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

Improving resiliency using graph based evolutionary algorithms

Resiliency is an important characteristic of any system. It signifies the ability of a system to survive and recover from unprecedented disruptions. Various characteristics exist that indicate the level of resiliency in a system. One of these attributes is the adaptability of the system. This adaptability can be enhanced by redundancy present within the system. In the context of system design, redundancy can be achieved by having a diverse set of good designs for that particular system. Evolutionary algorithms are widely used in creating designs for engineering systems, as they perform well on discontinuous and/or high dimensional problems. One method to control the diversity of solutions within an evolutionary algorithm is the use of combinatorial graphs, or graph based evolutionary algorithms. This diversity of solutions is key factor to enhance the redundancy of a system design. In this work, the way how graph based evolutionary algorithms generate diverse solutions is investigated by examining the influence of representation and mutation. This allows for greater understanding of the exploratory nature of each representation and how they can control the number of solution generated within a trial. The results of this research are then applied to the Travelling [sic] Salesman Problem, a known NP hard problem often used as a surrogate for logistic or network design problems. When the redundancy in system design is improved, adaptability can be achieved by placing an agent to initiate a transfer to other good solutions in the event of a disruption in network connectivity, making it possible to improve the resiliency of the system --Abstract, page iii

Graph-based solution batch management for Multi-Objective Evolutionary Algorithms

In Alberto and Mateo [2], 2004, a graph-based structure used for manipulating populations of Multi-Objective Evolutionary Algorithms in a more efficient way than the structures existing at that point was defined. In this paper, an improvement of such tool is presented. It consists of the simultaneous insertion of a set of solutions (solution batch), instead of a single one, into the created graph structure. Furthermore, two experiments devoted to comparing the behavior of the new algorithms with the original version from Alberto and Mateo [2] and with a well-known non-dominated sorting algorithm are carried out. The first shows how the new version outperforms the original one in time and number of Pareto comparisons. The second experiment shows a reduction in the time needed in all the cases and an important reduction in the number of Pareto comparisons when inserting chains of dominated solutions. From these experiments it is verified that, in general, the new proposals save computational time and, in the majority of the cases, the number of Pareto comparisons carried out for the insertion. In addition, when the new proposals outperform the others, they increase their gain over them as the size of the population and/or the size of the batch increases. The new tool can also be used, for example, in parallel genetic algorithms such as the ones based on islands, to carry out the migrations of the solutions

Phylogenetic inference's algorithms

Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016

Evolving Graphs by Graph Programming

Graphs are a ubiquitous data structure in computer science and can be used to represent solutions to difficult problems in many distinct domains. This motivates the use of Evolutionary Algorithms to search over graphs and efficiently find approximate solutions. However, existing techniques often represent and manipulate graphs in an ad-hoc manner. In contrast, rule-based graph programming offers a formal mechanism for describing relations over graphs. This thesis proposes the use of rule-based graph programming for representing and implementing genetic operators over graphs. We present the Evolutionary Algorithm Evolving Graphs by Graph Programming and a number of its extensions which are capable of learning stateful and stateless digital circuits, symbolic expressions and Artificial Neural Networks. We demonstrate that rule-based graph programming may be used to implement new and effective constraint-respecting mutation operators and show that these operators may strictly generalise others found in the literature. Through our proposal of Semantic Neutral Drift, we accelerate the search process by building plateaus into the fitness landscape using domain knowledge of equivalence. We also present Horizontal Gene Transfer, a mechanism whereby graphs may be passively recombined without disrupting their fitness. Through rigorous evaluation and analysis of over 20,000 independent executions of Evolutionary Algorithms, we establish numerous benefits of our approach. We find that on many problems, Evolving Graphs by Graph Programming and its variants may significantly outperform other approaches from the literature. Additionally, our empirical results provide further evidence that neutral drift aids the efficiency of evolutionary search