A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data.

Accurate identification of human leukocyte antigen (HLA) alleles is essential for various clinical and research applications, such as transplant matching and drug sensitivities. Recent advances in RNA-seq technology have made it possible to impute HLA types from sequencing data, spurring the development of a large number of computational HLA typing tools. However, the relative performance of these tools is unknown, limiting the ability for clinical and biomedical research to make informed choices regarding which tools to use. Here we report the study design of a comprehensive benchmarking of the performance of 12 HLA callers across 682 RNA-seq samples from 8 datasets with molecularly defined gold standard at 5 loci, HLA-A, -B, -C, -DRB1, and -DQB1. For each HLA typing tool, we will comprehensively assess their accuracy, compare default with optimized parameters, and examine for discrepancies in accuracy at the allele and loci levels. We will also evaluate the computational expense of each HLA caller measured in terms of CPU time and RAM. We also plan to evaluate the influence of read length over the HLA region on accuracy for each tool. Most notably, we will examine the performance of HLA callers across European and African groups, to determine discrepancies in accuracy associated with ancestry. We hypothesize that RNA-Seq HLA callers are capable of returning high-quality results, but the tools that offer a good balance between accuracy and computational expensiveness for all ancestry groups are yet to be developed. We believe that our study will provide clinicians and researchers with clear guidance to inform their selection of an appropriate HLA caller.

KU-BdSL: An open dataset for Bengali sign language recognition.

Sign language is a form of communication medium for speech and hearing disabled people. It has various forms with different troublesome patterns, which are difficult for the general mass to comprehend. Bengali sign language (BdSL) is one of the difficult sign languages due to its immense number of alphabet, words, and expression techniques. Machine translation can ease the difficulty for disabled people to communicate with generals. From the machine learning (ML) domain, computer vision can be the solution for them, and every ML solution requires a optimized model and a proper dataset. Therefore, in this research work, we have created a BdSL dataset and named `KU-BdSL', which consists of 30 classes describing 38 consonants ('banjonborno') of the Bengali alphabet. The dataset includes 1500 images of hand signs in total, each representing Bengali consonant(s). Thirty-nine participants (30 males and 9 females) of different ages (21-38 years) participated in the creation of this dataset. We adopted smartphones to capture the images due to the availability of their high-definition cameras. We believe that this dataset can be beneficial to the deaf and dumb (D&D) community. Identification of Bengali consonants of BdSL from images or videos is feasible using the dataset. It can also be employed for a human-machine interface for disabled people. In the future, we will work on the vowels and word level of BdSL.

Exploring factors influencing the severity of pregnancy anemia in India: a study using proportional odds model.

Pregnancy-associated anemia is a significant health issue that poses negative consequences for both the mother and the developing fetus. This study explores the triggering factors of anemia among pregnant females in India, utilizing data from the Demographic and Health Survey 2019-21. Chi-squared and gamma tests were conducted to find out the relationship between anemia and various socioeconomic and sociodemographic elements. Furthermore, ordinal logistic regression and multinomial logistic regression were used to gain deeper insight into the factors that affect anemia among pregnant women in India. According to these findings, anemia affects about 50% of pregnant women in India. Anemia is significantly associated with various factors such as geographical location, level of education, and wealth index. The results of our study indicate that enhancing education and socioeconomic status may serve as viable approaches for mitigating the prevalence of anemia disease developed in pregnant females in India. Employing both Ordinal and Multinominal logistic regression provides a more comprehensive understanding of the risk factors associated with anemia, enabling the development of targeted interventions to prevent and manage this health condition. This paper aims to enhance the efficacy of anemia prevention and management strategies for pregnant women in India by offering an in-depth understanding of the causative factors of anemia.

A Modified Aquila-Based Optimized XGBoost Framework for Detecting Probable Seizure Status in Neonates.

Electroencephalography (EEG) is increasingly being used in pediatric neurology and provides opportunities to diagnose various brain illnesses more accurately and precisely. It is thought to be one of the most effective tools for identifying newborn seizures, especially in Neonatal Intensive Care Units (NICUs). However, EEG interpretation is time-consuming and requires specialists with extensive training. It can be challenging and time-consuming to distinguish between seizures since they might have a wide range of clinical characteristics and etiologies. Technological advancements such as the Machine Learning (ML) approach for the rapid and automated diagnosis of newborn seizures have increased in recent years. This work proposes a novel optimized ML framework to eradicate the constraints of conventional seizure detection techniques. Moreover, we modified a novel meta-heuristic optimization algorithm (MHOA), named Aquila Optimization (AO), to develop an optimized model to make our proposed framework more efficient and robust. To conduct a comparison-based study, we also examined the performance of our optimized model with that of other classifiers, including the Decision Tree (DT), Random Forest (RF), and Gradient Boosting Classifier (GBC). This framework was validated on a public dataset of Helsinki University Hospital, where EEG signals were collected from 79 neonates. Our proposed model acquired encouraging results showing a 93.38% Accuracy Score, 93.9% Area Under the Curve (AUC), 92.72% F1 score, 65.17% Kappa, 93.38% sensitivity, and 77.52% specificity. Thus, it outperforms most of the present shallow ML architectures by showing improvements in accuracy and AUC scores. We believe that these results indicate a major advance in the detection of newborn seizures, which will benefit the medical community by increasing the reliability of the detection process.

A Bibliometric Analysis on Arrhythmia Detection and Classification from 2005 to 2022.

Bibliometric analysis is a widely used technique for analyzing large quantities of academic literature and evaluating its impact in a particular academic field. In this paper bibliometric analysis has been used to analyze the academic research on arrhythmia detection and classification from 2005 to 2022. We have followed PRISMA 2020 framework to identify, filter and select the relevant papers. This study has used the Web of Science database to find related publications on arrhythmia detection and classification. "Arrhythmia detection", "arrhythmia classification" and "arrhythmia detection and classification" are three keywords for gathering the relevant articles. 238 publications in total were selected for this research. In this study, two different bibliometric techniques, "performance analysis" and "science mapping", were applied. Different bibliometric parameters such as publication analysis, trend analysis, citation analysis, and networking analysis have been used to evaluate the performance of these articles. According to this analysis, the three countries with the highest number of publications and citations are China, the USA, and India in terms of arrhythmia detection and classification. The three most significant researchers in this field are those named U. R. Acharya, S. Dogan, and P. Plawiak. Machine learning, ECG, and deep learning are the three most frequently used keywords. A further finding of the study indicates that the popular topics for arrhythmia identification are machine learning, ECG, and atrial fibrillation. This research provides insight into the origins, current status, and future direction of arrhythmia detection research.

Detection of the chronic kidney disease using XGBoost classifier and explaining the influence of the attributes on the model using SHAP.

Chronic kidney disease (CKD) is a condition distinguished by structural and functional changes to the kidney over time. Studies show that 10% of adults worldwide are affected by some kind of CKD, resulting in 1.2 million deaths. Recently, CKD has emerged as a leading cause of mortality worldwide, making it necessary to develop a Computer-Aided Diagnostic (CAD) system to diagnose CKD automatically. Machine Learning (ML) based CAD system can be used by a clinician to automatically diagnoses mass people. Since ML models are considered a black box, it is also necessary to expose influential causes behind a model's prediction of a particular output. So that, a doctor can make a more rational decision based on the model's output and analysis of the features influence on the model. In this paper, we have used the XGBoost as the ML classifier to predict whether a patient has CKD or not. Using the XGBoost classifier, we have obtained an accuracy, precision, recall, and F1 score of [Formula: see text] and [Formula: see text] respectively using all [Formula: see text] features. Furthermore, we have used Biogeography Based Optimization (BBO) algorithm to find an effective subset of the features. The BBO algorithm selected almost half of the initial features. We have obtained an accuracy, precision, recall, and F1 score of [Formula: see text] and [Formula: see text] respectively using only 13 features selected by the BBO algorithm. Finally, we have explained the impact of the feature on the ML models using the SHapley Additive exPlanations (SHAP) analysis. Using SHAP analysis and BBO algorithm, we have found that hemoglobin and albumin mostly contribute to the detection of CKD.

Finding the influential clinical traits that impact on the diagnosis of heart disease using statistical and machine-learning techniques.

In recent years, the omnipresence of cardiac problems has been recognized as an epidemic. With the correct and quick diagnosis, both mortality and morbidity from cardiac disorders can be dramatically reduced. However, frequent medical check-ups are pricey and out of reach for a large number of people, particularly those living in low-income areas. In this paper, certain time-honored statistical techniques are used to determine the factors that lead to heart disease. Also, the findings were validated using various promising machine learning tools. Feature importance approach was employed to rank the clinical parameters of the patients based on the correlation of heart disease. In the case of statistical investigations, nonparametric tests such as the Mann Whitney U test and the Chi square test, as well as correlation analysis with Pearson correlation and Spearman Correlation were used. For additional validation, seven of the potential feature important based ML algorithms were applied. Moreover, Borda count was implemented to acknowledge the combined observation of those ML models. On top of that, SHAP value was calculated as a feature importance technique and for detailed evaluation. This research reveals two aspects of heart disease diagnosis.We found that eight clinical traits are sufficient to diagnose cardiac disorders, in which three traits are the most important sign of heart disease. One of the discoveries of this investigation uncovered chest pain, number of major blood vessels, thalassemia, age, maximum heart rate, cholesterol, oldpeak, and sex as sufficient clinical signs of individuals for the diagnosis of cardiac disorders. Over the above, considering the findings of all three approaches, chest pain, the number of major blood vessels, and thalassemia were identified as the prime factors of heart disease. The research also found, fasting blood sugar does not have a direct impact on cardiac disease. These findings will have the potency to be incredibly useful in clinical investigations as well as risk assessment for patients. Limiting the most critical features can have a significant impact on the diagnosis of heart disease and reduce the severity of health risks and death of patients.

LLDNet: A Lightweight Lane Detection Approach for Autonomous Cars Using Deep Learning.

Lane detection plays a vital role in making the idea of the autonomous car a reality. Traditional lane detection methods need extensive hand-crafted features and post-processing techniques, which make the models specific feature-oriented, and susceptible to instability for the variations on road scenes. In recent years, Deep Learning (DL) models, especially Convolutional Neural Network (CNN) models have been proposed and utilized to perform pixel-level lane segmentation. However, most of the methods focus on achieving high accuracy while considering structured roads and good weather conditions and do not put emphasis on testing their models on defected roads, especially ones with blurry lane lines, no lane lines, and cracked pavements, which are predominant in the real world. Moreover, many of these CNN-based models have complex structures and require high-end systems to operate, which makes them quite unsuitable for being implemented in embedded devices. Considering these shortcomings, in this paper, we have introduced a novel CNN model named LLDNet based on an encoder-decoder architecture that is lightweight and has been tested in adverse weather as well as road conditions. A channel attention and spatial attention module are integrated into the designed architecture to refine the feature maps for achieving outstanding results with a lower number of parameters. We have used a hybrid dataset to train our model, which was created by combining two separate datasets, and have compared the model with a few state-of-the-art encoder-decoder architectures. Numerical results on the utilized dataset show that our model surpasses the compared methods in terms of dice coefficient, IoU, and the size of the models. Moreover, we carried out extensive experiments on the videos of different roads in Bangladesh. The visualization results exhibit that our model can detect the lanes accurately in both structured and defected roads and adverse weather conditions. Experimental results elicit that our designed method is capable of detecting lanes accurately and is ready for practical implementation.

Whole-genome sequencing of a year-round fruiting jackfruit (Artocarpus heterophyllus Lam.) reveals high levels of single nucleotide variation.

Jackfruit (Artocarpus heterophyllus Lam.) is the national fruit of Bangladesh and produces fruit in the summer season only. However, jackfruit is not commercially grown in Bangladesh because of an extremely high variation in fruit quality, short seasonal fruiting (June-August) and susceptibility to abiotic stresses. Conversely, a year-round high yielding (ca. 4-fold higher than the seasonal variety) jackfruit variety, BARI Kanthal-3 developed by the Bangladesh Agricultural Research Institute (BARI) derived from a wild accession found in Ramgarh of Chattogram Hiltracts of Bangladesh, provides fruits from September to June. This study aimed to generate a draft whole-genome sequence (WGS) of BARI Kanthal-3 to obtain molecular insights including genes associated with year-round fruiting trait of this important unique variety. The estimated genome size of BARI Kanthal-3 was 1.04-gigabase-pair (Gbp) with a heterozygosity rate of 1.62%. De novo assembly yielded a scaffolded 817.7 Mb genome while a reference-guided approach, yielded 843 Mb of genome sequence. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 included 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are in inter-genic regions. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing identified orthologous gene groups in BARI Kanthal-3 with five closely and one distantly related species of 10,092 common orthogroups were found across the genomes of the six species. The phylogenetic analysis of the shared orthogroups showed that A. heterophyllus was the closest species to BARI Kanthal-3 and orthogroups related to flowering time were found to be more highly prevalent in BARI Kanthal-3 compared to the other Arctocarpus spp. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting of this highly nutritious fruit crop as well as providing a resource for molecular breeding.

Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh.

This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh.

A Pneumonia Diagnosis Scheme Based on Hybrid Features Extracted from Chest Radiographs Using an Ensemble Learning Algorithm.

Pneumonia is a fatal disease responsible for almost one in five child deaths worldwide. Many developing countries have high mortality rates due to pneumonia because of the unavailability of proper and timely diagnostic measures. Using machine learning-based diagnosis methods can help to detect the disease early and in less time and cost. In this study, we proposed a novel method to determine the presence of pneumonia and identify its type (bacterial or viral) through analyzing chest radiographs. We performed a three-class classification based on features containing diverse information of the samples. After using an augmentation technique to balance the dataset's sample sizes, we extracted the chest X-ray images' statistical features, as well as global features by employing a deep learning architecture. We then combined both sets of features and performed the final classification using the RandomForest classifier. A feature selection method was also incorporated to identify the features with the highest relevance. We tested the proposed method on a widely used (but relabeled) chest radiograph dataset to evaluate its performance. The proposed model can classify the dataset's samples with an 86.30% classification accuracy and 86.03% F-score, which assert the model's efficacy and reliability. However, results show that the classifier struggles while distinguishing between viral and bacterial pneumonia samples. Implementing this method will provide a fast and automatic way to detect pneumonia in a patient and identify its type.

A Machine Learning Approach to Diagnosing Lung and Colon Cancer Using a Deep Learning-Based Classification Framework.

The field of Medicine and Healthcare has attained revolutionary advancements in the last forty years. Within this period, the actual reasons behind numerous diseases were unveiled, novel diagnostic methods were designed, and new medicines were developed. Even after all these achievements, diseases like cancer continue to haunt us since we are still vulnerable to them. Cancer is the second leading cause of death globally; about one in every six people die suffering from it. Among many types of cancers, the lung and colon variants are the most common and deadliest ones. Together, they account for more than 25% of all cancer cases. However, identifying the disease at an early stage significantly improves the chances of survival. Cancer diagnosis can be automated by using the potential of Artificial Intelligence (AI), which allows us to assess more cases in less time and cost. With the help of modern Deep Learning (DL) and Digital Image Processing (DIP) techniques, this paper inscribes a classification framework to differentiate among five types of lung and colon tissues (two benign and three malignant) by analyzing their histopathological images. The acquired results show that the proposed framework can identify cancer tissues with a maximum of 96.33% accuracy. Implementation of this model will help medical professionals to develop an automatic and reliable system capable of identifying various types of lung and colon cancers.

A dataset for internet of things based fish farm monitoring and notification system.

Water quality depends on many factors. Some of them are essential for maintaining the minimum sustainability of water. Because of the great dependence of fishes on the condition of the aquatic environment, the water quality can directly affect their activity. Therefore monitoring water quality is a very important issue to consider, especially in the fish farming industry. In this paper a digital fish farm monitoring system is introduced and a collection of experimental data of water quality monitoring was presented, which were directly collected from a fish pond. As the quality factor of water affects its aquatic life form sustainability, therefore the quality factors of the water were measured using digital sensors. Temperature, pH factor and Turbidity were selected as the basic quality factors to measure. The dataset contains data recorded from two different water levels to analyze the aquatic environment more efficiently. Each level has 9623 sets of data of the selected parameters. Collection was continued all day long for several days. Later collected sensor data were analyzed as short period time series to find its properties. Machine Learning regression method was used to predict near future conditions. Moreover data were processed to find any repetitive patterns in its properties. This dataset represents the exact condition of the environment of the fish pond. Therefore it can be used to develop a system to monitor fish farms digitally. Using these data in machine learning, predicting the future is possible for advance monitoring of a fish farm. The dataset is available in Mendeley Data[1].

A Novel Method to Identify Pneumonia through Analyzing Chest Radiographs Employing a Multichannel Convolutional Neural Network.

Pneumonia is a virulent disease that causes the death of millions of people around the world. Every year it kills more children than malaria, AIDS, and measles combined and it accounts for approximately one in five child-deaths worldwide. The invention of antibiotics and vaccines in the past century has notably increased the survival rate of Pneumonia patients. Currently, the primary challenge is to detect the disease at an early stage and determine its type to initiate the appropriate treatment. Usually, a trained physician or a radiologist undertakes the task of diagnosing Pneumonia by examining the patient's chest X-ray. However, the number of such trained individuals is nominal when compared to the 450 million people who get affected by Pneumonia every year. Fortunately, this challenge can be met by introducing modern computers and improved Machine Learning techniques in Pneumonia diagnosis. Researchers have been trying to develop a method to automatically detect Pneumonia using machines by analyzing and the symptoms of the disease and chest radiographic images of the patients for the past two decades. However, with the development of cogent Deep Learning algorithms, the formation of such an automatic system is very much within the realms of possibility. In this paper, a novel diagnostic method has been proposed while using Image Processing and Deep Learning techniques that are based on chest X-ray images to detect Pneumonia. The method has been tested on a widely used chest radiography dataset, and the obtained results indicate that the model is very much potent to be employed in an automatic Pneumonia diagnosis scheme.

Controlling the Outbreak of COVID-19: A Noncooperative Game Perspective.

COVID-19 is a global epidemic. Till now, there is no remedy for this epidemic. However, isolation and social distancing are seemed to be effective preventive measures to control this pandemic. Therefore, in this article, an optimization problem is formulated that accommodates both isolation and social distancing features of the individuals. To promote social distancing, we solve the formulated problem by applying a noncooperative game that can provide an incentive for maintaining social distancing to prevent the spread of COVID-19. Furthermore, the sustainability of the lockdown policy is interpreted with the help of our proposed game-theoretic incentive model for maintaining social distancing where there exists a Nash equilibrium. Finally, we perform an extensive numerical analysis that shows the effectiveness of the proposed approach in terms of achieving the desired social-distancing to prevent the outbreak of the COVID-19 in a noncooperative environment. Numerical results show that the individual incentive increases more than 85% with an increasing percentage of home isolation from 25% to 100% for all considered scenarios. The numerical results also demonstrate that in a particular percentage of home isolation, the individual incentive decreases with an increasing number of individuals.

Histopathological Breast Cancer Image Classification by Deep Neural Network Techniques Guided by Local Clustering.

Breast Cancer is a serious threat and one of the largest causes of death of women throughout the world. The identification of cancer largely depends on digital biomedical photography analysis such as histopathological images by doctors and physicians. Analyzing histopathological images is a nontrivial task, and decisions from investigation of these kinds of images always require specialised knowledge. However, Computer Aided Diagnosis (CAD) techniques can help the doctor make more reliable decisions. The state-of-the-art Deep Neural Network (DNN) has been recently introduced for biomedical image analysis. Normally each image contains structural and statistical information. This paper classifies a set of biomedical breast cancer images (BreakHis dataset) using novel DNN techniques guided by structural and statistical information derived from the images. Specifically a Convolutional Neural Network (CNN), a Long-Short-Term-Memory (LSTM), and a combination of CNN and LSTM are proposed for breast cancer image classification. Softmax and Support Vector Machine (SVM) layers have been used for the decision-making stage after extracting features utilising the proposed novel DNN models. In this experiment the best Accuracy value of 91.00% is achieved on the 200x dataset, the best Precision value 96.00% is achieved on the 40x dataset, and the best F-Measure value is achieved on both the 40x and 100x datasets.

Involvement of Machine Learning for Breast Cancer Image Classification: A Survey.

Breast cancer is one of the largest causes of women's death in the world today. Advance engineering of natural image classification techniques and Artificial Intelligence methods has largely been used for the breast-image classification task. The involvement of digital image classification allows the doctor and the physicians a second opinion, and it saves the doctors' and physicians' time. Despite the various publications on breast image classification, very few review papers are available which provide a detailed description of breast cancer image classification techniques, feature extraction and selection procedures, classification measuring parameterizations, and image classification findings. We have put a special emphasis on the Convolutional Neural Network (CNN) method for breast image classification. Along with the CNN method we have also described the involvement of the conventional Neural Network (NN), Logic Based classifiers such as the Random Forest (RF) algorithm, Support Vector Machines (SVM), Bayesian methods, and a few of the semisupervised and unsupervised methods which have been used for breast image classification.