Modeling in higher dimensions to improve diagnostic testing accuracy: Theory and examples for multiplex saliva-based SARS-CoV-2 antibody assays.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the importance and challenges of correctly interpreting antibody test results. Identification of positive and negative samples requires a classification strategy with low error rates, which is hard to achieve when the corresponding measurement values overlap. Additional uncertainty arises when classification schemes fail to account for complicated structure in data. We address these problems through a mathematical framework that combines high dimensional data modeling and optimal decision theory. Specifically, we show that appropriately increasing the dimension of data better separates positive and negative populations and reveals nuanced structure that can be described in terms of mathematical models. We combine these models with optimal decision theory to yield a classification scheme that better separates positive and negative samples relative to traditional methods such as confidence intervals (CIs) and receiver operating characteristics. We validate the usefulness of this approach in the context of a multiplex salivary SARS-CoV-2 immunoglobulin G assay dataset. This example illustrates how our analysis: (i) improves the assay accuracy, (e.g. lowers classification errors by up to 42% compared to CI methods); (ii) reduces the number of indeterminate samples when an inconclusive class is permissible, (e.g. by 40% compared to the original analysis of the example multiplex dataset) and (iii) decreases the number of antigens needed to classify samples. Our work showcases the power of mathematical modeling in diagnostic classification and highlights a method that can be adopted broadly in public health and clinical settings.

Optimal classification and generalized prevalence estimates for diagnostic settings with more than two classes.

An accurate multiclass classification strategy is crucial to interpreting antibody tests. However, traditional methods based on confidence intervals or receiver operating characteristics lack clear extensions to settings with more than two classes. We address this problem by developing a multiclass classification based on probabilistic modeling and optimal decision theory that minimizes the convex combination of false classification rates. The classification process is challenging when the relative fraction of the population in each class, or generalized prevalence, is unknown. Thus, we also develop a method for estimating the generalized prevalence of test data that is independent of classification of the test data. We validate our approach on serological data with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) naïve, previously infected, and vaccinated classes. Synthetic data are used to demonstrate that (i) prevalence estimates are unbiased and converge to true values and (ii) our procedure applies to arbitrary measurement dimensions. In contrast to the binary problem, the multiclass setting offers wide-reaching utility as the most general framework and provides new insight into prevalence estimation best practices.

Modeling in higher dimensions to improve diagnostic testing accuracy: theory and examples for multiplex saliva-based SARS-CoV-2 antibody assays.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the importance and challenges of correctly interpreting antibody test results. Identification of positive and negative samples requires a classification strategy with low error rates, which is hard to achieve when the corresponding measurement values overlap. Additional uncertainty arises when classification schemes fail to account for complicated structure in data. We address these problems through a mathematical framework that combines high dimensional data modeling and optimal decision theory. Specifically, we show that appropriately increasing the dimension of data better separates positive and negative populations and reveals nuanced structure that can be described in terms of mathematical models. We combine these models with optimal decision theory to yield a classification scheme that better separates positive and negative samples relative to traditional methods such as confidence intervals (CIs) and receiver operating characteristics. We validate the usefulness of this approach in the context of a multiplex salivary SARS-CoV-2 immunoglobulin G assay dataset. This example illustrates how our analysis: (i) improves the assay accuracy (e.g. lowers classification errors by up to 42 % compared to CI methods); (ii) reduces the number of indeterminate samples when an inconclusive class is permissible (e.g. by 40 % compared to the original analysis of the example multiplex dataset); and (iii) decreases the number of antigens needed to classify samples. Our work showcases the power of mathematical modeling in diagnostic classification and highlights a method that can be adopted broadly in public health and clinical settings.

Dynamics and mechanisms for tear breakup (TBU) on the ocular surface.

The human tear film is rapidly established after each blink, and is essential for clear vision and eye health. This paper reviews mathematical models and theories for the human tear film on the ocular surface, with an emphasis on localized flows where the tear film may fail. The models attempt to identify the important physical processes, and their parameters, governing the tear film in health and disease.

Parameter Estimation for Mixed-Mechanism Tear Film Thinning.

Etiologies of tear breakup include evaporation-driven, divergent flow-driven, and a combination of these two. A mathematical model incorporating evaporation and lipid-driven tangential flow is fit to fluorescence imaging data. The lipid-driven motion is hypothesized to be caused by localized excess lipid, or "globs." Tear breakup quantities such as evaporation rates and tangential flow rates cannot currently be directly measured during breakup. We determine such variables by fitting mathematical models for tear breakup and the computed fluorescent intensity to experimental intensity data gathered in vivo. Parameter estimation is conducted via least squares minimization of the difference between experimental data and computed answers using either the trust-region-reflective or Levenberg-Marquardt algorithm. Best-fit determination of tear breakup parameters supports the notion that evaporation and divergent tangential flow can cooperate to drive breakup. The resulting tear breakup is typically faster than purely evaporative cases. Many instances of tear breakup may have similar causes, which suggests that interpretation of experimental results may benefit from considering multiple mechanisms.

Parameter Estimation for Evaporation-Driven Tear Film Thinning.

Many parameters affect tear film thickness and fluorescent intensity distributions over time; exact values or ranges for some are not well known. We conduct parameter estimation by fitting to fluorescent intensity data recorded from normal subjects' tear films. The fitting is done with thin film fluid dynamics models that are nonlinear partial differential equation models for the thickness, osmolarity and fluorescein concentration of the tear film for circular (spot) or linear (streak) tear film breakup. The corresponding fluorescent intensity is computed from the tear film thickness and fluorescein concentration. The least squares error between computed and experimental fluorescent intensity determines the parameters. The results vary across subjects and trials. The optimal values for variables that cannot be measured in vivo within tear film breakup often fall within accepted experimental ranges for related tear film dynamics; however, some instances suggest that a wider range of parameter values may be acceptable.