Detecting biomarkers from microarray data using distributed correlation based gene selection

The current study proposes a novel technique for feature selection by inculcating robustness in the conventional Signal to noise Ratio (SNR). The proposed method utilizes the robust measures of location i.e., the “Median” as well as the measures of variation i.e., “Median absolute deviation (MAD) and Interquartile range (IQR)” in the SNR. By this way, two independent robust signal-to-noise ratios have been proposed. The proposed method selects the most informative genes/features by combining the minimum subset of genes or features obtained via the greedy search approach with top-ranked genes selected through the robust signal-to-noise ratio (RSNR). The results obtained via the proposed method are compared with well-known gene/feature selection methods on the basis of performance metric i.e., classification error rate. A total of 5 gene expression datasets have been used in this study. Different subsets of informative genes are selected by the proposed and all the other methods included in the study, and their efficacy in terms of classification is investigated by using the classifier models such as support vector machine (SVM), Random forest (RF) and k-nearest neighbors (k-NN). The results of the analysis reveal that the proposed method (RSNR) produces minimum error rates than all the other competing feature selection methods in majority of the cases. For further assessment of the method, a detailed simulation study is also conducted.

Text mining is a special case of data mining which explore unstructured or semi-structured text documents, to establish valuable patterns and rules that indicate trends and significant features about specific topics. Text mining has been in pattern recognition, predictive studies, sentiment analysis and statistical theories in many areas of research, medicine, financial analysis, social life analysis, and business intelligence. Text mining uses concept of natural language processing and machine learning. Machine learning algorithms have been used and reported to give great results, but their performance of machine learning algorithms is affected by factors such as dataset domain, number of classes, length of the corpus, and feature selection techniques used. Redundant attribute affects the performance of the classification algorithm, but this can be reduced by using different feature selection techniques and dimensionality reduction techniques. Feature selection is a data preprocessing step that chooses a subset of input variable while eliminating features with little or no predictive information. Feature selection techniques are Information gain, Term Frequency, Term Frequency-Inverse document frequency, Mutual Information, and Chi-Square, which can use a filters, wrappers, or embedded approaches. To get the most value from machine learning, pairing the best algorithms with the right tools and processes is necessary. Little research has been done on the effect of feature selection techniques on classification accuracy for pairing of these algorithms with the best feature selection techniques for optimal results. In this research, a text classification experiment was conducted using incident management dataset, where incidents were classified into their resolver groups. Support vector machine (SVM), K-Nearest Neighbors (KNN), Naïve Bayes (NB) and Decision tree (DT) machine learning algorithms were examined. Filtering approach was used on the feature selection techniques, with different ranking indices applied for optimal feature set and classification accuracy results analyzed. The classification accuracy results obtained using TF were, 88% for SVM, 70% for NB, 79% for Decision tree, and KNN had 55%, while Boolean registered 90%, 83%, 82% and 75%, for SVM, NB, DT, and KNN respectively. TF-IDF, had 91%, 83%, 76%, and 56% for SVM, NB, DT, and KNN respectively. The results showed that algorithm performance is affected by feature selection technique applied. SVM performed best, followed by DT, KNN and finally NB. In conclusion, presence of noisy data leads to poor learning performance and increases the computational time. The classifiers performed differently depending on the feature selection technique applied. For optimal results, the classifier that performed best together with the feature selection technique with the best feature subset should be applied for all types of data for accurate classification performance. Keywords: Text Classification, Supervised Machine Learning, Feature Selection DOI : 10.7176/JIEA/9-3-06 Publication date :May 31 st 2019

This study evaluates the impact of three Feature Selection (FS) algorithms in an Object Based Image Analysis (OBIA) framework for Very-High-Resolution (VHR) Land Use-Land Cover (LULC) classification. The three selected FS algorithms, Correlation Based Selection (CFS), Mean Decrease in Accuracy (MDA) and Random Forest (RF) based Recursive Feature Elimination (RFE), were tested on Support Vector Machine (SVM), K-Nearest Neighbor, and Random Forest (RF) classifiers. The results demonstrate that the accuracy of SVM and KNN classifiers are the most sensitive to FS. The RF appeared to be more robust to high dimensionality, although a significant increase in accuracy was found by using the RFE method. In terms of classification accuracy, SVM performed the best using FS, followed by RF and KNN. Finally, only a small number of features is needed to achieve the highest performance using each classifier. This study emphasizes the benefits of rigorous FS for maximizing performance, as well as for minimizing model complexity and interpretation.

Today, video data, as a powerful multimedia component, is accompanied by some problems with increasing usage in communication, health, education, and social media in particular. Classification and detection of concepts in video data by automatic methods are some of these challenging problems. In this study, we propose a video classification system, which incorporates deep convolutional neural networks (CNNs) by leveraging feature selection and data fusion techniques to improve the accuracy of the classification. Principal Component Analysis (PCA) as a feature selection method and Discriminant Correlation Analysis (DCA) technique, which incorporates class associations into the correlation analysis of feature sets for data fusion, are applied to the problem at the feature level. Support Vector Machines (SVMs) have been trained with new feature vectors obtained from different deep convolutional neural networks by feature selection and data fusion methods. The proposed method is tested for 38 concepts on TRECVID 2013 SIN video task dataset and the results are evaluated. Our results show that the classification accuracy is improved by 4% with an accuracy of 50.27% when the proposed data fusion and feature selection techniques are used.

Feature selection (FS) plays a crucial role in medical imaging by reducing dimensionality, improving computational efficiency, and enhancing diagnostic accuracy. Traditional FS techniques, including filter, wrapper, and embedded methods, have been widely used but often struggle with high-dimensional and heterogeneous medical imaging data. Deep learning-based FS methods, particularly Convolutional Neural Networks (CNNs) and autoencoders, have demonstrated superior performance but lack interpretability. Hybrid approaches that combine classical and deep learning techniques have emerged as a promising solution, offering improved accuracy and explainability. Furthermore, integrating multi-modal imaging data (e.g., Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), and Ultrasound (US)) poses additional challenges in FS, necessitating advanced feature fusion strategies. Multi-modal feature fusion combines information from different imaging modalities to improve diagnostic accuracy. Recently, quantum computing has gained attention as a revolutionary approach for FS, providing the potential to handle high-dimensional medical data more efficiently. This systematic literature review comprehensively examines classical, Deep Learning (DL), hybrid, and quantum-based FS techniques in medical imaging. Key outcomes include a structured taxonomy of FS methods, a critical evaluation of their performance across modalities, and identification of core challenges such as computational burden, interpretability, and ethical considerations. Future research directions—such as explainable AI (XAI), federated learning, and quantum-enhanced FS—are also emphasized to bridge the current gaps. This review provides actionable insights for developing scalable, interpretable, and clinically applicable FS methods in the evolving landscape of medical imaging.

The complexity and high dimensionality of gene expression data pose significant challenges for effective feature selection and accurate classification in bioinformatics.This study introduces two novel algorithms, Support Vector Machine-Recursive Cluster Elimination (SVM-RCE) and its advanced version, SVM-RCE with Center Weights (SVM-RCE-CW), designed to optimize feature selection by leveraging clustering techniques and machine learning models.Both algorithms aim to reduce the feature space, thereby enhancing the interpretability and performance of classification models.We present a comprehensive comparison of these methods against traditional feature selection techniques, demonstrating their efficacy in achieving significant dimensionality reduction while maintaining or improving classification accuracy in several gene expression datasets.

Colon cancer heavily changes the composition of human genes (expressions). The deviation in the chemical composition of genes can be exploited to automatically diagnose colon cancer. The major challenge in the analysis of human gene based datasets is their large dimensionality. Therefore, efficient techniques are needed to select discerning genes. In this research article, we propose a novel classification technique that exploits the variations in gene expressions for classifying colon gene samples into normal and malignant classes, and quite intelligently tackles the larger dimensionality of gene based datasets. Previously individual feature selection techniques have been used for selection of discerning gene expressions, however, their performance is limited. In this research study, we propose a feed forward gene selection technique, wherein, two feature selection techniques are used one after the other. The genes selected by the first technique are fed as input to the second feature selection technique that selects genes from the given gene subset. The selected genes are then classified by using linear kernel of support vector machines (SVM). The feed forward approach of gene selection has shown improved performance. The proposed technique has been tested on three standard colon cancer datasets, and improved performance has been observed. It is observed that feed forward method of gene selection substantially reduces the size of gene based datasets, thereby reducing the computational time to a great extent. Performance of the proposed technique has also been compared with existing techniques of colon cancer diagnosis, and improved performance has been observed. Therefore, we hope that the proposed technique can be effectively used for diagnosis of colon cancer.

Gene selection and classification using Taguchi chaotic binary particle swarm optimization

Identifying important biomarkers to improve disease diagnosis and treatment is a significant topic of research in bioinformatics. However, bioinformatics datasets frequently have a large number of features per sample or instance. This problem, known as “high dimensionality,” can be alleviated through the use of dimension reducing techniques such as feature (gene) selection which remove unnecessary features. There are many versions of feature selection, with varying biases and predictive abilities. However, predictive power is but one factor to consider when choosing a feature selection technique: one must also consider the technique's stability, that is, its ability to create feature subsets which remain valid in the face of changes to the data. While there has been work in determining the relative stability of different feature selection techniques, this does not always help determine whether a chosen feature selection technique will give stable feature subsets for a specific dataset. Factors such as difficulty of learning (e.g., dataset difficulty) may also influence feature selection stability, making generally-true facts about different techniques not applicable to a given dataset. In this work, we study how dataset difficulty can affect the stability of feature selection techniques, leading to good performance from bad techniques and vice versa. We use a set of twenty-six DNA microarray datasets with varying levels of difficulty of learning, along with four levels of dataset perturbation, six feature selection techniques with various levels of stability, and twelve feature subset sizes. The results show that as the dataset difficulty increases, the stability decreases. However, the relative stability between the techniques remains the same. Additionally, the more difficult the dataset, the more the stability is affected by changes to the data. We also found that unstable rankers are more affected by the transition between Easy and Moderate datasets, whereas the stable techniques are more affected by the change between Moderate and Hard datasets. Lastly, as the feature subset size increases, the stability increases and the difference between the levels of dataset difficulty decreases. Overall, we conclude that difficulty of learning must be taken into account before interpreting stability results.

Information of built-up area is essential for various applications, such as sustainable development or urban planning. Built-up area extraction using optical data is challenging due to spectral confusion between built-up and other classes (bare land or river sand, etc.). Here an automated approach has been proposed to generate built-up maps using spectral-textural features and feature selection techniques. Eight Grey-Level Co-Occurrence Matrix based texture features are extracted using Landsat-8 Operational Land Imager bands and combined with multispectral data. The most informative features are selected from combined spectral-textural dataset using feature selection techniques. Further, Support Vector Machine (SVM) classifiers are trained on labelled samples using optimal features and results are compared with Back Propagation-Neural Network (BP-NN) and k-Nearest Neighbour (k-NN). The results show that inclusion of textural features and applying feature selection methods increases the highest overall accuracy of Linear-SVM, RBF-SVM, BP-NN, and k-NN by 9.20%, 9.09%, 8.42%, and 7.39%, respectively.

Heart disease is still one of the top causes of death globally, demanding early and effective prediction tools. Traditional predictive models frequently have limitations because they rely on single‐source statistics, which may not represent the entire scenario of a patient's complex health profile. Feature selection is an essential preprocessing step in machine learning that improves model efficiency by eliminating irrelevant or redundant features. This study evaluates the impact of feature selection on six classification modelsNaïve Bayes, Logistic Regression, Decision Tree, K‐Nearest Neighbors (KNN), Support Vector Machine (SVM), and Random Forestacross four datasets. Performance was assessed using accuracy, precision, recall, F1‐score, and area under the curve (AUC) before and after feature selection. The results indicate that feature selection had varying effects across different models and datasets. In Dataset‐01, Random Forest maintained its strong performance (98.70% accuracy) even after feature selection, while SVM and KNN saw noticeable drops, with accuracy decreasing from 88.96% to 79.87% and 87.01% to 81.17% respectively. For Dataset‐02, SVM showed improvement, increasing from 80.00% to 85.00%, while Naïve Bayes and KNN also improved, reaching 82.50% and 82.50% accuracy, respectively. In Dataset‐03, Logistic Regression and KNN experienced declines, with accuracy dropping from 88.76% to 83.71% and 91.57% to 87.08%, respectively, while Random Forest fell from 97.75% to 91.57%. Dataset‐04 showed mixed results, with Logistic Regression improving from 86.67% to 91.11%, but KNN and Random Forest dropping from 97.78% to 84.44% and 91.11% to 82.22%, respectively. These findings suggest that while feature selection enhances performance for some models, it can negatively impact others, particularly those reliant on a larger feature set. Future research should explore adaptive feature selection techniques to optimize model performance across diverse datasets.

DNA Microarrays are promising tool for cancer diagnosis and prognosis. DNA Microarrays are high-dimensional and gene selection is a difficult task. However, Bootstrap-based ensemble feature selection (Bagging) recently becomes popular and shows significant improvements in the field. This method aims to generate several slightly different sampled datasets, using bootstrap resampling, from training dataset. Afterwards, it aggregates all ranked feature lists, generated from sampled datasets, to obtain final (ensemble) feature list. Performance of bagging is proportional to diversity of generated sampled datasets. Therefore, it is proposed to use under-sampling of training set instead of using entire training set for bootstrap resampling to improve classification performance and gene selection stability. The proposed method was evaluated using support vector machine (SVM) as the classifier and recursive feature elimination (SVM-RFE) as the feature selection technique. Four microarray datasets were used for evaluation of the proposed method. The results show that 50% under-sampling approach have similar classification performance and outperforms conventional approach in terms of gene selection stability. In addition, 50% under-sampling uses only half of the samples of training dataset at each run of ensemble method so it has less computational cost.

Intelligent automated decision support systems are found to be useful for early detection of hepatitis for augmenting survivability. We present here an intelligent system for hepatitis disease diagnosis using UCI data set for experiment. We use multiple imputation technique for managing missing values in the UCI data set. One of the potential tools in this context is neural network for classification. For better diagnostic classification accuracy, various feature selection techniques are deployed as prerequisite. These features are considered to be more informative to the doctors for taking final decision. This work attempts rough set-based feature selection (RS) technique. For classification, we use incremental back propagation learning network (IBPLN), and Levenberg-Marquardt (LM) classification tested on UCI data base. We compare classification results in terms of classification accuracy, specificity, sensitivity and receiver-operating characteristics curve area(AUC).

One of the important practical applications of computer vision techniques is computer-aided diagnosis (CAD) in medical imaging. It has been shown that CAD can improve the accuracy of breast cancer detection and characterization by radiologists on mammograms. In this chapter, we discuss an important step — feature selection — in classifier design for CAD algorithms. Feature selection reduces the dimensionality of an available feature space and is therefore often used to prevent over-parameterization of a classifier. Many feature selection techniques have been proposed in the literature. We will illustrate the usefulness of genetic algorithms (GAs) for feature selection by comparing GA with a commonly used sequential selection method. A brief introduction to the GA is given and several examples using GA feature selection for the characterization of mammographic lesions are discussed. The examples illustrate the design of a fitness function for optimizing classification accuracy in terms of the receiver operating characteristics of the classifier, the dependence of GA performance on its evolution parameters, and the design of a fitness function tailored to a specific classification task.

Credit risk analysis forms an important criterion for the endurance of the banking sector. Understanding credit liability of customer enhances the security stability of the banker. This research is aimed at comparing the predictive accuracy of data mining techniques with feature selection and extraction techniques in the default of credit card clients and suggesting the most efficient technique for analyzing credit card default. Customer's default payments in Taiwan were used as the dataset. Machine Learning classification algorithms like K-nearest neighbor(KNN), Naive Bayesian(NB), Decision Tree(DT) and Support Vector Machines(SVM) were applied to the dataset. Feature filter methods like information gain (IG), gain ratio (GR) and chi-square (CS) and Wrapper based methods like Best First search(BFS) and Hill Climbing search (HCS) were used to identify minimum features required. Feature extraction methods such as Principal Component Analysis(PCA) and Linear Discriminant Anal-ysis(LDA) were also applied. The minimum features of feature selection algorithms along with PCA and LDA were then applied to Base classifiers and their accuracies were tabulated and compared. SVM with feature selection and extraction techniques had the best predictive accuracy.