Interaction-driven modeling of diseases over real-world contact data has been shown to promote the understanding of the spread of diseases in communities. This temporal modeling follows the path-preserving order and timing of the contacts, which are essential for accurate modeling. Yet, other important aspects were overlooked. Various airborne pathogens differ in the duration of exposure needed for infection. Also, from the individual perspective, Covid-19 progression differs between individuals, and its severity is statistically correlated with age. Here, we enrich an interaction-driven model of Covid-19 and similar airborne viral diseases with (a) meetings duration and (b) personal disease progression. The enriched model enables predicting outcomes at both the population and the individual levels. It further allows predicting individual risk of engaging in social interactions as a function of the virus characteristics and its prevalence in the population. We further showed that the enigmatic nature of asymptomatic transmission stems from the latent effect of the network density on this transmission and that asymptomatic transmission has a substantial impact only in sparse communities.
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The smoothing distribution of dynamic probit models with Gaussian state dynamics was recently proved to belong to the unified skew-normal family. Although this is computationally tractable in small-to-moderate settings, it may become computationally impractical in higher dimensions. In this work, adapting a recent more general class of expectation propagation (EP) algorithms, we derive an efficient EP routine to perform inference for such a distribution. We show that the proposed approximation leads to accuracy gains over available approximate algorithms in a financial illustration.
Bayesian binary regression is a prosperous area of research due to the computational challenges encountered by currently available methods either for high-dimensional settings or large datasets, or both. In the present work, we focus on the expectation propagation (EP) approximation of the posterior distribution in Bayesian probit regression under a multivariate Gaussian prior distribution. Adapting more general derivations in Anceschi et al. (2023), we show how to leverage results on the extended multivariate skew-normal distribution to derive an efficient implementation of the EP routine having a per-iteration cost that scales linearly in the number of covariates. This makes EP computationally feasible also in challenging high-dimensional settings, as shown in a detailed simulation study.
Binary responses arise in a multitude of statistical problems, including binary classification, bioassay, current status data problems and sensitivity estimation. There has been an interest in such problems in the Bayesian nonparametrics community since the early 1970s, but inference given binary data is intractable for a wide range of modern simulation-based models, even when employing MCMC methods. Recently, Christensen (2023) introduced a novel simulation technique based on counting permutations, which can estimate both posterior distributions and marginal likelihoods for any model from which a random sample can be generated. However, the accompanying implementation of this technique struggles when the sample size is too large (n > 250). Here we present perms, a new implementation of said technique which is substantially faster and able to handle larger data problems than the original implementation. It is available both as an R package and a Python library. The basic usage of perms is illustrated via two simple examples: a tractable toy problem and a bioassay problem. A more complex example involving changepoint analysis is also considered. We also cover the details of the implementation and illustrate the computational speed gain of perms via a simple simulation study.
The non-identifiability of the competing risks model requires researchers to work with restrictions on the model to obtain informative results. We present a new identifiability solution based on an exclusion restriction. Many areas of applied research use methods that rely on exclusion restrcitions. It appears natural to also use them for the identifiability of competing risks models. By imposing the exclusion restriction couple with an Archimedean copula, we are able to avoid any parametric restriction on the marginal distributions. We introduce a semiparametric estimation approach for the nonparametric marginals and the parametric copula. Our simulation results demonstrate the usefulness of the suggested model, as the degree of risk dependence can be estimated without parametric restrictions on the marginal distributions.
Trojans are one of the most threatening network attacks currently. HTTP-based Trojan, in particular, accounts for a considerable proportion of them. Moreover, as the network environment becomes more complex, HTTP-based Trojan is more concealed than others. At present, many intrusion detection systems (IDSs) are increasingly difficult to effectively detect such Trojan traffic due to the inherent shortcomings of the methods used and the backwardness of training data. Classical anomaly detection and traditional machine learning-based (TML-based) anomaly detection are highly dependent on expert knowledge to extract features artificially, which is difficult to implement in HTTP-based Trojan traffic detection. Deep learning-based (DL-based) anomaly detection has been locally applied to IDSs, but it cannot be transplanted to HTTP-based Trojan traffic detection directly. To solve this problem, in this paper, we propose a neural network detection model (HSTF-Model) based on hierarchical spatiotemporal features of traffic. Meanwhile, we combine deep learning algorithms with expert knowledge through feature encoders and statistical characteristics to improve the self-learning ability of the model. Experiments indicate that F1 of HSTF-Model can reach 99.4% in real traffic. In addition, we present a dataset BTHT consisting of HTTP-based benign and Trojan traffic to facilitate related research in the field.
Many researchers have identified distribution shift as a likely contributor to the reproducibility crisis in behavioral and biomedical sciences. The idea is that if treatment effects vary across individual characteristics and experimental contexts, then studies conducted in different populations will estimate different average effects. This paper uses ``generalizability" methods to quantify how much of the effect size discrepancy between an original study and its replication can be explained by distribution shift on observed unit-level characteristics. More specifically, we decompose this discrepancy into ``components" attributable to sampling variability (including publication bias), observable distribution shifts, and residual factors. We compute this decomposition for several directly-replicated behavioral science experiments and find little evidence that observable distribution shifts contribute appreciably to non-replicability. In some cases, this is because there is too much statistical noise. In other cases, there is strong evidence that controlling for additional moderators is necessary for reliable replication.
Deep neural networks have shown remarkable performance when trained on independent and identically distributed data from a fixed set of classes. However, in real-world scenarios, it can be desirable to train models on a continuous stream of data where multiple classification tasks are presented sequentially. This scenario, known as Continual Learning (CL) poses challenges to standard learning algorithms which struggle to maintain knowledge of old tasks while learning new ones. This stability-plasticity dilemma remains central to CL and multiple metrics have been proposed to adequately measure stability and plasticity separately. However, none considers the increasing difficulty of the classification task, which inherently results in performance loss for any model. In that sense, we analyze some limitations of current metrics and identify the presence of setup-induced forgetting. Therefore, we propose new metrics that account for the task's increasing difficulty. Through experiments on benchmark datasets, we demonstrate that our proposed metrics can provide new insights into the stability-plasticity trade-off achieved by models in the continual learning environment.
A significant limitation of one-class classification anomaly detection methods is their reliance on the assumption that unlabeled training data only contains normal instances. To overcome this impractical assumption, we propose two novel classification-based anomaly detection methods. Firstly, we introduce a semi-supervised shallow anomaly detection method based on an unbiased risk estimator. Secondly, we present a semi-supervised deep anomaly detection method utilizing a nonnegative (biased) risk estimator. We establish estimation error bounds and excess risk bounds for both risk minimizers. Additionally, we propose techniques to select appropriate regularization parameters that ensure the nonnegativity of the empirical risk in the shallow model under specific loss functions. Our extensive experiments provide strong evidence of the effectiveness of the risk-based anomaly detection methods.
Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as a compound parameter equal to the product of the proportion of susceptibles in the population and the transmission rate. This model allows us to estimate the effective reproduction number from concentrations of pathogen genomes while avoiding difficult to verify assumptions about the dynamics of the susceptible population. As a byproduct of our primary goal, we also produce a new model for estimating the effective reproduction number from case data using the same framework. We test this modeling framework in an agent-based simulation study with a realistic data generating mechanism which accounts for the time-varying dynamics of pathogen shedding. Finally, we apply our new model to estimating the effective reproduction number of SARS-CoV-2 in Los Angeles, California, using pathogen RNA concentrations collected from a large wastewater treatment facility.
Permutation tests are widely used for statistical hypothesis testing when the sampling distribution of the test statistic under the null hypothesis is analytically intractable or unreliable due to finite sample sizes. One critical challenge in the application of permutation tests in genomic studies is that an enormous number of permutations are often needed to obtain reliable estimates of very small $p$-values, leading to intensive computational effort. To address this issue, we develop algorithms for the accurate and efficient estimation of small $p$-values in permutation tests for paired and independent two-group genomic data, and our approaches leverage a novel framework for parameterizing the permutation sample spaces of those two types of data respectively using the Bernoulli and conditional Bernoulli distributions, combined with the cross-entropy method. The performance of our proposed algorithms is demonstrated through the application to two simulated datasets and two real-world gene expression datasets generated by microarray and RNA-Seq technologies and comparisons to existing methods such as crude permutations and SAMC, and the results show that our approaches can achieve orders of magnitude of computational efficiency gains in estimating small $p$-values. Our approaches offer promising solutions for the improvement of computational efficiencies of existing permutation test procedures and the development of new testing methods using permutations in genomic data analysis.
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