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Register a new userAn Evolutionary Approach to Drug-Design Using a Novel Neighbourhood Based Genetic Algorithm
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Added by
Avishek Ghosh
Publication date
2012
fields
Informatics Engineering
and research's language is
English
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The present work provides a new approach to evolve ligand structures which represent possible drug to be docked to the active site of the target protein. The structure is represented as a tree where each non-empty node represents a functional group. It is assumed that the active site configuration of the target protein is known with position of the essential residues. In this paper the interaction energy of the ligands with the protein target is minimized. Moreover, the size of the tree is difficult to obtain and it will be different for different active sites. To overcome the difficulty, a variable tree size configuration is used for designing ligands. The optimization is done using a novel Neighbourhood Based Genetic Algorithm (NBGA) which uses dynamic neighbourhood topology. To get variable tree size, a variable-length version of the above algorithm is devised. To judge the merit of the algorithm, it is initially applied on the well known Travelling Salesman Problem (TSP).
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There is considerable interest in the use of genetic algorithms to solve problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle the conflict between objectives and constraints that typically occurs in such problems. In order to overcome this, successful implementations frequently make use of problem specific knowledge. This paper is concerned with the development of a GA for a nurse rostering problem at a major UK hospital. The structure of the constraints is used as the basis for a co-evolutionary strategy using co-operating sub-populations. Problem specific knowledge is also used to define a system of incentives and disincentives, and a complementary mutation operator. Empirical results based on 52 weeks of live data show how these features are able to improve an unsuccessful canonical GA to the point where it is able to provide a practical solution to the problem
This paper describes a Genetic Algorithms approach to a manpower-scheduling problem arising at a major UK hospital. Although Genetic Algorithms have been successfully used for similar problems in the past, they always had to overcome the limitations of the classical Genetic Algorithms paradigm in handling the conflict between objectives and constraints. The approach taken here is to use an indirect coding based on permutations of the nurses, and a heuristic decoder that builds schedules from these permutations. Computational experiments based on 52 weeks of live data are used to evaluate three different decoders with varying levels of intelligence, and four well-known crossover operators. Results are further enhanced by introducing a hybrid crossover operator and by making use of simple bounds to reduce the size of the solution space. The results reveal that the proposed algorithm is able to find high quality solutions and is both faster and more flexible than a recently published Tabu Search approach.
Evolutionary algorithms (EA) have been widely accepted as efficient solvers for complex real world optimization problems, including engineering optimization. However, real world optimization problems often involve uncertain environment including noisy and/or dynamic environments, which pose major challenges to EA-based optimization. The presence of noise interferes with the evaluation and the selection process of EA, and thus adversely affects its performance. In addition, as presence of noise poses challenges to the evaluation of the fitness function, it may need to be estimated instead of being evaluated. Several existing approaches attempt to address this problem, such as introduction of diversity (hyper mutation, random immigrants, special operators) or incorporation of memory of the past (diploidy, case based memory). However, these approaches fail to adequately address the problem. In this paper we propose a Distributed Population Switching Evolutionary Algorithm (DPSEA) method that addresses optimization of functions with noisy fitness using a distributed population switching architecture, to simulate a distributed self-adaptive memory of the solution space. Local regression is used in the pseudo-populations to estimate the fitness. Successful applications to benchmark test problems ascertain the proposed methods superior performance in terms of both robustness and accuracy.
Transfer Optimization is an incipient research area dedicated to solving multiple optimization tasks simultaneously. Among the different approaches that can address this problem effectively, Evolutionary Multitasking resorts to concepts from Evolutionary Computation to solve multiple problems within a single search process. In this paper we introduce a novel adaptive metaheuristic algorithm to deal with Evolutionary Multitasking environments coined as Adaptive Transfer-guided Multifactorial Cellular Genetic Algorithm (AT-MFCGA). AT-MFCGA relies on cellular automata to implement mechanisms in order to exchange knowledge among the optimization problems under consideration. Furthermore, our approach is able to explain by itself the synergies among tasks that were encountered and exploited during the search, which helps us to understand interactions between related optimization tasks. A comprehensive experimental setup is designed to assess and compare the performance of AT-MFCGA to that of other renowned evolutionary multitasking alternatives (MFEA and MFEA-II). Experiments comprise 11 multitasking scenarios composed of 20 instances of 4 combinatorial optimization problems, yielding the largest discrete multitasking environment solved to date. Results are conclusive in regard to the superior quality of solutions provided by AT-MFCGA with respect to the rest of the methods, which are complemented by a quantitative examination of the genetic transferability among tasks throughout the search process.
During our earlier research, it was recognised that in order to be successful with an indirect genetic algorithm approach using a decoder, the decoder has to strike a balance between being an optimiser in its own right and finding feasible solutions. Previously this balance was achieved manually. Here we extend this by presenting an automated approach where the genetic algorithm itself, simultaneously to solving the problem, sets weights to balance the components out. Subsequently we were able to solve a complex and non-linear scheduling problem better than with a standard direct genetic algorithm implementation.
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