Examining applying high performance genetic data feature selection and classification algorithms for colon cancer diagnosis

Background and Objectives: This paper examines the accuracy and efficiency (time complexity) of high performance genetic data feature selection and classification algorithms for colon cancer diagnosis. The need for this research derives from the urgent and increasing need for accurate and efficient algorithms. Colon cancer is a leading cause of death worldwide, hence it is vitally important for the cancer tissues to be expertly identified and classified in a rapid and timely manner, to assure both a fast detection of the disease and to expedite the drug discovery process. Methods: In this research, a three-phase approach was proposed and implemented: Phases One and Two examined the feature selection algorithms and classification algorithms employed separately, and Phase Three examined the performance of the combination of these. Results: It was found from Phase One that the Particle Swarm Optimization (PSO) algorithm performed best with the colon dataset as a feature selection (29 genes selected) and from Phase Two that the Sup- port Vector Machine (SVM) algorithm outperformed other classifications, with an accuracy of almost 86%. It was also found from Phase Three that the combined use of PSO and SVM surpassed other algorithms in accuracy and performance, and was faster in terms of time analysis (94%). Conclusions: It is concluded that applying feature selection algorithms prior to classification algorithms results in better accuracy than when the latter are applied alone. This conclusion is important and significant to industry and society

Cancer prediction using graph-based gene selection and explainable classifier

Several Artificial Intelligence-based models have been developed for cancer prediction. In spite of the promise of artificial intelligence, there are very few models which bridge the gap between traditional human-centered prediction and the potential future of machine-centered cancer prediction. In this study, an efficient and effective model is developed for gene selection and cancer prediction. Moreover, this study proposes an artificial intelligence decision system to provide physicians with a simple and human-interpretable set of rules for cancer prediction. In contrast to previous deep learning-based cancer prediction models, which are difficult to explain to physicians due to their black-box nature, the proposed prediction model is based on a transparent and explainable decision forest model. The performance of the developed approach is compared to three state-of-the-art cancer prediction including TAGA, HPSO and LL. The reported results on five cancer datasets indicate that the developed model can improve the accuracy of cancer prediction and reduce the execution time

Breast Cancer Classification by Gene Expression Analysis using Hybrid Feature Selection and Hyper-heuristic Adaptive Universum Support Vector Machine

Comprehensive assessments of the molecular characteristics of breast cancer from gene expression patterns can aid in the early identification and treatment of tumor patients. The enormous scale of gene expression data obtained through microarray sequencing increases the difficulty of training the classifier due to large-scale features. Selecting pivotal gene features can minimize high dimensionality and the classifier complexity with improved breast cancer detection accuracy. However, traditional filter and wrapper-based selection methods have scalability and adaptability issues in handling complex gene features. This paper presents a hybrid feature selection method of Mutual Information Maximization - Improved Moth Flame Optimization (MIM-IMFO) for gene selection along with an advanced Hyper-heuristic Adaptive Universum Support classification model Vector Machine (HH-AUSVM) to improve cancer detection rates. The hybrid gene selection method is developed by performing filter-based selection using MIM in the first stage followed by the wrapper method in the second stage, to obtain the pivotal features and remove the inappropriate ones. This method improves standard MFO by a hybrid exploration/exploitation phase to accomplish a better trade-off between exploration and exploitation phases. The classifier HH-AUSVM is formulated by integrating the Adaptive Universum learning approach to the hyper- heuristics-based parameter optimized SVM to tackle the class samples imbalance problem. Evaluated on breast cancer gene expression datasets from Mendeley Data Repository, this proposed MIM-IMFO gene selection-based HH-AUSVM classification approach provided better breast cancer detection with high accuracies of 95.67%, 96.52%, 97.97% and 95.5% and less processing time of 4.28, 3.17, 9.45 and 6.31 seconds, respectively

Knowledge management overview of feature selection problem in high-dimensional financial data: Cooperative co-evolution and Map Reduce perspectives

The term big data characterizes the massive amounts of data generation by the advanced technologies in different domains using 4Vs volume, velocity, variety, and veracity-to indicate the amount of data that can only be processed via computationally intensive analysis, the speed of their creation, the different types of data, and their accuracy. High-dimensional financial data, such as time-series and space-Time data, contain a large number of features (variables) while having a small number of samples, which are used to measure various real-Time business situations for financial organizations. Such datasets are normally noisy, and complex correlations may exist between their features, and many domains, including financial, lack the al analytic tools to mine the data for knowledge discovery because of the high-dimensionality. Feature selection is an optimization problem to find a minimal subset of relevant features that maximizes the classification accuracy and reduces the computations. Traditional statistical-based feature selection approaches are not adequate to deal with the curse of dimensionality associated with big data. Cooperative co-evolution, a meta-heuristic algorithm and a divide-And-conquer approach, decomposes high-dimensional problems into smaller sub-problems. Further, MapReduce, a programming model, offers a ready-To-use distributed, scalable, and fault-Tolerant infrastructure for parallelizing the developed algorithm. This article presents a knowledge management overview of evolutionary feature selection approaches, state-of-The-Art cooperative co-evolution and MapReduce-based feature selection techniques, and future research directions

Computational models and approaches for lung cancer diagnosis

The success of treatment of patients with cancer depends on establishing an accurate diagnosis. To this end, the aim of this study is to developed novel lung cancer diagnostic models. New algorithms are proposed to analyse the biological data and extract knowledge that assists in achieving accurate diagnosis results

On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Hybrid ACO and SVM algorithm for pattern classification

Ant Colony Optimization (ACO) is a metaheuristic algorithm that can be used to solve a variety of combinatorial optimization problems. A new direction for ACO is to optimize continuous and mixed (discrete and continuous) variables. Support Vector Machine (SVM) is a pattern classification approach originated from statistical approaches. However, SVM suffers two main problems which include feature subset selection and parameter tuning. Most approaches related to tuning SVM parameters discretize the continuous value of the parameters which will give a negative effect on the classification performance. This study presents four algorithms for tuning the SVM parameters and selecting feature subset which improved SVM classification accuracy with smaller size of feature subset. This is achieved by performing the SVM parameters’ tuning and feature subset selection processes simultaneously. Hybridization algorithms between ACO and SVM techniques were proposed. The first two algorithms, ACOR-SVM and IACOR-SVM, tune the SVM parameters while the second two algorithms, ACOMV-R-SVM and IACOMV-R-SVM, tune the SVM parameters and select the feature subset simultaneously. Ten benchmark datasets from University of California, Irvine, were used in the experiments to validate the performance of the proposed algorithms. Experimental results obtained from the proposed algorithms are better when compared with other approaches in terms of classification accuracy and size of the feature subset. The average classification accuracies for the ACOR-SVM, IACOR-SVM, ACOMV-R and IACOMV-R algorithms are 94.73%, 95.86%, 97.37% and 98.1% respectively. The average size of feature subset is eight for the ACOR-SVM and IACOR-SVM algorithms and four for the ACOMV-R and IACOMV-R algorithms. This study contributes to a new direction for ACO that can deal with continuous and mixed-variable ACO

Hybrid feature selection of breast cancer gene expression microarray data based on metaheuristic methods: a comprehensive review

Breast cancer (BC) remains the most dominant cancer among women worldwide. Numerous BC gene expression microarray-based studies have been employed in cancer classification and prognosis. The availability of gene expression microarray data together with advanced classification methods has enabled accurate and precise classification. Nevertheless, the microarray datasets suffer from a large number of gene expression levels, limited sample size, and irrelevant features. Additionally, datasets are often asymmetrical, where the number of samples from different classes is not balanced. These limitations make it difficult to determine the actual features that contribute to the existence of cancer classification in the gene expression profiles. Various accurate feature selection methods exist, and they are being widely applied. The objective of feature selection is to search for a relevant, discriminant feature subset from the basic feature space. In this review, we aim to compile and review the latest hybrid feature selection methods based on bio-inspired metaheuristic methods and wrapper methods for the classification of BC and other types of cancer