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Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets

GIGASCIENCE 2016年第1期5卷 44页

作者： Narechania, Apurva Baker, Richard DeSalle, Rob Mathema, Barun Kolokotronis, Sergios-Orestis Kreiswirth, Barry Planet, Paul J. Amer Museum Nat Hist Sackler Inst Comparat Genom New York NY 10024 USA Rutgers Newark New Jersey Med Sch Publ Hlth Res Inst Ctr Newark NJ 07103 USA Childrens Hosp Philadelphia Dept Pediat Div Pediat Infect Dis Philadelphia PA 19104 USA Univ Penn Philadelphia PA 19104 USA Fordham Univ Dept Biol Sci Bronx NY 10458 USA Columbia Univ Mailman Sch Publ Hlth Dept Epidemiol New York NY 10032 USA

Background: Collective animal behavior, such as the flocking of birds or the shoaling of fish, has inspired a class of algorithms designed to optimize distance-based clusters in various applications, including document analysis and DNA microarrays. In a flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize, and clusters emerge without the need for partitional seeds. In addition to its unsupervised nature, flocking offers several computational advantages, including the potential to reduce the number of required comparisons. Findings: In the tool presented here, Clusterflock, we have implemented a flocking algorithm designed to locate groups (flocks) of orthologous gene families (OGFs) that share an evolutionary history. Pairwise distances that measure phylogenetic incongruence between OGFs guide flock formation. We tested this approach on several simulated datasets by varying the number of underlying topologies, the proportion of missing data, and evolutionary rates, and show that in datasets containing high levels of missing data and rate heterogeneity, Clusterflock outperforms other well-established clustering techniques. We also verified its utility on a known, large-scale recombination event in Staphylococcus aureus. By isolating sets of OGFs with divergent phylogenetic signals, we were able to pinpoint the recombined region without forcing a pre-determined number of groupings or defining a pre-determined incongruence threshold. Conclusions: Clusterflock is an open-source tool that can be used to discover horizontally transferred genes, recombined areas of chromosomes, and the phylogenetic 'core' of a genome. Although we used it here in an evolutionary context, it is generalizable to any clustering problem. Users can write extensions to calculate any distance metric on the unit interval, and can use these distances to 'flock' any type of data.

关键词： Swarms flocking algorithm Unsupervised clustering Data mining Horizontal gene transfer Recombination Staphylococcus aureus

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Distributed exploration algorithm for GPS-denied areas based on flocking rules

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INTERNATIONAL JOURNAL OF CONTROL 2025年

作者： Ribeiro, Rafael Santos, Francisco Silvestre, Daniel Silvestre, Carlos Inst Super Tecn Inst Syst & Robot Lisbon Portugal NOVA Univ Lisbon FCT UNL Sch Sci & Technol P-2829516 Caparica Portugal Lusofona Univ COPELABS Lisbon Portugal Univ Macau Fac Sci & Technol Dept Elect & Comp Engn Taipa Macau Peoples R China Univ Lisbon Inst Super Tecn Lisbon Portugal

This paper addresses the problem of having a multi-agent system (MAS) search for areas of higher relative importance as measured by an unknown utility function. In the envisioned scenario, there are inexpensive agents without localisation sensors and limited communication capabilities. More expensive nodes serve as fixed towers and forward noisy position and velocity measurements using directional antennae. There is no assumptions on initial network connectivity. By proposing a set of flocking rules and set-membership estimation, the formation drives to a vicinity of nearby local maximum of the function while having theoretical guarantees of no collisions. The performance of the method is evaluated both in Matlab simulations and using the Crazyswarm package under the robot operating system (ROS) environment, including cases of moving destinations, obstacles, undesirable zones, and different number of nodes and sizes of the mission plane.

关键词： flocking algorithm distributed exploration directional communication

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Extended flocking algorithm for Self-parameter Tuning

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ELECTRONICS AND COMMUNICATIONS IN JAPAN 2015年第4期98卷 44-51页

作者： Yamauchi, Sho Kawamura, Hidenori Suzuki, Keiji Hokkaido Univ Grad Sch Informat Sci Sapporo Hokkaido 060 Japan

flocking algorithms for a multiagent system are distributed algorithms that only have simple rules for each agent but generate complex formational movement. These algorithms are known as swarm intelligence and are robust and disaster tolerant for most cases. We consider that flocking algorithms that have these characteristics are the way to generate homeostasis in a system. We expect that by making use of this algorithm the system can tune its self-parameters and thus maintain a high performance. First, to apply a flocking algorithm to a system, we extended the flocking algorithm to form an arbitrary lattice for further flexibility. We then applied the extended flocking algorithm to position tracking camera system as an example. (C) 2015 Wiley Periodicals, Inc.

关键词： autonomous system flocking algorithm self-parameter tuning

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An Alternative flocking algorithm with Additional Dynamic Conditions 9

An Alternative Flocking Algorithm with Additional Dynamic Co...

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International Conference on Broadband and Wireless Computing, Communication and Applications (BWCCA)

作者： Sun, Ningping Tokunaga, Yusuke Kumamoto Natl Coll Technol Koshi Kumamoto Japan

ISBN: (纸本)9781479941735

flocking simulates the motion of a flock, which is well known as artificial life algorithms. By using the flocking, we can express the motion of the group such as fishes, birds, or crowded animals in computer graphics. In order to render flocking more realistically, we have devised a method that adds some dynamic conditions into flocking computation. The additional external force and the moving coordinated cameras within the three dimensional space can help us to apply the flocking algorithm into 3DCG system more extendedly and easily. In this paper we provide our algorithm and approaches.

关键词： artificial life boid model flocking algorithm computer graphics modeling and rendering

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Force-Based algorithm for Motion Planning of Large Agent

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IEEE TRANSACTIONS ON CYBERNETICS 2022年第1期52卷 654-665页

作者： Semnani, Samaneh Hosseini de Ruiter, Anton H. J. Liu, Hugh H. T. Isfahan Univ Technol Dept Elect & Comp Engn Esfahan *** Iran Ryerson Univ Aerosp Engn Dept Toronto ON M5B 2K3 Canada Univ Toronto Fac Appl Sci & Engn Toronto ON M3H 5T6 Canada

This article presents a distributed, efficient, scalable, and real-time motion planning algorithm for a large group of agents moving in 2-D or 3-D spaces. This algorithm enables autonomous agents to generate individual trajectories independently with only the relative position information of neighboring agents. Each agent applies a force-based control that contains two main terms: 1) collision avoidance and 2) navigational feedback. The first term keeps two agents separate with a certain distance, while the second term attracts each agent toward its goal location. Compared with existing collision-avoidance algorithms, the proposed force-based motion planning (FMP) algorithm can find collision-free motions with lower transition time, free from velocity state information of neighboring agents. It leads to less computational overhead. The performance of proposed FMP is examined over several dense and complex 2-D and 3-D benchmark simulation scenarios, with results outperforming existing methods.

关键词： Planning Heuristic algorithms Trajectory Real-time systems Navigation Computational complexity Force Collision avoidance distributed algorithms evolutionary computation flocking algorithm motion planning multiagent systems trajectory optimization

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UAV Swarm Control Based on Hybrid Bionic Swarm Intelligence

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Guidance, Navigation and Control 2023年第2期3卷 136-155页

作者： Ruitao Fan Jintao Wang Weixin Han Bin Xu School of Automation Northwestern Polytechnical UniversityXi'anP.R.China

Inspired by the pigeon behavior pattern,this paper proposes an Unmanned Aerial Vehicle(UAV)swarm control scheme based on hybrid bionic sw arm intelligence,which can realize multi-UAV obstacle avoidance d uring formation ***,the leadership mechanism of pigeon flock is mapped to UAV swamm,and the virtual leaders are introduced to solve the unfixed relative position of level-1 leader ***,the control law for UAV swarm formation is designed based on artificial potential field theory and analysis of the bionic *** avoid local minima,a guidance phase is added to the UAV formation *** analyzing the flocking algorithm,a cooperative interaction control model of UAV swarm is ***,the coopentive interactive control law for UAV sw arm obstacle avoidance is proposed based on improved artifcial potential feld *** the two bionic swarm control models are combined to realize the formation and obstacle avoidance of UAV swarm based on mixed bionic swarm ***,a series of simulations are conducted to demonstrate the proposed hybrid UAV sw arm control algorithm.

关键词： UAV formation control pigeon flock leadership mechanism obstacle avoidance flocking algorithm artificial potential field

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A distributed flocking control strategy for UAV groups

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COMPUTER COMMUNICATIONS 2020年第0期153卷 95-101页

作者： Liu, Wei Gao, Zhijun Shenyang Jianzhu Univ Network Ctr Shenyang Peoples R China Shenyang Jianzhu Univ Informat & Control Engn Fac Shenyang Peoples R China

To ensure the information security of UAV groups, maximize the detection range of the UAV group and minimize the communication range, this paper improves Olfati-Saber's flocking algorithm using virtual leader and integrates the multiple UAVs with real environment. The improved swarm control algorithm can help to make all agents accurately track the speed of virtual leaders. Then, we introduce the conception of virtual communication circle to control the communication power of each UAV, and the moving function of the target position is improved to meet the limited conditions of given communication distance, to ensure the non-collision and stable communication of the UAV during the moving process. All UAVs in the group system will keep converging, avoiding collision and the speed is the same as that of the virtual pilot. Therefore, multiple UAVs can track the virtual pilot for cluster flight and a distributed cooperative control strategy can be acquired. The simulation results show that the strategy proposed in this paper makes a better communication performance among UAVs in real time, and the UAV groups achieve the information more timely, which is proved to be an effective way to ensure the security communication among multiple UAVs.

关键词： Communication strategy UAV flocking algorithm Virtual leader Distributed control

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Development of a Virtual Pet Simulator for Pain and Stress Distraction for Pediatric Patients using Intelligent Techniques

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INTERNATIONAL JOURNAL OF ADVANCED COMPUTER SCIENCE AND APPLICATIONS 2021年第2期12卷 539-549页

作者： Solis-Vargas, Angie Contreras-Alcazar, Iam Sulla-Torres, Jose Univ Nacl San Agustin Arequipa Escuela Profes Ingn Sistemas Arequipa Peru

Pediatric medical procedures are often stressful and painful for children, so they can resist and make the work of doctors and nurses a little more complicated. This research aims to develop a virtual pet simulator to distract pediatric patients from pain and stress using smart techniques. The methodology used is SUM. The primary data for the development of the simulator were gravity, the player's position, the speed, and the mass for the calculation of the predictive physics in the toy to interact with the pet. As part of the intelligent techniques, the A-star algorithm was used for the pet to follow the user and the flocking algorithm to have a natural behavior of a group of animals and thus have a higher immersion level. Trials were conducted with pediatric patients where those who made use of the virtual pet simulator during the medical procedure felt less pain and stress than those who did not try the simulator. Therefore, it is highly recommended to use alternatives such as the one developed to reduce pain and stress in pediatric patients.

关键词： Virtual pet pediatric patients pain stress smart techniques A-star algorithm flocking algorithm

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Using Lazy Agents to Improve the flocking Efficiency of Multiple UAVs

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JOURNAL OF INTELLIGENT & ROBOTIC SYSTEMS 2021年第3期103卷 53-53页

作者： Song, Yeongho Gu, Myeonggeun Choi, Joonwon Oh, Hyondong Lim, Seunghan Shin, Hyo-Sang Tsourdos, Antonios Ulsan Natl Inst Sci & Technol Sch Mech Aerosp & Nucl Engn Ulsan 44919 South Korea PABLO AIR Co Ltd Incheon South Korea Cranfield Univ Inst Aerosp Sci Cranfield MK43 0AL Beds England

A group of agents can form a flock using the augmented Cucker-Smale (C-S) model. The model autonomously aligns them to a common velocity and maintains a relative distance among the agents in a distributed manner by sharing the information among neighbors. This paper introduces the concept of inactiveness to the augmented C-S model for improving the flocking performance. It involves controlling the energy and convergence time required to form a stable flock. Inspired by the natural world where a few lazy (or inactive) workers are helpful to the group performance in social insect colonies. In this study, we analyzed different levels of inactiveness as a degree of control input effectiveness for multiple fixed-wing UAVs in the flocking algorithm. To find the appropriate inactiveness level for each flock member, the particle swarm optimization-based approach is used as the first step, based on the initial condition of the flock. However, as the significant computational burden may cause difficulties in implementing the optimization-based approach in real time, we also propose a heuristic adaptive inactiveness approach, which changes the inactivity level of selected agents adaptively according to their position and heading relative to the flock center. The performance of the proposed approaches using the concept of lazy (or inactive) agents is verified with numerical simulations by comparing them with the conventional flocking algorithm in various scenarios.

关键词： Multi-agent system flocking algorithm Augmented Cucker-Smale model Inactiveness Particle swarm optimization

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flocking Control under Virtual Leader of USVs with Obstacle Avoidance 39

Flocking Control under Virtual Leader of USVs with Obstacle ...

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39th Chinese Control Conference (CCC)

作者： Wang, Yuanhui Xie, Weijie Zhang, Xiaoyun Harbin Engn Univ Coll Automat Harbin 150001 Peoples R China Harbin Marine Boiler & Turbine Res Inst Harbin 150078 Peoples R China

ISBN: (纸本)9789881563903

It focuses on solving the problem of autonomous obstacle avoidance for unmanned surface vehicles(USVs) formation mission. Firstly, a three-degree-of-freedom kinematics and dynamic model of USV is established. Secondly, the flocking algorithm is used to solve the problem of autonomous formation control for USVs. Considering the flocking algorithm is generally applied to particle-based model, it can't be directly applied to underactuated USVs. Thus, a virtual force point is introduced and a force analysis is carried out, which converts the control inputs in the flocking algorithm into the longitudinal control and heading control. In this case, it can achieve the autonomous formation of the USVs and the purpose of tracking virtual leader. Thirdly, combining obstacle avoidance algorithm based on potential function with flocking algorithm to achieve obstacle avoidance for the formation control. Finally, the effectiveness of the algorithm and model is verified by simulation experiments.

关键词： USV Formation Control Obstacle Avoidance flocking algorithm Virtual Leader

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