Cuckoo search epistasis: a new method for exploring significant genetic interactions

The advent of high-throughput sequencing technology has resulted in the ability to measure millions of single-nucleotide polymorphisms (SNPs) from thousands of individuals. Although these high-dimensional data have paved the way for better understanding of the genetic architecture of common diseases, they have also given rise to challenges in developing computational methods for learning epistatic relationships among genetic markers. We propose a new method, named cuckoo search epistasis (CSE) for identifying significant epistatic interactions in population-based association studies with a case-control design. This method combines a computationally efficient Bayesian scoring function with an evolutionary-based heuristic search algorithm, and can be efficiently applied to high-dimensional genome-wide SNP data. The experimental results from synthetic data sets show that CSE outperforms existing methods including multifactorial dimensionality reduction and Bayesian epistasis association mapping. In addition, on a real genome-wide data set related to Alzheimer's disease, CSE identified SNPs that are consistent with previously reported results, and show the utility of CSE for application to genome-wide data. © 2014 Macmillan Publishers Limited All rights reserved

Gnowee: A Hybrid Metaheuristic Optimization Algorithm for Constrained, Black Box, Combinatorial Mixed-Integer Design

This paper introduces Gnowee, a modular, Python-based, open-source hybrid metaheuristic optimization algorithm (Available from https://github.com/SlaybaughLab/Gnowee). Gnowee is designed for rapid convergence to nearly globally optimum solutions for complex, constrained nuclear engineering problems with mixed-integer and combinatorial design vectors and high-cost, noisy, discontinuous, black box objective function evaluations. Gnowee's hybrid metaheuristic framework is a new combination of a set of diverse, robust heuristics that appropriately balance diversification and intensification strategies across a wide range of optimization problems. This novel algorithm was specifically developed to optimize complex nuclear design problems; the motivating research problem was the design of material stack-ups to modify neutron energy spectra to specific targeted spectra for applications in nuclear medicine, technical nuclear forensics, nuclear physics, etc. However, there are a wider range of potential applications for this algorithm both within the nuclear community and beyond. To demonstrate Gnowee's behavior for a variety of problem types, comparisons between Gnowee and several well-established metaheuristic algorithms are made for a set of eighteen continuous, mixed-integer, and combinatorial benchmarks. These results demonstrate Gnoweee to have superior flexibility and convergence characteristics over a wide range of design spaces. We anticipate this wide range of applicability will make this algorithm desirable for many complex engineering applications.Comment: 43 pages, 7 tables, 6 figure

Feature Selection for Document Classification : Case Study of Meta-heuristic Intelligence and Traditional Approaches

Doctor of Philosophy (Computer Engineering), 2020Nowadays, the culture for accessing news around the world is changed from paper to electronic format and the rate of publication for newspapers and magazines on website are increased dramatically. Meanwhile, text feature selection for the automatic document classification (ADC) is becoming a big challenge because of the unstructured nature of text feature, which is called “multi-dimension feature problem”. On the other hand, various powerful schemes dealing with text feature selection are being developed continuously nowadays, but there still exists a research gap for “optimization of feature selection problem (OFSP)”, which can be looked for the global optimal features. Meanwhile, the capacity of meta-heuristic intelligence for knowledge discovery process (KDP) is also become the critical role to overcome NP-hard problem of OFSP by providing effective performance and efficient computation time. Therefore, the idea of meta-heuristic based approach for optimization of feature selection is proposed in this research to search the global optimal features for ADC. In this thesis, case study of meta-heuristic intelligence and traditional approaches for feature selection optimization process in document classification is observed. It includes eleven meta-heuristic algorithms such as Ant Colony search, Artificial Bee Colony search, Bat search, Cuckoo search, Evolutionary search, Elephant search, Firefly search, Flower search, Genetic search, Rhinoceros search, and Wolf search, for searching the optimal feature subset for document classification. Then, the results of proposed model are compared with three traditional search algorithms like Best First search (BFS), Greedy Stepwise (GS), and Ranker search (RS). In addition, the framework of data mining is applied. It involves data preprocessing, feature engineering, building learning model and evaluating the performance of proposed meta-heuristic intelligence-based feature selection using various performance and computation complexity evaluation schemes. In data processing, tokenization, stop-words handling, stemming and lemmatizing, and normalization are applied. In feature engineering process, n-gram TF-IDF feature extraction is used for implementing feature vector and both filter and wrapper approach are applied for observing different cases. In addition, three different classifiers like J48, Naïve Bayes, and Support Vector Machine, are used for building the document classification model. According to the results, the proposed system can reduce the number of selected features dramatically that can deteriorate learning model performance. In addition, the selected global subset features can yield better performance than traditional search according to single objective function of proposed model