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1. A robust pooled testing approach to expand COVID-19 screening capacity

   https://doi.org/10.1371/journal.pone.0246285  

   Bish, Douglas R.; Bish, Ebru K.; El-Hajj, Hussein; Aprahamian, Hrayer (February 2021, PLOS ONE)

   Pantea, Casian (Ed.)

   Limited testing capacity for COVID-19 has hampered the pandemic response. Pooling is a testing method wherein samples from specimens (e.g., swabs) from multiple subjects are combined into a pool and screened with a single test. If the pool tests positive, then new samples from the collected specimens are individually tested, while if the pool tests negative, the subjects are classified as negative for the disease. Pooling can substantially expand COVID-19 testing capacity and throughput, without requiring additional resources. We develop a mathematical model to determine the best pool size for different risk groups , based on each group’s estimated COVID-19 prevalence. Our approach takes into consideration the sensitivity and specificity of the test, and a dynamic and uncertain prevalence, and provides a robust pool size for each group. For practical relevance, we also develop a companion COVID-19 pooling design tool (through a spread sheet). To demonstrate the potential value of pooling, we study COVID-19 screening using testing data from Iceland for the period, February-28-2020 to June-14-2020, for subjects stratified into high- and low-risk groups. We implement the robust pooling strategy within a sequential framework, which updates pool sizes each week, for each risk group, based on prior week’s testing data. Robust pooling reduces the number of tests, over individual testing, by 88.5% to 90.2%, and 54.2% to 61.9%, respectively, for the low-risk and high-risk groups (based on test sensitivity values in the range [0.71, 0.98] as reported in the literature). This results in much shorter times, on average, to get the test results compared to individual testing (due to the higher testing throughput), and also allows for expanded screening to cover more individuals. Thus, robust pooling can potentially be a valuable strategy for COVID-19 screening. 

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2. Generalized additive regression for group testing data

   https://doi.org/10.1093/biostatistics/kxaa003  

   Liu, Yan; McMahan, Christopher S; Tebbs, Joshua M; Gallagher, Colin M; Bilder, Christopher R (February 2020, Biostatistics)

   Summary In screening applications involving low-prevalence diseases, pooling specimens (e.g., urine, blood, swabs, etc.) through group testing can be far more cost effective than testing specimens individually. Estimation is a common goal in such applications and typically involves modeling the probability of disease as a function of available covariates. In recent years, several authors have developed regression methods to accommodate the complex structure of group testing data but often under the assumption that covariate effects are linear. Although linearity is a reasonable assumption in some applications, it can lead to model misspecification and biased inference in others. To offer a more flexible framework, we propose a Bayesian generalized additive regression approach to model the individual-level probability of disease with potentially misclassified group testing data. Our approach can be used to analyze data arising from any group testing protocol with the goal of estimating multiple unknown smooth functions of covariates, standard linear effects for other covariates, and assay classification accuracy probabilities. We illustrate the methods in this article using group testing data on chlamydia infection in Iowa. 

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3. Array testing for multiplex assays

   https://doi.org/10.1093/biostatistics/kxy058  

   Hou, Peijie; Tebbs, Joshua M; Wang, Dewei; McMahan, Christopher S; Bilder, Christopher R (October 2018, Biostatistics)

   null (Ed.)

   Summary Group testing involves pooling individual specimens (e.g., blood, urine, swabs, etc.) and testing the pools for the presence of disease. When the proportion of diseased individuals is small, group testing can greatly reduce the number of tests needed to screen a population. Statistical research in group testing has traditionally focused on applications for a single disease. However, blood service organizations and large-scale disease surveillance programs are increasingly moving towards the use of multiplex assays, which measure multiple disease biomarkers at once. Tebbs and others (2013, Two-stage hierarchical group testing for multiple infections with application to the Infertility Prevention Project. Biometrics69, 1064–1073) and Hou and others (2017, Hierarchical group testing for multiple infections. Biometrics73, 656–665) were the first to examine hierarchical group testing case identification procedures for multiple diseases. In this article, we propose new non-hierarchical procedures which utilize two-dimensional arrays. We derive closed-form expressions for the expected number of tests per individual and classification accuracy probabilities and show that array testing can be more efficient than hierarchical procedures when screening individuals for multiple diseases at once. We illustrate the potential of using array testing in the detection of chlamydia and gonorrhea for a statewide screening program in Iowa. Finally, we describe an R/Shiny application that will help practitioners identify the best multiple-disease case identification algorithm. 

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4. Novel Pooling Strategies for Genetic Testing, with Application to Newborn Screening

   https://doi.org/10.1287/mnsc.2021.4289  

   El Hajj, Hussein; Bish, Douglas R.; Bish, Ebru K.; Kay, Denise M. (March 2022, Management Science)

   Newborn screening (NBS) is a state-level initiative that detects life-threatening genetic disorders for which early treatment can substantially improve health outcomes. Cystic fibrosis (CF) is among the most prevalent disorders in NBS. CF can be caused by a large number of mutation variants to the CFTR gene. Most states use a multitest CF screening process that includes a genetic test (DNA). However, due to cost concerns, DNA is used only on a small subset of newborns (based on a low-cost biomarker test with low classification accuracy), and only for a small subset of CF-causing variants. To overcome the cost barriers of expanded genetic testing, we explore a novel approach, of multipanel pooled DNA testing. This approach leads not only to a novel optimization problem (variant selection for screening, variant partition into multipanels, and pool size determination for each panel), but also to novel CF NBS processes. We establish key structural properties of optimal multipanel pooled DNA designs; develop a methodology that generates a family of optimal designs at different costs; and characterize the conditions under which a 1-panel versus a multipanel design is optimal. This methodology can assist decision-makers to design a screening process, considering the cost versus accuracy trade-off. Our case study, based on published CF NBS data from the state of New York, indicates that the multipanel and pooling aspects of genetic testing work synergistically, and the proposed NBS processes have the potential to substantially improve both the efficiency and accuracy of current practices. This paper was accepted by Stefan Scholtes, healthcare management. 

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5. An uncertainty-aware deep learning framework-based robust design optimization of metamaterial units

   https://doi.org/10.1007/s00158-025-03979-z  

   Wang, Zihan; Bhaduri, Anindya; Xu, Hongyi; Wang, Liping (March 2025, Structural and Multidisciplinary Optimization)

   Mechanical metamaterials represent an innovative class of artificial structures, distinguished by their extraordinary mechanical characteristics, which are beyond the scope of traditional natural materials. The use of deep generative models has become increasingly popular in the design of metamaterial units. The effectiveness of using deep generative models lies in their capacity to compress complex input data into a simplified, lower-dimensional latent space, while also enabling the creation of novel optimal designs through sampling within this space. However, the design process does not take into account the effect of model uncertainty due to data sparsity or the effect of input data uncertainty due to inherent randomness in the data. This might lead to the generation of undesirable structures with high sensitivity to the uncertainties in the system. To address this issue, a novel uncertainty-aware deep learning framework-based robust design approach is proposed for the design of metamaterial units with optimal target properties. The proposed approach utilizes the probabilistic nature of the deep learning framework and quantifies both aleatoric and epistemic uncertainties associated with surrogate-based design optimization. We demonstrate that the proposed design approach is capable of designing high-performance metamaterial units with high reliability. To showcase the effectiveness of the proposed design approach, a single-objective design optimization problem and a multi-objective design optimization problem are presented. The optimal robust designs obtained are validated by comparing them to the designs obtained from the topology optimization method as well as the designs obtained from a deterministic deep learning framework-based design optimization where none of the uncertainties in the system are explicitly considered. 

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