Simulated Real Data Research Articles

Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks

In a multi-host system, understanding host-species contribution to transmission is key to appropriately targeting control and preventive measures. Outbreak reconstruction methods aiming to identify who-infected-whom by combining epidemiological and genetic data could contribute to achieving this goal. However, the majority of these methods remain untested on realistic simulated multi-host data. Mycobacterium bovis is a slowly evolving multi-host pathogen and previous studies on outbreaks involving both cattle and wildlife have identified observation biases. Indeed, contrary to cattle, sampling wildlife is difficult. The aim of our study was to evaluate and compare the performances of three existing outbreak reconstruction methods (seqTrack, outbreaker2 and TransPhylo) on M. bovis multi-host data simulated with and without biases. Extending an existing transmission model, we simulated 30 bTB outbreaks involving cattle, badgers and wild boars and defined six sampling schemes mimicking observation biases. We estimated general and specific to multi-host systems epidemiological indicators. We tested four alternative transmission scenarios changing the mutation rate or the composition of the epidemiological system. The reconstruction of who-infected-whom was sensitive to the mutation rate and seqTrack reconstructed prolific super-spreaders. TransPhylo and outbreaker2 poorly estimated the contribution of each host-species and could not reconstruct the presence of a dead-end epidemiological host. However, the host-species of cattle (but not badger) index cases was correctly reconstructed by seqTrack and outbreaker2. These two specific indicators improved when considering an observation bias. We found an overall poor performance for the three methods on simulated biased and unbiased bTB data. This seemed partly attributable to the low evolutionary rate characteristic of M. bovis leading to insufficient genetic information, but also to the complexity of the simulated multi-host system. This study highlights the importance of an integrated approach and the need to develop new outbreak reconstruction methods adapted to complex epidemiological systems and tested on realistic multi-host data.

Simulation experiment design for calibration via active learning

Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from the system that is being simulated. When simulation models are expensive, emulators are built with simulation data as a computationally efficient approximation of an expensive model. An emulator then can be used to predict model outputs, instead of repeatedly running an expensive simulation model during the calibration process. Sequential design with an intelligent selection criterion can guide the process of collecting simulation data to build an emulator, making the calibration process more efficient and effective. This article proposes two novel criteria for sequentially acquiring new simulation data in an active learning setting by considering uncertainties on the posterior density of parameters. Analysis of several simulation experiments and real-data simulation experiments from epidemiology demonstrates that proposed approaches result in improved posterior and field predictions.

Continuous Emission Ultrasound: A New Paradigm to Ultrafast Ultrasound Imaging.

Current imaging techniques in echography rely on the pulse-echo (PE) paradigm which provides a straight-forward access to the in-depth structure of tissues. They inherently face two major challenges: the limitation of the pulse repetition frequency, directly linked to the imaging framerate, and, due to the emission scheme, their blindness to the phenomena that happen in the medium during the majority of the acquisition time. To overcome these limitations, we propose a new paradigm for ultrasound imaging, denoted by continuous emission ultrasound imaging (CEUI) [1], for a single input single output (SISO) device. A continuous insonification of the medium is done by the probe using a coded waveform inspired from the radar and sonar literature. A framework coupling a sliding window approach (SWA) and pulse compression methods processes the recorded echoes to rebuild a motion-mode (M-mode) image from the medium with a high temporal resolution compared to state-of-the-art ultrafast imaging methods. A study on realistic simulated data, with regards to the motion of the medium, has been carried out and, achieved results assess an unequivocal improvement of the slow time frequency up to, at least, two orders of magnitude compared to ultrafast US imaging methods. This enhancement leads, therefore, to a ten times improvement in the temporal separability of the imaging system. In addition, it demonstrates the capability of CEUI to catch relatively short and quick events, in comparison to the imaging period of PE methods, at any instant of the acquisition.

Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios

BackgroundSingle-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.ResultsWe systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.ConclusionsNo method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.

Efficient Class of Variance Estimators for Population using Supplementary Information in Stratified Random Sampling

This paper addresses an efficient class of variance estimators for population using stratified random sampling. The suggested class of estimators using supplementary information has been studied in different circumstances. The expressions of bias and mean square error (MSE) of the proposed estimators are derived up to the first degree of approximation. The theoretical comparison of the proposed and considered estimators is also discussed, which shows that the proposed estimators are more efficient than the existing estimators. Theoretical findings are validated by three different types of real data sets and simulation studies. The numerical results of the proposed and existing estimators are compared in terms of mean square error, percentage relative efficiency and diagrams. It is observed that all the proposed estimators outperform the existing estimators. For instance, the traditional unbiased estimator Ozel et.al [6] and other existing estimators. Lastly, appropriate recommendations have been provided for researchers to use these suggested estimators to solve real-world issues.

Empirical uncertainty evaluation for the pose of a kinematic LiDAR-based multi-sensor system

Abstract Kinematic multi-sensor systems (MSS) describe their movements through six-degree-of-freedom trajectories, which are often evaluated primarily for accuracy. However, understanding their self-reported uncertainty is crucial, especially when operating in diverse environments like urban, industrial, or natural settings. This is important, so the following algorithms can provide correct and safe decisions, i.e. for autonomous driving. In the context of localization, light detection and ranging sensors (LiDARs) are widely applied for tasks such as generating, updating, and integrating information from maps supporting other sensors to estimate trajectories. However, popular low-cost LiDARs deviate from other geodetic sensors in their uncertainty modeling. This paper therefore demonstrates the uncertainty evaluation of a LiDAR-based MSS localizing itself using an inertial measurement unit (IMU) and matching LiDAR observations to a known map. The necessary steps for accomplishing the sensor data fusion in a novel Error State Kalman filter (ESKF) will be presented considering the influences of the sensor uncertainties and their combination. The results provide new insights into the impact of random and systematic deviations resulting from parameters and their uncertainties established in prior calibrations. The evaluation is done using the Mahalanobis distance to consider the deviations of the trajectory from the ground truth weighted by the self-reported uncertainty, and to evaluate the consistency in hypothesis testing. The evaluation is performed using a real data set obtained from an MSS consisting of a tactical grade IMU and a Velodyne Puck in combination with reference data by a Laser Tracker in a laboratory environment. The data set consists of measurements for calibrations and multiple kinematic experiments. In the first step, the data set is simulated based on the Laser Tracker measurements to provide a baseline for the results under assumed perfect corrections. In comparison, the results using a more realistic simulated data set and the real IMU and LiDAR measurements provide deviations about a factor of five higher leading to an inconsistent estimation. The results offer insights into the open challenges related to the assumptions for integrating low-cost LiDARs in MSSs.

Proportion Estimation Using Enhanced Class of Estimators Under Simple Random Sampling: Application with Real Data Sets and Simulation

ABSTRACT This study aims to suggest a generalized class of estimators for population proportion under simple random sampling, which uses auxiliary attributes. The bias and MSEs are considered derived to the first degree approximation. The validity of the suggested and existing estimators is assessed via an empirical investigation. The performance of estimators has been evaluated using real data sets and a simulation study. We found that the suggested estimators have minimum mean squared error (MSE) and a higher percentage relative efficiency when compared to existing estimators based on real data sets and simulation studies. The suggested estimator performs better than the existing ones, according to the theoretical and empirical findings.

Logistics Hub and Route Optimization in the Physical Internet Paradigm

Background: The global logistics industry is facing looming challenges related to labor shortages and low-efficiency problems due to the lack of logistics facilities and resources, resulting in increased logistics delays. The Physical Internet is seen as a way to take logistics into the next generation of transformation. This research proposes a Physical Internet-enabled system that allows multiple companies to efficiently share warehouses and trucks to achieve operational efficiency and reduce CO2 emissions. Methods: We propose a novel demography-weighted combinatorial optimization model utilizing a genetic algorithm and the Lin–Kernighan heuristic. The model is tested with real data simulations to evaluate its performance. Results: The results show that compared to the existing model presented in a previous study, our proposed model improves location optimality and distributive routing efficiency and reduces CO2 emissions by 54%. Conclusions: By providing a well-founded novel model, this research makes an important contribution to the implementation of the Physical Internet by computing optimal logistics hubs and routes as well as providing a solution to cut CO2 emissions by half.

Neutrosophic robust ratio type estimator for estimating finite population mean

Various authors have put their sincere efforts into proposing ratio estimators for estimating the population's mean and variance under different situations and sampling methods. But the problem arises when data is unstable, imprecise, ambiguous, incomplete and vague. In such situations, classical methods of estimation do not yield precise results, as these methods are not meant for such problems. Given this difficulty, Neutrosophic statistics are the only alternative as it deals with indeterminacy. So in this study, we have proposed a generalized Neutrosophic robust ratio type estimator which can be used to provide good results in such situations, as well as in the case of the presence of outliers. For the evaluation point of view, we have made use of real data set and simulation study to check the efficacy of our suggested estimators over the mentioned existed estimators.

Estimation of off-the grid sparse spikes with over-parametrized projected gradient descent: theory and application

In this article, we study the problem of recovering sparse spikes with over-parametrized projected descent. We first provide a theoretical study of approximate recovery with our chosen initialization method: Continuous Orthogonal Matching Pursuit without Sliding. Then we study the effect of over-parametrization on the gradient descent which highlights the benefits of the projection step. Finally, we show the improved calculation times of our algorithm compared to state-of-the-art model-based methods on realistic simulated microscopy data.

A High-loss Power Line Theft Detection Method Based on Segmented Dynamic Time Warping Distance

Most of the existing electricity theft detection approach of distribution lines identifies anomaly users with large volume of electricity usage data. Since users’ electricity usage data and loss of associated distribution lines are highly correlated, this could be analysed to identify the dishonest user of electricity theft. A segmented dynamic time bending distance based electricity theft detection approach of high-loss line is proposed in this paper. Firstly, the heuristic segmentation algorithm is used to transform the time series of electricity usage of each user and line loss to implement feature extraction and data reduction. Thereafter, dynamic time bending distance is employed to find out the user whose electricity usage is most similar to that of the line loss. The user whose electricity consumption has most similarity to that of line loss with the same fluctuation direction is assigned as the suspected user of electricity theft. Numerical simulation of real world metering data of high-loss lines suggest that the proposed approach has better accuracy and lower false positive rate as compared to the comparison method.

On the reliable estimation of sequential Monod kinetic parameters

While dozens of studies have attempted to estimate the Monod kinetic parameters of microbial reductive dechlorination, published values in the literature vary by 2–6 orders of magnitude. This lack of consensus can be attributed in part to limitations of both experimental design and parameter estimation techniques. To address these issues, Hamiltonian Monte Carlo was used to produce more than one million sets of realistic simulated microcosm data under a variety of experimental conditions. These data were then employed in model fitting experiments using a number of parameter estimation algorithms for determining Monod kinetic parameters. Analysis of data from conventional triplicate microcosms yielded parameter estimates characterized by high collinearity, resulting in poor estimation accuracy and precision. Additionally, confidence intervals computed by commonly used classical regression analysis techniques contained true parameter values much less frequently than their nominal confidence levels. Use of an alternative experimental design, requiring the same number of analyses as conventional experiments but comprised of microcosms with varying initial chlorinated ethene concentrations, is shown to result in order-of-magnitude decreases in parameter uncertainty. A Metropolis algorithm which can be run on a typical personal computer is demonstrated to return more reliable parameter interval estimates.

Interpretable deep learning methods for multiview learning

BackgroundTechnological advances have enabled the generation of unique and complementary types of data or views (e.g. genomics, proteomics, metabolomics) and opened up a new era in multiview learning research with the potential to lead to new biomedical discoveries.ResultsWe propose iDeepViewLearn (Interpretable Deep Learning Method for Multiview Learning) to learn nonlinear relationships in data from multiple views while achieving feature selection. iDeepViewLearn combines deep learning flexibility with the statistical benefits of data and knowledge-driven feature selection, giving interpretable results. Deep neural networks are used to learn view-independent low-dimensional embedding through an optimization problem that minimizes the difference between observed and reconstructed data, while imposing a regularization penalty on the reconstructed data. The normalized Laplacian of a graph is used to model bilateral relationships between variables in each view, therefore, encouraging selection of related variables. iDeepViewLearn is tested on simulated and three real-world data for classification, clustering, and reconstruction tasks. For the classification tasks, iDeepViewLearn had competitive classification results with state-of-the-art methods in various settings. For the clustering task, we detected molecular clusters that differed in their 10-year survival rates for breast cancer. For the reconstruction task, we were able to reconstruct handwritten images using a few pixels while achieving competitive classification accuracy. The results of our real data application and simulations with small to moderate sample sizes suggest that iDeepViewLearn may be a useful method for small-sample-size problems compared to other deep learning methods for multiview learning.ConclusioniDeepViewLearn is an innovative deep learning model capable of capturing nonlinear relationships between data from multiple views while achieving feature selection. It is fully open source and is freely available at https://github.com/lasandrall/iDeepViewLearn.

Statistical inference of inverted Nadarajah–Haghighi distribution under type-II generalized hybrid censoring competing risks data

Tahir et al. (J Stat Comput Simul 88(14):2775–2798, 2018) introduced the inverse Nadarajah–Haghighi distribution (INHD) and demonstrated its ability to model positive real data sets with decreasing and upside-down bathtub hazard rate shapes. This article focuses on the inference of unknown parameters using a generalized Type-II hybrid censoring scheme (GT-II HCS) for the INHD in the presence of competing risks. The maximum likelihood (ML) and Bayes approaches are used to estimate the model parameters. Based on the squared error loss function, we compute Bayes estimates using Markov Chain Monte Carlo (MCMC) by applying Metropolis-Hasting (M-H) algorithm. Furthermore, the asymptotic confidence intervals, bootstrap confidence intervals (BCIs) and the highest posterior density (HPD) credible intervals are constructed. Using real data sets and simulation studies, we examined the introduced methods of inference with different sample sizes.

Matrix variate receiver operating characteristic curve for binary classification

In recent years, the study of Receiver Operating Characteristic (ROC) curve analysis has gained significant attention as a means of accurately assessing test performance and determining optimal cutoff points. Traditionally, ROC models have been developed for bi-distributional univariate and multivariate data, such as Bi-normal, Bi-Exponential, Multivariate ROC models, and so forth. However, in current practical scenarios, the prevalence of high-dimensional matrix variate data poses a challenge for accurate test evaluation. To address this issue, this paper presents a novel ROC model that incorporates matrix variate normal distribution to effectively explain the accuracy of a test in the context of matrix data. Further, the accuracy measure, Area under the Curve (AUC) is derived, which helps in explaining the variability of the curve and provides the sensitivity at a particular value of specificity and vice versa. The proposed methodology is supported by a real data set and simulation studies.

Optimizing the Simulation of Conveyor Systems through Digital Shadow Integration to Increase Assembly Efficiency

In today's highly competitive industrial environment, continuous improvement of efficiency and optimization of processes is crucial. This paper presents an approach to the optimization of conveyor systems that uses the concept of a digital shadow. A digital shadow, as an exact digital replica of a physical conveyor system, enables detailed simulation and analysis of real operational data, providing a basis for in-depth analysis and identification of areas for improvement. The aim of this approach is not only to improve the understanding of the dynamics and performance of existing conveyor systems, but also to increase the overall efficiency through predictive simulations and optimization algorithms. In this work, we demonstrate how the integration of a digital shadow into the simulation process can contribute to a better reaction to changes in the production environment, to the reduction of downtime and to the optimization of production flows. Our methodology combines data collection / analysis, and enables the creation of accurate and flexible models of conveyor systems. These models are then used in simulations that help identify optimal settings for different production scenarios and predict potential problems before they occur. The results of applying our approach on a test laboratory line show a significant improvement in efficiency and a reduction in operating costs. This study provides important insights and practical guidelines for engineers and production managers focused on the use of digital shadow to increase the efficiency of conveyor systems. It also contributes to the development of intelligent production technologies in the era of Industry 4.0.

A Bayesian approach on asymmetric heavy tailed mixture of factor analyzer

<abstract> <p>A Mixture of factor analyzer (MFA) model is a powerful tool to reduce the number of free parameters in high-dimensional data through the factor-analyzer technique based on the covariance matrices. This model also prepares an efficient methodology to determine latent groups in data. In this paper, we use an MFA model with a rich and flexible class of distributions called hidden truncation hyperbolic (HTH) distribution and a Bayesian structure with several computational benefits. The MFA based on the HTH family allows the factor scores and the error component can be skewed and heavy-tailed. Therefore, using the HTH family leads to the robustness of the MFA in modeling asymmetrical datasets with/without outliers. Furthermore, the HTH family, because of several desired properties, including analytical flexibility, provides steps in the estimation of parameters that are computationally tractable. In the present study, the advantages of MFA based on the HTH family have been discussed and the suitable efficiency of the introduced MFA model has been demonstrated by using real data examples and simulation.</p> </abstract>

Time warping between main epidemic time series in epidemiological surveillance.

The most common reported epidemic time series in epidemiological surveillance are the daily or weekly incidence of new cases, the hospital admission count, the ICU admission count, and the death toll, which played such a prominent role in the struggle to monitor the Covid-19 pandemic. We show that pairs of such curves are related to each other by a generalized renewal equation depending on a smooth time varying delay and a smooth ratio generalizing the reproduction number. Such a functional relation is also explored for pairs of simultaneous curves measuring the same indicator in two neighboring countries. Given two such simultaneous time series, we develop, based on a signal processing approach, an efficient numerical method for computing their time varying delay and ratio curves, and we verify that its results are consistent. Indeed, they experimentally verify symmetry and transitivity requirements and we also show, using realistic simulated data, that the method faithfully recovers time delays and ratios. We discuss several real examples where the method seems to display interpretable time delays and ratios. The proposed method generalizes and unifies many recent related attempts to take advantage of the plurality of these health data across regions or countries and time, providing a better understanding of the relationship between them. An implementation of the method is publicly available at the EpiInvert CRAN package.

Higher Order Partial Least Squares Path Modeling Using Binary Data: An Application on Multidimensional Poverty and Social Protection in East Java Province

The standard partial least squares path modeling (PLS-PM) estimation process assumes the observed data as continuous variables. With slight modifications, this estimation algorithm can be used for data on a binary scale and even for more complex models such as higher order constructs. This study aims to determine by simulation and application of real data the performance of the higher-order construct modeling approach, which of the repeated indicator and two-stage approaches provides better results. From simulation study it was found that the repeated indicator approach with binary data (BinPLS) was better than the two-stage approach. Empirical results also show that the BinPLS measurement model with the repeated indicator approach is better than standard PLS. Evaluation of the structural model also shows that BinPLS with a repeated indicator approach is the best because it produces path coefficients and the power to explain multidimensional poverty and social protection models that are better than BinPLS with a two-stage approach and standard PLS.

Application of Sampling Variance Smoothing Methods for Small Area Proportion Estimation

Abstract Sampling variance smoothing is an important topic in small area estimation. In this article, we propose sampling variance smoothing methods for small area proportion estimation. In particular, we consider the generalized variance function and design effect methods for sampling variance smoothing. We evaluate and compare the smoothed sampling variances and small area estimates based on the smoothed variance estimates through analysis of survey data from Statistics Canada. The results from real data analysis and simulation study indicate that the proposed sampling variance smoothing methods perform very well for small area estimation.