Forecasting the occurrence and absence of novel disease outbreaks is essential for disease management. Here, we develop a general model, with no real-world training data, that accurately forecasts outbreaks and non-outbreaks. We propose a novel framework, using a feature-based time series classification method to forecast outbreaks and non-outbreaks. We tested our methods on synthetic data from a Susceptible-Infected-Recovered model for slowly changing, noisy disease dynamics. Outbreak sequences give a transcritical bifurcation within a specified future time window, whereas non-outbreak (null bifurcation) sequences do not. We identified incipient differences in time series of infectives leading to future outbreaks and non-outbreaks. These differences are reflected in 22 statistical features and 5 early warning signal indicators. Classifier performance, given by the area under the receiver-operating curve, ranged from 0.99 for large expanding windows of training data to 0.7 for small rolling windows. Real-world performances of classifiers were tested on two empirical datasets, COVID-19 data from Singapore and SARS data from Hong Kong, with two classifiers exhibiting high accuracy. In summary, we showed that there are statistical features that distinguish outbreak and non-outbreak sequences long before outbreaks occur. We could detect these differences in synthetic and real-world data sets, well before potential outbreaks occur.
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We explore different aspects of cognitive diversity and its effect on the success of group deliberation. To evaluate this, we use 500 dialogues from small, online groups discussing the Wason Card Selection task - the DeliData corpus. Leveraging the corpus, we perform quantitative analysis evaluating three different measures of cognitive diversity. First, we analyse the effect of group size as a proxy measure for diversity. Second, we evaluate the effect of the size of the initial idea pool. Finally, we look into the content of the discussion by analysing discussed solutions, discussion patterns, and how conversational probing can improve those characteristics. Despite the reputation of groups for compounding bias, we show that small groups can, through dialogue, overcome intuitive biases and improve individual decision-making. Across a large sample and different operationalisations, we consistently find that greater cognitive diversity is associated with more successful group deliberation. Code and data used for the analysis are available in the repository: //github.com/gkaradzhov/cognitive-diversity-groups-cogsci24.
The use of propensity score (PS) methods has become ubiquitous in causal inference. At the heart of these methods is the positivity assumption. Violation of the positivity assumption leads to the presence of extreme PS weights when estimating average causal effects of interest, such as the average treatment effect (ATE) or the average treatment effect on the treated (ATT), which renders invalid related statistical inference. To circumvent this issue, trimming or truncating the extreme estimated PSs have been widely used. However, these methods require that we specify a priori a threshold and sometimes an additional smoothing parameter. While there are a number of methods dealing with the lack of positivity when estimating ATE, surprisingly there is no much effort in the same issue for ATT. In this paper, we first review widely used methods, such as trimming and truncation in ATT. We emphasize the underlying intuition behind these methods to better understand their applications and highlight their main limitations. Then, we argue that the current methods simply target estimands that are scaled ATT (and thus move the goalpost to a different target of interest), where we specify the scale and the target populations. We further propose a PS weight-based alternative for the average causal effect on the treated, called overlap weighted average treatment effect on the treated (OWATT). The appeal of our proposed method lies in its ability to obtain similar or even better results than trimming and truncation while relaxing the constraint to choose a priori a threshold (or even specify a smoothing parameter). The performance of the proposed method is illustrated via a series of Monte Carlo simulations and a data analysis on racial disparities in health care expenditures.
We consider the problem of robustly detecting changepoints in the variability of a sequence of independent multivariate functions. We develop a novel changepoint procedure, called the functional Kruskal--Wallis for covariance (FKWC) changepoint procedure, based on rank statistics and multivariate functional data depth. The FKWC changepoint procedure allows the user to test for at most one changepoint (AMOC) or an epidemic period, or to estimate the number and locations of an unknown amount of changepoints in the data. We show that when the ``signal-to-noise'' ratio is bounded below, the changepoint estimates produced by the FKWC procedure attain the minimax localization rate for detecting general changes in distribution in the univariate setting (Theorem 1). We also provide the behavior of the proposed test statistics for the AMOC and epidemic setting under the null hypothesis (Theorem 2) and, as a simple consequence of our main result, these tests are consistent (Corollary 1). In simulation, we show that our method is particularly robust when compared to similar changepoint methods. We present an application of the FKWC procedure to intraday asset returns and f-MRI scans. As a by-product of Theorem 1, we provide a concentration result for integrated functional depth functions (Lemma 2), which may be of general interest.
When modeling scientific and industrial problems, geometries are typically modeled by explicit boundary representations obtained from computer-aided design software. Unfitted (also known as embedded or immersed) finite element methods offer a significant advantage in dealing with complex geometries, eliminating the need for generating unstructured body-fitted meshes. However, current unfitted finite elements on nonlinear geometries are restricted to implicit (possibly high-order) level set geometries. In this work, we introduce a novel automatic computational pipeline to approximate solutions of partial differential equations on domains defined by explicit nonlinear boundary representations. For the geometrical discretization, we propose a novel algorithm to generate quadratures for the bulk and surface integration on nonlinear polytopes required to compute all the terms in unfitted finite element methods. The algorithm relies on a nonlinear triangulation of the boundary, a kd-tree refinement of the surface cells that simplify the nonlinear intersections of surface and background cells to simple cases that are diffeomorphically equivalent to linear intersections, robust polynomial root-finding algorithms and surface parameterization techniques. We prove the correctness of the proposed algorithm. We have successfully applied this algorithm to simulate partial differential equations with unfitted finite elements on nonlinear domains described by computer-aided design models, demonstrating the robustness of the geometric algorithm and showing high-order accuracy of the overall method.
When the marginal causal effect comparing the same treatment pair is available from multiple trials, we wish to transport all results to make inference on the target population effect. To account for the differences between populations, statistical analysis is often performed controlling for relevant variables. However, when transportability assumptions are placed on conditional causal effects, rather than the distribution of potential outcomes, we need to carefully choose these effect measures. In particular, we present identifiability results in two cases: target population average treatment effect for a continuous outcome and causal mean ratio for a positive outcome. We characterize the semiparametric efficiency bounds of the causal effects under the respective transportability assumptions and propose estimators that are doubly robust against model misspecifications. We highlight an important discussion on the tension between the non-collapsibility of conditional effects and the variational independence induced by transportability in the case of multiple source trials.
Deep orthogonal decomposition: a continuously adaptive data-driven approach to model order reduction
We develop a novel deep learning technique, termed Deep Orthogonal Decomposition (DOD), for dimensionality reduction and reduced order modeling of parameter dependent partial differential equations. The approach consists in the construction of a deep neural network model that approximates the solution manifold through a continuously adaptive local basis. In contrast to global methods, such as Principal Orthogonal Decomposition (POD), the adaptivity allows the DOD to overcome the Kolmogorov barrier, making the approach applicable to a wide spectrum of parametric problems. Furthermore, due to its hybrid linear-nonlinear nature, the DOD can accommodate both intrusive and nonintrusive techniques, providing highly interpretable latent representations and tighter control on error propagation. For this reason, the proposed approach stands out as a valuable alternative to other nonlinear techniques, such as deep autoencoders. The methodology is discussed both theoretically and practically, evaluating its performances on problems featuring nonlinear PDEs, singularities, and parametrized geometries.
In many modern regression applications, the response consists of multiple categorical random variables whose probability mass is a function of a common set of predictors. In this article, we propose a new method for modeling such a probability mass function in settings where the number of response variables, the number of categories per response, and the dimension of the predictor are large. Our method relies on a functional probability tensor decomposition: a decomposition of a tensor-valued function such that its range is a restricted set of low-rank probability tensors. This decomposition is motivated by the connection between the conditional independence of responses, or lack thereof, and their probability tensor rank. We show that the model implied by such a low-rank functional probability tensor decomposition can be interpreted in terms of a mixture of regressions and can thus be fit using maximum likelihood. We derive an efficient and scalable penalized expectation maximization algorithm to fit this model and examine its statistical properties. We demonstrate the encouraging performance of our method through both simulation studies and an application to modeling the functional classes of genes.
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.
Diagnosticians use an observed proportion as a direct estimate of the posterior probability of a diagnosis. Therefore, a diagnostician might regard a continuous Gaussian probability distribution of possible numerical outcomes conditional on the information in the study methods and data as posterior probabilities. Similarly, they might regard the distribution of possible means based on a SEM as a posterior probability distribution too. If the converse likelihood distribution of the observed mean conditional on any hypothetical mean (e.g. the null hypothesis) is assumed to be the same as the above posterior distribution (as is customary) then by Bayes rule, the prior distribution of all possible hypothetical means is uniform. It follows that the probability Q of any theoretically true mean falling into a tail beyond a null hypothesis would be equal to that tails area as a proportion of the whole. It also follows that the P value (the probability of the observed mean or something more extreme conditional on the null hypothesis) is equal to Q. Replication involves doing two independent studies, thus doubling the variance for the combined posterior probability distribution. So, if the original effect size was 1.96, the number of observations was 100, the SEM was 1 and the original P value was 0.025, the theoretical probability of a replicating study getting a P value of up to 0.025 again is only 0.283. By applying this double variance to achieve a power of 80%, the required number of observations is doubled compared to conventional approaches. If some replicating study is to achieve a P value of up to 0.025 yet again with a probability of 0.8, then this requires 3 times as many observations in the power calculation. This might explain the replication crisis.
Out of the participants in a randomized experiment with anticipated heterogeneous treatment effects, is it possible to identify which subjects have a positive treatment effect? While subgroup analysis has received attention, claims about individual participants are much more challenging. We frame the problem in terms of multiple hypothesis testing: each individual has a null hypothesis (stating that the potential outcomes are equal, for example) and we aim to identify those for whom the null is false (the treatment potential outcome stochastically dominates the control one, for example). We develop a novel algorithm that identifies such a subset, with nonasymptotic control of the false discovery rate (FDR). Our algorithm allows for interaction -- a human data scientist (or a computer program) may adaptively guide the algorithm in a data-dependent manner to gain power. We show how to extend the methods to observational settings and achieve a type of doubly-robust FDR control. We also propose several extensions: (a) relaxing the null to nonpositive effects, (b) moving from unpaired to paired samples, and (c) subgroup identification. We demonstrate via numerical experiments and theoretical analysis that the proposed method has valid FDR control in finite samples and reasonably high identification power.
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