A Multiobjective Proposal Based on the Firefly Algorithm for Inferring Phylogenies

In this paper, we proposed an MOEA approach, called PhyloMOEA which solves the phylogenetic inference problem using maximum parsimony and maximum likelihood criteria. The PhyloMOEA's development was motivated by several studies in the literature (Huelsenbeck, 1995; Jin & Nei, 1990; Kuhner & Felsenstein, 1994; Tateno et al., 1994), which point out that various phylogenetic inference methods lead to inconsistent solutions. Techniques using parsimony and likelihood criteria yield to different trees when they are applied separately to the four nucleotide datasets used in the experiments. On the other hand, PhyloMOEA was applied to the four datasets and found a set of trees that represents a trade-off between these criteria. POS and FS trees obtained by PhyloMOEA were statistically evaluated using the SH-test. The results of this test suggest that several PhyloMOEA solutions are consistent with the criteria used. It is important to observe that the PhyloMOEA trees are not directly comparable with trees obtained by other phylogenetic reconstruction programs since these programs consider only one optimality criterion. Moreover, support values for clades included in trees obtained by PhyloMOEA were calculated. The clades were classified into several types according to the type of trees the clade is in: maximum parsimony, maximum likelihood or intermediate trees. Support values were compared with clade posterior probabilities reported by Mr.Bayes for the four test datasets used. The results show that PhyloMOEA clade support closely approximates Mr.Bayes posterior probabilities if the clades found in the set of trees correspond to intermediate and maximum likelihood/maximum parsimony trees. Despite the relevant results found by PhyloMOEA, there are aspects that could be addressed in order to improve the algorithm and corresponding results: · PhyloMOEA requires several hours to find acceptable Pareto-solutions if initial trees are poorly estimated. This problem can be improved taking into account local search strategies (Guindon & Gascuel, 2003; Stamatakis & Meier, 2004). PhyloMOEA's performance is also decreased by the likelihood calculation, which is computationally intensive. As mentioned in Section 5.3, there are other techniques that address this problem (Larget & Simon, 1998; Stamatakis & Meier, 2004); · The proposed algorithm does not optimize parameters of the evolution model employed in the likelihood calculation. These values can be included in each solution such that they can be optimized during the algorithm execution (Lewis, 1998); · PhyloMOEA uses only Fitch parsimony which has a unitary state change cost matrix. The use of more complex parsimony models or even generalized parsimony can improve the results (Swofford et al., 1996); · Clade support obtained from PhyloMOEA trees can be also compared with bootstrap support values. A bootstrap analysis, using parsimony and likelihood criteria separately, enables the separation of clades that best support the maximum parsimony and maximum likelihood trees. This could lead to a better comparison between PhyloMOEA and bootstrap clade support values; · This research has not investigated the metrics for convergence and diversity of the obtained Pareto front. Measurements for convergence are difficult to obtain since the Pareto front is unknown in this case. On the other hand, various diversity metrics found in the literature (Deb, 2001) can be investigated; The experiments have shown that PhyloMOEA can make relevant contributions to phylogenetic inference. Moreover, there are remaining aspects that can be investigated to improve the current approach.

The aim of this book is to present and analyse theoretical advances and also emerging practical applications of swarm and evolutionary intelligence. It comprises nine chapters. Chapter 1 provides a theoretical introduction of the computational optimization techniques regarding the gradient-based methods such as steepest descent, conjugate gradient, newton and quasi-Newton methods and also the non-gradient methods such as genetic algorithm and swarm intelligence algorithms. Chapter 2, discusses evolutionary computation techniques and genetic algorithm. Swarm intelligence theory and particle swarm optimization algorithm are reviewed in Chapter 3. Also, several variations of particle swarm optimization algorithm are analysed and explained such as Geometric PSO, PSO with mutation, Chaotic PSO with mutation, multi-objective PSO and Quantum mechanics – based PSO algorithm. Chapter 4 deals with two essential colony bio-inspired algorithms: Ant colony optimization (ACO) and Artificial bee colony (ABC). Chapter 5, presents and analyses Cuckoo search and Bat swarm algorithms and their latest variations. In chapter 6, several other metaheuristic algorithms are discussed such as: Firefly algorithm (FA), Harmony search (HS), Cat swarm optimization (CSO) and their improved algorithm modifications. The latest Bio-Inspired Swarm Algorithms are discussed in chapter 7, such as: Grey Wolf Optimization (GWO) Algorithm, Whale Optimization Algorithm (WOA), Grasshopper Optimization Algorithm (GOA) and other algorithm variations such as binary and chaotic versions. Chapter 8 presents machine learning applications of swarm and evolutionary algorithms. Illustrative real-world examples are presented with real datasets regarding neural network optimization and feature selection, using: genetic algorithm, Geometric PSO, Chaotic Harmony Search, Chaotic Cuckoo Search, and Evolutionary Algorithm and also crime forecasting using swarm optimized SVM. In chapter 9, applications of swarm intelligence on deep long short-term memory (LSTM) networks and Deep Convolutional Neural Networks (CNNs) are discussed, including LSTM hyperparameter tuning and Covid19 diagnosis from chest X-Ray images. The aim of the book is to present and discuss several state-of-theart swarm intelligence and evolutionary algorithms together with their variances and also several illustrative applications on machine learning and deep learning.

A large amount of calculation exists in a complex engineering optimization problem. The swarm intelligence algorithm can improve calculation efficiency and accuracy of complex engineering optimization. In the existing research, the surrogate model and the swarm intelligence algorithm are only two independent tools to solve the optimization problem. In this paper, we propose the surrogate-assisted crow swarm intelligent search optimization algorithm (SACSA) by combining the characteristics of swarm intelligence algorithm and surrogate model. The proposed algorithm utilizes the initial samples to construct the surrogate model, and then the improved crow search algorithm (CSA) is applied to obtain optimal solution. Finally, the proposed algorithm is compared with EGO, MSSR, ARSM-ISES, AMGO and SEUMRE, MPS, HAM algorithms. The comparison results show that the proposed algorithm can find a global optimal solution with fewer samples and is beneficial to improving the efficiency and accuracy of calculation.

In the last decades, nature-inspired algorithms have been widely used to solve complex combinatorial optimisation problems. Among them, Evolutionary Algorithms (EAs) and Swarm Intelligence (SI) algorithms have been extensively employed as search and optimisation tools in various problem domains. Evolutionary and Swarm Intelligent algorithms are Artificial Intelligence (AI) techniques, inspired by natural evolution and adaptation. This paper presents two new nature-inspired algorithms, which use concepts of EAs and SI. The combination of EAs and SI algorithms can unify the fast speed of EAs to find global solutions and the good precision of SI algorithms to find good solutions using the feedback information. The proposed algorithms are applied to a complex NP-hard optimisation problem - the Terminal Assignment Problem (TAP). The objective is to minimise the link cost to form a network. The proposed algorithms are compared with several EAs and SI algorithms from literature. We show that the propose...

Image processing technology has always been a hot and difficult topic in the field of artificial intelligence. With the rise and development of machine learning and deep learning methods, swarm intelligence algorithms have become a hot research direction, and combining image processing technology with swarm intelligence algorithms has become a new and effective improvement method. Swarm intelligence algorithm refers to an intelligent computing method formed by simulating the evolutionary laws, behavior characteristics, and thinking patterns of insects, birds, natural phenomena, and other biological populations. It has efficient and parallel global optimization capabilities and strong optimization performance. In this paper, the ant colony algorithm, particle swarm optimization algorithm, sparrow search algorithm, bat algorithm, thimble colony algorithm, and other swarm intelligent optimization algorithms are deeply studied. The model, features, improvement strategies, and application fields of the algorithm in image processing, such as image segmentation, image matching, image classification, image feature extraction, and image edge detection, are comprehensively reviewed. The theoretical research, improvement strategies, and application research of image processing are comprehensively analyzed and compared. Combined with the current literature, the improvement methods of the above algorithms and the comprehensive improvement and application of image processing technology are analyzed and summarized. The representative algorithms of the swarm intelligence algorithm combined with image segmentation technology are extracted for list analysis and summary. Then, the unified framework, common characteristics, different differences of the swarm intelligence algorithm are summarized, existing problems are raised, and finally, the future trend is projected.

The application of swarm intelligence (SI) in the optimization field has been gaining much popularity, and various SI algorithms have been proposed in last decade. However, with the increased number of SI algorithms, most research focuses on the implementation of a specific choice of SI algorithms, and there has been rare research analyzing the common features among SI algorithms coherently. More importantly, no general principles for the implementation and improvement of SI algorithms exist for solving various optimization problems. In this research, aiming to cover such a research gap, a unified framework towards SI is proposed inspired by the in-depth analysis of SI algorithms. The unified framework consists of the most frequently used operations and strategies derived from typical examples of SI algorithms. Following the proposed unified framework, the intrinsic features of SI algorithms can be understood straightforwardly and the implementation and improvement of SI algorithms can be achieved effortlessly, which is of great importance in practice. The numerical experiments examine the effects of the possible strategies employed in the unified framework, and provide pilot attempts to validate the performance of different combinations of strategies, which can not only facilitate specific SI algorithm application, but also can motivate SI algorithm innovation.

In this chapter, the necessity of having developmental learning embedded in a swarm intelligence algorithm is confirmed by briefly considering brain evolution, brain development, brainstorming process, etc. Several swarm intelligence algorithms are looked at from a developmental learning perspective. A framework of a developmental swarm intelligence algorithm, which contains capacity developing stage and capability learning stage, is further given to help understand developmental swarm intelligence (DSI) algorithms, and to guide to design and/or implement any new developmental swarm intelligence algorithm and/or any developmental evolutionary algorithm. Following DSI, innovation is discussed and an innovation-inspired optimization (IO) algorithm is designed and developed. Finally, by combing the DSI and IO algorithm together, a unified swarm intelligence algorithm is proposed, which contains capacity developing stage and capability learning stage and with three search operators in its capability learning stage to mimic the three levels of innovations.

The integration of Swarm Intelligence (SI) algorithms and Evolutionary algorithms (EAs) might be one of the future approaches in the Evolutionary Computation (EC). This work narrates the early research on using Stochastic Diffusion Search (SDS) -- a swarm intelligence algorithm -- to empower the Differential Evolution (DE) -- an evolutionary algorithm -- over a set of optimisation problems. The results reported herein suggest that the powerful resource allocation mechanism deployed in SDS has the potential to improve the optimisation capability of the classical evolutionary algorithm used in this experiment. Different performance measures and statistical analyses were utilised to monitor the behaviour of the final coupled algorithm.

This paper presents a new approach to solve Fractional Programming Problems (FPPs) based on two different Swarm Intelligence (SI) algorithms. The two algorithms are: Particle Swarm Optimization, and Firefly Algorithm. The two algorithms are tested using several FPP benchmark examples and two selected industrial applications. The test aims to prove the capability of the SI algorithms to solve any type of FPPs. The solution results employing the SI algorithms are compared with a number of exact and metaheuristic solution methods used for handling FPPs. Swarm Intelligence can be denoted as an effective technique for solving linear or nonlinear, non-differentiable fractional objective functions. Problems with an optimal solution at a finite point and an unbounded constraint set, can be solved using the proposed approach. Numerical examples are given to show the feasibility, effectiveness, and robustness of the proposed algorithm. The results obtained using the two SI algorithms revealed the superiority of the proposed technique among others in computational time. A better accuracy was remarkably observed in the solution results of the industrial application problems.

Text document clustering refers to the unsupervised classification of textual documents into clusters based on content similarity and can be applied in applications such as search optimization and extracting hidden information from data generated by IoT sensors. Swarm intelligence (SI) algorithms use stochastic and heuristic principles that include simple and unintelligent individuals that follow some simple rules to accomplish very complex tasks. By mapping features of problems to parameters of SI algorithms, SI algorithms can achieve solutions in a flexible, robust, decentralized, and self-organized manner. Compared to traditional clustering algorithms, these solving mechanisms make swarm algorithms suitable for resolving complex document clustering problems. However, each SI algorithm shows a different performance based on its own strengths and weaknesses. In this paper, to find the best performing SI algorithm in text document clustering, we performed a comparative study for the PSO, bat, grey wolf optimization (GWO), and K-means algorithms using six data sets of various sizes, which were created from BBC Sport news and 20 newsgroups. Based on our experimental results, we discuss the features of a document clustering problem with the nature of SI algorithms and conclude that the PSO and GWO SI algorithms are better than K-means, and among those algorithms, the PSO performs best in terms of finding the optimal solution.

Value function approximation, such as Q-learning, is widely used in the discrete control rather than the continuous one because the optimal action in the discrete setting is more easily selected. Optimizing the action is a non-convex optimization problem with respect to the complex value function. Some notable studies simplify the non-convex optimization problem by assuming the value function as quadratic in the actions or by discretizing the action space. However, the performance of the output policy will decline if these studies’ premises do not hold. In order to address the problem, we propose a framework that combines swarm intelligence algorithms with value-based Reinforcement Learning, where the swarm intelligence algorithms are employed to search for the optimal action with respect to the state and the value function. To ensure the correctness of this framework, we conditionally claim the convergence rate of swarm intelligence algorithms with high probability. We then implement it by searching the batch optimal actions to various states on the GPU platform for the batch training. Furthermore, we employ the population-based atomic actions for the compatibility with the existing related work about solving discrete control problems. Four classical control models and four robot simulation environments are utilized in the comparisons. According to empirical results, our framework outputs a policy comparable with that of the policy-based algorithms by 10% timesteps in the continuous control. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This paper is motivated by the exploration-exploitation dilemma of Reinforcement Learning to solve continuous control tasks. To balance the exploration and exploitation, the stochastic exploration and the prioritized exploration are roughly two feasible ways, where the prioritized one is a better choice due to the higher data efficiency than the stochastic one, e.g. <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\varepsilon$</tex-math> </inline-formula> -greedy. Normally, the prioritized exploration works well in the value-based Reinforcement Learning algorithms rather than the policy-based ones; meanwhile, the policy-based algorithms are more suitable to continuous control tasks than the value-based ones. To tackle this conflict, we especially design a particle swarm optimization to maximize the Q-value of action in Q-learning. Our design can be hybridized by various swarm intelligence and value-based Reinforcement Learning algorithms. Also, it can be embedded in most intelligent control systems easily. The aim of this study is to solve the continuous control tasks by value-based algorithms as the first step of applying the prioritized exploration. The simulative results verify the effectiveness and efficiency of our design.

One of the most relevant problems in Bioinformaticsand Computational Biology is the search and reconstruction ofthe most accurate phylogenetic tree that explains, as exactly aspossible, the evolutionary relationships among species from agiven dataset. Different criteria have been employed to evaluatethe accuracy of evolutionary hypothesis in order to guide a searchalgorithm towards the best tree. However, these criteria may leadto distinct phylogenies, which are often conflicting among them.Therefore, a multi-objective approach can be useful. In this work,we present a phylogenetic adaptation of a multiobjective variablemesh optimization algorithm for inferring phylogenies, to tacklethe phylogenetic inference problem according to two optimalitycriteria: maximum parsimony and maximum likelihood. Theaim of this approach is to propose a complementary view ofphylogenetics in order to generate a set of trade-off phylogenetictopologies that represent a consensus between both criteria.Experiments on four real nucleotide datasets show that ourproposal can achieve promising results, under both multiobjectiveand biological approaches, with regard to other classical andrecent multiobjective metaheuristics from the state-of-the-art.

A survey of swarm intelligence for dynamic optimization: Algorithms and applications

Swarm Intelligence (SI) algorithms are frequently applied to tackle complex optimization problems. SI is especially used when good solutions are requested for NP hard problems within a reasonable response time. And when such problems possess a very high dimensionality, a dynamic nature, or present intrinsic complex intertwined independent variables, computational costs for SI algorithms may still be too high. Therefore, new approaches and hardware support are needed to speed up processing. Nowadays, with the popularization of GPU and multi-core processing, parallel versions of SI algorithms can provide the required performance on those though problems. This paper aims to describe the state of the art of such approaches, to summarize the key points addressed, and also to identify the research gaps that could be addressed better. The scope of this review considers recent papers mainly focusing on parallel implementations of the most frequently used SI algorithms. The use of nested parallelism is of particular interest, since one level of parallelism is often not sufficient to exploit the computational power of contemporary parallel hardware. The sources were main scientific databases and filtered accordingly to the set requirements of this literature review.

All inferences in comparative biology depend on accurate estimates of evolutionary relationships. Recent phylogenetic analyses have turned away from maximum parsimony towards the probabilistic techniques of maximum likelihood and bayesian Markov chain Monte Carlo (BMCMC). These probabilistic techniques represent a parametric approach to statistical phylogenetics, because their criterion for evaluating a topology--the probability of the data, given the tree--is calculated with reference to an explicit evolutionary model from which the data are assumed to be identically distributed. Maximum parsimony can be considered nonparametric, because trees are evaluated on the basis of a general metric--the minimum number of character state changes required to generate the data on a given tree--without assuming a specific distribution. The shift to parametric methods was spurred, in large part, by studies showing that although both approaches perform well most of the time, maximum parsimony is strongly biased towards recovering an incorrect tree under certain combinations of branch lengths, whereas maximum likelihood is not. All these evaluations simulated sequences by a largely homogeneous evolutionary process in which data are identically distributed. There is ample evidence, however, that real-world gene sequences evolve heterogeneously and are not identically distributed. Here we show that maximum likelihood and BMCMC can become strongly biased and statistically inconsistent when the rates at which sequence sites evolve change non-identically over time. Maximum parsimony performs substantially better than current parametric methods over a wide range of conditions tested, including moderate heterogeneity and phylogenetic problems not normally considered difficult.