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Empirical likelihood enables a nonparametric, likelihood-driven style of inference without restrictive assumptions routinely made in parametric models. We develop a framework for applying empirical likelihood to the analysis of experimental designs, addressing issues that arise from blocking and multiple hypothesis testing. In addition to popular designs such as balanced incomplete block designs, our approach allows for highly unbalanced, incomplete block designs. We derive an asymptotic multivariate chi-square distribution for a set of empirical likelihood test statistics and propose two single-step multiple testing procedures: asymptotic Monte Carlo and nonparametric bootstrap. Both procedures asymptotically control the generalised family-wise error rate and efficiently construct simultaneous confidence intervals for comparisons of interest without explicitly considering the underlying covariance structure. A simulation study demonstrates that the performance of the procedures is robust to violations of standard assumptions of linear mixed models. We also present an application to experiments on a pesticide.

Although there is substantial literature on identifying structural changes for continuous spatio-temporal processes, the same is not true for categorical spatio-temporal data. This work bridges that gap and proposes a novel spatio-temporal model to identify changepoints in ordered categorical data. The model leverages an additive mean structure with separable Gaussian space-time processes for the latent variable. Our proposed methodology can detect significant changes in the mean structure as well as in the spatio-temporal covariance structures. We implement the model through a Bayesian framework that gives a computational edge over conventional approaches. From an application perspective, our approach's capability to handle ordinal categorical data provides an added advantage in real applications. This is illustrated using county-wise COVID-19 data (converted to categories according to CDC guidelines) from the state of New York in the USA. Our model identifies three changepoints in the transmission levels of COVID-19, which are indeed aligned with the ``waves'' due to specific variants encountered during the pandemic. The findings also provide interesting insights into the effects of vaccination and the extent of spatial and temporal dependence in different phases of the pandemic.

Deep learning-based approaches have produced models with good insect classification accuracy; Most of these models are conducive for application in controlled environmental conditions. One of the primary emphasis of researchers is to implement identification and classification models in the real agriculture fields, which is challenging because input images that are wildly out of the distribution (e.g., images like vehicles, animals, humans, or a blurred image of an insect or insect class that is not yet trained on) can produce an incorrect insect classification. Out-of-distribution (OOD) detection algorithms provide an exciting avenue to overcome these challenge as it ensures that a model abstains from making incorrect classification prediction of non-insect and/or untrained insect class images. We generate and evaluate the performance of state-of-the-art OOD algorithms on insect detection classifiers. These algorithms represent a diversity of methods for addressing an OOD problem. Specifically, we focus on extrusive algorithms, i.e., algorithms that wrap around a well-trained classifier without the need for additional co-training. We compared three OOD detection algorithms: (i) Maximum Softmax Probability, which uses the softmax value as a confidence score, (ii) Mahalanobis distance-based algorithm, which uses a generative classification approach; and (iii) Energy-Based algorithm that maps the input data to a scalar value, called energy. We performed an extensive series of evaluations of these OOD algorithms across three performance axes: (a) \textit{Base model accuracy}: How does the accuracy of the classifier impact OOD performance? (b) How does the \textit{level of dissimilarity to the domain} impact OOD performance? and (c) \textit{Data imbalance}: How sensitive is OOD performance to the imbalance in per-class sample size?

The development of new manufacturing techniques such as 3D printing have enabled the creation of previously infeasible chemical reactor designs. Systematically optimizing the highly parameterized geometries involved in these new classes of reactor is vital to ensure enhanced mixing characteristics and feasible manufacturability. Here we present a framework to rapidly solve this nonlinear, computationally expensive, and derivative-free problem, enabling the fast prototype of novel reactor parameterizations. We take advantage of Gaussian processes to adaptively learn a multi-fidelity model of reactor simulations across a number of different continuous mesh fidelities. The search space of reactor geometries is explored through an amalgam of different, potentially lower, fidelity simulations which are chosen for evaluation based on weighted acquisition function, trading off information gain with cost of simulation. Within our framework we derive a novel criteria for monitoring the progress and dictating the termination of multi-fidelity Bayesian optimization, ensuring a high fidelity solution is returned before experimental budget is exhausted. The class of reactor we investigate are helical-tube reactors under pulsed-flow conditions, which have demonstrated outstanding mixing characteristics, have the potential to be highly parameterized, and are easily manufactured using 3D printing. To validate our results, we 3D print and experimentally validate the optimal reactor geometry, confirming its mixing performance. In doing so we demonstrate our design framework to be extensible to a broad variety of expensive simulation-based optimization problems, supporting the design of the next generation of highly parameterized chemical reactors.

The prediction of stochastic dynamical systems and the capture of dynamical behaviors are profound problems. In this article, we propose a data-driven framework combining Reservoir Computing and Normalizing Flow to study this issue, which mimics error modeling to improve the traditional Reservoir Computing performance and takes advantage of both approaches. This model-free method successfully predicts the long-term evolution of stochastic dynamical systems and replicates dynamical behaviors. With few assumptions about the underlying stochastic dynamical systems, we deal with Markov/non-Markov and stationary/non-stationary stochastic processes defined by linear/nonlinear stochastic differential equations or stochastic delay differential equations. We verify the effectiveness of the proposed framework in five experiments, including the Ornstein-Uhlenbeck process, Double-Well system, El Ni\~no Southern Oscillation simplified model, and stochastic Lorenz system. Additionally, we explore the noise-induced tipping phenomena and the replication of the strange attractor.

Survival analysis is the problem of estimating probability distributions for future event times, which can be seen as a problem in uncertainty quantification. Although there are fundamental theories on strictly proper scoring rules for uncertainty quantification, little is known about those for survival analysis. In this paper, we investigate extensions of four major strictly proper scoring rules for survival analysis and we prove that these extensions are proper under certain conditions, which arise from the discretization of the estimation of probability distributions. We also compare the estimation performances of these extended scoring rules by using real datasets, and the extensions of the logarithmic score and the Brier score performed the best.

The Coronavirus Disease 2019 (COVID-19) has a profound impact on global health and economy, making it crucial to build accurate and interpretable data-driven predictive models for COVID-19 cases to improve policy making. The extremely large scale of the pandemic and the intrinsically changing transmission characteristics pose great challenges for effective COVID-19 case prediction. To address this challenge, we propose a novel hybrid model in which the interpretability of the Autoregressive model (AR) and the predictive power of the long short-term memory neural networks (LSTM) join forces. The proposed hybrid model is formalized as a neural network with an architecture that connects two composing model blocks, of which the relative contribution is decided data-adaptively in the training procedure. We demonstrate the favorable performance of the hybrid model over its two component models as well as other popular predictive models through comprehensive numerical studies on two data sources under multiple evaluation metrics. Specifically, in county-level data of 8 California counties, our hybrid model achieves 4.173% MAPE on average, outperforming the composing AR (5.629%) and LSTM (4.934%). In country-level datasets, our hybrid model outperforms the widely-used predictive models - AR, LSTM, SVM, Gradient Boosting, and Random Forest - in predicting COVID-19 cases in 8 countries around the world. In addition, we illustrate the interpretability of our proposed hybrid model, a key feature not shared by most black-box predictive models for COVID-19 cases. Our study provides a new and promising direction for building effective and interpretable data-driven models, which could have significant implications for public health policy making and control of the current and potential future pandemics.

Kemeny's rule is one of the most studied and well-known voting schemes with various important applications in computational social choice and biology. Recently, Kemeny's rule was generalized via a set-wise approach by Gilbert et. al. Following this paradigm, we have shown in \cite{Phung-Hamel-2023} that the $3$-wise Kemeny voting scheme induced by the $3$-wise Kendall-tau distance presents interesting advantages in comparison with the classical Kemeny rule. While the $3$-wise Kemeny problem, which consists of computing the set of $3$-wise consensus rankings of a voting profile, is NP-hard, we establish in this paper several generalizations of the Major Order Theorems, as obtained in \cite{Milosz-Hamel-2020} for the classical Kemeny rule, for the $3$-wise Kemeny voting scheme to achieve a substantial search space reduction by efficiently determining in polynomial time the relative orders of pairs of alternatives. Essentially, our theorems quantify precisely the non-trivial property that if the preference for an alternative over another one in an election is strong enough, not only in the head-to-head competition but even when taking into consideration one or two more alternatives, then the relative order of these two alternatives in every $3$-wise consensus ranking must be as expected. Moreover, we show that the well-known $3/4$-majority rule of Betzler et al. for the classical Kemeny rule is only valid for elections with no more than $5$ alternatives with respect to the $3$-wise Kemeny scheme. Examples are also provided to show that the $3$-wise Kemeny rule is more resistant to manipulation than the classical one.

We study numerical integration over bounded regions in $\mathbb{R}^s, s\ge1$ with respect to some probability measure. We replace random sampling with quasi-Monte Carlo methods, where the underlying point set is derived from deterministic constructions that aim to fill the space more evenly than random points. Such quasi-Monte Carlo point sets are ordinarily designed for the uniform measure, and the theory only works for product measures when a coordinate-wise transformation is applied. Going beyond this setting, we first consider the case where the target density is a mixture distribution where each term in the mixture comes from a product distribution. Next we consider target densities which can be approximated with such mixture distributions. We require the approximation to be a sum of coordinate-wise products and the approximation to be positive everywhere (so that they can be re-scaled to probability density functions). We use tensor product hat function approximations for this purpose here, since a hat function approximation of a positive function is itself positive. We also study more complex algorithms, where we first approximate the target density with a general Gaussian mixture distribution and approximate the mixtures with an adaptive hat function approximation on rotated intervals. The Gaussian mixture approximation allows us to locate the essential parts of the target density, whereas the adaptive hat function approximation allows us to approximate the finer structure of the target density. We prove convergence rates for each of the integration techniques based on quasi-Monte Carlo sampling for integrands with bounded partial mixed derivatives. The employed algorithms are based on digital $(t,s)$-sequences over the finite field $\mathbb{F}_2$ and an inversion method. Numerical examples illustrate the performance of the algorithms for some target densities and integrands.

According to ICH Q8 guidelines, the biopharmaceutical manufacturer submits a design space (DS) definition as part of the regulatory approval application, in which case process parameter (PP) deviations within this space are not considered a change and do not trigger a regulatory post approval procedure. A DS can be described by non-linear PP ranges, i.e., the range of one PP conditioned on specific values of another. However, independent PP ranges (linear combinations) are often preferred in biopharmaceutical manufacturing due to their operation simplicity. While some statistical software supports the calculation of a DS comprised of linear combinations, such methods are generally based on discretizing the parameter space - an approach that scales poorly as the number of PPs increases. Here, we introduce a novel method for finding linear PP combinations using a numeric optimizer to calculate the largest design space within the parameter space that results in critical quality attribute (CQA) boundaries within acceptance criteria, predicted by a regression model. A precomputed approximation of tolerance intervals is used in inequality constraints to facilitate fast evaluations of this boundary using a single matrix multiplication. Correctness of the method was validated against different ground truths with known design spaces. Compared to stateof-the-art, grid-based approaches, the optimizer-based procedure is more accurate, generally yields a larger DS and enables the calculation in higher dimensions. Furthermore, a proposed weighting scheme can be used to favor certain PPs over others and therefore enabling a more dynamic approach to DS definition and exploration. The increased PP ranges of the larger DS provide greater operational flexibility for biopharmaceutical manufacturers.