Improved nonparametric survival prediction using CoxPH, Random Survival Forest & DeepHit Neural Network.

In recent times, time-to-event data such as time to failure or death is routinely collected alongside high-throughput covariates. These high-dimensional bioinformatics data often challenge classical survival models, which are either infeasible to fit or produce low prediction accuracy due to overfitting. To address this issue, the focus has shifted towards introducing a novel approaches for feature selection and survival prediction. In this article, we propose a new hybrid feature selection approach that handles high-dimensional bioinformatics datasets for improved survival prediction. This study explores the efficacy of four distinct variable selection techniques: LASSO, RSF-vs, SCAD, and CoxBoost, in the context of non-parametric biomedical survival prediction. Leveraging these methods, we conducted comprehensive variable selection processes. Subsequently, survival analysis models-specifically CoxPH, RSF, and DeepHit NN-were employed to construct predictive models based on the selected variables. Furthermore, we introduce a novel approach wherein only variables consistently selected by a majority of the aforementioned feature selection techniques are considered. This innovative strategy, referred to as the proposed method, aims to enhance the reliability and robustness of variable selection, subsequently improving the predictive performance of the survival analysis models. To evaluate the effectiveness of the proposed method, we compare the performance of the proposed approach with the existing LASSO, RSF-vs, SCAD, and CoxBoost techniques using various performance metrics including integrated brier score (IBS), concordance index (C-Index) and integrated absolute error (IAE) for numerous high-dimensional survival datasets. The real data applications reveal that the proposed method outperforms the competing methods in terms of survival prediction accuracy.

A novel flexible exponent power-X family of distributions with applications to COVID-19 mortality rate in Mexico and Canada.

This paper aims to introduce a novel family of probability distributions by the well-known method of the T-X family of distributions. The proposed family is called a "Novel Generalized Exponent Power X Family" of distributions. A three-parameters special sub-model of the proposed method is derived and named a "Novel Generalized Exponent Power Weibull" distribution (NGEP-Wei for short). For the proposed family, some statistical properties are derived including the hazard rate function, moments, moment generating function, order statistics, residual life, and reverse residual life. The well-known method of estimation, the maximum likelihood estimation method is used for estimating the model parameters. Besides, a comprehensive Monte Carlo simulation study is conducted to assess the efficacy of this estimation method. Finally, the model selection criterion such as Akaike information criterion (AINC), the correct information criterion (CINC), the Bayesian information criterion (BINC), the Hannan-Quinn information criterion (HQINC), the Cramer-von-Misses (CRMI), and the ANDA (Anderson-Darling) are used for comparison purpose. The comparison of the NGEP-Wei with other rival distributions is made by Two COVID-19 data sets. In terms of performance, we show that the proposed method outperforms the other competing methods included in this study.

Sequence based model using deep neural network and hybrid features for identification of 5-hydroxymethylcytosine modification.

RNA modifications are pivotal in the development of newly synthesized structures, showcasing a vast array of alterations across various RNA classes. Among these, 5-hydroxymethylcytosine (5HMC) stands out, playing a crucial role in gene regulation and epigenetic changes, yet its detection through conventional methods proves cumbersome and costly. To address this, we propose Deep5HMC, a robust learning model leveraging machine learning algorithms and discriminative feature extraction techniques for accurate 5HMC sample identification. Our approach integrates seven feature extraction methods and various machine learning algorithms, including Random Forest, Naive Bayes, Decision Tree, and Support Vector Machine. Through K-fold cross-validation, our model achieved a notable 84.07% accuracy rate, surpassing previous models by 7.59%, signifying its potential in early cancer and cardiovascular disease diagnosis. This study underscores the promise of Deep5HMC in offering insights for improved medical assessment and treatment protocols, marking a significant advancement in RNA modification analysis.

Monitoring the process mean under the Bayesian approach with application to hard bake process.

This study introduces the Bayesian adaptive exponentially weighted moving average (AEWMA) control chart within the framework of measurement error, examining two separate loss functions: the squared error loss function and the linex loss function. We conduct an analysis of the posterior and posterior predictive distributions utilizing a conjugate prior. In the presence of measurement error (ME), we employ a linear covariate model to assess the control chart's effectiveness. Additionally, we explore the impacts of measurement error by investigating multiple measurements and a method involving linearly increasing variance. We conduct a Monte Carlo simulation study to assess the control chart's performance under ME, examining its run length profile. Subsequently, we offer a specific numerical instance related to the hard-bake process in semiconductor manufacturing, serving to verify the functionality and practical application of the suggested Bayesian AEWMA control chart when confronted with ME.

Monitoring of manufacturing process using bayesian EWMA control chart under ranked based sampling designs.

Control charts, including exponentially moving average (EWMA) , are valuable for efficiently detecting small to moderate shifts. This study introduces a Bayesian EWMA control chart that employs ranked set sampling (RSS) with known prior information and two distinct loss functions (LFs), the Square Error Loss function (SELF) and the Linex Loss function (LLF), for posterior and posterior predictive distributions. The chart's performance is assessed using average run length (ARL) and standard deviation of run length (SDRL) profiles, and it is compared to the Bayesian EWMA control chart based on simple random sampling (SRS). The results indicate that the proposed control chart detects small to moderate shifts more effectively. The application in semiconductor manufacturing provides concrete evidence that the Bayesian EWMA control chart, when implemented with RSS schemes, demonstrates a higher degree of sensitivity in detecting deviations from normal process behavior. Comparison to the Bayesian EWMA control chart using SRS, it exhibits a superior ability to identify and flag instances where the manufacturing process is going out of control. This heightened sensitivity is critical for promptly addressing and rectifying issues, which ultimately contributes to improved quality control in semiconductor production.

Performance of Bayesian EWMA control chart with measurement error under ranked set sampling schemes with application in industrial engineering.

The objective of this study is to investigate the behavior of the Bayesian exponentially weighted moving average (EWMA) control chart in the presence of measurement error (ME). It explores the impact of different ranked set sampling designs and loss functions on the performance of the control chart when ME is present. The analysis incorporates a covariate model, multiple measurement methods, and a conjugate prior to account for ME. The performance evaluation of the proposed Bayesian EWMA control chart with ME includes metrics such as average run length and standard deviation of run lengths. The findings, obtained through Monte Carlo simulation and real data application, indicated that ME significantly affects the performance of the Bayesian EWMA control chart when RSS schemes are employed. Particularly noteworthy is the superior performance of the median RSS scheme compared to the other two schemes in the presence of ME.

Adaptive EWMA control chart using Bayesian approach under ranked set sampling schemes with application to Hard Bake process.

The memory-type control charts, such as cumulative sum (CUSUM) and exponentially weighted moving average control chart, are more desirable for detecting a small or moderate shift in the production process of a location parameter. In this article, a novel Bayesian adaptive EWMA (AEWMA) control chat utilizing ranked set sampling (RSS) designs is proposed under two different loss functions, i.e., square error loss function (SELF) and linex loss function (LLF), and with informative prior distribution to monitor the mean shift of the normally distributed process. The extensive Monte Carlo simulation method is used to check the performance of the suggested Bayesian-AEWMA control chart using RSS schemes. The effectiveness of the proposed AEWMA control chart is evaluated through the average run length (ARL) and standard deviation of run length (SDRL). The results indicate that the proposed Bayesian control chart applying RSS schemes is more sensitive in detecting mean shifts than the existing Bayesian AEWAM control chart based on simple random sampling (SRS). Finally, to demonstrate the effectiveness of the proposed Bayesian-AEWMA control chart under different RSS schemes, we present a numerical example involving the hard-bake process in semiconductor fabrication. Our results show that the Bayesian-AEWMA control chart using RSS schemes outperforms the EWMA and AEWMA control charts utilizing the Bayesian approach under simple random sampling in detecting out-of-control signals.

Temporal analysis and opinion dynamics of COVID-19 vaccination tweets using diverse feature engineering techniques.

The outbreak of the COVID-19 pandemic has also triggered a tsunami of news, instructions, and precautionary measures related to the disease on social media platforms. Despite the considerable support on social media, a large number of fake propaganda and conspiracies are also circulated. People also reacted to COVID-19 vaccination on social media and expressed their opinions, perceptions, and conceptions. The present research work aims to explore the opinion dynamics of the general public about COVID-19 vaccination to help the administration authorities to devise policies to increase vaccination acceptance. For this purpose, a framework is proposed to perform sentiment analysis of COVID-19 vaccination-related tweets. The influence of term frequency-inverse document frequency, bag of words (BoW), Word2Vec, and combination of TF-IDF and BoW are explored with classifiers including random forest, gradient boosting machine, extra tree classifier (ETC), logistic regression, Naïve Bayes, stochastic gradient descent, multilayer perceptron, convolutional neural network (CNN), bidirectional encoder representations from transformers (BERT), long short-term memory (LSTM), and recurrent neural network (RNN). Results reveal that ETC outperforms using BoW with a 92% of accuracy and is the most suitable approach for sentiment analysis of COVID-19-related tweets. Opinion dynamics show that sentiments in favor of vaccination have increased over time.

Short-Term Prediction of COVID-19 Using Novel Hybrid Ensemble Empirical Mode Decomposition and Error Trend Seasonal Model.

In this article, a new hybrid time series model is proposed to predict COVID-19 daily confirmed cases and deaths. Due to the variations and complexity in the data, it is very difficult to predict its future trajectory using linear time series or mathematical models. In this research article, a novel hybrid ensemble empirical mode decomposition and error trend seasonal (EEMD-ETS) model has been developed to forecast the COVID-19 pandemic. The proposed hybrid model decomposes the complex, nonlinear, and nonstationary data into different intrinsic mode functions (IMFs) from low to high frequencies, and a single monotone residue by applying EEMD. The stationarity of each IMF component is checked with the help of the augmented Dicky-Fuller (ADF) test and is then used to build up the EEMD-ETS model, and finally, future predictions have been obtained from the proposed hybrid model. For illustration purposes and to check the performance of the proposed model, four datasets of daily confirmed cases and deaths from COVID-19 in Italy, Germany, the United Kingdom (UK), and France have been used. Similarly, four different statistical metrics, i.e., root mean square error (RMSE), symmetric mean absolute parentage error (sMAPE), mean absolute error (MAE), and mean absolute percentage error (MAPE) have been used for a comparison of different time series models. It is evident from the results that the proposed hybrid EEMD-ETS model outperforms the other time series and machine learning models. Hence, it is worthy to be used as an effective model for the prediction of COVID-19.

Prediction of Multidrug-Resistant Tuberculosis Using Machine Learning Algorithms in SWAT, Pakistan.

In this paper, we have focused on machine learning (ML) feature selection (FS) algorithms for identifying and diagnosing multidrug-resistant (MDR) tuberculosis (TB). MDR-TB is a universal public health problem, and its early detection has been one of the burning issues. The present study has been conducted in the Malakand Division of Khyber Pakhtunkhwa, Pakistan, to further add to the knowledge on the disease and to deal with the issues of identification and early detection of MDR-TB by ML algorithms. These models also identify the most important factors causing MDR-TB infection whose study gives additional insights into the matter. ML algorithms such as random forest, k-nearest neighbors, support vector machine, logistic regression, leaset absolute shrinkage and selection operator (LASSO), artificial neural networks (ANNs), and decision trees are applied to analyse the case-control dataset. This study reveals that close contacts of MDR-TB patients, smoking, depression, previous TB history, improper treatment, and interruption in first-line TB treatment have a great impact on the status of MDR. Accordingly, weight loss, chest pain, hemoptysis, and fatigue are important symptoms. Based on accuracy, sensitivity, and specificity, SVM and RF are the suggested models to be used for patients' classifications.

Robust proportional overlapping analysis for feature selection in binary classification within functional genomic experiments.

In this paper, a novel feature selection method called Robust Proportional Overlapping Score (RPOS), for microarray gene expression datasets has been proposed, by utilizing the robust measure of dispersion, i.e., Median Absolute Deviation (MAD). This method robustly identifies the most discriminative genes by considering the overlapping scores of the gene expression values for binary class problems. Genes with a high degree of overlap between classes are discarded and the ones that discriminate between the classes are selected. The results of the proposed method are compared with five state-of-the-art gene selection methods based on classification error, Brier score, and sensitivity, by considering eleven gene expression datasets. Classification of observations for different sets of selected genes by the proposed method is carried out by three different classifiers, i.e., random forest, k-nearest neighbors (k-NN), and support vector machine (SVM). Box-plots and stability scores of the results are also shown in this paper. The results reveal that in most of the cases the proposed method outperforms the other methods.

Forecasting COVID-19 in Pakistan.

OBJECTIVES: Forecasting epidemics like COVID-19 is of crucial importance, it will not only help the governments but also, the medical practitioners to know the future trajectory of the spread, which might help them with the best possible treatments, precautionary measures and protections. In this study, the popular autoregressive integrated moving average (ARIMA) will be used to forecast the cumulative number of confirmed, recovered cases, and the number of deaths in Pakistan from COVID-19 spanning June 25, 2020 to July 04, 2020 (10 days ahead forecast). METHODS: To meet the desire objectives, data for this study have been taken from the Ministry of National Health Service of Pakistan's website from February 27, 2020 to June 24, 2020. Two different ARIMA models will be used to obtain the next 10 days ahead point and 95% interval forecast of the cumulative confirmed cases, recovered cases, and deaths. Statistical software, RStudio, with "forecast", "ggplot2", "tseries", and "seasonal" packages have been used for data analysis. RESULTS: The forecasted cumulative confirmed cases, recovered, and the number of deaths up to July 04, 2020 are 231239 with a 95% prediction interval of (219648, 242832), 111616 with a prediction interval of (101063, 122168), and 5043 with a 95% prediction interval of (4791, 5295) respectively. Statistical measures i.e. root mean square error (RMSE) and mean absolute error (MAE) are used for model accuracy. It is evident from the analysis results that the ARIMA and seasonal ARIMA model is better than the other time series models in terms of forecasting accuracy and hence recommended to be used for forecasting epidemics like COVID-19. CONCLUSION: It is concluded from this study that the forecasting accuracy of ARIMA models in terms of RMSE, and MAE are better than the other time series models, and therefore could be considered a good forecasting tool in forecasting the spread, recoveries, and deaths from the current outbreak of COVID-19. Besides, this study can also help the decision-makers in developing short-term strategies with regards to the current number of disease occurrences until an appropriate medication is developed.

The analysis of risk factors associated with tonsillitis in district Mardan, Pakistan.

OBJECTIVE: To assess the risk factors associated with tonsillitis. METHODS: The cross-sectional study was conducted at Mardan Medical Complex and District Headquarter Hospital, Mardan, Pakistan, from January to June 2018, and comprised tonsillitis patients. Data was collected using a questionnaire which included different risk factors like age 1-10 years, gender, residential area, dietary habit etc. Data was analysed using SPSS 20. RESULTS: Of the 325 subjects, 200(61.54%), were clinically diagnosed with tonsillitis; 138(69%) being males. Age, unhygienic living condition, balanced diet, stressful environment and the use of sore/spicy foods were identified as significantly associated factors (p<0.05). CONCLUSIONS: Age, unhygienic living condition, balanced diet, stressful environment and the use of sore/spicy food were found to have a strong association with tonsillitis.

A New Extended-X Family of Distributions: Properties and Applications.

During the past couple of years, statistical distributions have been widely used in applied areas such as reliability engineering, medical, and financial sciences. In this context, we come across a diverse range of statistical distributions for modeling heavy tailed data sets. Well-known distributions are log-normal, log-t, various versions of Pareto, log-logistic, Weibull, gamma, exponential, Rayleigh and its variants, and generalized beta of the second kind distributions, among others. In this paper, we try to supplement the distribution theory literature by incorporating a new model, called a new extended Weibull distribution. The proposed distribution is very flexible and exhibits desirable properties. Maximum likelihood estimators of the model parameters are obtained, and a Monte Carlo simulation study is conducted to assess the behavior of these estimators. Finally, we provide a comparative study of the newly proposed and some other existing methods via analyzing three real data sets from different disciplines such as reliability engineering, medical, and financial sciences. It has been observed that the proposed method outclasses well-known distributions on the basis of model selection criteria.

A Flexible Reduced Logarithmic-X Family of Distributions with Biomedical Analysis.

Statistical distributions play a prominent role in applied sciences, particularly in biomedical sciences. The medical data sets are generally skewed to the right, and skewed distributions can be used quite effectively to model such data sets. In the present study, therefore, we propose a new family of distributions to model right skewed medical data sets. The proposed family may be named as a flexible reduced logarithmic-X family. The proposed family can be obtained via reparameterizing the exponentiated Kumaraswamy G-logarithmic family and the alpha logarithmic family of distributions. A special submodel of the proposed family called, a flexible reduced logarithmic-Weibull distribution, is discussed in detail. Some mathematical properties of the proposed family and certain related characterization results are presented. The maximum likelihood estimators of the model parameters are obtained. A brief Monte Carlo simulation study is done to evaluate the performance of these estimators. Finally, for the illustrative purposes, three applications from biomedical sciences are analyzed and the goodness of fit of the proposed distribution is compared to some well-known competitors.

Regulatory genes identification within functional genomics experiments for tissue classification into binary classes via machine learning techniques.

OBJECTIVE: The aim of this study is to filter out the most informative genes that mainly regulate the target tissue class, increase classification accuracy, reduce the curse of dimensionality, and discard redundant and irrelevant genes. METHOD: This paper presented the idea of gene selection using bagging sub-forest (BSF). The proposed method provided genes importance grounded on the idea specified in the standard random forest algorithm. The new method is compared with three state-of-the art methods, i.e., Wilcoxon, masked painter and proportional overlapped score (POS). These methods were applied on 5 data sets, i.e. Colon, Lymph node breast cancer, Leukaemia, Serrated colorectal carcinomas, and Breast Cancer. Comparison was done by selecting top 20 genes by applying the gene selection methods and applying random forest (RF) and support vector machine (SVM) classifiers to assess their predictive performance on the datasets with selected genes. Classification accuracy, Brier score, and sensitivity have been used as performance measures. RESULTS: The proposed method gave better results than the other methods using both random forest and SVM classifiers on all the datasets among all the feature selection methods. CONCLUSIONS: The proposed method showed improved performance in terms of classification accuracy, Brier score and sensitivity, and hence, could be used as a novel method for gene selection to classify tissue samples into their correct classes.

Risk factors associated with childhood asthma in District Mardan, Pakistan.

OBJECTIVE: To estimate the prevalence of asthma in children aged <10 years, and to identify important risk factors for asthma.. METHODS: The case-control study was conducted at Mardan Medical Complex and District Head Quarters Hospital, Mardan, Pakistan, from June to September 2017. Data was collected from paediatric patients of asthma as well as healthy controls through a self-designed questionnaire. SPSS 19 was used for data analysis. RESULTS: Of the 647 subjects, 349(54%) were asthmatic cases and 298(46%) were controls. Among the cases, 201(57.6%) were females, while 148(42.4%) were males. There were 332(51%) subjects whose fathers were smokers, and of them 224(67%) had asthma and 125(37%) were non-asthmatic. Overall, 323(50%) subjects had carpet in their rooms, and of them 221(68%) had asthma. Among other risk factors, subjects aged <5 years had 1.49 time more likely to have asthma with (odds ratio: 1.49, 95% confidence interval: 0.963-1.988). CONCLUSIONS: Female gender, fathers' smoking, having carpet in the room and age <5 year were found to be the main risk factors associated with asthma.

Sample size issues in multilevel logistic regression models.

Educational researchers, psychologists, social, epidemiological and medical scientists are often dealing with multilevel data. Sometimes, the response variable in multilevel data is categorical in nature and needs to be analyzed through Multilevel Logistic Regression Models. The main theme of this paper is to provide guidelines for the analysts to select an appropriate sample size while fitting multilevel logistic regression models for different threshold parameters and different estimation methods. Simulation studies have been performed to obtain optimum sample size for Penalized Quasi-likelihood (PQL) and Maximum Likelihood (ML) Methods of estimation. Our results suggest that Maximum Likelihood Method performs better than Penalized Quasi-likelihood Method and requires relatively small sample under chosen conditions. To achieve sufficient accuracy of fixed and random effects under ML method, we established ''50/50" and ''120/50" rule respectively. On the basis our findings, a ''50/60" and ''120/70" rules under PQL method of estimation have also been recommended.

The frequency of various diseases among patients attending Tehsil Headquarter Hospital Khwazakela, Swat.

This hospital-based study was conducted in THQ (Tehsil Headquarter) Hospital Khwazakhela, district Swat in April 2018, to determine the incidence of various diseases among patients in general and the cases attended in the OPD (out patients department) in particular. One year of data was taken from April 2017 to March 2018, of all the patients who attended the THQ Hospital to check the frequency of individual diseases, month wise, gender wise, age wise as well as, case wise. Information on patients attending OPD with respiratory, gastro intestinal, urinary tract diseases and other communicable diseases were compiled. A total of 219,056 patients attended Civil Hospital Khwazakhela during that period, with an average of 18,254.66 patients per month. This comprised 104,349(47.63%) males and 114,707 (52.36%) females. Most patients were in the age group of 15 to 59 years which comprised a total of 109,217 (49.85%) patients. In this age group 42,713 (39.10%) were males and 66,504 (60.89%) were females. A total of 77,286 patients attended OPD having respiratory, gastro intestinal, urinary tract diseases and communicable diseases. Among these patients, about 28,115 (36.37%) had respiratory diseases, 23,045 (29.81%) had gastro intestinal diseases, 18,060 (23.36%) had urinary tract diseases and 8,066 (10.43%) had other communicable diseases. Respiratory diseases were the most common in our study. The ratio of female cases was higher than males. Most of the patients were in the age group of 15-59 years. The emerging challenges for health practitioners are to prevent respiratory diseases that pose a major healthcare burden in the region.

Quinazolinone Synthesis through Base-Promoted SNAr Reaction of ortho-Fluorobenzamides with Amides Followed by Cyclization.

A transition-metal-free synthesis of quinazolin-4-ones by Cs2CO3-promoted SNAr reaction of ortho-fluorobenzamides with amides followed by cyclization in dimethyl sulfoxide has been developed. The present procedure can provide efficient synthetic methods for the formation of both 2-substituted and 2,3-disubstituted quinazolin-4-one rings depending on the use of easily available starting materials and an efficient, one-pot protocol for the synthesis of the marketed drug product of methaqualone.