Genetic Algorithm Based Feature Selection Research Articles

Genetic algorithm-based feature selection in high-resolution NMR spectra

High-resolution nuclear magnetic resonance (NMR) spectroscopy has provided a new means for detection and recognition of metabolic changes in biological systems in response to pathophysiological stimuli and to the intake of toxins or nutrition. To identify meaningful patterns from NMR spectra, various statistical pattern recognition methods have been applied to reduce their complexity and uncover implicit metabolic patterns. In this paper, we present a genetic algorithm (GA)-based feature selection method to determine major metabolite features to play a significant role in discrimination of samples among different conditions in high-resolution NMR spectra. In addition, an orthogonal signal filter was employed as a preprocessor of NMR spectra in order to remove any unwanted variation of the data that is unrelated to the discrimination of different conditions. The results of k-nearest neighbors and the partial least squares discriminant analysis of the experimental NMR spectra from human plasma showed the potential advantage of the features obtained from GA-based feature selection combined with an orthogonal signal filter.

Enhanced prediction of misalignment conditions from spectral data using feature selection and filtering

This paper proposes a novel method for the use of genetic algorithm-based feature selection and signal filtering to construct reliable calibration models of shaft misalignment. Determination and selection of the key feature(s) is crucial to the predictive performance of calibration models. Even with proper feature selection, the predictive performance of calibration models can be enhanced by filtering the raw spectral data. This improvement results because a filter removes the unwanted variation of predictor variables that is orthogonal to response variables. This is the first work that attempts to develop a systematic calibration model based on genetic algorithm-based feature selection and orthogonal filtering. A case study shows that the proposed calibration model for shaft misalignment conditions produces better predictive performance than traditional multivariate statistical approaches such as principal component regression and partial least squares.

Differential diagnosis of CT focal liver lesions using texture features, feature selection and ensemble driven classifiers

The aim of the present study is to define an optimally performing computer-aided diagnosis (CAD) architecture for the classification of liver tissue from non-enhanced computed tomography (CT) images into normal liver (C1), hepatic cyst (C2), hemangioma (C3), and hepatocellular carcinoma (C4). To this end, various CAD architectures, based on texture features and ensembles of classifiers (ECs), are comparatively assessed. Number of regions of interests (ROIs) corresponding to C1-C4 have been defined by experienced radiologists in non-enhanced liver CT images. For each ROI, five distinct sets of texture features were extracted using first order statistics, spatial gray level dependence matrix, gray level difference method, Laws' texture energy measures, and fractal dimension measurements. Two different ECs were constructed and compared. The first one consists of five multilayer perceptron neural networks (NNs), each using as input one of the computed texture feature sets or its reduced version after genetic algorithm-based feature selection. The second EC comprised five different primary classifiers, namely one multilayer perceptron NN, one probabilistic NN, and three k-nearest neighbor classifiers, each fed with the combination of the five texture feature sets or their reduced versions. The final decision of each EC was extracted by using appropriate voting schemes, while bootstrap re-sampling was utilized in order to estimate the generalization ability of the CAD architectures based on the available relatively small-sized data set. The best mean classification accuracy (84.96%) is achieved by the second EC using a fused feature set, and the weighted voting scheme. The fused feature set was obtained after appropriate feature selection applied to specific subsets of the original feature set. The comparative assessment of the various CAD architectures shows that combining three types of classifiers with a voting scheme, fed with identical feature sets obtained after appropriate feature selection and fusion, may result in an accurate system able to assist differential diagnosis of focal liver lesions from non-enhanced CT images.

Soil differentiation using fingerprint Fourier transform infrared spectroscopy, chemometrics and genetic algorithm-based feature selection

Soil is a complex environmental medium, particularly with respect to its biological and organic characteristics. Analytical approaches based on specific aspects of biological or organic variation may fail to detect broader differences in function or composition. Fourier transform infrared spectroscopy (FT-IR) spectra provide a more comprehensive description of soil characteristics in the form of complex multivariate data sets. Soils at different stages of recovery from degradation following opencast mining and from undisturbed land were investigated to evaluate the use of powerful chemometric approaches to differentiate their FT-IR spectra. FT-IR data sets were first subjected to principal component analysis (PCA), then discriminant function analysis (PC-DFA), with genetic algorithms (GAs) subsequently used to determine important discriminatory variables (wavenumbers) in the PC-DFA models. Whilst PCA of spectra was partially successful in grouping soils, PC-DFA discriminated undisturbed from reclaimed soils and differentiated between reclaimed soils of differing age. GA-DFA analyses identified wave numbers related to stretching of aromatic and aliphatic C–H bonds, and C–O or C–OH groups in glycopeptides or complex carbohydrates, as important discriminatory variables. GA-multiple linear regression (GA-MLR) analyses indicated that the recovery of disturbed soils may not be complete after 50 years. Chemometric analyses of FT-IR spectra offer a potentially efficient approach to screen for complex changes in soils and to indicate their nature. Additional work across a range of soils, comparing outputs from this approach with those from other widely used analyses, would further evaluate its effectiveness and aid in the interpretation of findings.

Context based mixture model for cell phase identification in automated fluorescence microscopy.

BackgroundAutomated identification of cell cycle phases of individual live cells in a large population captured via automated fluorescence microscopy technique is important for cancer drug discovery and cell cycle studies. Time-lapse fluorescence microscopy images provide an important method to study the cell cycle process under different conditions of perturbation. Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task.ResultsThe data is generated from Hela H2B GFP cells imaged during a 2-day period with images acquired 15 minutes apart using an automated time-lapse fluorescence microscopy. The patterns are described with four kinds of features, including twelve general features, Haralick texture features, Zernike moment features, and wavelet features. To generate a new set of features with more discriminate power, the commonly used feature reduction techniques are used, which include Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), Maximum Margin Criterion (MMC), Stepwise Discriminate Analysis based Feature Selection (SDAFS), and Genetic Algorithm based Feature Selection (GAFS). Then, we propose a Context Based Mixture Model (CBMM) for dealing with the time-series cell sequence information and compare it to other traditional classifiers: Support Vector Machine (SVM), Neural Network (NN), and K-Nearest Neighbor (KNN). Being a standard practice in machine learning, we systematically compare the performance of a number of common feature reduction techniques and classifiers to select an optimal combination of a feature reduction technique and a classifier. A cellular database containing 100 manually labelled subsequence is built for evaluating the performance of the classifiers. The generalization error is estimated using the cross validation technique. The experimental results show that CBMM outperforms all other classifies in identifying prophase and has the best overall performance.ConclusionThe application of feature reduction techniques can improve the prediction accuracy significantly. CBMM can effectively utilize the contextual information and has the best overall performance when combined with any of the previously mentioned feature reduction techniques.

Computer aided diagnosis based on medical image processing and artificial intelligence methods

Advances in imaging technology and computer science have greatly enhanced interpretation of medical images, and contributed to early diagnosis. The typical architecture of a Computer Aided Diagnosis (CAD) system includes image pre-processing, definition of region(s) of interest, features extraction and selection, and classification. In this paper, the principles of CAD systems design and development are demonstrated by means of two examples. The first one focuses on the differentiation between symptomatic and asymptomatic carotid atheromatous plaques. For each plaque, a vector of texture and motion features was estimated, which was then reduced to the most robust ones by means of ANalysis of VAriance (ANOVA). Using fuzzy c-means, the features were then clustered into two classes. Clustering performances of 74%, 79%, and 84% were achieved for texture only, motion only, and combinations of texture and motion features, respectively. The second CAD system presented in this paper supports the diagnosis of focal liver lesions and is able to characterize liver tissue from Computed Tomography (CT) images as normal, hepatic cyst, hemangioma, and hepatocellular carcinoma. Five texture feature sets were extracted for each lesion, while a genetic algorithm based feature selection method was applied to identify the most robust features. The selected feature set was fed into an ensemble of neural network classifiers. The achieved classification performance was 100%, 93.75% and 90.63% in the training, validation and testing set, respectively. It is concluded that computerized analysis of medical images in combination with artificial intelligence can be used in clinical practice and may contribute to more efficient diagnosis.

An Empirical Study of Univariate and Genetic Algorithm-Based Feature Selection in Binary Classification with Microarray Data

We consider both univariate- and multivariate-based feature selection for the problem of binary classification with microarray data. The idea is to determine whether the more sophisticated multivariate approach leads to better misclassification error rates because of the potential to consider jointly significant subsets of genes (but without overfitting the data). We present an empirical study in which 10-fold cross-validation is applied externally to both a univariate-based and two multivariate- (genetic algorithm (GA)-) based feature selection processes. These procedures are applied with respect to three supervised learning algorithms and six published two-class microarray datasets. Considering all datasets, and learning algorithms, the average 10-fold external cross-validation error rates for the univariate-, single-stage GA-, and two-stage GA-based processes are 14.2%, 14.6%, and 14.2%, respectively. We also find that the optimism bias estimates from the GA analyses were half that of the univariate approach, but the selection bias estimates from the GA analyses were 2.5 times that of the univariate results. We find that the 10-fold external cross-validation misclassification error rates were very comparable. Further, we find that a two-stage GA approach did not demonstrate a significant advantage over a 1-stage approach. We also find that the univariate approach had higher optimism bias and lower selection bias compared to both GA approaches.

Neural vs. statistical classifier in conjunction with genetic algorithm based feature selection

Digital mammography is one of the most suitable methods for early detection of breast cancer. It uses digital mammograms to find suspicious areas containing benign and malignant microcalcifications. However, it is very difficult to distinguish benign and malignant microcalcifications. This is reflected in the high percentage of unnecessary biopsies that are performed and many deaths caused by late detection or misdiagnosis. A computer based feature selection and classification system can provide a second opinion to the radiologists in assessment of microcalcifications. The research in this paper proposes and investigates a neural-genetic algorithm for feature selection in conjunction with neural and statistical classifiers to classify microcalcification patterns in digital mammograms. The obtained results show that the proposed approach is able to find an appropriate feature subset and neural classifier achieves better results than two statistical models.

Predicting Protein‐Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine‐Learning Methods.

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure−activity relationship (QSAR) approach is introduced for scoring protein−ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.

Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods.

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure-activity relationship (QSAR) approach is introduced for scoring protein-ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.

Genetic algorithm based feature selection for target detection in SAR images

A genetic algorithm (GA) approach is presented to select a set of features to discriminate the targets from the natural clutter false alarms in SAR images. Four stages of an automatic target detection system are developed: the rough target detection, feature extraction from the potential target regions, GA based feature selection and the final Bayesian classification. A new fitness function based on minimum description length principle (MDLP) is proposed to drive GA and it is compared with three other fitness functions. Experimental results show that the new fitness function outperforms the other three fitness functions and the GA driven by it selected a good subset of features to discriminate the targets from clutters effectively.

FAULT DETECTION USING SUPPORT VECTOR MACHINES AND ARTIFICIAL NEURAL NETWORKS, AUGMENTED BY GENETIC ALGORITHMS

Artificial neural networks (ANNs) have been used to detect faults in rotating machinery for a number of years, using statistical methods to preprocess the vibration signals as input features. ANNs have been shown to be highly successful in this type of application; in comparison, support vector machines (SVMs) are a more recent development, and little use has been made of them in the condition monitoring arena. The availability of a limited amount of training data creates certain problems for the use of SVMs, and a strategy is advanced to improve the generalisation performance in cases where only limited training data is available. This paper examines the performance of both types of classifiers in two-class fault/no-fault recognition examples and the attempts to improve the overall generalisation performance of both techniques through the use of genetic algorithm based feature selection process.

Neural Net Based Hybrid Modeling of the Methanol Synthesis Process

A Hybrid modeling approach, combining an analytical model with a radial basis function neural network is introduced in this paper. The modeling procedure is combined with genetic algorithm based feature selection designed to select informative variables from the set of available measurements. By only using informative inputs, the model's generalization ability can be enhanced. The approach proposed is applied to modeling of the liquid–phase methanol synthesis. It is shown that a hybrid modeling approach exploiting available a priori knowledge and experimental data can considerably outperform a purely analytical approach.

Multistrategic data mining in a clinical meningoencephalitis database

This project aims at inducing as much information as possible from clinical databases. Until now, the following six methods are applied to a clinical database (meningoencephalitis):1. association rule induction,2. decision trees with genetic algorithm based feature selection,3. decision tree induction with random sampling,4. rough set based rule induction,5. logit analysis6. linear discriminant analysis.Experimental results show that knowledge which medical experts did not expect was extracted by different methods. The research will be extended to other methods and databases.

Application of neural networks and genetic algorithms in the classification of endothelial cells

This paper deals with developing automatic classification algorithms for identifying images of F-actin distribution in endothelial cells with different treatment of drugs. A novel combination of genetic algorithm based feature selection, used to obtain an optimal feature set, and artificial neural network methods including the multilayer feedforward network and the functional link network was used in the classification.