Conventional Machine Learning Classifiers Research Articles

NaII-Pred: An ensemble-learning framework for the identification and interpretation of sodium ion inhibitors by fusing multiple feature representation

High-affinity ligand peptides for ion channels are essential for controlling the flow of ions across the plasma membrane. These peptides are now being investigated as possible therapeutic possibilities for a variety of illnesses, including cancer and cardiovascular disease. So, the identification and interpretation of ligand peptide inhibitors to control ion flow across cells become pivotal for exploration. In this work, we developed an ensemble-based model, NaII-Pred, for the identification of sodium ion inhibitors. The ensemble model was trained, tested, and evaluated on three different datasets. The NaII-Pred method employs six different descriptors and a hybrid feature set in conjunction with five conventional machine learning classifiers to create 35 baseline models. Through an ensemble approach, the top five baseline models trained on the hybrid feature set were integrated to yield the final predictive model, NaII-Pred. Our proposed model, NaII-Pred, outperforms the baseline models and the current predictors on both datasets. We believe NaII-Pred will play a critical role in screening and identifying potential sodium ion inhibitors and will be an invaluable tool.

Independent Video Steganalysis Framework Perspective of Secure Video Processing

We have designed an algorithm of cross-domain feature set extraction for cross-domain video steganalysis of video steganography in multiple domains. For video steganography, we implemented the recently proposed steganography methods such as PMs, MVs, and IPMs. The outcomes of these techniques have fed as input to the proposed Steganalysis approach. We have designed a cross-domain technique for Steganalysis in which the global feature set is extracted according to common statistical properties. After the extraction of global features, the domain-specific features have been extracted in the local features set. Both global and local features are set to form the cross-domain steganalysis technique. The classification has been performed by using the conventional machine learning classifiers such as Support Vector Machine (SVM) and Artificial Neural Network (ANN).

Using Ensemble Learning for Anomaly Detection in Cyber–Physical Systems

The swift embrace of Industry 4.0 paradigms has led to the growing convergence of Information Technology (IT) networks and Operational Technology (OT) networks. Traditionally isolated on air-gapped and fully trusted networks, OT networks are now becoming more interconnected with IT networks due to the advancement and applications of IoT. This expanded attack surface has led to vulnerabilities in Cyber–Physical Systems (CPSs), resulting in increasingly frequent compromises with substantial economic and life safety repercussions. The existing methods for the anomaly detection of security threats typically use simple threshold-based strategies or apply Machine Learning (ML) algorithms to historical data for the prediction of future anomalies. However, due to the high levels of heterogeneity across different CPS environments, minimizing the opportunities for transfer learning, and the scarcity of real-world data for training, the existing ML-based anomaly detection techniques suffer from a poor predictive performance. This paper introduces a hybrid anomaly detection approach designed to identify threats to CPSs by combining the signature-based anomaly detection typically utilized in IT networks, the threshold-based anomaly detection typically utilized in OT networks, and behavioural-based anomaly detection using Ensemble Learning (EL), which leverages the strengths of multiple ML algorithms against the same dataset to increase the accuracy. Multiple public research datasets were used to validate the proposed approach, with the hybrid methodology employing a divide-and-conquer strategy to offload the detection of certain cyber threats to computationally inexpensive signature-based and threshold-based methods using domain knowledge to minimize the size of the behavioural-based data needed for ML model training, thus achieving a higher accuracy over a reduced timeframe. The experimental results showed accuracy improvements of 4–7% over those of the conventional ML classifiers in performing anomaly detection across multiple datasets, which is particularly important to the operators of CPS environments due to the high financial and life safety costs associated with interruptions to system availability.

Real-time classification of tumour and non-tumour tissue in colorectal cancer using diffuse reflectance spectroscopy and neural networks to aid margin assessment.

Colorectal cancer is the third most commonly diagnosed malignancy and the second leading cause of mortality worldwide. A positive resection margin following surgery for colorectal cancer is linked with higher rates of local recurrence and poorer survival. We investigated diffuse reflectance spectroscopy (DRS) to distinguish tumour and non-tumour tissue in ex vivo colorectal specimens, to aid margin assessment and provide augmented visual maps to the surgeon in real-time. Patients undergoing elective colorectal cancer resection surgery at a London-based hospital were prospectively recruited. A hand-held DRS probe was used on the surface of freshly resected ex vivo colorectal tissue. Spectral data was acquired for tumour and non-tumour tissue. Binary classification was achieved using conventional machine learning classifiers and a convolutional neural network (CNN), which were evaluated in terms of sensitivity, specificity, accuracy and the area under the curve. A total of 7692 mean spectra were obtained for tumour and non-tumour colorectal tissue. The CNN-based classifier was the best performing machine learning algorithm, when compared to contrastive approaches, for differentiating tumour and non-tumour colorectal tissue, with an overall diagnostic accuracy of 90.8% and area under the curve of 96.8%. Live on-screen classification of tissue type was achieved using a graduated colourmap. A high diagnostic accuracy for a DRS probe and tracking system to differentiate ex vivo tumour and non-tumour colorectal tissue in real-time with on-screen visual feedback was highlighted by this study. Further in vivo studies are needed to ensure integration into a surgical workflow.

An integrative machine learning model for the identification of tumor T-cell antigens

The escalating global incidence of cancer poses significant health challenges, underscoring the need for innovative and more efficacious treatments. Cancer immunotherapy, a promising approach leveraging the body’s immune system against cancer, emerges as a compelling solution. Consequently, the identification and characterization of tumor T-cell antigens (TTCAs) have become pivotal for exploration. In this manuscript, we introduce TTCA-IF, an integrative machine learning-based framework designed for TTCAs identification. TTCA-IF employs ten feature encoding types in conjunction with five conventional machine learning classifiers. To establish a robust foundation, these classifiers are trained, resulting in the creation of 150 baseline models. The outputs from these baseline models are then fed back into the five classifiers, generating their respective meta-models. Through an ensemble approach, the five meta-models are seamlessly integrated to yield the final predictive model, the TTCA-IF model. Our proposed model, TTCA-IF, surpasses both baseline models and existing predictors in performance. In a comparative analysis involving nine novel peptide sequences, TTCA-IF demonstrated exceptional accuracy by correctly identifying 8 out of 9 peptides as TTCAs. As a tool for screening and pinpointing potential TTCAs, we anticipate TTCA-IF to be invaluable in advancing cancer immunotherapy.

Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features

DNA-binding proteins (DBPs) play a significant role in all phases of genetic processes, including DNA recombination, repair, and modification. They are often utilized in drug discovery as fundamental elements of steroids, antibiotics, and anticancer drugs. Predicting them poses the most challenging task in proteomics research. Conventional experimental methods for DBP identification are costly and sometimes biased toward prediction. Therefore, developing powerful computational methods that can accurately and rapidly identify DBPs from sequence information is an urgent need. In this study, we propose a novel deep learning-based method called Deep-WET to accurately identify DBPs from primary sequence information. In Deep-WET, we employed three powerful feature encoding schemes containing Global Vectors, Word2Vec, and fastText to encode the protein sequence. Subsequently, these three features were sequentially combined and weighted using the weights obtained from the elements learned through the differential evolution (DE) algorithm. To enhance the predictive performance of Deep-WET, we applied the SHapley Additive exPlanations approach to remove irrelevant features. Finally, the optimal feature subset was input into convolutional neural networks to construct the Deep-WET predictor. Both cross-validation and independent tests indicated that Deep-WET achieved superior predictive performance compared to conventional machine learning classifiers. In addition, in extensive independent test, Deep-WET was effective and outperformed than several state-of-the-art methods for DBP prediction, with accuracy of 78.08%, MCC of 0.559, and AUC of 0.805. This superior performance shows that Deep-WET has a tremendous predictive capacity to predict DBPs. The web server of Deep-WET and curated datasets in this study are available at https://deepwet-dna.monarcatechnical.com/. The proposed Deep-WET is anticipated to serve the community-wide effort for large-scale identification of potential DBPs.

AttentiveSkin: To Predict Skin Corrosion/Irritation Potentials of Chemicals via Explainable Machine Learning Methods.

Skin Corrosion/Irritation (Corr./Irrit.) has long been a health hazard in the Globally Harmonized System (GHS). Several in silico models have been built to predict Skin Corr./Irrit. as an alternative to the increasingly restricted animal testing. However, current studies are limited by data amount/quality and model availability. To address these issues, we compiled a traceable consensus GHS data set comprising 731 Corr., 1283 Irrit., and 1205 negative (Neg.) samples from 6 governmental databases and 2 external data sets. Then, a series of binary classifiers were developed with five machine learning (ML) algorithms and six molecular representations. For 10-fold cross-validation, the best Corr. vs Neg. classifier achieved an Area Under the Receiver Operating Characteristic Curve (AUC) of 97.1%, while the best Irrit. vs Neg. classifier achieved an AUC of 84.7%. Compared with existing in silico tools on external validation, our Attentive FP classifiers showed the highest metrics on Corr. vs Neg. and the second highest accuracy on Irrit. vs Neg. The SHapley Additive exPlanation approach was further applied to figure out important molecular features, and the attention weights were visualized to perform interpretable prediction. Structural alerts associated with Skin Corr./Irrit. were also identified. The interpretable Attentive FP classifiers were integrated into the software AttentiveSkin at https://github.com/BeeBeeWong/AttentiveSkin. The conventional ML classifiers are also provided on our platform admetSAR at http://lmmd.ecust.edu.cn/admetsar2/. Considering the data deficiency and the limited model availability of Skin Corr./Irrit., we believe that our data set and models could facilitate chemical safety assessment and relevant studies.

StackER: a novel SMILES-based stacked approach for the accelerated and efficient discovery of ERα and ERβ antagonists

The role of estrogen receptors (ERs) in breast cancer is of great importance in both clinical practice and scientific exploration. However, around 15–30% of those affected do not see benefits from the usual treatments owing to the innate resistance mechanisms, while 30–40% will gain resistance through treatments. In order to address this problem and facilitate community-wide efforts, machine learning (ML)-based approaches are considered one of the most cost-effective and large-scale identification methods. Herein, we propose a new SMILES-based stacked approach, termed StackER, for the accelerated and efficient identification of ERα and ERβ inhibitors. In StackER, we first established an up-to-date dataset consisting of 1,996 and 1,207 compounds for ERα and ERβ, respectively. Using the up-to-date dataset, StackER explored a wide range of different SMILES-based feature descriptors and ML algorithms in order to generate probabilistic features (PFs). Finally, the selected PFs derived from the two-step feature selection strategy were used for the development of an efficient stacked model. Both cross-validation and independent tests showed that StackER surpassed several conventional ML classifiers and the existing method in precisely predicting ERα and ERβ inhibitors. Remarkably, StackER achieved MCC values of 0.829–0.847 and 0.712–0.786 in terms of the cross-validation and independent tests, respectively, which were 5.92–8.29 and 1.59–3.45% higher than the existing method. In addition, StackER was applied to determine useful features for being ERα and ERβ inhibitors and identify FDA-approved drugs as potential ERα inhibitors in efforts to facilitate drug repurposing. This innovative stacked method is anticipated to facilitate community-wide efforts in efficiently narrowing down ER inhibitor screening.

Strength of ensemble learning in automatic sleep stages classification using single-channel EEG and ECG signals.

Healthy sleep plays an essential role in human daily life. Classification of sleep stages is a crucial tool for assisting physicians in diagnosing and treating sleep disorders. In this study, a strong ensemble learning model is proposed to enhance the ability of classification models in accurate sleep staging, particularly in multi-class classification. We asserted that high-accuracy sleep classification is achievable using only single-channel electroencephalogram (EEG) and electrocardiogram (ECG) by combining their best-extractable features in the time and frequency domains we recommended. More importantly, the superiority of the recommended method, which is the simultaneous use of stacking and bagging, over conventional machine learning classifiers in sleep staging was demonstrated, using the MIT-BIH Polysomnographic and Sleep-EDF expanded databases. Finally, K-fold cross-validation was used to fairly estimate these models. The best mean test accuracy rates for distinguishing between two classes of "sleep vs. wake," "rapid vs. non-rapid eye movement," and "deep vs. light sleep," were obtained 99.93%, 99.64%, and 99.69%, respectively. Furthermore, our proposed method achieved accuracies of 97.14%, 95.18%, 92.7%, and 85.64% for separating three, four, five, and six sleep classes, respectively. Compared to recent studies, our method outperforms other sleep stage classification schemes, especially in multi-class staging.

A Deep Survey on Human Activity Recognition Using Mobile and Wearable Sensors

Activity-based wellness management is thought to be a powerful application for mobile health. It is possible to provide context-aware wellness services and track human activity thanks to accessing for multiple devices as well as gadgets that we use every day. Generally in smart gadgets like phones, watches, rings etc., the embedded sensors having a wealth data that can be incorporated to person task tracking identification. In a real-world setting, all researchers shown effective boosting algorithms can extract information in person task identification. Identifying basic person tasks such as talk, walk, sit along sleep. Our findings demonstrate that boosting classifiers perform better than conventional machine learning classifiers. Moreover, the feature engineering for differentiating an activity detection capability for smart phones and smart watches. For the purpose of improving the classification of fundamental human activities, upcoming mechanisms give the guidelines for identification for various sensors and wearable devices.

IF-AIP: A machine learning method for the identification of anti-inflammatory peptides using multi-feature fusion strategy

Background:The most commonly used therapy currently for inflammatory and autoimmune diseases is nonspecific anti-inflammatory drugs, which have various hazardous side effects. Recently, some anti-inflammatory peptides (AIPs) have been found to be a substitute therapy for inflammatory diseases like rheumatoid arthritis and Alzheimer’s. Therefore, the identification of these AIPs is an emerging topic that is equally important. Methods:In this work, we have proposed an identification model for AIPs using a voting classifier. We used eight different feature descriptors and five conventional machine-learning classifiers. The eight feature encodings were concatenated to get a hybrid feature set. The five baseline models trained on the hybrid feature set were integrated via a voting classifier. Finally, a feature selection algorithm was used to select the optimal feature set for the construction of our final model, named IF-AIP. Results:We tested the proposed model on two independent datasets. On independent data 1, the IF-AIP model shows an improvement of 3%–5.6% in terms of accuracies and 6.7%–10.8% in terms of MCC compared to the existing methods. On the independent dataset 2, our model IF-AIP shows an overall improvement of 2.9%–5.7% in terms of accuracy and 8.3%–8.6% in terms of MCC score compared to the existing methods. A comparative performance analysis was conducted between the proposed model and existing methods using a set of 24 novel peptide sequences. Notably, the IF-AIP method exhibited exceptional accuracy, correctly identifying all 24 peptides as AIPs. The source code, pre-trained models, and all datasets are made available at https://github.com/Mir-Saima/IF-AIP.

Deep learning-based meta-learner strategy for electricity theft detection

Electricity theft damages power grid infrastructure and is also responsible for huge revenue losses for electric utilities. Integrating smart meters in traditional power grids enables real-time monitoring and collection of consumers’ electricity consumption (EC) data. Based on the collected data, it is possible to identify the normal and malicious behavior of consumers by analyzing the data using machine learning (ML) and deep learning methods. This paper proposes a deep learning-based meta-learner model to distinguish between normal and malicious patterns in EC data. The proposed model consists of two stages. In Fold-0, the ML classifiers extract diverse knowledge and learns based on EC data. In Fold-1, a multilayer perceptron is used as a meta-learner, which takes the prediction results of Fold-0 classifiers as input, automatically learns non-linear relationships among them, and extracts hidden complicated features to classify normal and malicious behaviors. Therefore, the proposed model controls the overfitting problem and achieves high accuracy. Moreover, extensive experiments are conducted to compare its performance with boosting, bagging, standalone conventional ML classifiers, and baseline models published in top-tier outlets. The proposed model is evaluated using a real EC dataset, which is provided by the Energy Informatics Group in Pakistan. The model achieves 0.910 ROC-AUC and 0.988 PR-AUC values on the test dataset, which are higher than those of the compared models.

TROLLOPE: A novel sequence-based stacked approach for the accelerated discovery of linear T-cell epitopes of hepatitis C virus.

Hepatitis C virus (HCV) infection is a concerning health issue that causes chronic liver diseases. Despite many successful therapeutic outcomes, no effective HCV vaccines are currently available. Focusing on T cell activity, the primary effector for HCV clearance, T cell epitopes of HCV (TCE-HCV) are considered promising elements to accelerate HCV vaccine efficacy. Thus, accurate and rapid identification of TCE-HCVs is recommended to obtain more efficient therapy for chronic HCV infection. In this study, a novel sequence-based stacked approach, termed TROLLOPE, is proposed to accurately identify TCE-HCVs from sequence information. Specifically, we employed 12 different sequence-based feature descriptors from heterogeneous perspectives, such as physicochemical properties, composition-transition-distribution information and composition information. These descriptors were used in cooperation with 12 popular machine learning (ML) algorithms to create 144 base-classifiers. To maximize the utility of these base-classifiers, we used a feature selection strategy to determine a collection of potential base-classifiers and integrated them to develop the meta-classifier. Comprehensive experiments based on both cross-validation and independent tests demonstrated the superior predictive performance of TROLLOPE compared with conventional ML classifiers, with cross-validation and independent test accuracies of 0.745 and 0.747, respectively. Finally, a user-friendly online web server of TROLLOPE (http://pmlabqsar.pythonanywhere.com/TROLLOPE) has been developed to serve research efforts in the large-scale identification of potential TCE-HCVs for follow-up experimental verification.

Relevance of deep sequence models for recognising automated construction activities: a case study on a low-rise construction system

Recognising activities of construction equipment is essential for monitoring productivity, construction progress, safety, and environmental impacts. While there have been many studies on activity recognition of earth excavation and moving equipment, activity identification of Automated Construction Systems (ACS) has been rarely attempted. Especially for low-rise ACS that offers energy-efficient, cost-effective solutions for urgent housing needs, and provides more affordable living options for a broader population. Deep learning methods have gained a lot of attention because of their ability to perform classification without manually extracting relevant features. This study evaluates the feasibility of deep sequence models for developing an activity recognition framework for low-rise automated construction equipment. Time series acceleration data was collected from the structure to identify major operation classes of an ACS. Long Short Term Memory Networks (LSTM) were applied for identifying the activity classes and the performance was compared with that of traditional machine learning classifiers. Diverse augmentation methods were adopted for generating datasets for training the deep learning classifiers. Several recently published literature seem to establish the superiority of complex deep learning techniques over traditional machine learning algorithms regardless of the application context. However, the results of this study show that all the conventional machine learning classifiers perform equivalently or better than deep learning classifiers in identifying activities of the ACS. The performance of the deep learning classifiers is affected by the lack of diversity in the initial dataset. If the augmented dataset significantly alters the characteristics of the original dataset, it may not deliver good recognition results.

Self-Supervision for Medical Image Classification: State-of-the-Art Performance with ~100 Labeled Training Samples per Class.

Is self-supervised deep learning (DL) for medical image analysis already a serious alternative to the de facto standard of end-to-end trained supervised DL? We tackle this question for medical image classification, with a particular focus on one of the currently most limiting factor of the field: the (non-)availability of labeled data. Based on three common medical imaging modalities (bone marrow microscopy, gastrointestinal endoscopy, dermoscopy) and publicly available data sets, we analyze the performance of self-supervised DL within the self-distillation with no labels (DINO) framework. After learning an image representation without use of image labels, conventional machine learning classifiers are applied. The classifiers are fit using a systematically varied number of labeled data (1-1000 samples per class). Exploiting the learned image representation, we achieve state-of-the-art classification performance for all three imaging modalities and data sets with only a fraction of between 1% and 10% of the available labeled data and about 100 labeled samples per class.

A simple scoring rule to predict survival to discharge after out of hospital cardiac arrest at the time of ED arrival

BackgroundIt is important to be able to predict the chance of survival to hospital discharge upon ED arrival in order to determine whether to continue or terminate resuscitation efforts after out of hospital cardiac arrest. This study was conducted to develop and validate a simple scoring rule that could predict survival to hospital discharge at the time of ED arrival. MethodsThis was a multicenter retrospective cohort study based on a nationwide registry (Korean Cardiac Arrest Research Consortium) of out of hospital cardiac arrest (OHCA). The study included adult OHCA patients older than 18 years old, who visited one of 33 tertiary hospitals in South Korea from September 1st, 2015 to June 30th, 2020. Among 12,321 screened, 5471 patients were deemed suitable for analysis after exclusion. Pre-hospital ROSC, pre-hospital witness, shockable rhythm, initial pH, and age were selected as the independent variables. The dependent variable was set to be the survival to hospital discharge. Multivariable logistic regression (LR) was performed, and the beta-coefficients were rounded to the nearest integer to formulate the scoring rule. Several machine learning algorithms including the random forest classifier (RF), support vector machine (SVM), and K-nearest neighbor classifier (K−NN) were also trained via 5-fold cross-validation over a pre-specified grid, and validated on the test data. The prediction performances and the calibration curves of each model were obtained. Pre-processing of the registry was done using R, model training & optimization using Python. ResultsA total of 5471 patients were included in the analysis. The AUROC of the scoring rule over the test data was 0.7620 (0.7311–0.7929). The AUROCs of the machine learning classifiers (LR, SVM, k-NN, RF) were 0.8126 (0.7748–0.8505), 0.7920 (0.7512–0.8329), 0.6783 (0.6236–0.7329), and 0.7879 (0.7465–0.8294), respectively. ConclusionA simple scoring rule consisting of five, binary variables could aid in the prediction of the survival to hospital discharge at the time of ED arrival, showing comparable results to conventional machine learning classifiers.

Objective assessment of sleep parameters using multimodal AX3 data in older participants

AbstractBackgroundSleep disturbances are both risk factors for and symptoms of dementia. Current methods for assessing sleep disturbances are largely based on either polysomnography (PSG) which is costly and inconvenient, or self‐ or care‐giver reports which are prone to measurement error. Low‐cost methods to monitor sleep disturbances longitudinally and at scale can be useful for assessing symptom development. Here, we develop deep learning models that use multimodal variables (accelerometers and temperature) recorded by the AX3 to accurately identify sleep and wake epochs and derive sleep parameters.MethodEighteen men and women (65‐80y) participated in a sleep laboratory‐based study in which multiple devices for sleep monitoring were evaluated. PSGs were recorded over a 10‐h period and scored according to established criteria per 30 sec epochs. Tri‐axial accelerometers and temperature signals were captured with an Axivity AX3, at 100Hz and 1Hz, respectively, throughout a 19‐h period, including 10‐h concurrent PSG recording and 9‐h of wakefulness. We developed and evaluated a supervised deep learning algorithm to detect sleep and wake epochs and determine sleep parameters from the multimodal AX3 raw data. We validated our results with gold standard PSG measurements and compared our algorithm to the Biobank accelerometer analysis toolbox. Single modality (accelerometer or temperature) and multimodality (both signals) approaches were evaluated using the 3‐fold cross‐validation.ResultThe proposed deep learning model outperformed baseline models such as the Biobank accelerometer analysis toolbox and conventional machine learning classifiers (Random Forest and Support Vector Machine) by up to 25%. Using multimodal data improved sleep and wake classification performance (up to 18% higher) compared with the single modality. In terms of the sleep parameters, our approach boosted the accuracy of estimations by 11% on average compared to the Biobank accelerometer analysis toolbox.ConclusionIn older adults without dementia, combining multimodal data from AX3 with deep learning methods allows satisfactory quantification of sleep and wakefulness. This approach holds promise for monitoring sleep behaviour and deriving accurate sleep parameters objectively and longitudinally from a low‐cost wearable sensor. A limitation of our current study is that the participants were healthy older adults: future work will focus on people living with dementia.

KNN-Based Machine Learning Classifier Used on Deep Learned Spatial Motion Features for Human Action Recognition.

Human action recognition is an essential process in surveillance video analysis, which is used to understand the behavior of people to ensure safety. Most of the existing methods for HAR use computationally heavy networks such as 3D CNN and two-stream networks. To alleviate the challenges in the implementation and training of 3D deep learning networks, which have more parameters, a customized lightweight directed acyclic graph-based residual 2D CNN with fewer parameters was designed from scratch and named HARNet. A novel pipeline for the construction of spatial motion data from raw video input is presented for the latent representation learning of human actions. The constructed input is fed to the network for simultaneous operation over spatial and motion information in a single stream, and the latent representation learned at the fully connected layer is extracted and fed to the conventional machine learning classifiers for action recognition. The proposed work was empirically verified, and the experimental results were compared with those for existing methods. The results show that the proposed method outperforms state-of-the-art (SOTA) methods with a percentage improvement of 2.75% on UCF101, 10.94% on HMDB51, and 0.18% on the KTH dataset.

Driving drowsiness detection using spectral signatures of EEG-based neurophysiology.

Introduction: Drowsy driving is a significant factor causing dire road crashes and casualties around the world. Detecting it earlier and more effectively can significantly reduce the lethal aftereffects and increase road safety. As physiological conditions originate from the human brain, so neurophysiological signatures in drowsy and alert states may be investigated for this purpose. In this preface, A passive brain-computer interface (pBCI) scheme using multichannel electroencephalography (EEG) brain signals is developed for spatially localized and accurate detection of human drowsiness during driving tasks. Methods: This pBCI modality acquired electrophysiological patterns of 12 healthy subjects from the prefrontal (PFC), frontal (FC), and occipital cortices (OC) of the brain. Neurological states are recorded using six EEG channels spread over the right and left hemispheres in the PFC, FC, and OC of the sleep-deprived subjects during simulated driving tasks. In post-hoc analysis, spectral signatures of the δ, θ, α, and β rhythms are extracted in terms of spectral band powers and their ratios with a temporal correlation over the complete span of the experiment. Minimum redundancy maximum relevance, Chi-square, and ReliefF feature selection methods are used and aggregated with a Z-score based approach for global feature ranking. The extracted drowsiness attributes are classified using decision trees, discriminant analysis, logistic regression, naïve Bayes, support vector machines, k-nearest neighbors, and ensemble classifiers. The binary classification results are reported with confusion matrix-based performance assessment metrics. Results: In inter-classifier comparison, the optimized ensemble model achieved the best results of drowsiness classification with 85.6% accuracy and precision, 89.7% recall, 87.6% F1-score, 80% specificity, 70.3% Matthews correlation coefficient, 70.2% Cohen's kappa score, and 91% area under the receiver operating characteristic curve with 76-ms execution time. In inter-channel comparison, the best results were obtained at the F8 electrode position in the right FC of the brain. The significance of all the results was validated with a p-value of less than 0.05 using statistical hypothesis testing methods. Conclusions: The proposed scheme has achieved better results for driving drowsiness detection with the accomplishment of multiple objectives. The predictor importance approach has reduced the feature extraction cost and computational complexity is minimized with the use of conventional machine learning classifiers resulting in low-cost hardware and software requirements. The channel selection approach has spatially localized the most promising brain region for drowsiness detection with only a single EEG channel (F8) which reduces the physical intrusiveness in normal driving operation. This pBCI scheme has a good potential for practical applications requiring earlier, more accurate, and less disruptive drowsiness detection using the spectral information of EEG biosignals.

Pretoria: An effective computational approach for accurate and high-throughput identification of CD8+ t-cell epitopes of eukaryotic pathogens

T-cells recognize antigenic epitopes present on major histocompatibility complex (MHC) molecules, triggering an adaptive immune response in the host. T-cell epitope (TCE) identification is challenging because of the extensive number of undetermined proteins found in eukaryotic pathogens, as well as MHC polymorphisms. In addition, conventional experimental approaches for TCE identification are time-consuming and expensive. Thus, computational approaches that can accurately and rapidly identify CD8+ T-cell epitopes (TCEs) of eukaryotic pathogens based solely on sequence information may facilitate the discovery of novel CD8+ TCEs in a cost-effective manner. Here, Pretoria (Predictor of CD8+ TCEs of eukaryotic pathogens) is proposed as the first stack-based approach for accurate and large-scale identification of CD8+ TCEs of eukaryotic pathogens. In particular, Pretoria enabled the extraction and exploration of crucial information embedded in CD8+ TCEs by employing a comprehensive set of 12 well-known feature descriptors extracted from multiple groups, including physicochemical properties, composition-transition-distribution, pseudo-amino acid composition, and amino acid composition. These feature descriptors were then utilized to construct a pool of 144 different machine learning (ML)-based classifiers based on 12 popular ML algorithms. Finally, the feature selection method was used to effectively determine the important ML classifiers for the construction of our stacked model. The experimental results indicated that Pretoria is an accurate and effective computational approach for CD8+ TCE prediction; it was superior to several conventional ML classifiers and the existing method in terms of the independent test, with an accuracy of 0.866, MCC of 0.732, and AUC of 0.921. Additionally, to maximize user convenience for high-throughput identification of CD8+ TCEs of eukaryotic pathogens, a user-friendly web server of Pretoria (http://pmlabstack.pythonanywhere.com/Pretoria) was developed and made freely available.