An Enhanced Multi-Objective Biogeography-Based Optimization Algorithm for Automatic Detection of Overlapping Communities in a Social Network with Node Attributes

Community detection is one of the most important and interesting issues in social network analysis. In recent years, simultaneous considering of nodes' attributes and topological structures of social networks in the process of community detection has attracted the attentions of many scholars, and this consideration has been recently used in some community detection methods to increase their efficiencies and to enhance their performances in finding meaningful and relevant communities. But the problem is that most of these methods tend to find non-overlapping communities, while many real-world networks include communities that often overlap to some extent. In order to solve this problem, an evolutionary algorithm called MOBBO-OCD, which is based on multi-objective biogeography-based optimization (BBO), is proposed in this paper to automatically find overlapping communities in a social network with node attributes with synchronously considering the density of connections and the similarity of nodes' attributes in the network. In MOBBO-OCD, an extended locus-based adjacency representation called OLAR is introduced to encode and decode overlapping communities. Based on OLAR, a rank-based migration operator along with a novel two-phase mutation strategy and a new double-point crossover are used in the evolution process of MOBBO-OCD to effectively lead the population into the evolution path. In order to assess the performance of MOBBO-OCD, a new metric called alpha_SAEM is proposed in this paper, which is able to evaluate the goodness of both overlapping and non-overlapping partitions with considering the two aspects of node attributes and linkage structure. Quantitative evaluations reveal that MOBBO-OCD achieves favorable results which are quite superior to the results of 15 relevant community detection algorithms in the literature

Proposal and Comparative Study of Evolutionary Algorithms for Optimum Design of a Gear System

This paper proposes a novel metaheuristic framework using a Differential Evolution (DE) algorithm with the Non-dominated Sorting Genetic Algorithm-II (NSGA-II). Both algorithms are combined employing a collaborative strategy with sequential execution, which is called DE-NSGA-II. The DE-NSGA-II takes advantage of the exploration abilities of the multi-objective evolutionary algorithms strengthened with the ability to search global mono-objective optimum of DE, that enhances the capability of finding those extreme solutions of Pareto Optimal Front (POF) difficult to achieve. Numerous experiments and performance comparisons between different evolutionary algorithms were performed on a referent problem for the mono-objective and multi-objective literature, which consists of the design of a double reduction gear train. A preliminary study of the problem, solved in an exhaustive way, discovers the low density of solutions in the vicinity of the optimal solution (mono-objective case) as well as in some areas of the POF of potential interest to a decision maker (multi-objective case). This characteristic of the problem would explain the considerable difficulties for its resolution when exact methods and/or metaheuristics are used, especially in the multi-objective case. However, the DE-NSGA-II framework exceeds these difficulties and obtains the whole POF which significantly improves the few previous multi-objective studies.Fil: Méndez Babey, Máximo. Universidad de Las Palmas de Gran Canaria; EspañaFil: Rossit, Daniel Alejandro. Universidad Nacional del Sur. Departamento de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Matemática Bahía Blanca. Universidad Nacional del Sur. Departamento de Matemática. Instituto de Matemática Bahía Blanca; ArgentinaFil: González, Begoña. Universidad de Las Palmas de Gran Canaria; EspañaFil: Frutos, Mariano. Universidad Nacional del Sur. Departamento de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Económicas y Sociales del Sur. Universidad Nacional del Sur. Departamento de Economía. Instituto de Investigaciones Económicas y Sociales del Sur; Argentin

Community Detection in Networks using Bio-inspired Optimization: Latest Developments, New Results and Perspectives with a Selection of Recent Meta-Heuristics

Detecting groups within a set of interconnected nodes is a widely addressed prob- lem that can model a diversity of applications. Unfortunately, detecting the opti- mal partition of a network is a computationally demanding task, usually conducted by means of optimization methods. Among them, randomized search heuristics have been proven to be efficient approaches. This manuscript is devoted to pro- viding an overview of community detection problems from the perspective of bio-inspired computation. To this end, we first review the recent history of this research area, placing emphasis on milestone studies contributed in the last five years. Next, we present an extensive experimental study to assess the performance of a selection of modern heuristics over weighted directed network instances. Specifically, we combine seven global search heuristics based on two different similarity metrics and eight heterogeneous search operators designed ad-hoc. We compare our methods with six different community detection techniques over a benchmark of 17 Lancichinetti-Fortunato-Radicchi network instances. Ranking statistics of the tested algorithms reveal that the proposed methods perform com- petitively, but the high variability of the rankings leads to the main conclusion: no clear winner can be declared. This finding aligns with community detection tools available in the literature that hinge on a sequential application of different algorithms in search for the best performing counterpart. We end our research by sharing our envisioned status of this area, for which we identify challenges and opportunities which should stimulate research efforts in years to come

Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America. 
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Evolutionary Optimization of Atrial Fibrillation Diagnostic Algorithms

The goal of this research is to introduce an improved method for detecting atrial fibrillation (AF). The foundation of our algorithm is the irregularity of the RR intervals in the electrocardiogram (ECG) signal, and their correlation with AF. Three statistical techniques, including root mean squares of successive differences (RMSSD), turning points ratio (TPR), and Shannon entropy (SE), are used to detect RR interval irregularity. We use the Massachusetts Institution of Technology / Beth Israel Hospital (MIT-BIH) atrial fibrillation databases and their annotations to tune the parameters of the statistical methods by biogeography-based optimization (BBO), which is an evolutionary optimization algorithm. We trained each statistical method to diagnose AF on each database. Then each trained method was tested on the rest of the databases. We were able to obtain accuracy levels as high as 99 for the detection of AF in the trained databases. We obtained accuracy levels of up to 75 in the tested database

Evolutionary Optimization of Atrial Fibrillation Diagnostic Algorithms

The goal of this research is to introduce an improved method for detecting atrial fibrillation (AF). The foundation of our algorithm is the irregularity of the RR intervals in the electrocardiogram (ECG) signal, and their correlation with AF. Three statistical techniques, including root mean squares of successive differences (RMSSD), turning points ratio (TPR), and Shannon entropy (SE), are used to detect RR interval irregularity. We use the Massachusetts Institution of Technology / Beth Israel Hospital (MIT-BIH) atrial fibrillation databases and their annotations to tune the parameters of the statistical methods by biogeography-based optimization (BBO), which is an evolutionary optimization algorithm. We trained each statistical method to diagnose AF on each database. Then each trained method was tested on the rest of the databases. We were able to obtain accuracy levels as high as 99 for the detection of AF in the trained databases. We obtained accuracy levels of up to 75 in the tested database

Gap Analysis and the Geographical Distribution of Parasites

Sampling biases can have enormous impacts on studies of parasite biogeography. While complete sampling is sometimes possible for local or regional patterns of parasitism, continental and global analyses often rely on data collected in a heterogeneous manner. At these larger scales, spatially-explicit methods to quantify and correct for geographic sampling biases are necessary. Approaches based on “gap analysis” can contribute to the development of corrective measures by identifying geographical variation in our knowledge of parasites and quantifying how sampling varies in relation to host characteristics and habitat features. In this chapter, we review these methods and describe how they have been applied to study gaps in our knowledge of primate parasites.Human Evolutionary Biolog

Multi-objective community detection applied to social and COVID-19 constructed networks

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonCommunity Detection plays an integral part in network analysis, as it facilitates understanding the structures and functional characteristics of the network. Communities organize real-world networks into densely connected groups of nodes. This thesis provides a critical analysis of the Community Detection and highlights the main areas including algorithms, evaluation metrics, applications, and datasets in social networks. After defining the research gap, this thesis proposes two Attribute-Based Label Propagation algorithms that maximizes both Modularity and homogeneity. Homogeneity is considered as an objective function one time, and as a constraint another time. To better capture the homogeneity of real-world networks, a new Penalized Homogeneity degree (PHd) is proposed, that can be easily personalized based on the network characteristics. For the first time, COVID-19 tracing data are utilized to form two dataset networks: one is based on the virus transition between the world countries. While the second dataset is an attributed network based on the virus transition among the contact-tracing in the Kingdom of Bahrain. This type of networks that is concerned in tracking a disease was not formed based on COVID-19 virus and has never been studied as a community detection problem. The proposed datasets are validated and tested in several experiments. The proposed Penalized Homogeneity measure is personalized and used to evaluate the proposed attributed network. Extensive experiments and analysis are carried out to evaluate the proposed methods and benchmark the results with other well-known algorithms. The results are compared in terms of Modularity, proposed PHd, and accuracy measures. The proposed methods have achieved maximum performance among other methods, with 26.6% better performance in Modularity, and 33.96% in PHd on the proposed dataset, as well as noteworthy results on benchmarking datasets with improvement in Modularity measures of 7.24%, and 4.96% respectively, and proposed PHd values 27% and 81.9%

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

Elucidating the demographic and phylogeographic histories of species provides insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of histories and demographic parameters with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Even with genomic estimates of historical demographic parameters, we found the prominent diversification hypotheses to be untestable. We conclude that investigations into the multifarious processes shaping species histories, aided by genomic datasets, will provide greater resolution of diversification in the Neotropics, but that future efforts should focus on understanding the processes shaping the histories of lineages rather than trying to reconcile these histories with landscape and climatic events in Earth history.Comment: 61 pages, 4 figures (+3 supplemental), 3 tables (+6 supplemental

Multi-Objective Evolutionary Algorithms to Find Community Structures in Large Networks

Real-world complex systems are often modeled by networks such that the elements are represented by vertices and their interactions are represented by edges. An important characteristic of these networks is that they contain clusters of vertices densely linked amongst themselves and more sparsely connected to nodes outside the cluster. Community detection in networks has become an emerging area of investigation in recent years, but most papers aim to solve single-objective formulations, often focused on optimizing structural metrics, including the modularity measure. However, several studies have highlighted that considering modularityas a unique objective often involves resolution limit and imbalance inconveniences. This paper opens a new avenue of research in the study of multi-objective variants of the classical community detection problem by applying multi-objective evolutionary algorithms that simultaneously optimize different objectives. In particular, they analyzed two multi-objective variants involving not only modularity but also the conductance metric and the imbalance in the number of nodes of the communities. With this aim, a new Pareto-based multi-objective evolutionary algorithm is presented that includes advanced initialization strategies and search operators. The results obtained when solving large-scale networks representing real-life power systems show the good performance of these methods and demonstrate that it is possible to obtain a balanced number of nodes in the clusters formed while also having high modularity and conductance values