On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

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

Adaptive and learning-based formation control of swarm robots

Autonomous aerial and wheeled mobile robots play a major role in tasks such as search and rescue, transportation, monitoring, and inspection. However, these operations are faced with a few open challenges including robust autonomy, and adaptive coordination based on the environment and operating conditions, particularly in swarm robots with limited communication and perception capabilities. Furthermore, the computational complexity increases exponentially with the number of robots in the swarm. This thesis examines two different aspects of the formation control problem. On the one hand, we investigate how formation could be performed by swarm robots with limited communication and perception (e.g., Crazyflie nano quadrotor). On the other hand, we explore human-swarm interaction (HSI) and different shared-control mechanisms between human and swarm robots (e.g., BristleBot) for artistic creation. In particular, we combine bio-inspired (i.e., flocking, foraging) techniques with learning-based control strategies (using artificial neural networks) for adaptive control of multi- robots. We first review how learning-based control and networked dynamical systems can be used to assign distributed and decentralized policies to individual robots such that the desired formation emerges from their collective behavior. We proceed by presenting a novel flocking control for UAV swarm using deep reinforcement learning. We formulate the flocking formation problem as a partially observable Markov decision process (POMDP), and consider a leader-follower configuration, where consensus among all UAVs is used to train a shared control policy, and each UAV performs actions based on the local information it collects. In addition, to avoid collision among UAVs and guarantee flocking and navigation, a reward function is added with the global flocking maintenance, mutual reward, and a collision penalty. We adapt deep deterministic policy gradient (DDPG) with centralized training and decentralized execution to obtain the flocking control policy using actor-critic networks and a global state space matrix. In the context of swarm robotics in arts, we investigate how the formation paradigm can serve as an interaction modality for artists to aesthetically utilize swarms. In particular, we explore particle swarm optimization (PSO) and random walk to control the communication between a team of robots with swarming behavior for musical creation

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de

Swarm robotics:design and implementation

This project presents a swarming and herding behaviour using simple robots. The main goal is to demonstrate the applicability of artificial intelligence (AI) in simple robotics that can then be scaled to industrial and consumer markets to further the ability of automation. AI can be achieved in many different ways; this paper explores the possible platforms on which to build a simple AI robots from consumer grade microcontrollers. Emphasis on simplicity is the main focus of this paper. Cheap and 8 bit microcontrollers were used as the brain of each robot in a decentralized swarm environment were each robot is autonomous but still a part of the whole. These simple robots don’t communicate directly with each other. They will utilize simple IR sensors to sense each other and simple limit switches to sense other obstacles in their environment. Their main objective is to assemble at certain location after initial start from random locations, and after converging they would move as a single unit without collisions. Using readily available microcontrollers and simple circuit design, semiconsistent swarming behaviour was achieved. These robots don’t follow a set path but will react dynamically to different scenarios, guided by their simple AI algorithm

2010 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Abstract book for the Second Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: November 19 - 20, 2010Plenary speaker: Abdul-Aziz Yakubu, Professor and Chair of the Department of Mathematics, Howard UniversityFeatured speaker: Jory Weintraub, Assistant Director Education and Outreach, National Evolutionary Synthesis Cente

Energy Efficient Routing Algorithms for Wireless Sensor Networks and Performance Evaluation of Quality of Service for IEEE 802.15.4 Networks

The popularity of Wireless Sensor Networks (WSN) have increased tremendously in recent time due to growth in Micro-Electro-Mechanical Systems (MEMS) technology. WSN has the potentiality to connect the physical world with the virtual world by forming a network of sensor nodes. Here, sensor nodes are usually battery-operated devices, and hence energy saving of sensor nodes is a major design issue. To prolong the network‘s lifetime, minimization of energy consumption should be implemented at all layers of the network protocol stack starting from the physical to the application layer including cross-layer optimization. In this thesis, clustering based routing protocols for WSNs have been discussed. In cluster-based routing, special nodes called cluster heads form a wireless backbone to the sink. Each cluster heads collects data from the sensors belonging to its cluster and forwards it to the sink. In heterogeneous networks, cluster heads have powerful energy devices in contrast to homogeneous networks where all nodes have uniform and limited resource energy. So, it is essential to avoid quick depletion of cluster heads. Hence, the cluster head role rotates, i.e., each node works as a cluster head for a limited period of time. Energy saving in these approaches can be obtained by cluster formation, cluster-head election, data aggregation at the cluster-head nodes to reduce data redundancy and thus save energy. The first part of this thesis discusses methods for clustering to improve energy efficiency of homogeneous WSN. It also proposes Bacterial Foraging Optimization (BFO) as an algorithm for cluster head selection for WSN. The simulation results show improved performance of BFO based optimization in terms of total energy dissipation and no of alive nodes of the network system over LEACH, K-Means and direct methods. IEEE 802.15.4 is the emerging next generation standard designed for low-rate wireless personal area networks (LR-WPAN). The second part of the work reported here in provides performance evaluation of quality of service parameters for WSN based on IEEE 802.15.4 star and mesh topology. The performance studies have been evaluated for varying traffic loads using MANET routing protocol in QualNet 4.5. The data packet delivery ratio, average end-to-end delay, total energy consumption, network lifetime and percentage of time in sleep mode have been used as performance metrics. Simulation results show that DSR (Dynamic Source Routing) performs better than DYMO (Dynamic MANET On-demand) and AODV (Ad–hoc On demand Distance Vector) routing protocol for varying traffic loads rates

Development of New Global Optimization Algorithms Using Stochastic Level Set Method with Application in: Topology Optimization, Path Planning and Image Processing

A unique mathematical tool is developed to deal with global optimization of a set of engineering problems. These include image processing, mechanical topology optimization, and optimal path planning in a variational framework, as well as some benchmark problems in parameter optimization. The optimization tool in these applications is based on the level set theory by which an evolving contour converges toward the optimum solution. Depending upon the application, the objective function is defined, and then the level set theory is used for optimization. Level set theory, as a member of active contour methods, is an extension of the steepest descent method in conventional parameter optimization to the variational framework. It intrinsically suffers from trapping in local solutions, a common drawback of gradient based optimization methods. In this thesis, methods are developed to deal with this drawbacks of the level set approach. By investigating the current global optimization methods, one can conclude that these methods usually cannot be extended to the variational framework; or if they can, the computational costs become drastically expensive. To cope with this complexity, a global optimization algorithm is first developed in parameter space and compared with the existing methods. This method is called "Spiral Bacterial Foraging Optimization" (SBFO) method because it is inspired by the aggregation process of a particular bacterium called, Dictyostelium Discoideum. Regardless of the real phenomenon behind the SBFO, it leads to new ideas in developing global optimization methods. According to these ideas, an effective global optimization method should have i) a stochastic operator, and/or ii) a multi-agent structure. These two properties are very common in the existing global optimization methods. To improve the computational time and costs, the algorithm may include gradient-based approaches to increase the convergence speed. This property is particularly available in SBFO and it is the basis on which SBFO can be extended to variational framework. To mitigate the computational costs of the algorithm, use of the gradient based approaches can be helpful. Therefore, SBFO as a multi-agent stochastic gradient based structure can be extended to multi-agent stochastic level set method. In three steps, the variational set up is formulated: i) A single stochastic level set method, called "Active Contours with Stochastic Fronts" (ACSF), ii) Multi-agent stochastic level set method (MSLSM), and iii) Stochastic level set method without gradient such as E-ARC algorithm. For image processing applications, the first two steps have been implemented and show significant improvement in the results. As expected, a multi agent structure is more accurate in terms of ability to find the global solution but it is much more computationally expensive. According to the results, if one uses an initial level set with enough holes in its topology, a single stochastic level set method can achieve almost the same level of accuracy as a multi-agent structure can obtain. Therefore, for a topology optimization problem for which a high level of calculations (at each iteration a finite element model should be solved) is required, only ACSF with initial guess with multiple holes is implemented. In some applications, such as optimal path planning, objective functions are usually very complicated; finding a closed-form equation for the objective function and its gradient is therefore impossible or sometimes very computationally expensive. In these situations, the level set theory and its extensions cannot be directly employed. As a result, the Evolving Arc algorithm that is inspired by "Electric Arc" in nature, is proposed. The results show that it can be a good solution for either unconstrained or constrained problems. Finally, a rigorous convergence analysis for SBFO and ACSF is presented that is new amongst global optimization methods in both parameter and variational framework

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

An Empirical Study on Collective Intelligence Algorithms for Video Games Problem-Solving

Computational intelligence (CI), such as evolutionary computation or swarm intelligence methods, is a set of bio-inspired algorithms that have been widely used to solve problems in areas like planning, scheduling or constraint satisfaction problems. Constrained satisfaction problems (CSP) have taken an important attention from the research community due to their applicability to real problems. Any CSP problem is usually modelled as a constrained graph where the edges represent a set of restrictions that must be verified by the variables (represented as nodes in the graph) which will define the solution of the problem. This paper studies the performance of two particular CI algorithms, ant colony optimization (ACO) and genetic algorithms (GA), when dealing with graph-constrained models in video games problems. As an application domain, the "Lemmings" video game has been selected, where a set of lemmings must reach the exit point of each level. In order to do that, each level is represented as a graph where the edges store the allowed movements inside the world. The goal of the algorithms is to assign the best skills in each position on a particular level, to guide the lemmings to reach the exit. The paper describes how the ACO and GA algorithms have been modelled and applied to the selected video game. Finally, a complete experimental comparison between both algorithms, based on the number of solutions found and the levels solved, is analysed to study the behaviour of those algorithms in the proposed domain