Genetic algorithm in ab initio protein structure prediction using low resolution model : a review

Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution

Applications of Artificial Intelligence in Power Systems

Artificial intelligence tools, which are fast, robust and adaptive can overcome the drawbacks of traditional solutions for several power systems problems. In this work, applications of AI techniques have been studied for solving two important problems in power systems. The first problem is static security evaluation (SSE). The objective of SSE is to identify the contingencies in planning and operations of power systems. Numerical conventional solutions are time-consuming, computationally expensive, and are not suitable for online applications. SSE may be considered as a binary-classification, multi-classification or regression problem. In this work, multi-support vector machine is combined with several evolutionary computation algorithms, including particle swarm optimization (PSO), differential evolution, Ant colony optimization for the continuous domain, and harmony search techniques to solve the SSE. Moreover, support vector regression is combined with modified PSO with a proposed modification on the inertia weight in order to solve the SSE. Also, the correct accuracy of classification, the speed of training, and the final cost of using power equipment heavily depend on the selected input features. In this dissertation, multi-object PSO has been used to solve this problem. Furthermore, a multi-classifier voting scheme is proposed to get the final test output. The classifiers participating in the voting scheme include multi-SVM with different types of kernels and random forests with an adaptive number of trees. In short, the development and performance of different machine learning tools combined with evolutionary computation techniques have been studied to solve the online SSE. The performance of the proposed techniques is tested on several benchmark systems, namely the IEEE 9-bus, 14-bus, 39-bus, 57-bus, 118-bus, and 300-bus power systems. The second problem is the non-convex, nonlinear, and non-differentiable economic dispatch (ED) problem. The purpose of solving the ED is to improve the cost-effectiveness of power generation. To solve ED with multi-fuel options, prohibited operating zones, valve point effect, and transmission line losses, genetic algorithm (GA) variant-based methods, such as breeder GA, fast navigating GA, twin removal GA, kite GA, and United GA are used. The IEEE systems with 6-units, 10-units, and 15-units are used to study the efficiency of the algorithms

Applications of Artificial Intelligence in Power Systems

Artificial intelligence tools, which are fast, robust and adaptive can overcome the drawbacks of traditional solutions for several power systems problems. In this work, applications of AI techniques have been studied for solving two important problems in power systems. The first problem is static security evaluation (SSE). The objective of SSE is to identify the contingencies in planning and operations of power systems. Numerical conventional solutions are time-consuming, computationally expensive, and are not suitable for online applications. SSE may be considered as a binary-classification, multi-classification or regression problem. In this work, multi-support vector machine is combined with several evolutionary computation algorithms, including particle swarm optimization (PSO), differential evolution, Ant colony optimization for the continuous domain, and harmony search techniques to solve the SSE. Moreover, support vector regression is combined with modified PSO with a proposed modification on the inertia weight in order to solve the SSE. Also, the correct accuracy of classification, the speed of training, and the final cost of using power equipment heavily depend on the selected input features. In this dissertation, multi-object PSO has been used to solve this problem. Furthermore, a multi-classifier voting scheme is proposed to get the final test output. The classifiers participating in the voting scheme include multi-SVM with different types of kernels and random forests with an adaptive number of trees. In short, the development and performance of different machine learning tools combined with evolutionary computation techniques have been studied to solve the online SSE. The performance of the proposed techniques is tested on several benchmark systems, namely the IEEE 9-bus, 14-bus, 39-bus, 57-bus, 118-bus, and 300-bus power systems. The second problem is the non-convex, nonlinear, and non-differentiable economic dispatch (ED) problem. The purpose of solving the ED is to improve the cost-effectiveness of power generation. To solve ED with multi-fuel options, prohibited operating zones, valve point effect, and transmission line losses, genetic algorithm (GA) variant-based methods, such as breeder GA, fast navigating GA, twin removal GA, kite GA, and United GA are used. The IEEE systems with 6-units, 10-units, and 15-units are used to study the efficiency of the algorithms

PSA 2016

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2016

Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction

The schemata theorem, on which the working of Genetic Algorithm (GA) is based in its current form, has a fallacious selection procedure and incomplete crossover operation. In this paper, generalization of the schemata theorem has been provided by correcting and removing these limitations. The analysis shows that similarity growth within GA population is inherent due to its stochastic nature. While the stochastic property helps in GA’s convergence. The similarity growth is responsible for stalling and becomes more prevalent for hard optimization problem like protein structure prediction (PSP). While it is very essential that GA should explore the vast and complicated search landscape, in reality, it is often stuck in local minima. This paper shows that, removal of members of population having certain percentage of similarity would keep GA perform better, balancing and maintaining convergence property intact as well as avoids stalling

Training issues and learning algorithms for feedforward and recurrent neural networks

Ph.DDOCTOR OF PHILOSOPH

Gaining Insight into Determinants of Physical Activity using Bayesian Network Learning

Contains fulltext : 228326pre.pdf (preprint version ) (Open Access) Contains fulltext : 228326pub.pdf (publisher's version ) (Open Access)BNAIC/BeneLearn 202

Logic Mining Approach: Shoppers’ Purchasing Data Extraction via Evolutionary Algorithm

Online shopping is a multi-billion-dollar industry worldwide. However, several challenges related to purchase intention can impact the sales of e-commerce. For example, e-commerce platforms are unable to identify which factors contribute to the high sales of a product. Besides, online sellers have difficulty finding products that align with customers’ preferences. Therefore, this work will utilize an artificial neural network to provide knowledge extraction for the online shopping industry or e-commerce platforms that might improve their sales and services. There are limited attempts to propose knowledge extraction with neural network models in the online shopping field, especially research revolving around online shoppers’ purchasing intentions. In this study, 2-satisfiability logic was used to represent the shopping attribute and a special recurrent artificial neural network named Hopfield neural network was employed. In reducing the learning complexity, a genetic algorithm was implemented to optimize the logical rule throughout the learning phase in performing a 2-satisfiability-based reverse analysis method, implemented during the learning phase as this method was compared. The performance of the genetic algorithm with 2-satisfiability-based reverse analysis was measured according to the selected performance evaluation metrics. The simulation suggested that the proposed model outperformed the existing model in doing logic mining for the online shoppers dataset

31th International Conference on Information Modelling and Knowledge Bases

Information modelling is becoming more and more important topic for researchers, designers, and users of information systems.The amount and complexity of information itself, the number of abstractionlevels of information, and the size of databases and knowledge bases arecontinuously growing. Conceptual modelling is one of the sub-areas ofinformation modelling. The aim of this conference is to bring together experts from different areas of computer science and other disciplines, who have a common interest in understanding and solving problems on information modelling and knowledge bases, as well as applying the results of research to practice. We also aim to recognize and study new areas on modelling and knowledge bases to which more attention should be paid. Therefore philosophy and logic, cognitive science, knowledge management, linguistics and management science are relevant areas, too. In the conference, there will be three categories of presentations, i.e. full papers, short papers and position papers

Search-Based Software Maintenance and Testing

2012 - 2013In software engineering there are many expensive tasks that are performed during development and maintenance activities. Therefore, there has been a lot of e ort to try to automate these tasks in order to signi cantly reduce the development and maintenance cost of software, since the automation would require less human resources. One of the most used way to make such an automation is the Search-Based Software Engineering (SBSE), which reformulates traditional software engineering tasks as search problems. In SBSE the set of all candidate solutions to the problem de nes the search space while a tness function di erentiates between candidate solutions providing a guidance to the optimization process. After the reformulation of software engineering tasks as optimization problems, search algorithms are used to solve them. Several search algorithms have been used in literature, such as genetic algorithms, genetic programming, simulated annealing, hill climbing (gradient descent), greedy algorithms, particle swarm and ant colony. This thesis investigates and proposes the usage of search based approaches to reduce the e ort of software maintenance and software testing with particular attention to four main activities: (i) program comprehension; (ii) defect prediction; (iii) test data generation and (iv) test suite optimiza- tion for regression testing. For program comprehension and defect prediction, this thesis provided their rst formulations as optimization problems and then proposed the usage of genetic algorithms to solve them. More precisely, this thesis investigates the peculiarity of source code against textual documents written in natural language and proposes the usage of Genetic Algorithms (GAs) in order to calibrate and assemble IR-techniques for di erent software engineering tasks. This thesis also investigates and proposes the usage of Multi-Objective Genetic Algorithms (MOGAs) in or- der to build multi-objective defect prediction models that allows to identify defect-prone software components by taking into account multiple and practical software engineering criteria. Test data generation and test suite optimization have been extensively investigated as search- based problems in literature . However, despite the huge body of works on search algorithms applied to software testing, both (i) automatic test data generation and (ii) test suite optimization present several limitations and not always produce satisfying results. The success of evolutionary software testing techniques in general, and GAs in particular, depends on several factors. One of these factors is the level of diversity among the individuals in the population, which directly a ects the exploration ability of the search. For example, evolutionary test case generation techniques that employ GAs could be severely a ected by genetic drift, i.e., a loss of diversity between solutions, which lead to a premature convergence of GAs towards some local optima. For these reasons, this thesis investigate the role played by diversity preserving mechanisms on the performance of GAs and proposed a novel diversity mechanism based on Singular Value Decomposition and linear algebra. Then, this mechanism has been integrated within the standard GAs and evaluated for evolutionary test data generation. It has been also integrated within MOGAs and empirically evaluated for regression testing. [edited by author]XII n.s