Prevalence Estimation and Optimal Classification Methods to Account for Time Dependence in Antibody Levels

Serology testing can identify past infection by quantifying the immune response of an infected individual providing important public health guidance. Individual immune responses are time-dependent, which is reflected in antibody measurements. Moreover, the probability of obtaining a particular measurement changes due to prevalence as the disease progresses. Taking into account these personal and population-level effects, we develop a mathematical model that suggests a natural adaptive scheme for estimating prevalence as a function of time. We then combine the estimated prevalence with optimal decision theory to develop a time-dependent probabilistic classification scheme that minimizes error. We validate this analysis by using a combination of real-world and synthetic SARS-CoV-2 data and discuss the type of longitudinal studies needed to execute this scheme in real-world settings.Comment: 29 pages, 11 figure

Minimal Assumptions for Optimal Serology Classification: Theory and Implications for Multidimensional Settings and Impure Training Data

Minimizing error in prevalence estimates and diagnostic classifiers remains a challenging task in serology. In theory, these problems can be reduced to modeling class-conditional probability densities (PDFs) of measurement outcomes, which control all downstream analyses. However, this task quickly succumbs to the curse of dimensionality, even for assay outputs with only a few dimensions (e.g. target antigens). To address this problem, we propose a technique that uses empirical training data to classify samples and estimate prevalence in arbitrary dimension without direct access to the conditional PDFs. We motivate this method via a lemma that relates relative conditional probabilities to minimum-error classification boundaries. This leads us to formulate an optimization problem that: (i) embeds the data in a parameterized, curved space; (ii) classifies samples based on their position relative to a coordinate axis; and (iii) subsequently optimizes the space by minimizing the empirical classification error of pure training data, for which the classes are known. Interestingly, the solution to this problem requires use of a homotopy-type method to stabilize the optimization. We then extend the analysis to the case of impure training data, for which the classes are unknown. We find that two impure datasets suffice for both prevalence estimation and classification, provided they satisfy a linear independence property. Lastly, we discuss how our analysis unifies discriminative and generative learning techniques in a common framework based on ideas from set and measure theory. Throughout, we validate our methods in the context of synthetic data and a research-use SARS-CoV-2 enzyme-linked immunosorbent (ELISA) assay

A Practical Algorithm for General Large Scale Nonlinear Optimization Problems

We provide an effective and efficient implementation of a sequential quadratic programming (SQP) algorithm for the general large scale nonlinear programming problem. In this algorithm the quadratic programming subproblems are solved by an interior point method that can be prematurely halted by a trust region constraint. Numerous computational enhancements to improve the numerical performance are presented. These include a dynamic procedure for adjusting the merit function parameter and procedures for adjusting the trust region radius. Numerical results and comparisons are presented

An Infeasible Point Method for Minimizing the Lennard-Jones Potential

Minimizing the Lennard-Jones potential, the most-studied modelproblem for molecular conformation, is an unconstrained globaloptimization problem with a large number of local minima. In thispaper, the problem is reformulated as an equality constrainednonlinear programming problem with only linear constraints. Thisformulation allows the solution to approached through infeasibleconfigurations, increasing the basin of attraction of the globalsolution. In this way the likelihood of finding a global minimizeris increased. An algorithm for solving this nonlinear program isdiscussed, and results of numerical tests are presented.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44788/1/10589_2004_Article_140555.pd

Long-term thermal sensitivity of Earth’s tropical forests

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate

Consistent patterns of common species across tropical tree communities

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1,2,3,4,5,6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.Publisher PDFPeer reviewe