The importance of data classification using machine learning methods in microarray data

The detection of genetic mutations has attracted global attention. several methods have proposed to detect diseases such as cancers and tumours. One of them is microarrays, which is a type of representation for gene expression that is helpful in diagnosis. To unleash the full potential of microarrays, machine-learning algorithms and gene selection methods can be implemented to facilitate processing on microarrays and to overcome other potential challenges. One of these challenges involves high dimensional data that are redundant, irrelevant, and noisy. To alleviate this problem, this representation should be simplified. For example, the feature selection process can be implemented by reducing the number of features adopted in clustering and classification. A subset of genes can be selected from a pool of gene expression data recorded on DNA micro-arrays. This paper reviews existing classification techniques and gene selection methods. The effectiveness of emerging techniques, such as the swarm intelligence technique in feature selection and classification in microarrays, are reported as well. These emerging techniques can be used in detecting cancer. The swarm intelligence technique can be combined with other statistical methods for attaining better results

HYBRID FLOWER POLLINATION ALGORITHM AND SUPPORT VECTOR MACHINE FOR BREAST CANCER CLASSIFICATION

Microarray technology is a system that enable experts to examine gene profile at molecular level for early disease detection. Machine learning algorithms such as classification are used in detection of dieses from data generated by microarray. It increases the potentials of classification and diagnosis of many diseases such as cancer at gene expression level. Though, numerous difficulties may affect the performance of machine learning algorithms which includes vast number of genes features comprised in the original data. Many of these features may be unrelated to the intended analysis. Therefore, feature selection is necessary to be performed in the data preprocessing. Many feature selection algorithms are developed and applied on microarray which including the metaheuristic optimization algorithms. This paper proposed a new technique for feature selection and classification of breast cancer based on Flower Pollination algorithm (FPA) and Support Vector machine (SVM) using microarray data. The result for this research reveals that FPA-SVM is promising by outperforming the state of the earth Particle Swam Optimization algorithm with 80.11% accuracy. Â

Survey analysis for optimization algorithms applied to electroencephalogram

This paper presents a survey for optimization approaches that analyze and classify Electroencephalogram (EEG) signals. The automatic analysis of EEG presents a significant challenge due to the high-dimensional data volume. Optimization algorithms seek to achieve better accuracy by selecting practical features and reducing unwanted features. Forty-seven reputable research papers are provided in this work, emphasizing the developed and executed techniques divided into seven groups based on the applied optimization algorithm particle swarm optimization (PSO), ant colony optimization (ACO), artificial bee colony (ABC), grey wolf optimizer (GWO), Bat, Firefly, and other optimizer approaches). The main measures to analyze this paper are accuracy, precision, recall, and F1-score assessment. Several datasets have been utilized in the included papers like EEG Bonn University, CHB-MIT, electrocardiography (ECG) dataset, and other datasets. The results have proven that the PSO and GWO algorithms have achieved the highest accuracy rate of around 99% compared with other techniques

Mutable composite firefly algorithm for gene selection in microarray based cancer classification

Cancer classification is critical due to the strenuous effort required in cancer treatment and the rising cancer mortality rate. Recent trends with high throughput technologies have led to discoveries in terms of biomarkers that successfully contributed to cancerrelated issues. A computational approach for gene selection based on microarray data analysis has been applied in many cancer classification problems. However, the existing hybrid approaches with metaheuristic optimization algorithms in feature selection (specifically in gene selection) are not generalized enough to efficiently classify most cancer microarray data while maintaining a small set of genes. This leads to the classification accuracy and genes subset size problem. Hence, this study proposed to modify the Firefly Algorithm (FA) along with the Correlation-based Feature Selection (CFS) filter for the gene selection task. An improved FA was proposed to overcome FA slow convergence by generating mutable size solutions for the firefly population. In addition, a composite position update strategy was designed for the mutable size solutions. The proposed strategy was to balance FA exploration and exploitation in order to address the local optima problem. The proposed hybrid algorithm known as CFS-Mutable Composite Firefly Algorithm (CFS-MCFA) was evaluated on cancer microarray data for biomarker selection along with the deployment of Support Vector Machine (SVM) as the classifier. Evaluation was performed based on two metrics: classification accuracy and size of feature set. The results showed that the CFS-MCFA-SVM algorithm outperforms benchmark methods in terms of classification accuracy and genes subset size. In particular, 100 percent accuracy was achieved on all four datasets and with only a few biomarkers (between one and four). This result indicates that the proposed algorithm is one of the competitive alternatives in feature selection, which later contributes to the analysis of microarray data

Elephant Search with Deep Learning for Microarray Data Analysis

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, a novel elephant search (ES) based optimization is proposed to select best gene expressions from the large volume of microarray data. Further, a promising machine learning method is envisioned to leverage such high dimensional and complex microarray dataset for extracting hidden patterns inside to make a meaningful prediction and most accurate classification. In particular, stochastic gradient descent based Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on nine most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning (ESDL) approach are compared with most recent published article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl

Swarm Intelligence Based Feature Selection for High Dimensional Classification: A Literature Survey

Feature selection is an important and challenging task in machine learning and data mining techniques to avoid the curse of dimensionality and maximize the classification accuracy. Moreover, feature selection helps to reduce computational complexity of learning algorithm, improve prediction performance, better data understanding and reduce data storage space. Swarm intelligence based feature selection approach enables to find an optimal feature subset from an extremely large dimensionality of features for building the most accurate classifier model. There is still a type of researches that is not done yet in data mining. In this paper, the utilization of swarm intelligence algorithms for feature selection process in high dimensional data focusing on medical data classification is form the subject matter. The results shows that swarm intelligence algorithms reviewed based on state-of-the-art literature have a promising capability that can be applied in feature selections techniques. The significance of this work is to present the comparison and various alternatives of swarm algorithms to be applied in feature selections for high dimensional classification

Hybrid Feature Selection Approach Based on GRASP for Cancer Microarray Data

Microarray data usually contain a large number of genes, but a small number of samples. Feature subset selection for microarray data aims at reducing the number of genes so that useful information can be extracted from the samples. Reducing the dimension of data sets further helps in improving the computational efficiency of the learning model. In this paper, we propose a modified algorithm based on the tabu search as local search procedures to a Greedy Randomized Adaptive Search Procedure (GRASP) for high dimensional microarray data sets. The proposed Tabu based Greedy Randomized Adaptive Search Procedure algorithm is named as TGRASP. In TGRASP, a new parameter has been introduced named as Tabu Tenure and the existing parameters, NumIter and size have been modified. We observed that different parameter settings affect the quality of the optimum. The second proposed algorithm known as FFGRASP (Firefly Greedy Randomized Adaptive Search Procedure) uses a firefly optimization algorithm in the local search optimzation phase of the greedy randomized adaptive search procedure (GRASP). Firefly algorithm is one of the powerful algorithms for optimization of multimodal applications. Experimental results show that the proposed TGRASP and FFGRASP algorithms are much better than existing algorithm with respect to three performance parameters viz. accuracy, run time, number of a selected subset of features. We have also compared both the approaches with a unified metric (Extended Adjusted Ratio of Ratios) which has shown that TGRASP approach outperforms existing approach for six out of nine cancer microarray datasets and FFGRASP performs better on seven out of nine datasets

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