Visual and computational analysis of structure-activity relationships in high-throughput screening data

Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets

A Study Of Vantage Point Neighbourhood Search In The Bees Algorithm For Combinatorial Optimization Problems

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2014Thesis (M.Sc. ) -- İstanbul Technical University, Institute of Science and Technology, 2014Bu tez çalışmasının temel amacı arıların kaynak arama davranışlarını modelleyen arı algoritmasının, kombinatoryal uzaylarda komşuluk arama fazına yeni bir yaklaşım geliştirilmesidir. Geliştirilen yaklaşım Gezgin Satıcı Problemine uygulanarak Gezgin Satıcı Problemi çözümünün en iyilenmesi amaçlanmıştır.This thesis focuses on nature-inspired optimisation algorithms, in particular, the Bees Algorithm that developed for combinatorial domains with new local search procedure and applied to Traveller Salesman Problem (TSP). An efficient and robust local neighborhood search algorithm is proposed for combinatorial domains to increase the efficiency of the Bees Algorithm.Yüksek LisansM.Sc

Accelerating ant colony optimization by using local search

This thesis report is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Computer Science and Engineering, 2015.Cataloged from PDF version of thesis report.Includes bibliographical references (page 42-45).Optimization is very important fact in terms of taking decision in mathematics, statistics, computer science and real life problem solving or decision making application. Many different optimization techniques have been developed for solving such functional problem. In order to solving various problem computer Science introduce evolutionary optimization algorithm and their hybrid. In recent years, test functions are using to validate new optimization algorithms and to compare the performance with other existing algorithm. There are many Single Object Optimization algorithm proposed earlier. For example: ACO, PSO, ABC. ACO is a popular optimization technique for solving hard combination mathematical optimization problem. In this paper, we run ACO upon five benchmark function and modified the parameter of ACO in order to perform SBX crossover and polynomial mutation. The proposed algorithm SBXACO is tested upon some benchmark function under both static and dynamic to evaluate performances. We choose wide range of benchmark function and compare results with existing DE and its hybrid DEahcSPX from other literature are also presented here.Nabila TabassumMaruful HaqueB. Computer Science and Engineerin

How Fitch-Margoliash Algorithm can Benefit from Multi Dimensional Scaling

Whatever the phylogenetic method, genetic sequences are often described as strings of characters, thus molecular sequences can be viewed as elements of a multi-dimensional space. As a consequence, studying motion in this space (ie, the evolutionary process) must deal with the amazing features of high-dimensional spaces like concentration of measured phenomenon

A new pheromone trail-based genetic algorithm for comparative genome assembly

Gap closing is considered one of the most challenging and time-consuming tasks in bacterial genome sequencing projects, especially with the emergence of new sequencing technologies, such as pyrosequencing, which may result in large amounts of data without the benefit of large insert libraries for contig scaffolding. We propose a novel algorithm to align contigs with more than one reference genome at a time. This approach can successfully overcome the limitations of low degrees of conserved gene order for the reference and target genomes. A pheromone trail-based genetic algorithm (PGA) was used to search globally for the optimal placement for each contig. Extensive testing on simulated and real data sets shows that PGA significantly outperforms previous methods, especially when assembling genomes that are only moderately related. An extended version of PGA can predict additional candidate connections for each contig and can thus increase the likelihood of identifying the correct arrangement of each contig. The software and test data sets can be accessed at http://sourceforge.net/projects/pga4genomics/

The development and application of metaheuristics for problems in graph theory: A computational study

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.It is known that graph theoretic models have extensive application to real-life discrete optimization problems. Many of these models are NP-hard and, as a result, exact methods may be impractical for large scale problem instances. Consequently, there is a great interest in developing e±cient approximate methods that yield near-optimal solutions in acceptable computational times. A class of such methods, known as metaheuristics, have been proposed with success. This thesis considers some recently proposed NP-hard combinatorial optimization problems formulated on graphs. In particular, the min- imum labelling spanning tree problem, the minimum labelling Steiner tree problem, and the minimum quartet tree cost problem, are inves- tigated. Several metaheuristics are proposed for each problem, from classical approximation algorithms to novel approaches. A compre- hensive computational investigation in which the proposed methods are compared with other algorithms recommended in the literature is reported. The results show that the proposed metaheuristics outper- form the algorithms recommended in the literature, obtaining optimal or near-optimal solutions in short computational running times. In addition, a thorough analysis of the implementation of these methods provide insights for the implementation of metaheuristic strategies for other graph theoretic problems

Using swarm intelligence for distributed job scheduling on the grid

With the rapid growth of data and computational needs, distributed systems and computational Grids are gaining more and more attention. Grids are playing an important and growing role in today networks. The huge amount of computations a Grid can fulfill in a specific time cannot be done by the best super computers. However, Grid performance can still be improved by making sure all the resources available in the Grid are utilized by a good load balancing algorithm. The purpose of such algorithms is to make sure all nodes are equally involved in Grid computations. This research proposes two new distributed swarm intelligence inspired load balancing algorithms. One is based on ant colony optimization and is called AntZ, the other one is based on particle swarm optimization and is called ParticleZ. Distributed load balancing does not incorporate a single point of failure in the system. In the AntZ algorithm, an ant is invoked in response to submitting a job to the Grid and this ant surfs the network to find the best resource to deliver the job to. In the ParticleZ algorithm, each node plays a role as a particle and moves toward other particles by sharing its workload among them. We will be simulating our proposed approaches using a Grid simulation toolkit (GridSim) dedicated to Grid simulations. The performance of the algorithms will be evaluated using several performance criteria (e.g. makespan and load balancing level). A comparison of our proposed approaches with a classical approach called State Broadcast Algorithm and two random approaches will also be provided. Experimental results show the proposed algorithms (AntZ and ParticleZ) can perform very well in a Grid environment. In particular, the use of particle swarm optimization, which has not been addressed in the literature, can yield better performance results in many scenarios than the ant colony approach

Traveling Salesman Problem

This book is a collection of current research in the application of evolutionary algorithms and other optimal algorithms to solving the TSP problem. It brings together researchers with applications in Artificial Immune Systems, Genetic Algorithms, Neural Networks and Differential Evolution Algorithm. Hybrid systems, like Fuzzy Maps, Chaotic Maps and Parallelized TSP are also presented. Most importantly, this book presents both theoretical as well as practical applications of TSP, which will be a vital tool for researchers and graduate entry students in the field of applied Mathematics, Computing Science and Engineering