIQUE problem. We measure the performance of a standard genetic algorithm on an elementary set of problem instances consisting of embedded cliques in random graphs. We indicate the need for improvement, and introduce a new genetic algorithm, the multi-phase annealed GA, which exhibits superior performance on the same problem set. As we scale up the problem size and test on \hard" benchmark instances, we notice a degraded performance in the algorithm caused by premature convergence to local minima. To alleviate this problem, a sequence of modi cations are implemented ranging from changes in input representation to systematic local search. The most recent version, called union GA, incorporates the features of union cross-over, greedy replacement, and diversity enhancement. It shows a marked speed-up in the number of iterations required to find a given solution, as well as some improvement in the clique size found. We discuss issues related to the SIMD implementation of the genetic algorithms on a Thinking Machines CM-5, which was necessitated by the intrinsically high time complexity (O(n3)) of the serial algorithm for computing one iteration. Our preliminary conclusions are: (1) a genetic algorithm needs to be heavily customized to work "well" for the clique problem; (2) a GA is computationally very expensive, and its use is only recommended if it is known to find larger cliques than other algorithms; (3) although our customization e ort is bringing forth continued improvements, there is no clear evidence, at this time, that a GA will have better success in circumventing local minima.NSF (CCR-9204284

Reconstructing (super)trees from data sets with missing distances: Not all is lost

The wealth of phylogenetic information accumulated over many decades of biological research, coupled with recent technological advances in molecular sequence generation, present significant opportunities for researchers to investigate relationships across and within the kingdoms of life. However, to make best use of this data wealth, several problems must first be overcome. One key problem is finding effective strategies to deal with missing data. Here, we introduce Lasso, a novel heuristic approach for reconstructing rooted phylogenetic trees from distance matrices with missing values, for datasets where a molecular clock may be assumed. Contrary to other phylogenetic methods on partial datasets, Lasso possesses desirable properties such as its reconstructed trees being both unique and edge-weighted. These properties are achieved by Lasso restricting its leaf set to a large subset of all possible taxa, which in many practical situations is the entire taxa set. Furthermore, the Lasso approach is distance-based, rendering it very fast to run and suitable for datasets of all sizes, including large datasets such as those generated by modern Next Generation Sequencing technologies. To better understand the performance of Lasso, we assessed it by means of artificial and real biological datasets, showing its effectiveness in the presence of missing data. Furthermore, by formulating the supermatrix problem as a particular case of the missing data problem, we assessed Lasso's ability to reconstruct supertrees. We demonstrate that, although not specifically designed for such a purpose, Lasso performs better than or comparably with five leading supertree algorithms on a challenging biological data set. Finally, we make freely available a software implementation of Lasso so that researchers may, for the first time, perform both rooted tree and supertree reconstruction with branch lengths on their own partial datasets

A novel evolutionary formulation of the maximum independent set problem

We introduce a novel evolutionary formulation of the problem of finding a maximum independent set of a graph. The new formulation is based on the relationship that exists between a graph's independence number and its acyclic orientations. It views such orientations as individuals and evolves them with the aid of evolutionary operators that are very heavily based on the structure of the graph and its acyclic orientations. The resulting heuristic has been tested on some of the Second DIMACS Implementation Challenge benchmark graphs, and has been found to be competitive when compared to several of the other heuristics that have also been tested on those graphs

A maximal clique based multiobjective evolutionary algorithm for overlapping community detection

Detecting community structure has become one im-portant technique for studying complex networks. Although many community detection algorithms have been proposed, most of them focus on separated communities, where each node can be-long to only one community. However, in many real-world net-works, communities are often overlapped with each other. De-veloping overlapping community detection algorithms thus be-comes necessary. Along this avenue, this paper proposes a maxi-mal clique based multiobjective evolutionary algorithm for over-lapping community detection. In this algorithm, a new represen-tation scheme based on the introduced maximal-clique graph is presented. Since the maximal-clique graph is defined by using a set of maximal cliques of original graph as nodes and two maximal cliques are allowed to share the same nodes of the original graph, overlap is an intrinsic property of the maximal-clique graph. Attributing to this property, the new representation scheme al-lows multiobjective evolutionary algorithms to handle the over-lapping community detection problem in a way similar to that of the separated community detection, such that the optimization problems are simplified. As a result, the proposed algorithm could detect overlapping community structure with higher partition accuracy and lower computational cost when compared with the existing ones. The experiments on both synthetic and real-world networks validate the effectiveness and efficiency of the proposed algorithm

Uncovering the overlapping community structure of complex networks in nature and society

Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of communities, we apply an efficient technique for exploring overlapping communities on a large scale. We find that overlaps are significant, and the distributions we introduce reveal universal features of networks. Our studies of collaboration, word-association and protein interaction graphs show that the web of communities has non-trivial correlations and specific scaling properties.Comment: The free academic research software, CFinder, used for the publication is available at the website of the publication: http://angel.elte.hu/clusterin