Epidemiological delays, such as incubation periods, serial intervals, and hospital lengths of stay, are among key quantities in infectious disease epidemiology that inform public health policy and clinical practice. This information is used to inform mathematical and statistical models, which in turn can inform control strategies. There are three main challenges that make delay distributions difficult to estimate. First, the data are commonly censored (e.g., symptom onset may only be reported by date instead of the exact time of day). Second, delays are often right truncated when being estimated in real time (not all events that have occurred have been observed yet). Third, during a rapidly growing or declining outbreak, overrepresentation or underrepresentation, respectively, of recently infected cases in the data can lead to bias in estimates. Studies that estimate delays rarely address all these factors and sometimes report several estimates using different combinations of adjustments, which can lead to conflicting answers and confusion about which estimates are most accurate. In this work, we formulate a checklist of best practices for estimating and reporting epidemiological delays with a focus on the incubation period and serial interval. We also propose strategies for handling common biases and identify areas where more work is needed. Our recommendations can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.
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Accurately extracting clinical information from speech is critical to the diagnosis and treatment of many neurological conditions. As such, there is interest in leveraging AI for automatic, objective assessments of clinical speech to facilitate diagnosis and treatment of speech disorders. We explore transfer learning using foundation models, focusing on the impact of layer selection for the downstream task of predicting pathological speech features. We find that selecting an optimal layer can greatly improve performance (~15.8% increase in balanced accuracy per feature as compared to worst layer, ~13.6% increase as compared to final layer), though the best layer varies by predicted feature and does not always generalize well to unseen data. A learned weighted sum offers comparable performance to the average best layer in-distribution (only ~1.2% lower) and had strong generalization for out-of-distribution data (only 1.5% lower than the average best layer).
The emergence of cooperative behavior, despite natural selection favoring rational self-interest, presents a significant evolutionary puzzle. Evolutionary game theory elucidates why cooperative behavior can be advantageous for survival. However, the impact of non-uniformity in the frequency of actions, particularly when actions are altered in the short term, has received little scholarly attention. To demonstrate the relationship between the non-uniformity in the frequency of actions and the evolution of cooperation, we conducted multi-agent simulations of evolutionary games. In our model, each agent performs actions in a chain-reaction, resulting in a non-uniform distribution of the number of actions. To achieve a variety of non-uniform action frequency, we introduced two types of chain-reaction rules: one where an agent's actions trigger subsequent actions, and another where an agent's actions depend on the actions of others. Our results revealed that cooperation evolves more effectively in scenarios with even slight non-uniformity in action frequency compared to completely uniform cases. In addition, scenarios where agents' actions are primarily triggered by their own previous actions more effectively support cooperation, whereas those triggered by others' actions are less effective. This implies that a few highly active individuals contribute positively to cooperation, while the tendency to follow others' actions can hinder it.
After decades of attention, emergence continues to lack a centralized mathematical definition that leads to a rigorous emergence test applicable to physical flocks and swarms, particularly those containing both deterministic elements (eg, interactions) and stochastic perturbations like measurement noise. This study develops a heuristic test based on singular value curve analysis of data matrices containing deterministic and Gaussian noise signals. The minimum detection criteria are identified, and statistical and matrix space analysis developed to determine upper and lower bounds. This study applies the analysis to representative examples by using recorded trajectories of mixed deterministic and stochastic trajectories for multi-agent, cellular automata, and biological video. Examples include Cucker Smale and Vicsek flocking, Gaussian noise and its integration, recorded observations of bird flocking, and 1D cellular automata. Ensemble simulations including measurement noise are performed to compute statistical variation and discussed relative to random matrix theory noise bounds. The results indicate singular knee analysis of recorded trajectories can detect gradated levels on a continuum of structure and noise. Across the eight singular value decay metrics considered, the angle subtended at the singular value knee emerges with the most potential for supporting cross-embodiment emergence detection, the size of noise bounds is used as an indication of required sample size, and the presence of a large fraction of singular values inside noise bounds as an indication of noise.
We consider the problem of a graph subjected to adversarial perturbations, such as those arising from cyber-attacks, where edges are covertly added or removed. The adversarial perturbations occur during the transmission of the graph between a sender and a receiver. To counteract potential perturbations, we explore a repetition coding scheme with sender-assigned binary noise and majority voting on the receiver's end to rectify the graph's structure. Our approach operates without prior knowledge of the attack's characteristics. We provide an analytical derivation of a bound on the number of repetitions needed to satisfy probabilistic constraints on the quality of the reconstructed graph. We show that the method can accurately decode graphs that were subjected to non-random edge removal, namely, those connected to vertices with the highest eigenvector centrality, in addition to random addition and removal of edges by the attacker.
Neighborhood disadvantage is associated with worse health and cognitive outcomes. Morphological similarity network (MSN) is a promising approach to elucidate cortical network patterns underlying complex cognitive functions. We hypothesized that MSNs could capture changes in cortical patterns related to neighborhood disadvantage and cognitive function. This cross-sectional study included cognitively unimpaired participants from two large Alzheimers studies at University of Wisconsin-Madison. Neighborhood disadvantage status was obtained using the Area Deprivation Index (ADI). Cognitive performance was assessed on memory, processing speed and executive function. Morphological Similarity Networks (MSN) were constructed for each participant based on the similarity in distribution of cortical thickness of brain regions, followed by computation of local and global network features. Association of ADI with cognitive scores and MSN features were examined using linear regression and mediation analysis. ADI showed negative association with category fluency,implicit learning speed, story recall and modified pre-clinical Alzheimers cognitive composite scores, indicating worse cognitive function among those living in more disadvantaged neighborhoods. Local network features of frontal and temporal regions differed based on ADI status. Centrality of left lateral orbitofrontal region showed a partial mediating effect between association of neighborhood disadvantage and story recall performance. Our preliminary findings suggest differences in local cortical organization by neighborhood disadvantage, which partially mediated the relationship between ADI and cognitive performance, providing a possible network-based mechanism to, in-part, explain the risk for poor cognitive functioning associated with disadvantaged neighborhoods.
Difference-in-differences (DID) is a popular approach to identify the causal effects of treatments and policies in the presence of unmeasured confounding. DID identifies the sample average treatment effect in the treated (SATT). However, a goal of such research is often to inform decision-making in target populations outside the treated sample. Transportability methods have been developed to extend inferences from study samples to external target populations; these methods have primarily been developed and applied in settings where identification is based on conditional independence between the treatment and potential outcomes, such as in a randomized trial. We present a novel approach to identifying and estimating effects in a target population, based on DID conducted in a study sample that differs from the target population. We present a range of assumptions under which one may identify causal effects in the target population and employ causal diagrams to illustrate these assumptions. In most realistic settings, results depend critically on the assumption that any unmeasured confounders are not effect measure modifiers on the scale of the effect of interest (e.g., risk difference, odds ratio). We develop several estimators of transported effects, including g-computation, inverse odds weighting, and a doubly robust estimator based on the efficient influence function. Simulation results support theoretical properties of the proposed estimators. As an example, we apply our approach to study the effects of a 2018 US federal smoke-free public housing law on air quality in public housing across the US, using data from a DID study conducted in New York City alone.
Error bounds are derived for sampling and estimation using a discretization of an intrinsically defined Langevin diffusion with invariant measure $\text{d}\mu_\phi \propto e^{-\phi} \mathrm{dvol}_g $ on a compact Riemannian manifold. Two estimators of linear functionals of $\mu_\phi $ based on the discretized Markov process are considered: a time-averaging estimator based on a single trajectory and an ensemble-averaging estimator based on multiple independent trajectories. Imposing no restrictions beyond a nominal level of smoothness on $\phi$, first-order error bounds, in discretization step size, on the bias and variance/mean-square error of both estimators are derived. The order of error matches the optimal rate in Euclidean and flat spaces, and leads to a first-order bound on distance between the invariant measure $\mu_\phi$ and a stationary measure of the discretized Markov process. This order is preserved even upon using retractions when exponential maps are unavailable in closed form, thus enhancing practicality of the proposed algorithms. Generality of the proof techniques, which exploit links between two partial differential equations and the semigroup of operators corresponding to the Langevin diffusion, renders them amenable for the study of a more general class of sampling algorithms related to the Langevin diffusion. Conditions for extending analysis to the case of non-compact manifolds are discussed. Numerical illustrations with distributions, log-concave and otherwise, on the manifolds of positive and negative curvature elucidate on the derived bounds and demonstrate practical utility of the sampling algorithm.
There are some global tests for heterogeneity of variance in k-sample one-way layouts, but few consider pairwise comparisons between treatment levels. For experimental designs with a control, comparisons of the variances between the treatment levels and the control are of interest - in analogy to the location parameter with the Dunnett (1955) procedure. Such a many-to-one approach for variances is proposed using the Levene transformation, a kind of residuals. Its properties are characterized with simulation studies and corresponding data examples are evaluated with R code.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
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