W2V-repeated index: Prediction of enhancers and their strength based on repeated fragments.

Enhancers are crucial in gene expression regulation, dictating the specificity and timing of transcriptional activity, which highlights the importance of their identification for unravelling the intricacies of genetic regulation. Therefore, it is critical to identify enhancers and their strengths. Repeated sequences in the genome are repeats of the same or symmetrical fragments. There has been a great deal of evidence that repetitive sequences contain enormous amounts of genetic information. Thus, We introduce the W2V-Repeated Index, designed to identify enhancer sequence fragments and evaluates their strength through the analysis of repeated K-mer sequences in enhancer regions. Utilizing the word2vector algorithm for numerical conversion and Manta Ray Foraging Optimization for feature selection, this method effectively captures the frequency and distribution of K-mer sequences. By concentrating on repeated K-mer sequences, it minimizes computational complexity and facilitates the analysis of larger K values. Experiments indicate that our method performs better than all other advanced methods on almost all indicators.

Diagnosis of Obstructive Sleep Apnea Using Feature Selection, Classification Methods, and Data Grouping Based Age, Sex, and Race.

Obstructive sleep apnea (OSA) is a prevalent sleep disorder that affects approximately 3-7% of males and 2-5% of females. In the United States alone, 50-70 million adults suffer from various sleep disorders. OSA is characterized by recurrent episodes of breathing cessation during sleep, thereby leading to adverse effects such as daytime sleepiness, cognitive impairment, and reduced concentration. It also contributes to an increased risk of cardiovascular conditions and adversely impacts patient overall quality of life. As a result, numerous researchers have focused on developing automated detection models to identify OSA and address these limitations effectively and accurately. This study explored the potential benefits of utilizing machine learning methods based on demographic information for diagnosing the OSA syndrome. We gathered a comprehensive dataset from the Torr Sleep Center in Corpus Christi, Texas, USA. The dataset comprises 31 features, including demographic characteristics such as race, age, sex, BMI, Epworth score, M. Friedman tongue position, snoring, and more. We devised a novel process encompassing pre-processing, data grouping, feature selection, and machine learning classification methods to achieve the research objectives. The classification methods employed in this study encompass decision tree (DT), naive Bayes (NB), k-nearest neighbor (kNN), support vector machine (SVM), linear discriminant analysis (LDA), logistic regression (LR), and subspace discriminant (Ensemble) classifiers. Through rigorous experimentation, the results indicated the superior performance of the optimized kNN and SVM classifiers for accurately classifying sleep apnea. Moreover, significant enhancements in model accuracy were observed when utilizing the selected demographic variables and employing data grouping techniques. For instance, the accuracy percentage demonstrated an approximate improvement of 4.5%, 5%, and 10% with the feature selection approach when applied to the grouped data of Caucasians, females, and individuals aged 50 or below, respectively. Furthermore, a comparison with prior studies confirmed that effective data grouping and proper feature selection yielded superior performance in OSA detection when combined with an appropriate classification method. Overall, the findings of this research highlight the importance of leveraging demographic information, employing proper feature selection techniques, and utilizing optimized classification models for accurate and efficient OSA diagnosis.

Classification framework for faulty-software using enhanced exploratory whale optimizer-based feature selection scheme and random forest ensemble learning.

Software Fault Prediction (SFP) is an important process to detect the faulty components of the software to detect faulty classes or faulty modules early in the software development life cycle. In this paper, a machine learning framework is proposed for SFP. Initially, pre-processing and re-sampling techniques are applied to make the SFP datasets ready to be used by ML techniques. Thereafter seven classifiers are compared, namely K-Nearest Neighbors (KNN), Naive Bayes (NB), Linear Discriminant Analysis (LDA), Linear Regression (LR), Decision Tree (DT), Support Vector Machine (SVM), and Random Forest (RF). The RF classifier outperforms all other classifiers in terms of eliminating irrelevant/redundant features. The performance of RF is improved further using a dimensionality reduction method called binary whale optimization algorithm (BWOA) to eliminate the irrelevant/redundant features. Finally, the performance of BWOA is enhanced by hybridizing the exploration strategies of the grey wolf optimizer (GWO) and harris hawks optimization (HHO) algorithms. The proposed method is called SBEWOA. The SFP datasets utilized are selected from the PROMISE repository using sixteen datasets for software projects with different sizes and complexity. The comparative evaluation against nine well-established feature selection methods proves that the proposed SBEWOA is able to significantly produce competitively superior results for several instances of the evaluated dataset. The algorithms' performance is compared in terms of accuracy, the number of features, and fitness function. This is also proved by the 2-tailed P-values of the Wilcoxon signed ranks statistical test used. In conclusion, the proposed method is an efficient alternative ML method for SFP that can be used for similar problems in the software engineering domain.

Recognizing seizure using Poincaré plot of EEG signals and graphical features in DWT domain.

Electroencephalography (EEG) signals are considered one of the oldest techniques for detecting disorders in medical signal processing. However, brain complexity and the non-stationary nature of EEG signals represent a challenge when applying this technique. The current paper proposes new geometrical features for classification of seizure (S) and seizure-free (SF) EEG signals with respect to the Poincaré pattern of discrete wavelet transform (DWT) coefficients. DWT decomposes EEG signal to four levels, and thus Poincaré plot is shown for coefficients. Due to patterns of the Poincaré plot, novel geometrical features are computed from EEG signals. The computed features are involved in standard descriptors of 2­D projection (STD), summation of triangle area using consecutive points (STA), as well as summation of shortest distance from each point relative to the 45-degree line (SSHD), and summation of distance from each point relative to the coordinate center (SDTC). The proposed procedure leads to discriminate features between S and SF EEG signals. Thereafter, a binary particle swarm optimization (BPSO) is developed as an appropriate technique for feature selection. Finally, k-nearest neighbor (KNN) and support vector machine (SVM) classifiers are used for classifying features in S and SF groups. By developing the proposed method, we have archived classification accuracy of 99.3 % with respect to the proposed geometrical features. Accordingly, S and SF EEG signals have been classified. Also, Poincaré plot of SF EEG signals has more regular geometrical shapes as compared to S group. As a final remark, we notice that the Poincaré plot of coefficients in S EEG signals has occupied more space as compared to SF EEG signals (Tab. 3, Fig. 11, Ref. 57). Text in PDF www.elis.sk Keywords: EEG signal, DWT, Poincaré plot, geometrical feature, BPSO, SVM, KNN.

Exploiting Feature Selection and Neural Network Techniques for Identification of Focal and Nonfocal EEG Signals in TQWT Domain.

For drug resistance patients, removal of a portion of the brain as a cause of epileptic seizures is a surgical remedy. However, before surgery, the detailed analysis of the epilepsy localization area is an essential and logical step. The Electroencephalogram (EEG) signals from these areas are distinct and are referred to as focal, while the EEG signals from other normal areas are known as nonfocal. The visual inspection of multiple channels for detecting the focal EEG signal is time-consuming and prone to human error. To address this challenge, we propose a novel method based on differential operator and Tunable Q-factor wavelet transform (TQWT) to distinguish the focal and nonfocal signals. For this purpose, first, the EEG signal was differenced and then decomposed by TQWT. Second, several entropy-based features were derived from the TQWT subbands. Third, the efficacy of the six binary feature selection algorithms, binary bat algorithm (BBA), binary differential evolution (BDE) algorithm, firefly algorithm (FA), genetic algorithm (GA), grey wolf optimization (GWO), and particle swarm optimization (PSO), was evaluated. In the end, the selected features were fed to several machine learning and neural network classifiers. We observed that the PSO with neural networks provides an effective solution for the application of focal EEG signal detection. The proposed framework resulted in an average classification accuracy of 97.68%, a sensitivity of 97.26%, and a specificity of 98.11% in a tenfold cross-validation strategy, which is higher than the state of the art used in the public Bern-Barcelona EEG database.

Feature Selection of OMIC Data by Ensemble Swarm Intelligence Based Approaches.

OMIC datasets have high dimensions, and the connection among OMIC features is very complicated. It is difficult to establish linkages among these features and certain biological traits of significance. The proposed ensemble swarm intelligence-based approaches can identify key biomarkers and reduce feature dimension efficiently. It is an end-to-end method that only relies on the rules of the algorithm itself, without presets such as the number of filtering features. Additionally, this method achieves good classification accuracy without excessive consumption of computing resources.