An improved Binary Particle Swarm Optimization (iBPSO) for Gene Selection and Cancer Classification using DNA Microarrays

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.

DNA microarrays can simultaneously measure the expression level of thousands of gene within a particular mRNA sample that provide information about the state of cells and tissues. Though these expressive values are useful in cancer classification, and understand the mechanisms involved in the genesis of disease processes, however, only a few genes out of these thousands of genes contribute towards disease classification. On this basis, usage of feature selection algorithm is favourable, as the main goal of feature selection algorithm is to identify the relevant features (here genes) efficiently. In this paper, we have applied four filter Feature Selection (FS) methods, namely, Mutual Information (MI), Pearson Correlation Coefficient (PCC), Chi <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , ReliefF along with three well-known classifiers, namely, Random Forest (RF), Decision Tree (DT), and K-Nearest Neighbour (KNN) on six microarray datasets (both binary and multi-class) namely, Leukemia, Lung, Lymphoma and Leukemia, Gastric, SRBCT and Childhood Tumor and recorded the accuracies.

The aim of this paper is twofold. First, we present a thorough experimental study to show the superiority of the generalization capability of the support vector machine (SVM) approach in the automatic classification of electrocardiogram (ECG) beats. Second, we propose a novel classification system based on particle swarm optimization (PSO) to improve the generalization performance of the SVM classifier. For this purpose, we have optimized the SVM classifier design by searching for the best value of the parameters that tune its discriminant function, and upstream by looking for the best subset of features that feed the classifier. The experiments were conducted on the basis of ECG data from the Massachusetts Institute of Technology-Beth Israel Hospital (MIT-BIH) arrhythmia database to classify five kinds of abnormal waveforms and normal beats. In particular, they were organized so as to test the sensitivity of the SVM classifier and that of two reference classifiers used for comparison, i.e., the k-nearest neighbor (kNN) classifier and the radial basis function (RBF) neural network classifier, with respect to the curse of dimensionality and the number of available training beats. The obtained results clearly confirm the superiority of the SVM approach as compared to traditional classifiers, and suggest that further substantial improvements in terms of classification accuracy can be achieved by the proposed PSO-SVM classification system. On an average, over three experiments making use of a different total number of training beats (250, 500, and 750, respectively), the PSO-SVM yielded an overall accuracy of 89.72% on 40438 test beats selected from 20 patient records against 85.98%, 83.70%, and 82.34% for the SVM, the kNN, and the RBF classifiers, respectively.

Chapter 16 - An enhanced feature selection and cancer classification for microarray data using relaxed Lasso and support vector machine

Over the past few decades, DNA microarray technology has emerged as a prevailing process for early identification of cancer subtypes. Several feature selection (FS) techniques have been widely applied for identifying cancer from microarray gene data but only very few studies have been conducted on distributing the feature selection process for detecting cancer subtypes. Not all the gene expressions are needed in prediction, this research article objective is to select discriminative biomarkers by using distributed FS method which helps in accurately diagnosis of cancer subtype. Traditional feature selection techniques have several drawbacks like unrelated features that could perform well in terms of classification accuracy with a suitable subset of genes will be left out of the selection. To overcome the issue, in this paper a new filter-based method for gene selection is introduced which can select the highly relevant genes for distinguishing tissues from the gene expression dataset. In addition, it is used to compute the relation between gene-gene and gene-class and simultaneously identify subset of essential genes. Our method is tested on Diffuse Large B cell Lymphoma (DLBCL) dataset by using well-known classification techniques such as support vector machine, naïve Bayes, k-nearest neighbor, and decision tree. Results on biological DLBCL dataset demonstrate that the proposed method provides promising tools for the prediction of cancer type, with the prediction accuracy of 97.62%, precision of 94.23%, sensitivity of 94.12%, F-measure of 90.12%, and ROC value of 99.75%. The experimental results reveal the fact that the proposed method is significantly improved classification accuracy and execution time, compared to existing standard algorithms when applied to the non-partitioned dataset. Furthermore, the extracted genes are biologically sound and agree with the outcome of relevant biomedical studies.

Parkinson's disease (PD) is a neurological disorder which is progressive in nature. Although there is no cure to this disease, symptomatic treatments are available. These treatments can slow the progressive development of the symptoms. Medications can treat some of the symptoms of the PD up to a great extent that in turn may help the patients to live a normal life. Besides these medications, the patients can also be provided with various therapies based on the types of their symptoms. But for providing any treatment, detection of its symptoms at an early stage is very important. This can reduce its future complexities considerably. Early diagnosis along with proper medications may treat the symptoms of PD significantly. This motivates to propose a new and effective methodology for detection and analysis of PD. In this work, an approach has been proposed for identification of PD patients by using Electroencephalogram (EEG) signals. Here, the EEG signals of normal persons and PD patients are processed in three stages. First, the raw EEG signals are pre-processed for removal of noises and artefacts present. Out of various techniques, Wavelet transform is used for this purpose. In the MATLAB environment, de-noising can be executed by using the in-built functions. Performances of the de-noising techniques are examined with the performance parameters namely Root Mean Square Error (RMSE) as well as Signal to Noise Ratio (SNR). In the second stage, statistical features are extracted from the pre-processed EEG signals. In this work, five statistical features are considered for performing the classification. In the final stage, the extracted features are classified using Artificial Neural Network (ANN) and Support Vector Machine (SVM) techniques. ANN is an efficient classifier that predicts the human brain's working manners. SVM on the other hand has been proven as one of the most prevailing classification algorithms that gives highly accurate and robust results. This is a novel approach of analyzing the performances of the classification techniques by evaluating the best performing feature. In both the classifiers accuracy, precision, sensitivity and specificity are calculated from the confusion matrix evaluated from the values of the statistical features. In ANN, results using six different training algorithms at different hidden layers are calculated and compared. This proves the training algorithm Levenberg-Marquardt back-propagation with hidden layer 20 as the best combination for performing the classification. From the results it is seen that both ANN and SVM classifiers provide significant classification accuracies of 94.7% and 96.5% respectively. Amongst the five considered features, Mean performs the best in terms of classification accuracy.

기업의 부도를 예측하는 것은 회계나 재무 분야에서 중요한 연구주제이다. 지금까지 기업 부도예측을 위해 여러 가지 데이터마이닝 기법들이 적용되었으나 주로 단일 모형을 사용함으로서 복잡한 분류 문제에의 적용에 한계를 갖고 있었다. 본 논문에서는 최근에 각광받고 있는 SVM (support vector machine) 모형들을 결합한 앙상블 SVM 모형 (ensemble SVM model)을 부도예측에 사용하고자 한다. 제안된 앙상블 모형은 v-조각 교차 타당성 (v-fold cross-validation)에 의해 얻어진 여러 가지 모형 중에서 성능이 좋은 상위 k개의 단일 모형으로 구성하고 과반수 투표 방식 (majority voting)을 사용하여 미지의 클래스를 분류한다. 본 논문에서 제안된 앙상블 SVM 모형의 성능을 평가하기 위해 실제 기업의 재무비율 자료와 모의실험자료를 가지고 실험하였고, 실험결과 제안된 앙상블 모형이 여러 가지 평가척도 하에서 단일 SVM 모형들보다 좋은 성능을 보임을 알 수 있었다. Corporate bankruptcy prediction has been an important topic in the accounting and finance field for a long time. Several data mining techniques have been used for bankruptcy prediction. However, there are many limits for application to real classification problem with a single model. This study proposes ensemble SVM (support vector machine) model which assembles different SVM models with each different kernel functions. Our ensemble model is made and evaluated by v-fold cross-validation approach. The k top performing models are recruited into the ensemble. The classification is then carried out using the majority voting opinion of the ensemble. In this paper, we investigate the performance of ensemble SVM classifier in terms of accuracy, error rate, sensitivity, specificity, ROC curve, and AUC to compare with single SVM classifiers based on financial ratios dataset and simulation dataset. The results confirmed the advantages of our method: It is robust while providing good performance.

This paper presents a comparison between one-dimensional component analysis (1D-PCA) and two-dimensional principal component analysis (2D-PCA) under two different types of classification techniques namely k-nearest neighbor (kNN) and Support Vector Machines (SVM). These two techniques differ in the method to determine the image covariance matrix. 2DPCA used 2D image matrices instead of column vectors in 1DPCA. The eigenvectors derived from these matrices will result in images in reduced dimensions to be used for classification. K-nearest neighbor algorithm (kNN) and Support Vector Machines (SVM) were used for classification. The performance measures used for comparison were classification accuracy and computational time. The tests were performed on the ORL image database. The experimental results indicate that 2DPCA outperforms in terms of classification accuracy and computational complexity.

Using information technology such as search engine for collecting and monitoring of network public opinion is a practical and effective method. This paper puts forward an improved algorithm of SVM classifier based on incremental learning online, and then implements a topic crawler system for network public opinion and to grab the public opinion.

A query image based scene/image retrieval system is a system that analyzes the properties of a query image and identifies the class in which the image belongs and retrieves a number of images which are most alike and relevant to the query image. A scene/image classifier provides the first stage for this system. Scene classification is the process that analyzes the properties of various image features of a scene and organizes the scenes into categories. Programmed techniques for correlating scenes with labels have a high potential for improving the performance of computer vision applications such as searching, retrieval and object recognition. The scene category system uses the feature vectors extracted from image data to classify test images. We have implemented a k-nearest neighbour (kNN) classifier which uses gray scale and Scale Invariant Feature Transform (SIFT) features as input and used support vector machine (SVM) classifier that uses GIST features as input. kNN classifier is used, as it has an advantage of working with a large amount of data and SVM is robust even when the training sample has some bias. The performance measure of the classifier was evaluated using confusion matrix and classification accuracy. We considered MIT-8 scene category, leaves, Caltech-20 and deer data sets for our experiments. The classification accuracy was found to be good. Results show that classification accuracy is increased significantly for classification using GIST features in SVM classifiers. We are exploring methods to obtain optimal performance of classifiers.

Instance selection and construction methods were originally designed to improve the performance of the k-nearest neighbors classifier by increasing its speed and improving the classification accuracy. These goals were achieved by eliminating redundant and noisy samples, thus reducing the size of the training set. In this paper, the performance of instance selection methods is investigated in terms of classification accuracy and reduction of training set size. The classification accuracy of the following classifiers is evaluated: decision trees, random forest, Naive Bayes, linear model, support vector machine and k-nearest neighbors. The obtained results indicate that for the most of the classifiers compressing the training set affects prediction performance and only a small group of instance selection methods can be recommended as a general purpose preprocessing step. These are learning vector quantization based algorithms, along with the Drop2 and Drop3. Other methods are less efficient or provide low compression ratio.

Objective: To analyze the recurrence patterns and reasons in patients with nasopharyngeal carcinoma (NPC) treated with intensity-modulated radiotherapy (IMRT) and to investigate the feasibility of radiomics for analysis of radioresistance.Methods: We analyzed 306 NPC patients treated with IMRT from Jul-2009 to Aug-2016, 20 of whom developed with recurrence. For the NPCs with recurrence, CT, MR, or PET/CT images of recurrent disease were registered with the primary planning CT for dosimetry analysis. The recurrences were defined as in-field, marginal or out-of-field, according to dose-volume histogram (DVH) of the recurrence volume. To explore the predictive power of radiomics for NPCs with in-field recurrences (NPC-IFR), 16 NPCs with non-progression disease (NPC-NPD) were used for comparison. For these NPC-IFRs and NPC-NPDs, 1117 radiomic features were quantified from the tumor region using pre-treatment spectral attenuated inversion-recovery T2-weighted (SPAIR T2W) magnetic resonance imaging (MRI). Intraclass correlation coefficients (ICC) and Pearson correlation coefficient (PCC) was calculated to identify influential feature subset. Kruskal-Wallis test and receiver operating characteristic (ROC) analysis were employed to assess the capability of each feature on NPC-IFR prediction. Principal component analysis (PCA) was performed for feature reduction. Artificial neural network (ANN), k-nearest neighbor (KNN), and support vector machine (SVM) models were trained and validated by using stratified 10-fold cross validation.Results: The median follow up was 26.5 (range 8–65) months. 9/20 (45%) occurred in the primary tumor, 8/20 (40%) occurred in regional lymph nodes, and 3/20 (15%) patients developed a primary and regional failure. Dosimetric and target volume analysis of the recurrence indicated that there were 18 in-field, and 1 marginal as well as 1 out-of-field recurrence. With pre-therapeutic SPAIR T2W MRI images available, 11 NPC-IFRs (11 of 18 NPC-IFRs who had available pre-therapeutic MRI) and 16 NPC-NPDs were subsequently employed for radiomic analysis. Results showed that NPC-IFRs vs. NPC-NPDs could be differentiated by 8 features (AUCs: 0.727–0.835). The classification models showed potential in prediction of NPC-IFR with higher accuracies (ANN: 0.812, KNN: 0.775, SVM: 0.732).Conclusion: In-field and high-dose region relapse were the main recurrence patterns which may be due to the radioresistance. After integration in the clinical workflow, radiomic analysis can be served as imaging biomarkers to facilitate early salvage for NPC patients who are at risk of in-field recurrence.

This paper investigates the performance of three supervised machine learning algorithms K-Nearest Neighbor (KNN), Decision Tree (DT), and Support Vector Machine (SVM) for diabetes classification using the Pima Indians Diabetes Dataset. The study aims to provide a fair and consistent comparison by applying unified preprocessing procedures, including median imputation for clinically invalid values, feature standardization, and stratified 5-fold cross-validation. Model performance is evaluated using accuracy, precision, recall, and F1-score, with particular emphasis on recall for the diabetic class due to its clinical significance in reducing false negative diagnoses. Experimental results show that the Decision Tree model achieves the most balanced performance, with an average accuracy of 0.78 and an F1-score of 0.75, while maintaining higher recall for diabetic cases compared to KNN and SVM. Although SVM and KNN demonstrate acceptable overall accuracy, both models exhibit limitations in identifying minority-class instances. These findings highlight the importance of algorithm selection based not only on accuracy but also on clinical priorities such as interpretability and sensitivity to positive cases. The study contributes practical insights for the development of reliable machine learning–based decision support systems for early diabetes screening.

Landsat-like moderate resolution remote sensing images are widely used in land use and land cover (LULC) classification. Limited by coarser resolutions, most of the traditional LULC classifications that are based on moderate resolution remote sensing images focus on the spectral features of a single pixel. Inspired by the spatial evaluation methods in landscape ecology, this study proposed a new method to extract neighborhood characteristics around a pixel for moderate resolution images. 3 landscape-metric-like indexes, i.e., mean index, standard deviation index, and distance weighted value index, were defined as adjacent region features to include the surrounding environmental characteristics. The effects of the adjacent region features and the different feature set configurations on improving the LULC classification were evaluated by a series of well-controlled LULC classification experiments using K nearest neighbor (KNN) and support vector machine (SVM) classifiers on a Landsat 8 Operational Land Imager (OLI) image. When the adjacent region features were added, the overall accuracies of both the classifiers were higher than when only spectral features were used. For the KNN and SVM classifiers that used only spectral features, the overall accuracies of the LULC classification were 85.45% and 88.87%, respectively, and the accuracies were improved to 94.52% and 96.97%. The classification accuracies of all the LULC types improved. Highly heterogeneous LULC types that are easily misclassified achieved greater improvements. As comparisons, the grey-level co-occurrence matrix (GLCM) and convolutional neural network (CNN) approaches were also implemented on the same dataset. The results revealed that the new method outperformed GLCM and CNN approaches and can significantly improve the classification performance that is based on moderate resolution data.

Recent remote sensing literature has shown that support vector machine (SVM) methods generally outperform traditional statistical and neural methods in classification problems involving hyperspectral images. However, there are still open issues that, if suitably addressed, could allow further improvement of their performances in terms of classification accuracy. Two especially critical issues are: 1) the determination of the most appropriate feature subspace where to carry out the classification task and 2) model selection. In this paper, these two issues are addressed through a classification system that optimizes the SVM classifier accuracy for this kind of imagery. This system is based on a genetic optimization framework formulated in such a way as to detect the best discriminative features without requiring the a priori setting of their number by the user and to estimate the best SVM parameters (i.e., regularization and kernel parameters) in a completely automatic way. For these purposes, it exploits fitness criteria intrinsically related to the generalization capabilities of SVM classifiers. In particular, two criteria are explored, namely: 1) the simple support vector count and 2) the radius margin bound. The effectiveness of the proposed classification system in general and of these two criteria in particular is assessed both by simulated and real experiments. In addition, a comparison with classification approaches based on three different feature selection methods is reported, i.e., the steepest ascent (SA) algorithm and two other methods explicitly developed for SVM classifiers, namely: 1) the recursive feature elimination technique and 2) the radius margin bound minimization method