A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots

This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms

Software defect prediction: do different classifiers find the same defects?

Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.During the last 10 years, hundreds of different defect prediction models have been published. The performance of the classifiers used in these models is reported to be similar with models rarely performing above the predictive performance ceiling of about 80% recall. We investigate the individual defects that four classifiers predict and analyse the level of prediction uncertainty produced by these classifiers. We perform a sensitivity analysis to compare the performance of Random Forest, Naïve Bayes, RPart and SVM classifiers when predicting defects in NASA, open source and commercial datasets. The defect predictions that each classifier makes is captured in a confusion matrix and the prediction uncertainty of each classifier is compared. Despite similar predictive performance values for these four classifiers, each detects different sets of defects. Some classifiers are more consistent in predicting defects than others. Our results confirm that a unique subset of defects can be detected by specific classifiers. However, while some classifiers are consistent in the predictions they make, other classifiers vary in their predictions. Given our results, we conclude that classifier ensembles with decision-making strategies not based on majority voting are likely to perform best in defect prediction.Peer reviewedFinal Published versio

Methods for Amharic part-of-speech tagging

The paper describes a set of experiments involving the application of three state-of- the-art part-of-speech taggers to Ethiopian Amharic, using three different tagsets. The taggers showed worse performance than previously reported results for Eng- lish, in particular having problems with unknown words. The best results were obtained using a Maximum Entropy ap- proach, while HMM-based and SVM- based taggers got comparable results

Enhanced Ensemble Fusion Model for Stress Classification and Prediction

Stress has become a common phenomenon in modern society, and it has been identified as a major factor that affects people's health and well-being. Stress can be caused by various factors, such as work pressure, financial difficulties, relationship problems, and health issues. Prolonged exposure to stress can lead to physical and mental health problems, including anxiety, depression, cardiovascular diseases, and obesity. Accurate stress classification and prediction can help individuals and organizations identify the sources and levels of stress and take appropriate measures to manage stress and prevent negative outcomes. By identifying individuals who are at risk of stress, proactive interventions can be initiated to prevent negative outcomes. Additionally, stress classification and prediction can be useful for designing effective stress management programs and policies that can improve the well-being and productivity of individuals and organizations. Existing systems for stress classification and prediction have limitations in terms of accuracy and efficiency. To overcome these limitations, this paper proposes an Enhanced Ensemble Fusion (EEF) model that combines three ensemble classifiers, namely stacking, bagging, and boosting, using a blending classifier. The EEF model is composed of several classifiers, including the stacking classifier, the bagging classifier, and the boosting classifier, each using an Enhanced J48, Enhanced SVM, and Enhanced Naive Bayes classifier. An Enhanced Logistic Regression classifier is used as a meta-classifier for the stacking classifier. The model was evaluated on a Swell-EDA dataset and WESAD-EDA dataset, and the results show that it outperformed existing systems in terms of accuracy and robustness. The Enhanced Ensemble Fusion Model achieved an accuracy of 72.86% for WESAD-EDA dataset and 50% for Swell-EDA dataset which is significantly higher than the accuracy of individual classifiers and existing ensemble methods. The proposed model provides a promising approach for stress classification and prediction, which can be useful in various applications, such as healthcare, human resources, and education

The Diamond STING server

Diamond STING is a new version of the STING suite of programs for a comprehensive analysis of a relationship between protein sequence, structure, function and stability. We have added a number of new functionalities by both providing more structure parameters to the STING Database and by improving/expanding the interface for enhanced data handling. The integration among the STING components has also been improved. A new key feature is the ability of the STING server to handle local files containing protein structures (either modeled or not yet deposited to the Protein Data Bank) so that they can be used by the principal STING components: (Java)Protein Dossier ((J)PD) and STING Report. The current capabilities of the new STING version and a couple of biologically relevant applications are described here. We have provided an example where Diamond STING identifies the active site amino acids and folding essential amino acids (both previously determined by experiments) by filtering out all but those residues by selecting the numerical values/ranges for a set of corresponding parameters. This is the fundamental step toward a more interesting endeavor—the prediction of such residues. Diamond STING is freely accessible at and

Intrusion detection by machine learning = Behatolás detektálás gépi tanulás által

Since the early days of information technology, there have been many stakeholders who used the technological capabilities for their own benefit, be it legal operations, or illegal access to computational assets and sensitive information. Every year, businesses invest large amounts of effort into upgrading their IT infrastructure, yet, even today, they are unprepared to protect their most valuable assets: data and knowledge. This lack of protection was the main reason for the creation of this dissertation. During this study, intrusion detection, a field of information security, is evaluated through the use of several machine learning models performing signature and hybrid detection. This is a challenging field, mainly due to the high velocity and imbalanced nature of network traffic. To construct machine learning models capable of intrusion detection, the applied methodologies were the CRISP-DM process model designed to help data scientists with the planning, creation and integration of machine learning models into a business information infrastructure, and design science research interested in answering research questions with information technology artefacts. The two methodologies have a lot in common, which is further elaborated in the study. The goals of this dissertation were two-fold: first, to create an intrusion detector that could provide a high level of intrusion detection performance measured using accuracy and recall and second, to identify potential techniques that can increase intrusion detection performance. Out of the designed models, a hybrid autoencoder + stacking neural network model managed to achieve detection performance comparable to the best models that appeared in the related literature, with good detections on minority classes. To achieve this result, the techniques identified were synthetic sampling, advanced hyperparameter optimization, model ensembles and autoencoder networks. In addition, the dissertation set up a soft hierarchy among the different detection techniques in terms of performance and provides a brief outlook on potential future practical applications of network intrusion detection models as well