Efficient Two-Level Swarm Intelligence Approach for Multiple Sequence Alignment

This paper proposes two-level particle swarm optimization (TL-PSO), an efficient PSO variant that addresses two levels of optimization problem. Level one works on optimizing dimension for entire swarm, whereas level two works for optimizing each particle's position. The issue addressed here is one of the most challenging multiple sequence alignment (MSA) problem. TL-PSO deals with the arduous task of determination of exact sequence length with most suitable gap positions in MSA. The two levels considered here are: to obtain optimal sequence length in level one and to attain optimum gap positions for maximal alignment score in level two. The performance of TL-PSO has been assessed through a comparative study with two kinds of benchmark dataset of DNA and RNA. The efficiency of the proposed approach is evaluated with four popular scoring schemes at specific parameters. TL-PSO alignments are compared with four PSO variants, i.e. S-PSO, M-PSO, ED-MPSO and CPSO-Sk, and two leading alignment software, i.e. ClustalW and T-Coffee, at different alignment scores. Hence obtained results prove the competence of TL-PSO at accuracy aspects and conclude better score scheme

Multiple sequence alignment using particle swarm optimization

The recent advent of bioinformatics has given rise to the central and recurrent problem of optimally aligning biological sequences. Many techniques have been proposed in an attempt to solve this complex problem with varying degrees of success. This thesis investigates the application of a computational intelligence technique known as particle swarm optimization (PSO) to the multiple sequence alignment (MSA) problem. Firstly, the performance of the standard PSO (S-PSO) and its characteristics are fully analyzed. Secondly, a scalability study is conducted that aims at expanding the S-PSO’s application to complex MSAs, as well as studying the behaviour of three other kinds of PSOs on the same problems. Experimental results show that the PSO is efficient in solving the MSA problem and compares positively with well-known CLUSTAL X and T-COFFEE.Dissertation (MSc)--University of Pretoria, 2009.Computer ScienceUnrestricte

A Review of the Family of Artificial Fish Swarm Algorithms: Recent Advances and Applications

The Artificial Fish Swarm Algorithm (AFSA) is inspired by the ecological behaviors of fish schooling in nature, viz., the preying, swarming, following and random behaviors. Owing to a number of salient properties, which include flexibility, fast convergence, and insensitivity to the initial parameter settings, the family of AFSA has emerged as an effective Swarm Intelligence (SI) methodology that has been widely applied to solve real-world optimization problems. Since its introduction in 2002, many improved and hybrid AFSA models have been developed to tackle continuous, binary, and combinatorial optimization problems. This paper aims to present a concise review of the family of AFSA, encompassing the original ASFA and its improvements, continuous, binary, discrete, and hybrid models, as well as the associated applications. A comprehensive survey on the AFSA from its introduction to 2012 can be found in [1]. As such, we focus on a total of {\color{blue}123} articles published in high-quality journals since 2013. We also discuss possible AFSA enhancements and highlight future research directions for the family of AFSA-based models.Comment: 37 pages, 3 figure

High Order Contingency Selection using Particle Swarm Optimization and Tabu Search

There is a growing interest in investigating the high order contingency events that may result in large blackouts, which have been a great concern for power grid secure operation. The actual number of high order contingency is too huge for operators and planner to apply a brute-force enumerative analysis. This thesis presents a heuristic searching method based on particle swarm optimization (PSO) and tabu search to select severe high order contingencies. The original PSO algorithm gives an intelligent strategy to search the feasible solution space, but tends to find the best solution only. The proposed method combines the original PSO with tabu search such that a number of top candidates will be identified. This fits the need of high order contingency screening, which can be eventually the input to many other more complicate security analyses. Reordering of branches of test system based on severity of N-1 contingencies is applied as a pre-processing to increase the convergence properties and efficiency of the algorithm. With this reordering approach, many critical high order contingencies are located in a small area in the whole searching space. Therefore, the proposed algorithm tends to concentrate in searching this area such that the number of critical branch combinations searched will increase. Therefore, the speedup ratio is found to increase significantly. The proposed algorithm is tested for N-2 and N-3 contingencies using two test systems modified from the IEEE 118-bus and 30-bus systems. Variation of inertia weight, learning factors, and number of particles is tested and the range of values more suitable for this specific algorithm is suggested. Although illustrated and tested with N-2 and N-3 contingency analysis, the proposed algorithm can be extended to even higher order contingencies but visualization will be difficult because of the increase in the problem dimensions corresponding to the order of contingencies

Enhancement of Metaheuristic Algorithm for Scheduling Workflows in Multi-fog Environments

Whether in computer science, engineering, or economics, optimization lies at the heart of any challenge involving decision-making. Choosing between several options is part of the decision- making process. Our desire to make the "better" decision drives our decision. An objective function or performance index describes the assessment of the alternative's goodness. The theory and methods of optimization are concerned with picking the best option. There are two types of optimization methods: deterministic and stochastic. The first is a traditional approach, which works well for small and linear problems. However, they struggle to address most of the real-world problems, which have a highly dimensional, nonlinear, and complex nature. As an alternative, stochastic optimization algorithms are specifically designed to tackle these types of challenges and are more common nowadays. This study proposed two stochastic, robust swarm-based metaheuristic optimization methods. They are both hybrid algorithms, which are formulated by combining Particle Swarm Optimization and Salp Swarm Optimization algorithms. Further, these algorithms are then applied to an important and thought-provoking problem. The problem is scientific workflow scheduling in multiple fog environments. Many computer environments, such as fog computing, are plagued by security attacks that must be handled. DDoS attacks are effectively harmful to fog computing environments as they occupy the fog's resources and make them busy. Thus, the fog environments would generally have fewer resources available during these types of attacks, and then the scheduling of submitted Internet of Things (IoT) workflows would be affected. Nevertheless, the current systems disregard the impact of DDoS attacks occurring in their scheduling process, causing the amount of workflows that miss deadlines as well as increasing the amount of tasks that are offloaded to the cloud. Hence, this study proposed a hybrid optimization algorithm as a solution for dealing with the workflow scheduling issue in various fog computing locations. The proposed algorithm comprises Salp Swarm Algorithm (SSA) and Particle Swarm Optimization (PSO). In dealing with the effects of DDoS attacks on fog computing locations, two Markov-chain schemes of discrete time types were used, whereby one calculates the average network bandwidth existing in each fog while the other determines the number of virtual machines existing in every fog on average. DDoS attacks are addressed at various levels. The approach predicts the DDoS attack’s influences on fog environments. Based on the simulation results, the proposed method can significantly lessen the amount of offloaded tasks that are transferred to the cloud data centers. It could also decrease the amount of workflows with missed deadlines. Moreover, the significance of green fog computing is growing in fog computing environments, in which the consumption of energy plays an essential role in determining maintenance expenses and carbon dioxide emissions. The implementation of efficient scheduling methods has the potential to mitigate the usage of energy by allocating tasks to the most appropriate resources, considering the energy efficiency of each individual resource. In order to mitigate these challenges, the proposed algorithm integrates the Dynamic Voltage and Frequency Scaling (DVFS) technique, which is commonly employed to enhance the energy efficiency of processors. The experimental findings demonstrate that the utilization of the proposed method, combined with the Dynamic Voltage and Frequency Scaling (DVFS) technique, yields improved outcomes. These benefits encompass a minimization in energy consumption. Consequently, this approach emerges as a more environmentally friendly and sustainable solution for fog computing environments

An Approach Based on Particle Swarm Optimization for Inspection of Spacecraft Hulls by a Swarm of Miniaturized Robots

The remoteness and hazards that are inherent to the operating environments of space infrastructures promote their need for automated robotic inspection. In particular, micrometeoroid and orbital debris impact and structural fatigue are common sources of damage to spacecraft hulls. Vibration sensing has been used to detect structural damage in spacecraft hulls as well as in structural health monitoring practices in industry by deploying static sensors. In this paper, we propose using a swarm of miniaturized vibration-sensing mobile robots realizing a network of mobile sensors. We present a distributed inspection algorithm based on the bio-inspired particle swarm optimization and evolutionary algorithm niching techniques to deliver the task of enumeration and localization of an a priori unknown number of vibration sources on a simplified 2.5D spacecraft surface. Our algorithm is deployed on a swarm of simulated cm-scale wheeled robots. These are guided in their inspection task by sensing vibrations arising from failure points on the surface which are detected by on-board accelerometers. We study three performance metrics: (1) proximity of the localized sources to the ground truth locations, (2) time to localize each source, and (3) time to finish the inspection task given a 75% inspection coverage threshold. We find that our swarm is able to successfully localize the present so

Adaptive Estimation and Heuristic Optimization of Nonlinear Spacecraft Attitude Dynamics

For spacecraft conducting on-orbit operations, changes to the structure of the spacecraft are not uncommon. These planned or unanticipated changes in inertia properties couple with the spacecraft\u27s attitude dynamics and typically require estimation. For systems with time-varying inertia parameters, multiple model adaptive estimation (MMAE) routines can be utilized for parameter and state estimates. MMAE algorithms involve constructing a bank of recursive estimators, each assuming a different hypothesis for the systems dynamics. This research has three distinct, but related, contributions to satellite attitude dynamics and estimation. In the first part of this research, MMAE routines employing parallel banks of unscented attitude filters are applied to analytical models of spacecraft with time-varying mass moments of inertia (MOI), with the objective of estimating the MOI and classifying the spacecraft\u27s behavior. New adaptive estimation techniques were either modified or developed that can detect discontinuities in MOI up to 98 of the time in the specific problem scenario.Second, heuristic optimization techniques and numerical methods are applied to Wahba\u27s single-frame attitude estimation problem,decreasing computation time by an average of nearly 67 . Finally, this research poses MOI estimation as an ODE parameter identification problem, achieving successful numerical estimates through shooting methods and exploiting the polhodes of rigid body motion with results, on average, to be within 1 to 5 of the true MOI values

Multiobjective overtaking maneuver planning of autonomous ground vehicles

This paper proposes a computational trajectory optimization framework for solving the problem of multi-objective automatic parking motion planning. Constrained automatic parking maneuver problem is usually difficult to solve because of some practical limitations and requirements. This problem becomes more challenging when multiple objectives are required to be optimized simultaneously. The designed approach employs a swarm intelligent algorithm to produce the trade-off front along the objective space. In order to enhance the local search ability of the algorithm, a gradient operation is utilized to update the solution. In addition, since the evolutionary process tends to be sensitive with respect to the flight control parameters, a novel adaptive parameter controller is designed and incorporated in the algorithm framework such that the proposed method can dynamically balance the exploitation and exploration. The performance of using the designed multi-objective strategy is validated and analyzed by performing a number of simulation and experimental studies. The results indicate that the present approach can provide reliable solutions and it can outperform other existing approaches investigated in this paper

Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction

Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computed structures and identify the functions of these sequences. Developing methods that will satisfy these needs both efficiently and accurately is of paramount importance for advances in many biomedical fields, for a better basic understanding of aberrant states of stress and disease, including drug discovery and discovery of biomarkers. Several aspects of secondary structure predictions and other protein structure-related predictions are investigated using different types of information such as data obtained from knowledge-based potentials derived from amino acids in protein sequences, physicochemical properties of amino acids and propensities of amino acids to appear at the ends of secondary structures. Investigating the performance of these secondary structure predictions by type of amino acid highlights some interesting aspects relating to the influences of the individual amino acid types on formation of secondary structures and points toward ways to make further gains. Other research areas include Relative Solvent Accessibility (RSA) predictions and predictions of phosphorylation sites, which is one of the Post-Translational Modification (PTM) sites in proteins. Protein secondary structures and other features of proteins are predicted efficiently, reliably, less expensively and more accurately. A novel method called Fast Learning Optimized PREDiction (FLOPRED) Methodology is proposed for predicting protein secondary structures and other features, using knowledge-based potentials, a Neural Network based Extreme Learning Machine (ELM) and advanced Particle Swarm Optimization (PSO) techniques that yield better and faster convergence to produce more accurate results. These techniques yield superior classification of secondary structures, with a training accuracy of 93.33% and a testing accuracy of 92.24% with a standard deviation of 0.48% obtained for a small group of 84 proteins. We have a Matthew\u27s correlation-coefficient ranging between 80.58% and 84.30% for these secondary structures. Accuracies for individual amino acids range between 83% and 92% with an average standard deviation between 0.3% and 2.9% for the 20 amino acids. On a larger set of 415 proteins, we obtain a testing accuracy of 86.5% with a standard deviation of 1.38%. These results are significantly higher than those found in the literature. Prediction of protein secondary structure based on amino acid sequence is a common technique used to predict its 3-D structure. Additional information such as the biophysical properties of the amino acids can help improve the results of secondary structure prediction. A database of protein physicochemical properties is used as features to encode protein sequences and this data is used for secondary structure prediction using FLOPRED. Preliminary studies using a Genetic Algorithm (GA) for feature selection, Principal Component Analysis (PCA) for feature reduction and FLOPRED for classification give promising results. Some amino acids appear more often at the ends of secondary structures than others. A preliminary study has indicated that secondary structure accuracy can be improved as much as 6% by including these effects for those residues present at the ends of alpha-helix, beta-strand and coil. A study on RSA prediction using ELM shows large gains in processing speed compared to using support vector machines for classification. This indicates that ELM yields a distinct advantage in terms of processing speed and performance for RSA. Additional gains in accuracies are possible when the more advanced FLOPRED algorithm and PSO optimization are implemented. Phosphorylation is a post-translational modification on proteins often controls and regulates their activities. It is an important mechanism for regulation. Phosphorylated sites are known to be present often in intrinsically disordered regions of proteins lacking unique tertiary structures, and thus less information is available about the structures of phosphorylated sites. It is important to be able to computationally predict phosphorylation sites in protein sequences obtained from mass-scale sequencing of genomes. Phosphorylation sites may aid in the determination of the functions of a protein and to better understanding the mechanisms of protein functions in healthy and diseased states. FLOPRED is used to model and predict experimentally determined phosphorylation sites in protein sequences. Our new PSO optimization included in FLOPRED enable the prediction of phosphorylation sites with higher accuracy and with better generalization. Our preliminary studies on 984 sequences demonstrate that this model can predict phosphorylation sites with a training accuracy of 92.53% , a testing accuracy 91.42% and Matthew\u27s correlation coefficient of 83.9%. In summary, secondary structure prediction, Relative Solvent Accessibility and phosphorylation site prediction have been carried out on multiple sets of data, encoded with a variety of information drawn from proteins and the physicochemical properties of their constituent amino acids. Improved and efficient algorithms called S-ELM and FLOPRED, which are based on Neural Networks and Particle Swarm Optimization are used for classifying and predicting protein sequences. Analysis of the results of these studies provide new and interesting insights into the influence of amino acids on secondary structure prediction. S-ELM and FLOPRED have also proven to be robust and efficient for predicting relative solvent accessibility of proteins and phosphorylation sites. These studies show that our method is robust and resilient and can be applied for a variety of purposes. It can be expected to yield higher classification accuracy and better generalization performance compared to previous methods