A hybrid feature weighted attention based deep learning approach for an intrusion detection system using the random forest algorithm.

Due to the recent advances in the Internet and communication technologies, network systems and data have evolved rapidly. The emergence of new attacks jeopardizes network security and make it really challenging to detect intrusions. Multiple network attacks by an intruder are unavoidable. Our research targets the critical issue of class imbalance in intrusion detection, a reflection of the real-world scenario where legitimate network activities significantly out number malicious ones. This imbalance can adversely affect the learning process of predictive models, often resulting in high false-negative rates, a major concern in Intrusion Detection Systems (IDS). By focusing on datasets with this imbalance, we aim to develop and refine advanced algorithms and techniques, such as anomaly detection, cost-sensitive learning, and oversampling methods, to effectively handle such disparities. The primary goal is to create models that are highly sensitive to intrusions while minimizing false alarms, an essential aspect of effective IDS. This approach is not only practical for real-world applications but also enhances the theoretical understanding of managing class imbalance in machine learning. Our research, by addressing these significant challenges, is positioned to make substantial contributions to cybersecurity, providing valuable insights and applicable solutions in the fight against digital threats and ensuring robustness and relevance in IDS development. An intrusion detection system (IDS) checks network traffic for security, availability, and being non-shared. Despite the efforts of many researchers, contemporary IDSs still need to further improve detection accuracy, reduce false alarms, and detect new intrusions. The mean convolutional layer (MCL), feature-weighted attention (FWA) learning, a bidirectional long short-term memory (BILSTM) network, and the random forest algorithm are all parts of our unique hybrid model called MCL-FWA-BILSTM. The CNN-MCL layer for feature extraction receives data after preprocessing. After convolution, pooling, and flattening phases, feature vectors are obtained. The BI-LSTM and self-attention feature weights are used in the suggested method to mitigate the effects of class imbalance. The attention layer and the BI-LSTM features are concatenated to create mapped features before feeding them to the random forest algorithm for classification. Our methodology and model performance were validated using NSL-KDD and UNSW-NB-15, two widely available IDS datasets. The suggested model's accuracies on binary and multi-class classification tasks using the NSL-KDD dataset are 99.67% and 99.88%, respectively. The model's binary and multi-class classification accuracies on the UNSW-NB15 dataset are 99.56% and 99.45%, respectively. Further, we compared the suggested approach with other previous machine learning and deep learning models and found it to outperform them in detection rate, FPR, and F-score. For both binary and multiclass classifications, the proposed method reduces false positives while increasing the number of true positives. The model proficiently identifies diverse network intrusions on computer networks and accomplishes its intended purpose. The suggested model will be helpful in a variety of network security research fields and applications.

Analysis of Parkinson's Disease Using an Imbalanced-Speech Dataset by Employing Decision Tree Ensemble Methods.

Parkinson's disease (PD) currently affects approximately 10 million people worldwide. The detection of PD positive subjects is vital in terms of disease prognostics, diagnostics, management and treatment. Different types of early symptoms, such as speech impairment and changes in writing, are associated with Parkinson disease. To classify potential patients of PD, many researchers used machine learning algorithms in various datasets related to this disease. In our research, we study the dataset of the PD vocal impairment feature, which is an imbalanced dataset. We propose comparative performance evaluation using various decision tree ensemble methods, with or without oversampling techniques. In addition, we compare the performance of classifiers with different sizes of ensembles and various ratios of the minority class and the majority class with oversampling and undersampling. Finally, we combine feature selection with best-performing ensemble classifiers. The result shows that AdaBoost, random forest, and decision tree developed for the RUSBoost imbalanced dataset perform well in performance metrics such as precision, recall, F1-score, area under the receiver operating characteristic curve (AUROC) and the geometric mean. Further, feature selection methods, namely lasso and information gain, were used to screen the 10 best features using the best ensemble classifiers. AdaBoost with information gain feature selection method is the best performing ensemble method with an F1-score of 0.903.

DBP-iDWT: Improving DNA-Binding Proteins Prediction Using Multi-Perspective Evolutionary Profile and Discrete Wavelet Transform.

DNA-binding proteins (DBPs) have crucial biotic activities including DNA replication, recombination, and transcription. DBPs are highly concerned with chronic diseases and are used in the manufacturing of antibiotics and steroids. A series of predictors were established to identify DBPs. However, researchers are still working to further enhance the identification of DBPs. This research designed a novel predictor to identify DBPs more accurately. The features from the sequences are transformed by F-PSSM (Filtered position-specific scoring matrix), PSSM-DPC (Position specific scoring matrix-dipeptide composition), and R-PSSM (Reduced position-specific scoring matrix). To eliminate the noisy attributes, we extended DWT (discrete wavelet transform) to F-PSSM, PSSM-DPC, and R-PSSM and introduced three novel descriptors, namely, F-PSSM-DWT, PSSM-DPC-DWT, and R-PSSM-DWT. Onward, the training of the four models were performed using LiXGB (Light eXtreme gradient boosting), XGB (eXtreme gradient boosting, ERT (extremely randomized trees), and Adaboost. LiXGB with R-PSSM-DWT has attained 6.55% higher accuracy on training and 5.93% on testing dataset than the best existing predictors. The results reveal the excellent performance of our novel predictor over the past studies. DBP-iDWT would be fruitful for establishing more operative therapeutic strategies for fatal disease treatment.

DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features.

In the domain of genome annotation, the identification of DNA-binding protein is one of the crucial challenges. DNA is considered a blueprint for the cell. It contained all necessary information for building and maintaining the trait of an organism. It is DNA, which makes a living thing, a living thing. Protein interaction with DNA performs an essential role in regulating DNA functions such as DNA repair, transcription, and regulation. Identification of these proteins is a crucial task for understanding the regulation of genes. Several methods have been developed to identify the binding sites of DNA and protein depending upon the structures and sequences, but they were costly and time-consuming. Therefore, we propose a methodology named "DNAPred_Prot", which uses various position and frequency-dependent features from protein sequences for efficient and effective prediction of DNA-binding proteins. Using testing techniques like 10-fold cross-validation and jackknife testing an accuracy of 94.95% and 95.11% was yielded, respectively. The results of SVM and ANN were also compared with those of a random forest classifier. The robustness of the proposed model was evaluated by using the independent dataset PDB186, and an accuracy of 91.47% was achieved by it. From these results, it can be predicted that the suggested methodology performs better than other extant methods for the identification of DNA-binding proteins.

iAcety-SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest.

Acetylation is the most important post-translation modification (PTM) in eukaryotes; it has manifold effects on the level of protein that transform an acetyl group from an acetyl coenzyme to a specific site on a polypeptide chain. Acetylation sites play many important roles, including regulating membrane protein functions and strongly affecting the membrane interaction of proteins and membrane remodeling. Because of these properties, its correct identification is essential to understand its mechanism in biological systems. As such, some traditional methods, such as mass spectrometry and site-directed mutagenesis, are used, but they are tedious and time-consuming. To overcome such limitations, many computer models are being developed to correctly identify their sequences from non-acetyl sequences, but they have poor efficiency in terms of accuracy, sensitivity, and specificity. This work proposes an efficient and accurate computational model for predicting Acetylation using machine learning approaches. The proposed model achieved an accuracy of 100 percent with the 10-fold cross-validation test based on the Random Forest classifier, along with a feature extraction approach using statistical moments. The model is also validated by the jackknife, self-consistency, and independent test, which achieved an accuracy of 100, 100, and 97, respectively, results far better as compared to the already existing models available in the literature.

DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning.

DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver cancer) and chronic diseases (i.e. AIDS/HIV, asthma), while other kinds are involved in antibiotics, steroids, and anti-inflammatory drugs designing. These crucial processes are closely related to DBPs types. DBPs are categorized into single-stranded DNA-binding proteins (ssDBPs) and double-stranded DNA-binding proteins (dsDBPs). Few computational predictors have been reported for discriminating ssDBPs and dsDBPs. However, due to the limitations of the existing methods, an intelligent computational system is still highly desirable. In this work, features from protein sequences are discovered by extending the notion of dipeptide composition (DPC), evolutionary difference formula (EDF), and K-separated bigram (KSB) into the position-specific scoring matrix (PSSM). The highly intrinsic information was encoded by a compression approach named discrete cosine transform (DCT) and the model was trained with support vector machine (SVM). The prediction performance was further boosted by the genetic algorithm (GA) ensemble strategy. The novel predictor (DBP-GAPred) acquired 1.89%, 0.28%, and 6.63% higher accuracies on jackknife, 10-fold, and independent dataset tests, respectively than the best predictor. These outcomes confirm the superiority of our method over the existing predictors.

The Number of Confirmed Cases of Covid-19 by using Machine Learning: Methods and Challenges.

Covid-19 is one of the biggest health challenges that the world has ever faced. Public health policy makers need the reliable prediction of the confirmed cases in future to plan medical facilities. Machine learning methods learn from the historical data and make predictions about the events. Machine learning methods have been used to predict the number of confirmed cases of Covid-19. In this paper, we present a detailed review of these research papers. We present a taxonomy that groups them in four categories. We further present the challenges in this field. We provide suggestions to the machine learning practitioners to improve the performance of machine learning methods for the prediction of confirmed cases of Covid-19.

iHyd-PseAAC (EPSV): Identifying Hydroxylation Sites in Proteins by Extracting Enhanced Position and Sequence Variant Feature via Chou's 5-Step Rule and General Pseudo Amino Acid Composition.

BACKGROUND: In various biological processes and cell functions, Post Translational Modifications (PTMs) bear critical significance. Hydroxylation of proline residue is one kind of PTM, which occurs following protein synthesis. The experimental determination of hydroxyproline sites in an uncharacterized protein sequence requires extensive, time-consuming and expensive tests. METHODS: With the torrential slide of protein sequences produced in the post-genomic age, certain remarkable computational strategies are desired to overwhelm the issue. Keeping in view the composition and sequence order effect within polypeptide chains, an innovative in-silico> predictor via a mathematical model is proposed. RESULTS: Later, it was stringently verified using self-consistency, cross-validation and jackknife tests on benchmark datasets. It was established after a rigorous jackknife test that the new predictor values are superior to the values predicted by previous methodologies. CONCLUSION: This new mathematical technique is the most appropriate and encouraging as compared with the existing models.

iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou's 5-steps Rule and Pseudo Components.

BACKGROUND: The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological pro-cesses. Thus its identification is necessary to understand its mechanism. Experimental determination through site-directed mutagenesis and high throughput mass spectrometry is a costly and time taking process, thus, the reliable computational model is required for identification of sulfotyrosine sites. METHODOLOGY: In this paper, we present a computational model for the prediction of the sulfotyrosine sites named iSulfoTyr-PseAAC in which feature vectors are constructed using statistical moments of protein amino acid sequences and various position/composition relative features. These features are in-corporated into PseAAC. The model is validated by jackknife, cross-validation, self-consistency and in-dependent testing. RESULTS: Accuracy determined through validation was 93.93% for jackknife test, 95.16% for cross-validation, 94.3% for self-consistency and 94.3% for independent testing. CONCLUSION: The proposed model has better performance as compared to the existing predictors, how-ever, the accuracy can be improved further, in future, due to increasing number of sulfotyrosine sites in proteins.